Thursday, February 23, 2012

What evidence is found for the first life on earth?

First and foremost, we now have evidence for photosynthetic life suddenly appearing on earth, as soon as water appeared on the earth, in the oldest sedimentary rocks ever found on earth.

The Sudden Appearance Of Photosynthetic Life On Earth - video
http://www.metacafe.com/watch/4262918

When Did Life on Earth Begin? Ask a Rock (3.85 bya)
http://www.astrobio.net/exclusive/293/
When did oxygenic photosynthesis evolve? - Roger Buick - 2008
Excerpt:,, U–Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.
http://rstb.royalsocietypublishing.org/content/363/1504/2731.long

New study: Oxygenic photosynthesis goes back three billion years - September 26, 2013 - vjtorley
Excerpt: If Buick is correct here, then oxygenic photosynthesis goes right back to the very dawn of life. (also see comment #8 for more detailed notes on photosynthesis at 3.8 billion years ago)
http://www.uncommondescent.com/intelligent-design/new-study-oxygenic-photosynthesis-goes-back-three-billion-years/

Team Claims It Has Found Oldest Fossils By NICHOLAS WADE - August 2011
Excerpt: Rocks older than 3.5 billion years have been so thoroughly cooked as to destroy all cellular structures, but chemical traces of life can still be detected. Chemicals indicative of life have been reported in rocks 3.5 billion years old in the Dresser Formation of Western Australia and, with less certainty, in rocks 3.8 billion years old in Greenland.
http://www.nytimes.com/2011/08/22/science/earth/22fossil.html?_r=1

Does the Chemistry of the Cell Point to Its Origin in Darwin's "Warm Little Pond"? - February 23, 2012
Excerpt: Studies have indicated that the earliest life may be older than the oldest known rocks, which are dated at 4 billion years old.
http://www.evolutionnews.org/2012/02/does_the_cells056641.html
Earliest (Bacteria) fossils found in Australia, 3.4 bya
http://www.uncommondescent.com/origin-of-life/earliest-fossils-found-in-australia-3-4-bya/

Dr. Hugh Ross - Origin Of Life Paradox (No prebiotic chemical signatures)- video
http://www.metacafe.com/watch/4012696

Isotopic Evidence For Life Immediately Following Late Bombardment - Graph
http://cdn.physorg.com/newman/gfx/news/hires/2014/oldestbitofc.jpg
"We get that evidence from looking at carbon 12 to carbon 13 analysis. And it tells us that in Earth's oldest (sedimentary) rock, which dates at 3.80 billion years ago, we find an abundance for the carbon signature of living systems. Namely, that life prefers carbon 12. And so if you see a higher ratio of carbon 12 to carbon 13 that means that carbon has been processed by life. And it is that kind of evidence that tells us that life has been abundant on earth as far back as 3.80 billion years ago (when water was first present on earth).,,, And that same carbon 12 to carbon 13 analysis tells us that planet earth, over it entire 4.5662 billion year history has never had prebiotics. Prebiotics would have a higher ratio of carbon 13 to carbon 12. All the carbonaceous material, we see in the entire geological record of the earth, has the signature of being post-biotic not pre-biotic. Which means planet earth never had a primordial soup. And the origin of life on earth took place in a geological instant" (as soon as it was possible for life to exist on earth).
- Hugh Ross - quote as stated in preceding video - italics are added

Archaean Microfossils and the Implications for Intelligent Design - August 2011
Excerpt: This dramatically limits the amount of time, and thus the probabilistic resources, available to those who wish to invoke purely unguided and purposeless material processes to explain the origin of life.
http://www.evolutionnews.org/2011/08/surprisingly_soon_archaean_mic049921.html
Could Impacts Jump-Start the Origin of Life? - Hugh Ross - article
http://www.reasons.org/could-impacts-jump-start-origin-life

Moreover, the atmosphere is found not to be 'reducing' on the early earth as is commonly taught in materialistic origin of life scenarios;
Miller-Urey Experiment "Icon of Evolution" Alive and Well in Proposed Texas Instructional Materials - 2011
Excerpt: However, it has been known for decades that the Earth's early atmosphere probably was not composed of methane or ammonia, and thus would not have been conducive to Miller-Urey type chemistry. As origin of life theorist David Deamer explains, "This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers..."1 Theorist Jeffrey Bada and other experts have likewise observed that "Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used...
http://www.evolutionnews.org/2011/06/miller-urey_experiment_icon_of047271.html

Time to end speculation about a reducing atmosphere for the early Earth - David Tyler - December 2011
Excerpt: Using zircons dated to almost 4.4 Ga, the researchers have analysed their redox state (a measure of the degree of oxygenation of the mineral).,,, "[In] this issue, Trail et al. report their analysis of the sole mineral survivors of the Hadean, zircon samples more than 4 billion years old. Their findings allowed them to determine the 'fugacity' of oxygen in Hadean magmatic melts, a quantity that acts as a measure of magmatic redox conditions. Unexpectedly, the zircons record oxygen fugacities identical to those in the present-day mantle, leading the authors to conclude that Hadean volcanic gases were as highly oxidized as those emitted today."
http://www.arn.org/blogs/index.php/literature/2011/12/02/time_to_end_speculation_about_a_reducing

Top Five Problems with Current Origin-of-Life Theories - Casey Luskin - December 12, 2012
Overview:
Problem 1: No Viable Mechanism to Generate a Primordial Soup
Problem 2: Forming Polymers Requires Dehydration Synthesis
Problem 3: RNA World Hypothesis Lacks Confirming Evidence
Problem 4: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code
Problem 5: No Workable Model for the Origin of Life

http://www.evolutionnews.org/2012/12/top_five_probl067431.html
Late Heavy Bombardment - graph
http://www.reasons.org/Media/Default/Images/Archive/clip_image008_0000.jpg

Life - Its Sudden Origin and Extreme Complexity - Dr. Fazale Rana - video
http://www.metacafe.com/watch/4287513

The evidence scientists have discovered in the geologic record is stunning in its support of the anthropic hypothesis. The oldest sedimentary rocks on earth, known to science, originated underwater (and thus in relatively cool environs) 3.86 billion years ago. Those sediments, which are exposed at Isua in southwestern Greenland, also contain the earliest chemical evidence (fingerprint) of 'photosynthetic' life [Nov. 7, 1996, Nature]. This evidence had been fought by materialists since it is totally contrary to their evolutionary theory. Yet, Danish scientists were able to bring forth another line of geological evidence to substantiate the primary line of geological evidence for photo-synthetic life in the earth’s earliest sedimentary rocks.

U-rich Archaean sea-floor sediments from Greenland - indications of +3700 Ma oxygenic photosynthesis (2003)
http://adsabs.harvard.edu/abs/2004E&PSL.217..237R

Moreover, evidence for 'sulfate reducing' bacteria has been discovered alongside the evidence for photosynthetic bacteria:
When Did Life First Appear on Earth? - Fazale Rana - December 2010
Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
http://www.reasons.org/when-did-life-first-appear-earth

Iron in Primeval Seas Rusted by Bacteria - Apr. 23, 2013
Excerpt: The oldest known iron ores were deposited in the Precambrian period and are up to four billion years old (the Earth itself is estimated to be about 4.6 billion years old). ,,,
This research not only provides the first clear evidence that microorganisms were directly involved in the deposition of Earth's oldest iron formations; it also indicates that large populations of oxygen-producing cyanobacteria were at work in the shallow areas of the ancient oceans, while deeper water still reached by the light (the photic zone) tended to be populated by anoxyenic or micro-aerophilic iron-oxidizing bacteria which formed the iron deposits.,,,

http://www.sciencedaily.com/releases/2013/04/130423110750.htm
Thus we now have fairly conclusive evidence for bacterial life in the oldest sedimentary rocks ever found by scientists on earth.

These following sites have illustrations that shows some of the interdependent, ‘life-enabling’, biogeochemical complexity of different types of bacterial life on Earth.,,,

Biologically mediated cycles for hydrogen, carbon, nitrogen, oxygen, sulfur, and iron – image of interdependent ‘biogeochemical’ web
http://www.sciencemag.org/content/320/5879/1034/F2.large.jpg
Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13
Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages.
http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1
Microbial Mat Ecology – Image on page 92 (third page down)
http://www.dsls.usra.edu/biologycourse/workbook/Unit2.2.pdf

,,,Please note, that if even one type of bacteria group did not exist in this complex cycle of biogeochemical interdependence, that was illustrated on the third page of the preceding site, then all of the different bacteria would soon die out. This essential biogeochemical interdependence, of the most primitive different types of bacteria that we have evidence of on ancient earth, makes the origin of life ‘problem’ for neo-Darwinists that much worse. For now not only do neo-Darwinists have to explain how the ‘miracle of life’ happened once with the origin of photosynthetic bacteria, but they must now also explain how all these different types bacteria, that photosynthetic bacteria are dependent on, in this irreducibly complex biogeochemical web, miraculously arose just in time to supply the necessary nutrients, in their biogeochemical link in the chain, for photosynthetic bacteria to continue to survive. As well, though not clearly illustrated in the illustration on the preceding site, please note that a long term tectonic cycle, of the turnover the Earth’s crustal rocks, must also be fine-tuned to a certain degree with the bacteria and thus plays a important ‘foundational’ role in the overall ecology of the biogeochemical system that must be accounted for as well.
Ancient Earth Crust Stored in Deep Mantle - Apr. 24, 2013
Excerpt: New research,, demonstrates that oceanic volcanic rocks contain samples of recycled crust dating back to the Archean era 2.5 billion years ago.,, This indicates that the sulfur comes from a deep mantle reservoir containing crustal material subducted before the Great Oxidation Event and preserved for over half the age of Earth.
"These measurements place the first firm age estimates of recycled material in oceanic hotspots," Hauri said. "They confirm the cycling of sulfur from the atmosphere and oceans into mantle and ultimately back to the surface," Hauri said.

http://www.sciencedaily.com/releases/2013/04/130424132705.htm
As a side issue to these complex interdependent biogeochemical relationships, of the 'simplest' bacteria on Earth, that provide the foundation for a 'friendly' environment on Earth that is hospitable to higher lifeforms above them to eventually appear on earth, it is interesting to note man's failure to build a miniature, self-enclosed, ecology in which humans could live for any extended periods of time.
Biosphere 2 – What Went Wrong?
Excerpt: Other Problems
Biosphere II’s water systems became polluted with too many nutrients. The crew had to clean their water by running it over mats of algae, which they later dried and stored.
Also, as a symptom of further atmospheric imbalances, the level of dinitrogen oxide became dangerously high. At these levels, there was a risk of brain damage due to a reduction in the synthesis of vitamin B12.

http://biology.kenyon.edu/slonc/bio3/2000projects/carroll_d_walker_e/whatwentwrong.html
The simplest photosynthetic life on earth is exceedingly complex, too complex to happen by accident even if the primeval oceans had been full of pre-biotic soup.
Scientists unlock some key secrets of photosynthesis - July 2, 2012
Excerpt: "The photosynthetic system of plants is nature's most elaborate nanoscale biological machine," said Lakshmi. "It converts light energy at unrivaled efficiency of more than 95 percent compared to 10 to 15 percent in the current man-made solar technologies.,, "Photosystem II is the engine of life," Lakshmi said. "It performs one of the most energetically demanding reactions known to mankind, splitting water, with remarkable ease and efficiency.",,, "Water is a very stable molecule and it takes four photons of light to split water," she said. "This is a challenge for chemists and physicists around the world (to imitate) as the four-photon reaction has very stringent requirements."
http://phys.org/news/2012-07-scientists-key-secrets-photosynthesis.html
The Miracle Of Photosynthesis - electron transport - video
http://www.youtube.com/watch?v=hj_WKgnL6MI

Electron transport and ATP synthesis during photosynthesis - Illustration
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.figgrp.1672

Consider the following paradox of photosynthesis,,, Plants perform photosynthesis. Plants use massively complex machinery within their cells to capture the light from the Sun and produce sugars (food). The benefit of this is, of course, that they eventually provide food for animals and humans.
But plants also then break down the very food that they make by using another set of extremely complex machinery to get ATP (the 'energy currency' molecule of the cell) from the sugars that they initially built.
Yet, this makes no sense from an evolutionary perspective because the plants should have only formed the complex machinery (if evolution had any power to create complex machinery in the first place) to take the power of light and convert it directly to ATP so that they could use it themselves instead of producing more 'food' than is necessary...that would be more energetically feasible. But, lo, that's not what happens,,,

Moreover photosynthesis is found to be widespread among different bacteria phyla with no clear evolutionary relationships between them:
The Elaborate Nanoscale Machine Called Photosynthesis: No Vestige of a Beginning - Cornelius Hunter - July 2012
Excerpt: "The ability to do photosynthesis is widely distributed throughout the bacterial domain in six different phyla, with no apparent pattern of evolution. Photosynthetic phyla include the cyanobacteria, proteobacteria (purple bacteria), green sulfur bacteria (GSB), firmicutes (heliobacteria), filamentous anoxygenic phototrophs (FAPs, also often called the green nonsulfur bacteria), and acidobacteria (Raymond, 2008)."
http://darwins-god.blogspot.com/2012/07/elaborate-nanoscale-machine-called.html?showComment=1341739083709#c1202402748048253561

Early Evolution of Photosynthesis - Robert E. Blankenship - October 2010
Excerpt: A wealth of evidence indicates that photosynthesis is an ancient process that originated not long after the origin of life,,,
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949000/

"Despite its complexity, C4 photosynthesis is one of the best examples of 'convergent evolution', having evolved more than 50 times in at least 18 plant families (Sage 2004; Conway Morris 2006)."
http://mbe.oxfordjournals.org/content/26/8/1909.full.pdf

Psalm 104:14
He causes the grass to grow for the cattle, And vegetation for the labor of man, So that he may bring forth food from the earth,
There is actually a molecular machine, that surpasses man made machines in engineering parameters, that is integral to the photosynthetic process:

The ATP Synthase Enzyme - an exquisite motor necessary for first life - video
http://www.youtube.com/watch?v=W3KxU63gcF4

Here is a newer molecular animation of the ATP molecular machine:

Miniature Molecular Power Plant: ATP Synthase - January 2013 - video
http://www.youtube.com/watch?v=XI8m6o0gXDY

Of note:
ATP: The Perfect Energy Currency for the Cell - Jerry Bergman, Ph.D.
Excerpt: In manufacturing terms, the ATP (Synthase) molecule is a machine with a level of organization on the order of a research microscope or a standard television (Darnell, Lodish, and Baltimore, 1996).
http://www.trueorigin.org/atp.asp

ATP Synthase, an Energy-Generating Rotary Motor Engine - Jonathan M. May 15, 2013
Excerpt: ATP synthase has been described as "a splendid molecular machine," and "one of the most beautiful" of "all enzymes" .,, "bona fide rotary dynamo machine",,,
If such a unique and brilliantly engineered nanomachine bears such a strong resemblance to the engineering of manmade hydroelectric generators, and yet so impressively outperforms the best human technology in terms of speed and efficiency, one is led unsurprisingly to the conclusion that such a machine itself is best explained by intelligent design.

http://www.evolutionnews.org/2013/05/atp_synthase_an_1072101.html

Cells Know Their Physics - October 2010
Excerpt: the Complex I macromolecular complex. This machine employs a railroad-like piston and coupling-rod mechanism (07/07/2010, 09/22/2010) to create the proton gradient that drives ATP synthesis.“It is remarkable that the most fundamental energy-generating machinery in cells is based on the wave properties of electrons, which allow for an efficient transport of energy-carrying particles along the chain of redox cofactors toward molecular oxygen via quantum tunneling as demonstrated by this study.”
http://www.creationsafaris.com/crev201010.htm#20101027a

Your Motor/Generators Are 100% Efficient – October 2011
Excerpt: ATP synthase astounds again. The molecular machine that generates almost all the ATP (molecular “energy pellets”) for all life was examined by Japanese scientists for its thermodynamic efficiency. By applying and measuring load on the top part that synthesizes ATP, they were able to determine that one cannot do better at getting work out of a motor,,, The article was edited by noted Harvard expert on the bacterial flagellum, Howard Berg.
http://crev.info/content/111014-your_motor_generators

Thermodynamic efficiency and mechanochemical coupling of F1-ATPase - 2011
Excerpt:F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,,
Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase.

http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1
See also:
Davies et al., “Macromolecular organization of ATP synthase and complex I in whole mitochondria,” Proceedings of the National Academy of Sciences
and:
Tamás Beke-Somfai, Per Lincoln, and Bengt Nordén, “Double-lock ratchet mechanism revealing the role of [alpha]SER-344 in F0F1 ATP synthase,” Proceedings of the National Academy of Sciences

There is a profound 'chicken and egg' dilemma with ATP surrounding the Origin Of Life problem for evolutionists:
Evolutionist Has Another Honest Moment as “Thorny Questions Remain” - Cornelius Hunter - July 2012
Excerpt: It's a chicken and egg question. Scientists are in disagreement over what came first -- replication, or metabolism. But there is a third part to the equation -- and that is energy. … You need enzymes to make ATP and you need ATP to make enzymes. The question is: where did energy come from before either of these two things existed?
http://darwins-god.blogspot.com/2012/07/evolutionist-has-another-honest-moment.html
The 10 Step Glycolysis Pathway In ATP Production: An Overview - video
http://www.youtube.com/watch?v=8Kn6BVGqKd8

At the 6:00 minute mark of the following video, Chris Ashcraft, PhD – molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production:

Evolution vs ATP Synthase - Molecular Machine - video
http://www.metacafe.com/watch/4012706

Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways - Cornelius Hunter - July 2011
http://darwins-god.blogspot.com/2011/07/glycolysis-and-citric-acid-cycle.html

The photosynthetic process is clearly a irreducible complex condition:
"There is no question about photosynthesis being Irreducibly Complex. But it’s worse than that from an evolutionary perspective. There are 17 enzymes alone involved in the synthesis of chlorophyll. Are we to believe that all intermediates had selective value? Not when some of them form triplet states that have the same effect as free radicals like O2. In addition if chlorophyll evolved before antenna proteins, whose function is to bind chlorophyll, then chlorophyll would be toxic to cells. Yet the binding function explains the selective value of antenna proteins. Why would such proteins evolve prior to chlorophyll? and if they did not, how would cells survive chlorophyll until they did?" Uncommon Descent Blogger

Evolutionary biology: Out of thin air John F. Allen & William Martin:
The measure of the problem is here: “Oxygenetic photosynthesis involves about 100 proteins that are highly ordered within the photosynthetic membranes of the cell."
http://www.nature.com/nature/journal/v445/n7128/full/445610a.html
Of note: anoxygenic (without oxygen) photosynthesis is even more of a complex chemical pathway than oxygenic photosynthesis is:
"Remarkably, the biosynthetic routes needed to make the key molecular component of anoxygenic photosynthesis are more complex than the pathways that produce the corresponding component required for the oxygenic form.";
Early Life Remains Complex By Fazale R. Rana (FACTS for FAITH Issue 7, 2001)
Also of note: Anaerobic organisms, that live without oxygen, and most viruses are quickly destroyed by direct contact with oxygen.

In what I find to be a very fascinating discovery, it is found that photosynthetic life, which is an absolutely vital link that all higher life on earth is dependent on for food, uses ‘non-local’ quantum mechanical principles to accomplish photosynthesis. Moreover, this is direct evidence that a non-local, beyond space-time mass-energy, cause must be responsible for ‘feeding’ all life on earth, since all higher life on earth is eventually completely dependent on this non-local ‘photosynthetic energy’ in which to live their lives on this earth:

Non-Local Quantum Coherence In Photosynthesis - video with notes in description
http://vimeo.com/30235178

At the 21:00 minute mark of the following video, Dr Suarez explains why photosynthesis needs a 'non-local', beyond space and time, cause to explain its effect:

Nonlocality of Photosynthesis - Antoine Suarez - video - 2012
http://www.youtube.com/watch?v=dhMrrmlTXl4&feature=player_detailpage#t=1268s
Uncovering Quantum Secret in Photosynthesis - June 20, 2013
Excerpt: Photosynthetic organisms, such as plants and some bacteria, have mastered this process: In less than a couple of trillionths of a second, 95 percent of the sunlight they absorb is whisked away to drive the metabolic reactions that provide them with energy. The efficiency of photovoltaic cells currently on the market is around 20 percent.,,,
Van Hulst and his group have evaluated the energy transport pathways of separate individual but chemically identical, antenna proteins, and have shown that each protein uses a distinct pathway. The most surprising discovery was that the transport paths within single proteins can vary over time due to changes in the environmental conditions, apparently adapting for optimal efficiency. "These results show that coherence, a genuine quantum effect of superposition of states, is responsible for maintaining high levels of transport efficiency in biological systems, even while they adapt their energy transport pathways due to environmental influences" says van Hulst.

http://www.sciencedaily.com/releases/2013/06/130620142932.htm

Plants 'seen doing quantum physics' - By Jason Palmer - 21 June 2013
Excerpt: "What you see here is this photon comes in, and it sees many energy pathways," explained Prof van Hulst. "Where does it go? It goes to the one that's most efficient, the one where this quantum effect tells you it has the highest probability (of being put to use)," he told BBC News.
But the soft, flexible, warm conditions at room temperature mean that, as things move and jiggle - as life tends to do - that most efficient path can change. Remarkably, so did the evident path along the rings. ,,,- "this for me is something shocking," Prof van Hulst continued.

http://www.bbc.co.uk/news/science-environment-22996054

Quantum Mechanics Explains Efficiency of Photosynthesis - Jan. 9, 2014
Excerpt: Previous experiments suggest that energy is transferred in a wave-like manner, exploiting quantum phenomena, but crucially, a non-classical explanation could not be conclusively proved as the phenomena identified could equally be described using classical physics.,,,
Now, a team at UCL have attempted to identify features in these biological systems which can only be predicted by quantum physics, and for which no classical analogues exist.
,,,said Alexandra Olaya-Castro (UCL Physics & Astronomy), supervisor and co-author of the research. "We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer.",,,
Other biomolecular processes such as the transfer of electrons within macromolecules (like in reaction centres in photosynthetic systems), the structural change of a chromophore upon absorption of photons (like in vision processes) or the recognition of a molecule by another (as in olfaction processes), are influenced by specific vibrational motions. The results of this research therefore suggest that a closer examination of the vibrational dynamics involved in these processes could provide other biological prototypes exploiting truly non-classical phenomena,,

http://www.sciencedaily.com/releases/2014/01/140109092008.htm

Unlocking nature's quantum engineering for efficient solar energy - January 7, 2013
Excerpt: Certain biological systems living in low light environments have unique protein structures for photosynthesis that use quantum dynamics to convert 100% of absorbed light into electrical charge,,,
"Some of the key issues in current solar cell technologies appear to have been elegantly and rigorously solved by the molecular architecture of these PPCs – namely the rapid, lossless transfer of excitons to reaction centres.",,,
These biological systems can direct a quantum process, in this case energy transport, in astoundingly subtle and controlled ways – showing remarkable resistance to the aggressive, random background noise of biology and extreme environments. "This new understanding of how to maintain coherence in excitons, and even regenerate it through molecular vibrations, provides a fascinating glimpse into the intricate design solutions – seemingly including quantum engineering – ,,, and which could provide the inspiration for new types of room temperature quantum devices."

http://phys.org/news/2013-01-nature-quantum-efficient-solar-energy.html

Purple bacteria's light-harvesting prowess lies in highly symmetrical molecules - May 15, 2013
Excerpt: Purple bacteria are among Earth's oldest organisms, and among its most efficient in turning sunlight into usable chemical energy. Now, a key to their light-harvesting prowess has been explained through a detailed structural analysis by scientists at MIT.,,,
You would not expect a regular structure, almost a perfect structure," as is found in this primitive microbe, he says.
In these regular round complexes, Cao says, "nature only used certain symmetry numbers: mostly ninefold, some eightfold, very few tenfold. It's very selective." His group's mathematical analysis shows there are good reasons for that, he says.
These ring-shaped molecules, in turn, are arranged in a hexagonal pattern on the spherical photosynthetic membrane of purple bacteria, Cao says.
"With these symmetry numbers, the interactions between all pairs of the symmetric rings are optimized at the same time. … We believe that 'nature' found the most robust structures in terms of energy transfer," Cao says. Both eightfold and tenfold symmetries also work, though not as well: Only a lattice made up of ninefold symmetric complexes can tolerate an error in either direction. "You want consecutive numbers so it can tolerate such mistakes," Cao says.

http://phys.org/news/2013-05-secret-efficient-photosynthesis-purple-bacteria.html

What's quantum physics got to do with biology? - June 2012
Excerpt: certain bacteria can capture 95% of the light that hits them and turn it into useful energy. Solar panels also convert light from the Sun into energy—but they aren't nearly as good at it. The very best solar panels ever tested in a lab (i.e., not the ones actually available for sale and installation on your house) were able to convert about 34% of the light that hit them into electricity.,, Why can't we use the Sun's energy as effectively as bacteria can? The secret may be that the bacteria are using quantum physics to transmit energy.
http://boingboing.net/2012/06/01/quantum-biology.html

Unusual Quantum Effect Discovered in Earliest Stages of Photosynthesis - May 2012
Excerpt: "The behavior we were able to see at these very fast time scales implies a much more sophisticated mixing of electronic states," Tiede said. "It shows us that high-level biological systems could be tapped into very fundamental physics in a way that didn't seem likely or even possible."
The quantum effects observed in the course of the experiment hint that the natural light-harvesting processes involved in photosynthesis may be more efficient than previously indicated by classical biophysics, said chemist Gary Wiederrecht of Argonne's Center for Nanoscale Materials. "It leaves us wondering: how did Mother Nature create this incredibly elegant solution?" he said.

http://www.sciencedaily.com/releases/2012/05/120524092932.htm

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Gregory S. Engel, Nature (12 April 2007)
Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated.,,,, This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. ---- Conclusion? Obviously Photosynthesis is a brilliant piece of design by "Someone" who even knows how quantum mechanics works.
http://www.ncbi.nlm.nih.gov/pubmed/17429397

Quantum Mechanics at Work in Photosynthesis: Algae Familiar With These Processes for Nearly Two Billion Years - Feb. 2010
Excerpt: "We were astonished to find clear evidence of long-lived quantum mechanical states involved in moving the energy. Our result suggests that the energy of absorbed light resides in two places at once -- a quantum superposition state, or coherence -- and such a state lies at the heart of quantum mechanical theory.",,, "It suggests that algae knew about quantum mechanics nearly two billion years before humans," says Scholes.
http://www.sciencedaily.com/releases/2010/02/100203131356.htm

A few notes on the theistic implications of photosynthesis and of light itself:
https://docs.google.com/document/d/1_uX1w_iUOD3O8F-GvbkfG2GKuAunQuYRssSMb_t5kB8/edit

Life Masters Physics - Feb. 2010
Excerpt: Collini et al.2 report evidence suggesting that a process known as quantum coherence ‘wires’ together distant molecules in the light-harvesting apparatus of marine cryptophyte algae.,,,“Intriguingly, recent work has documented that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws at temperatures up to 180 K,”. ,,, “This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures.”
http://www.creationsafaris.com/crev201002.htm#20100210a
Materialists have tried to get around this crushing evidence for the sudden appearance of extremely complex, and elegant, photosynthetic life in the oldest sedimentary rocks ever found on earth by suggesting life could have originated in extreme conditions at hydrothermal vents. Yet, ignoring the fact that hydrothermal vents were themselves submerged in the water that produced the earliest sedimentary rocks that we find evidence for photosynthetic life in, the materialists are once again betrayed by the empirical evidence:
Refutation Of Hyperthermophile Origin Of Life scenario
Excerpt: While life, if appropriately designed, can survive under extreme physical and chemical conditions, it cannot originate under those conditions. High temperatures are especially catastrophic for evolutionary models. The higher the temperature climbs, the shorter the half-life for all the crucial building block molecules,
http://www.reasons.org/LateHeavyBombardmentIntensityandtheOriginofLife

The origin of life--did it occur at high temperatures?
Excerpt: Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 degrees C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine).
http://www.ncbi.nlm.nih.gov/pubmed/11539558

Chemist explores the membranous origins of the first living cell:
Excerpt: Conditions in geothermal springs and similar extreme environments just do not favor membrane formation, which is inhibited or disrupted by acidity, dissolved salts, high temperatures, and calcium, iron, and magnesium ions. Furthermore, mineral surfaces in these clay-lined pools tend to remove phosphates and organic chemicals from the solution. "We have to face up to the biophysical facts of life," Deamer said. "Hot, acidic hydrothermal systems are not conducive to self-assembly processes."
http://currents.ucsc.edu/05-06/04-03/deamer.asp

Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010
Excerpt: numerous problems abound for the hydrothermal vent hypothesis for the origin of life,,,, For example, as Stanley Miller has pointed out, the polymers are "too unstable to exist in a hot prebiotic environment." Miller has also noted that the RNA bases are destroyed very quickly in water when the water boils. Intense heating also has the tendency to degrade amino acids such as serine and threonine. A more damning problem lies in the fact that the homochirality of the amino acids is destroyed by heating.
Of course, accounting for the required building blocks is an interesting problem, but from the vantage of ID proponents, it is only one of many problems facing materialistic accounts of the origin of life. After all, it is the sequential arrangement of the chemical constituents -- whether that happens to be amino acids in proteins, or nucleotides in DNA or RNA -- to form complex specified information (a process which requires the production of specified irregularity), which compellingly points toward the activity of rational deliberation (Intelligence).

http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html

Origin-of-Life Theorists Fail to Explain Chemical Signatures in the Cell - Casey Luskin - February 15, 2012
Excerpt: (Nick) Lane also notes that the study has a significant conceptual flaw. "To suggest that the ionic composition of primordial cells should reflect the composition of the oceans is to suggest that cells are in equilibrium with their medium, which is close to saying that they are not alive," Lane says. "Cells require dynamic disequilibrium -- that is what being alive is all about.",,, Our uniform experience affirms that specified information-whether inscribed hieroglyphics, written in a book, encoded in a radio signal, or produced in a simulation experiment-always arises from an intelligent source, from a mind and not a strictly material process.
(Stephen Meyer - Signature in the Cell, p. 347)
http://www.evolutionnews.org/2012/02/origin-of-life_056391.html
Sometimes in a 'hot' origin of life scenario a Darwinist will reference 'proteinoids':
The Origin of Life
Excerpt: Heat is another way to join monomers into polymers. Scientists have shown that when organic monomers (like amino acids) are heated and splashed onto hot sand or rocks, the heat vaporizes the water and links the monomers into polymers – which scientists call ‘proteinoids’. http://www.biology.iupui.edu/biocourses/N100/ch8life.html
Yet 'proteinoids' are far from being truly functional proteins:
Protenoids are not fully functioning proteins. Here are some differences:
1. Proteinoids do not have anything coding their sequences, and the amino acids bond together randomly.
2. Proteinoids do not fold into a predictable three-dimensional conformation (since their sequences are not deterministic, for example).
3. Proteinoids contain both left- and right-handed amino acids in equal amounts, and even if the experiment begins will all left-handed amino acids, some are converted to the other form.
4. The amino acids in proteinoids are not all bonded together by alpha bonds: the amino acid chain in proteinoids is branched and “kinked” instead of being linear (due to incorrect bonding, for example, involving side groups).
5. Proteinoids have bonds other than peptide bonds joining their amino acids. Some of the starting amino acids are converted into pigments, which are incorporated into the proteinoid.

,,,those 5 points are followed by many excellent quotes refuting proteinoids as being nearly proteins,,,
http://www.uncommondescent.com/biomimicry/mechanical-gear-found-in-living-organism/#comment-471823
As to the 'lipid world' scenario, which uses clay on the ocean bottom to get started, a few problems that go unmentioned by Darwinists in that scenario are discussed in the following articles:

Pop Goes the Fatbubble Theory for the Origin of Life
http://www.creationsafaris.com/crev200409.htm#abiogenesis130

Darwinists Award New Inductee
http://www.creationsafaris.com/crev200612.htm#20061211a

Besides the implausibility of the 'hot' origin of life scenarios, some Darwinists have instead opted for promoting a 'cold' origin of life scenario with ice. Yet the cold origin of life scenario is also found to be implausible for several reasons.
The Peculiar Properties of Ice - August 2012
Excerpt: As we reported here, there are some fundamental problems that still need to be addressed for an ice-packed origin of life to be feasible. A cold origin-of-life scenario may seem to solve some difficulties with molecular stability and nucleotide concentration, but the tradeoffs, including a slower reaction rate, make this scenario untenable.
http://www.evolutionnews.org/2012/08/the_peculiar_pr_1062861.html
Besides the implausibility of hydrothermal vents and ice, it is also commonly, and erroneously, presumed in many grade school textbooks that life slowly arose in a primordial ocean of pre-biotic soup. Yet there are no chemical signatures in the geologic record indicating that a ocean of this pre-biotic soup ever existed. In fact, as stated earlier, the evidence indicates that complex photosynthetic life appeared on earth as soon as water appeared on earth with no chemical signature whatsoever of prebiotic activity.
The Primordial Soup Myth:
Excerpt: "Accordingly, Abelson(1966), Hull(1960), Sillen(1965), and many others have criticized the hypothesis that the primitive ocean, unlike the contemporary ocean, was a "thick soup" containing all of the micromolecules required for the next stage of molecular evolution. The concept of a primitive "thick soup" or "primordial broth" is one of the most persistent ideas at the same time that is most strongly contraindicated by thermodynamic reasoning and by lack of experimental support." - Sidney Fox, Klaus Dose on page 37 in Molecular Evolution and the Origin of Life.
http://theory-of-evolution.net/chap11/primordial-soup-myth.php

New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life - Feb. 2010
"Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life, But soup has no capacity for producing the energy vital for life."
William Martin - an evolutionary biologist
http://www.sciencedaily.com/releases/2010/02/100202101245.htm
Moreover, water is considered a 'universal solvent' which is a very thermodynamic obeying and thus origin of life defying fact.
Abiogenic Origin of Life: A Theory in Crisis - Arthur V. Chadwick, Ph.D.
Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.
http://origins.swau.edu/papers/life/chadwick/default.html

Professor Arthur E. Wilder-Smith "Any amounts of polypeptide which might be formed will be broken down into their initial components (amino acids) by the excess of water. The ocean is thus practically the last place on this or any other planet where the proteins of life could be formed spontaneously from amino acids. Yet nearly all text-books of biology teach this nonsense to support evolutionary theory and spontaneous biogenesis ... Has materialistic Neo-Darwinian philosophy overwhelmed us to such an extent that we forget or overlook the well-known facts of science and of chemistry in order to support this philosophy? ... Without exception all Miller's amino acids are completely unsuitable for any type of spontaneous biogenesis. And the same applies to all and any randomly formed substances and amino acids which form racemates. This statement is categorical and absolute and cannot be affected by special conditions."
http://theevolutioncrisis.org.uk/testimony3.php

A Substantial Conundrum Confronting The Chemical Origin Of Life - August 2011
Excerpt: 1. Peptide bond formation is an endothermic reaction. This means that the reaction requires the absorption of energy: It does not take place spontaneously.
2. Peptide bond formation is a condensation reaction. It hence involves the net removal of a water molecule. So not only can this reaction not happen spontaneously in an aqueous medium, but, in fact, the presence of water inhibits the reaction.

http://www.uncommondescent.com/origin-of-life/a-substantial-conundrum-confronting-the-chemical-origin-of-life/
Sea Salt only adds to this thermodynamic problem:
...even at concentrations seven times weaker than in today’s oceans. The ingredients of sea salt are very effective at dismembering membranes and preventing RNA units (monomers) from forming polymers any longer than two links (dimers). Creation Evolution News - Sept. 2002
The following article and videos have a fairly good overview of the major problems facing any naturalistic Origin Of Life scenario:
Origin of life researchers, approaching 2014 conference, sound glum about progress - Feb. 2014
Excerpt: The real mile stone came 1953 with Stanley Miller flask experiments, showing that amino acids can be formed under prebiotic conditions from a mixture of gas presumably present in the prebiotic atmosphere. Which conceptual progress have we made since then? It is too much to say that we didn’t really make any, if we look at data under really and honest prebiotic conditions?
Adding that this situation is not due to shortage of means and finances in the field- but to a real lack of difficulty to conceive conceptually how this nonliving-living passage really took place?

http://www.uncommondescent.com/origin-of-life/origin-of-life-researchers-approaching-2014-conference-sound-glum-about-progress/

The Shrouding of Origin of Life Research - Dec. 14, 2013
Excerpt: we’re up against these three or four paradoxes (for the origin of biological life),,, The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA.”,,,
http://www.darwinthenandnow.com/2013/12/the-shrouding-of-origin-of-life-research/
Origin Of Life - No Realistic Explanations - Charles Thaxton PhD. - video
http://www.metacafe.com/watch/5222490/

Here are two renowned Chemists who severely question the chemical origin of life:

Top Ten Most Cited Chemist in the World Knows That Evolution Doesn't Work - James Tour, Phd. - video
http://www.youtube.com/watch?v=A15p8f3wDM0

Dr. David Humphreys – The Origin of Life – video
http://www.youtube.com/watch?v=ozcmkD_f7bA

The Origin Of Life Requires Intelligence - Kirk Durston PhD - 2013 video
http://www.metacafe.com/w/10335610

Is the Chemical Origin of Life (Abiogenesis) a Realistic Scenario?
http://www.godandscience.org/evolution/chemlife.html

Evolution's Fatal Flaw - The Origin Of Life - Chris Ashcraft PhD - video
http://www.metacafe.com/watch/4347153

Evolutionary Assumptions - Life from dead chemicals? - video
http://www.youtube.com/watch?v=O1fteDkXLBE
"Shut up," Coyne Explained - January 2012
Excerpt: Coyne writes that Kuhn's criticisms of current origin-of-life research are "absurdly funny" -- even though such research (into the origin of life) has not led to the abiotic formation of a single functional protein, much less a living cell.
http://www.evolutionnews.org/2012/01/shut_up_coyne_e055421.html
Though the 1953 Miller-Urey experiment is often touted, by evolutionists, as evidence that life can spontaneously arise on the primitive earth, evolutionists always seem to fail to mention the severe problems that were found with the 1953 Miller-Urey experiment in which, among other severe problems, only a few of the building blocks for proteins, amino-acids, were ever actually produced in minute quantities in an artificial environment:
Miller-Urey Experiment
Excerpt: While successful in trapping some amino acids, this is now recognized as not being analogous to the real natural world - there are no known or even hypothesized protective traps observed in nature. What they made was 85% tar, 13% carboxylic acid add, (both toxic to life) and only 2% amino acids. Problem: mostly only 2 of the 20 different amino acids life needed were produced, and they are much more likely to bond with the tar or acid than they are with each other. Half of the amino acids were right-handed and half were left-handed. This is a problem because all proteins are left-handed and even the smallest proteins have 70-100 amino acids all in the precise order.
http://www.soulharvest.info/FAQ/Evolution/Commonlies/MillerUrey.html

On the Miller-Urey Experiment Wikipedia Offers a Citation Bluff - Casey Luskin - November 13, 2012
Excerpt: The bottom line is that these scenarios do NOT represent what would happen by unguided chemical reactions on the early earth or anywhere else. They need specialized intervention from a chemist -- i.e. an intelligent agent -- to carefully manipulate the conditions to get them to work. This paper is kind of like Sutherland's: one of the better pieces of work in the area but only convincing (or even impressive) for the already-convinced or the uninformed. Unfortunately, these kinds of papers leave non-specialists with a false impression that significant progress has been made. As you know, this is made much worse by a media that loves to promote these impressions.
http://www.evolutionnews.org/2012/11/on_the_miller-u066341.html

Why These 20 Amino Acids? - March 12, 2012 - Dr. Fazale Rana
Excerpt: Recent work from the University of Hawaii adds new insight, indicating that the set of amino acids used to make proteins is the optimal set.
http://www.reasons.org/articles/why-these-20-amino-acids

Rare Amino Acid Challenge to the Origin of Life
Excerpt: Granted that on early Earth arginine and lysine are either totally missing or available only at such extremely low abundance levels as to be irrelevant, and recognizing that arginine-and-lysine-containing proteins are essential for the crucial protein-DNA interactions, naturalistic explanations for the origin of life are ruled out.
http://www.reasons.org/rare-amino-acid-challenge-origin-life
Programming of Life - Amino Acids - video
http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/2/hixVhW-8ae0

The problem of 'left handed' homochirality found in the Miller-Urey experiment is of no small concern to any Origin Of Life scenario put forth by evolutionists:

Dr. Charles Garner on the problem of Chirality in nature and Origin of Life Research - audio
http://intelligentdesign.podomatic.com/player/web/2010-04-12T17_21_16-07_00

Origin Of Life - Problems With Proteins - Homochirality - Charles Thaxton PhD. - video
http://www.metacafe.com/watch/5222490
Homochirality and Darwin - Robert Sheldon - April 2010
Excerpt: there is no abiotic path from a racemic solution to a stereo-active solution of amino acid(s) that doesn't involve a biotic chiral agent, be it chiral beads or Louis Pasteur himself. Like many critiques of ID, the problem with these "Darwinist" solutions is that they always smuggle in some information, in this case, chiral agents.
http://rbsp.info/PROCRUSTES/homochirality-and-darwin/

Homochirality and Darwin: part 2 - Robert Sheldon - May 2010
Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn't imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos?
http://rbsp.info/PROCRUSTES/homochirality-and-darwin-part-2/
Left-Handed Amino Acids Explained Naturally? Not by a long shot! - January 2010
http://www.creationsafaris.com/crev201101.htm#20110110a

The deep unexplained mystery as to why biological molecules are chiral, 'either left- or right-handed', has, in large part, to do with the 'controllable circularly polarized coherent light output' of biological molecules. In other words, the mysterious chirality of biological molecules turns out to allow biological molecules to communicate using 'biological laser light';

Chirality and Biological Laser Light
https://docs.google.com/document/d/1avwUZsP_AsB16L72tD68cpC4kir6aa0W9CkYJUvc-lI/edit

The severity of the homochirality problem begins to highlight the number one question facing any Origin Of Life research. Namely, "Where is the specified complexity (information) coming from?" Even this recent 'evolution friendly' article readily admitted the staggering level of 'specified complexity' (information) being dealt with in the first cell:
Was our oldest ancestor a proton-powered rock? - Oct. 2009
Excerpt: “There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.”
http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html
So much for 'simple' life!
Colossians 1:16
For by him all things were created, in heaven and on earth, visible and invisible, whether thrones or dominions or rulers or authorities—all things were created through him and for him.
I think David Abel, the director of the Gene Emergence Project, does a very good job of highlighting just how crucial 'information' is to Origin of Life research:
Chance and necessity do not explain the origin of life: Trevors JT, Abel DL.
Excerpt: Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic--that is, it is programmatically and algorithmically organized and controlled.
http://www.ncbi.nlm.nih.gov/pubmed/15563395

Self-organization vs. self-ordering events in life-origin models - Abel; Trevors
Excerpt: No falsifiable theory of self-organization exists. “Self-organization” provides no mechanism and offers no detailed verifiable explanatory power. Care should be taken not to use the term “self-organization” erroneously to refer to low-informational, natural-process, self-ordering events, especially when discussing genetic information.
http://www.sciencedirect.com/science/article/pii/S1571064506000224
Does New Scientific Evidence About the Origin of Life Put an End to Darwinian Evolution? - Stephen Meyer - 4 part video
http://www.evolutionnews.org/2011/03/does_new_scientific_evidence_a045171.html

The "simplest" life currently found on the earth that is able to exist outside of a test tube, the parasitic Mycoplasmal, has between a 0.56-1.38 megabase genome. Yet Mycoplasma is still not a 'free living' cell but is a parasitic bacteria, with a stripped down genome, which is dependent on its host for a number of essential functions. A independent 'free-living' cell, such as a e-coli bacterium, has about 10 times as many genes as Mycoplasma (525 genes to 4,288 genes respectively):
Mycoplasma
Excerpt: There are no free-living Mycoplasma, they are strictly parasites. They parasitize a wide range of organism including humans, plants, animals, and insects. Mycoplasma grow very slowly, even under perfect conditions, with a generation time ranging up to nine hours in some species. They also have a very long lag phase, so it may take an entire week before colonies become visible on agar plates. Due to their degraded genome, and inability to perform basic functions, Mycoplasma rely on their host for much of their nutrition.
http://microbewiki.kenyon.edu/index.php/Mycoplasma#Ecology
Yet, even with this 'reduced complexity' in the parasitic Mycoplasma, we find that even the 'simplest' parasitic life on earth easily exceeds man's ability to produce such integrated complexity in his computer programs:
Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
"No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?"
http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf
Meet Mycoplasma, a parasitic bare-bones bacterium, with 484 genes - schematic representation of integrated enzyme cycles
http://www.pnas.org/content/103/2/425/F3.large.jpg

Mycoplasma Genitalium - The "Simplest" Life On Earth - video
http://www.metacafe.com/watch/4012738

The Dictionary of "Simplest" Life - Dr. Paul A. Nelson - video
http://www.youtube.com/watch?v=zJaetK9gvCo
First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009
Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
"At all three levels, we found M. pneumoniae was more complex than we expected,"

http://www.sciencedaily.com/releases/2009/11/091126173027.htm

There’s No Such Thing as a ‘Simple’ Organism - November 2009
Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function.
http://www.wired.com/wiredscience/2009/11/basics-of-life/

Simplest Microbes More Complex than Thought - Dec. 2009
Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes."
http://www.creationsafaris.com/crev200912.htm#20091229a

To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012
Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,
The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,,
,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,,

http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/
Here is the image, from the preceding article, on the integrated processes of M. genitalium
http://cdn.theatlantic.com/static/mt/assets/science/cellmodules.jpg
The Ham-Nye Creation Debate: A Huge Missed Opportunity - Casey Luskin - February 4, 2014
Ecerpt: "The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems."
(Sara Imari Walker and Paul C. W. Davies, "The algorithmic origins of life," Journal of the Royal Society Interface, 10: 20120869 (2012).)
http://www.evolutionnews.org/2014/02/the_ham-nye_deb081911.html

Comparing genomes to computer operating systems - Van - May 2010
Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,,
http://www.ncbi.nlm.nih.gov/pubmed/20439753
Programming of Life and its Prerequisites - Don Johnson - video
This presentation reviews the cell’s computers & computer programs, including computer, coding systems, & algorithmic requirements. The information questions unanswered as yet by science are highlighted.
http://vimeo.com/38531934

On top of the fact that we now know the genetic code of the simplest organism ever found on Earth is a highly advanced 'logic' code, which far surpasses man's ability to devise such codes, we also know for a fact no operation of logic ever performed by a computer will ever increase the algorithmic code inherent in a computer's program, i.e. Bill Gates will never use random number generators and selection software to write more highly advanced computer codes:
"... no operation performed by a computer can create new information."
Douglas G. Robertson, "Algorithmic Information Theory, Free Will and the Turing Test," Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34.
The 'simplest' life possible, by experiment, requires several hundred distinct interlocking protein types which further interlock with several hundred distinct genes in the DNA, which are all further interlocked with RNA, and the associated protein machinery, in an irreducibly complex manner that defies all attempts to reduce its complexity further.

William Dembski calls the DNA, RNA, Protein interlock problem :
"Irreducible Complexity on steroids".
Biological function and the genetic code are interdependent: Voie:
Life never ceases to astonish scientists as its secrets are more and more revealed. In particular the origin of life remains a mystery:
Chaos, Solitons and Fractals, 2006, Vol 28(4), 1000-1004.
http://home.online.no/~albvoie/index.cfm
Journey Inside The Cell - DNA to mRNA to Proteins - Stephen Meyer - Signature In The Cell - video
http://www.youtube.com/watch?v=1fiJupfbSpg

Simplified Protein Synthesis Animation Video
http://www.youtube.com/watch?v=Ikq9AcBcohA

At the 37 min. 15 sec. mark of this following video, Dr. Walter Bradley talks a little bit about the OOL problem and Watson and Crick's, the co-discoverers of the DNA helix, disbelieving reactions to the DNA, RNA, Protein, 'translation complexity' they found themselves to be dealing with:

Evidence for an Engineered Universe - Walter Bradley - video
http://www.youtube.com/watch?v=nLd_cPfysrE

Recently Craig Venter, of deciphering the human genome fame, created quite a stir, in the public imagination, by claiming to have 'created' synthetic life. The fact is that the claim was a gross exaggeration of what Venter's group had actually accomplished, for the truth is that they did not truly 'create' anything, not even a single protein or gene, they merely copied information that was already present in life before:
Is Craig Venter’s Synthetic Cell Really Life? - July 2010
Excerpt: David Baltimore was closer to the truth when he told the New York Times that the researchers had not created life so much as mimicked it. It might be still more accurate to say that the researchers mimicked one part and borrowed the rest.
http://www.uncommondescent.com/evolution/is-craig-venters-synthetic-cell-really-life/
“This is not life from scratch,” Venter says
http://www.uncommondescent.com/evolution/is-craig-venters-synthetic-cell-really-life/#comment-440685
Stephen Meyer Discusses Craig Venter's "Synthetic Life" on CBN - 9:30 minute mark of video
http://www.cbn.com/tv/1430349359001

Aside from the small, but impressive, technical feat of Venter's work, in reality researchers can't even say with 100% certainty what the minimal gene set for a genome is, much less are they anywhere near creating life from scratch in the laboratory:
John I. Glass et al., "Essential Genes of a Minimal Bacterium," PNAS, USA103 (2006): 425-30.
Excerpt: "An earlier study published in 1999 estimated the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.,,, Given the evolutionary path of extreme genome reduction taken by M. genitalium, it is likely that all its 482 protein-coding genes are in some way necessary for effective growth in its natural habitat"
http://www.pnas.org/content/103/2/425.full

The essential genome of a bacterium - 2011
Excerpt: Using hypersaturated transposon mutagenesis coupled with high-throughput sequencing, we determined the essential Caulobacter genome at 8bp resolution, including 1012 essential genome features: 480 ORFs, 402 regulatory sequences and 130 non-coding elements, including 90 intergenic segments of unknown function.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202797/pdf/msb201158.pdf

Life’s Minimum Complexity Supports ID - Fazale Rana - November 2011
Excerpt page 16: The Stanford investigators determined that the essential genome of C. crescentus consisted of just over 492,000 base pairs (genetic letters), which is close to 12 percent of the overall genome size. About 480 genes comprise the essential genome, along with nearly 800 sequence elements that play a role in gene regulation.,,, When the researchers compared the C. crescentus essential genome to other essential genomes, they discovered a limited match. For example, 320 genes of this microbe’s basic genome are found in the bacterium E. coli. Yet, of these genes, over one-third are nonessential for E. coli. This finding means that a gene is not intrinsically essential. Instead, it’s the presence or absence of other genes in the genome that determine whether or not a gene is essential.,,
http://www.reasons.org/files/ezine/ezine-2011-11/ezine-2011-11.pdf
The following study highlights the inherent fallacy in gene deletion/knockout experiments that have led many scientists astray in the past as to underestimating what the minimal genome for life should actually be:
Minimal genome should be twice the size - 2006
Excerpt: “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. “When you knock out one gene, the genome can compensate by using an alternative gene. “But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. “Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.
http://www.news-medical.net/news/2006/03/30/16976.aspx
Moreover Genetic Redundancy is incompatible with Darwinism:
The Problem Of Genetic Redundancy for Darwinism
Excerpt: the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the Darwinian (or: selectionist) concept. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes. Still, over 90% of the genes studies of model organisms were observed to be redundant [Conant GC et al, 2004; Kobayashi K et al, 2003; Baba T et al, 2006].
http://archive.is/YxXhd
Mouse Genome Knockout Experiment
http://www.uncommondescent.com/books-of-interest/new-book-junk-dna-junked-in-favour-of-what/comment-page-3/#comment-374647
Jonathan Wells on Darwinism, Science, and Junk DNA - November 2011
Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin​] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome(actually 1mb from a mouse genome is about .03%, not 1%.)—and that they could “see no effect in them.”
But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler​ said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.

http://www.uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
The probabilities against life 'spontaneously' originating are simply overwhelming:

In fact Dean Kenyon, who was a leading Origin Of Life researcher as well as a college textbook author on the subject in the 1970s, admitted after years of extensive research:
"We have not the slightest chance for the chemical evolutionary origin of even the simplest of cells".
Origin Of Life? - Probability Of Protein And The Information Of DNA - Dean Kenyon - video
http://www.youtube.com/watch?v=9VhR2BHhxeo

Probability of Simple Cell Spontaneously Forming - Jon Rittenhouse - Biola - video
http://www.metacafe.com/w/9742745

Probability Of A Protein and First Living Cell - Chris Ashcraft - video (notes in description)
http://vimeo.com/31536455

Stephen Meyer - Proteins by Design - Doing The Math - video
http://www.metacafe.com/watch/6332250/

Centre for Intelligent Design Lecture 2011 by Stephen Meyer on 'Signature in the Cell' - video
http://www.youtube.com/watch?v=NbluTDb1Nfs
Signature in the Cell - Book Review - Ken Peterson
Excerpt: If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell
In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

Professor Harold Morowitz shows the Origin of Life 'problem' escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,:
"The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!"
(Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)
Dr. Don Johnson lays out some of the probabilities for life in this following video:
Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video
a typical functional protein - 1 part in 10^175
the required enzymes for life - 1 part in 10^40,000
a living self replicating cell - 1 part in 10^340,000,000

http://www.vimeo.com/11706014

Increasing Genomic Information - Don Johnson - video
Excerpt: Forming the simplest life is 10^300,000,000 more likely that forming a human life
http://www.youtube.com/watch?v=VYFq9mpCT6c
Programming of Life - Probability of a Cell Evolving - video
http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/9/nyTUSe99z6o
Programming of Life - video playlist:
http://www.youtube.com/playlist?list=PLAFDF33F11E2FB840

Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number:
DID LIFE START BY CHANCE?
Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
http://members.tripod.com/~Black_J/chance.html
Punctured cell will never reassemble - Jonathan Wells - 2:40 mark of video
http://www.youtube.com/watch?v=WKoiivfe_mo

Also of interest is the information content that is derived in a cell when working from a thermodynamic perspective:
“a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong
http://books.google.com/books?id=yNev8Y-xN8YC&pg=PA112&lpg=PA112

'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica."
Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894
of note: The 10^12 bits of information number for a bacterium is derived from entropic considerations, which is, due to the tightly integrated relationship between information and entropy, considered the most accurate measure of the transcendent quantum information/entanglement constraining a 'simple' life form to be so far out of thermodynamic equilibrium.
"Is there a real connection between entropy in physics and the entropy of information? ....The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental..." Siegfried, Dallas Morning News, 5/14/90, [Quotes Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin]

Demonic device converts information to energy - 2010
Excerpt: "This is a beautiful experimental demonstration that information has a thermodynamic content," says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. "This tells us something new about how the laws of thermodynamics work on the microscopic scale," says Jarzynski.
http://www.scientificamerican.com/article.cfm?id=demonic-device-converts-inform
For calculations, from the thermodynamic perspective, please see the following site:
Moleular Biophysics – Information theory. Relation between information and entropy: - Setlow-Pollard, Ed. Addison Wesley
Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz' deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
http://www.astroscu.unam.mx/~angel/tsb/molecular.htm
It is interesting to note, long before DNA was discovered, just how far back in history that 'information' has been seen to be a insurmountable problem for purely material processes:
A brief history of design
Excerpt: Cicero (106–43 BC) continued his challenge to the evolutionism of Epicurus by marveling that anyone could persuade himself that chance collisions of particles could form anything as beautiful as the world. He said that this was on a par with believing that if the letters of the alphabet were thrown on the ground often enough they would spell out the Annals of Ennius.
http://creation.com/a-brief-history-of-design
Further comments:
The Theist holds the Intellectual High-Ground - March 2011
Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)
http://www.faithfulnews.com/contents/view_content2/49631/rabbi-moshe-averick-the-theist-holds-the-intellectual-high-ground-apologetics-christian-apologetics-defending-gospel

Scientists Prove Again that Life is the Result of Intelligent Design - Rabbi Moshe Averick - August 2011
Excerpt: “To go from bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.” - Dr. Lynn Margulis
http://www.algemeiner.com/2011/08/17/scientists-prove-again-that-life-is-the-result-of-intelligent-design/

“From the beginning of this book we have emphasized the enormous information content of even the simplest living systems. The information cannot in our view be generated by what are often called ‘natural’ processes, as for instance through meteorological and chemical processes occurring at the surface of a lifeless planet. As well as a suitable physical and chemical environment, a large initial store of information was also needed. We have argued that the requisite information came from an ‘intelligence’, -
Sir Fred Hoyle, Chandra Wickramasinghe - A Theory of Cosmic Creationism - pg. 150
http://www.creationscience.com/onlinebook/ReferencesandNotes32.html
Here is a related article with several more excellent quotes, by leading origin of life researchers, commenting on the 'problem' that the origin of life presents to 'science' (actually it is only a problem for atheists who 'believe' that 'science' equates strictly to their reductive materialistic view of reality):

Faye Flam: Atheist Writer Who is Long on Graciousness, Long on Civility… Short on Reason, Short on Scientific Realities - Rabbi Averick
http://www.algemeiner.com/2012/01/12/faye-flam-atheist-writer-who-is-long-on-graciousness-long-on-civility-short-on-reason-short-on-scientific-realities-2/

The following videos give a small glimpse into how the probabilities are calculated for the origin of life:

The Origin of Life - Lecture On Probability - John Walton - Professor Of Chemistry - short video
http://www.metacafe.com/watch/4012749
Entire Video:
http://edinburghcreationgroup.org/originoflife.xml

Protein Molecules and "Simple" Cells - video
http://www.youtube.com/watch?v=uFNwStNhHIc

Further notes:

Evolution: Possible or Impossible? - free e-book (with plenty of examples from math) - by Dr. James F. Coppedge
http://creationsafaris.com/epoi_toc.htm

Ilya Prigogine was an eminent chemist and physicist who received two Nobel Prizes in chemistry. Regarding the probability of life originating by accident, he said:
“The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.”
Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz, Physics Today 25, pp. 23-28. (Sourced Quote)
http://en.wikiquote.org/wiki/Western_Thought_on_Creation
http://www.miraclesormagic.com/intelligent-design-vs-evolution.html

Atheistic Science is Rapidly Sinking in the Quicksand - January 28, 2013 - Rabbi Moshe Averick
Excerpt: As Nobel Prize winner, Dr. Jacque Monod explains in his classic work, Chance and Necessity, there are no chemical or physical laws that determine any particular order of amino acids to build the first proteins (all amino acids can link together equally well) and similarly there are no chemical or physical laws that would determine the sequences of nucleotides that code for these proteins in DNA. The only option left for him is chance. He acknowledges that the random probability of such a system coming into being is “virtually zero.”
http://www.algemeiner.com/2013/01/28/atheistic-science-is-rapidly-sinking-in-the-quicksand/

The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012
Excerpt: Tompa and Rose calculate the "total number of possible distinct patterns of interactions," using yeast, a unicellular eukaryote, as their model system; this "total number" is the size of the space that must be searched. With approximately 4,500 proteins in yeast, the interactome search space "is on the order of 10^7200, an unimaginably large number," they write -- but "more realistic" estimates, they continue, are "yet more complicated." Proteins present many possible surfaces for chemical interaction. "In all," argue Tompa and Rose, "an average protein would have approximately 3540 distinguishable interfaces," and if one uses this number for the interactome space calculation, the result is 10 followed by the exponent 7.9 x 10^10.,,, the numbers preclude formation of a functional interactome (of 'simple' life) by trial and error,, within any meaningful span of time. This numerical exercise...is tantamount to a proof that the cell does not organize by random collisions of its interacting constituents. (i.e. that life did not arise, nor operate, by chance!)
http://www.evolutionnews.org/2012/10/a_revolutionary065521.html

Origins - Statistical Impossibility of Evolution with Ralph Muncaster - video
(Mr. Muncaster holds a BS in engineering and an MBA from the University of Colorado. A former atheist and hardcore Bible skeptic, Ralph had spent 15 years conducting research to dispute the Bible (and ended up becoming a believer.)
http://www.youtube.com/watch?v=DXIAbd8pYQM

On the Impossibility of Abiogenesis - June 2012
Excerpt: Modern science takes for granted that the naturalistic origin of life, called “abiogenesis” or “chemical evolution” or “pre-biotic evolution” is extremely improbable but not impossible. “Life” here means a single self-reproducing and self-sustaining biological cell. Science claims that life can arise from inorganic matter through natural processes. This unsupported claim is based on the conviction that all arrangements of atoms are possible and life is considered merely one such arrangement. In what follows I try to explain that such a believe is unfounded because abiogenesis is impossible in principle.
http://www.uncommondescent.com/intelligent-design/on-the-impossibility-of-abiogenesis/
Anyone who has debated an evolutionist, over the probability of life spontaneous arising, knows that it can be quite frustrating because eventually the person will realize that many times the evolutionist will not be reasonable on the matter and that he is operating on nothing but blind faith that life can spontaneously arise by unintelligent processes. Here are a few more links relating to the (im)probability of life:
Probability's Nature and Nature's Probability: A Call to Scientific Integrity - Donald E. Johnson
Excerpt: "one should not be able to get away with stating “it is possible that life arose from non-life by ...” or “it’s possible that a different form of life exists elsewhere in the universe” without first demonstrating that it is indeed possible (non-zero probability) using known science. One could, of course, state “it may be speculated that ... ,” but such a statement wouldn’t have the believability that its author intends to convey by the pseudo-scientific pronouncement."
http://www.amazon.com/Probabilitys-Nature-Natures-Probability-Scientific/dp/1439228620
Intelligent Design: Required by Biological Life? K.D. Kalinsky - Pg. 11
Excerpt: It is estimated that the simplest life form would require at least 382 protein-coding genes. Using our estimate in Case Four of 700 bits of functional information required for the average protein, we obtain an estimate of about 267,000 bits for the simplest life form. Again, this is well above Inat and it is about 10^80,000 times more likely that ID (Intelligent Design) could produce the minimal genome than mindless natural processes.
http://www.newscholars.com/papers/ID%20Web%20Article.pdf

Could Chance Arrange the Code for (Just) One Gene?
"our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)."
http://www.creationsafaris.com/epoi_c10.htm
Even the low end 'hypothetical' probability estimate given by a evolutionist, for life spontaneously arising, is fantastically impossible:
General and Special Evidence for Intelligent Design in Biology:
- The requirements for the emergence of a primitive, coupled replication-translation system, which is considered a candidate for the breakthrough stage in this paper, are much greater. At a minimum, spontaneous formation of: - two rRNAs with a total size of at least 1000 nucleotides - ~10 primitive adaptors of ~30 nucleotides each, in total, ~300 nucleotides - at least one RNA encoding a replicase, ~500 nucleotides (low bound) is required. In the above notation, n = 1800, resulting in E < 10^-1018. That is, the chance of life occurring by natural processes is 1 in 10 followed by 1018 zeros. (Koonin's intent was to show that short of postulating a multiverse of an infinite number of universes (Many Worlds), the chance of life occurring on earth is vanishingly small.)
http://www.conservapedia.com/General_and_Special_Evidence_for_Intelligent_Design_in_Biology
The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life - Eugene V Koonin
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892545/
Origin of life both one of the hardest and most important problems in science - November 2011
Excerpt: 'Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.' - Eugene V. Koonin, molecular biologist
http://www.uncommondescent.com/intelligent-design/he-said-it-origin-of-life-both-one-of-the-hardest-and-most-important-problems-in-science-and-the-solution-is/
It should be stressed that Dr. Koonin tries to account for the origination of the massive amount of functional information, required for the Origin of Life, by trying to access an 'unelucidated and undirected' mechanism of Quantum Mechanics called 'Many Worlds in one'(He is trying to invoke a ‘materialistic miracle’). Besides Dr. Koonin ignoring the fact that Quantum Events, on a whole, are strictly restricted to the transcendent universal laws/constants of the universe, including and especially the second law of thermodynamics, for as far back in time in the universe as we can 'observe', it is also fair to note, in criticism to Dr. Koonin’s scenario, that appealing to the undirected infinite probabilistic resource, of the quantum mechanics of the Many Worlds scenario, actually greatly increases the amount of totally chaotic information one would expect to see generated 'randomly' on the earth. In fact the Many Worlds scenario actually greatly increases the likelihood we would witness total chaos, instead of order, surrounding us as the following video points out:

Finely Tuned Big Bang, Elvis In Many Worlds, and the Schroedinger Equation – Granville Sewell – audio
http://www.metacafe.com/watch/4233012

Though Koonin appeals to a 'modern version' of Many Worlds, called 'Many Worlds in One' (Alex Vilenkin), 'Many Worlds' was originally devised because of the inability of materialistic scientists to find adequate causation for quantum wave collapse in the first place (i.e. that is, adequate causation that did not involve God!):
Quantum mechanics
Excerpt: The Everett many-worlds interpretation, formulated in 1956, holds that all the possibilities described by quantum theory simultaneously occur in a multiverse composed of mostly independent parallel universes.[39] This is not accomplished by introducing some new axiom to quantum mechanics, but on the contrary by removing the axiom of the collapse of the wave packet:
http://en.wikipedia.org/wiki/Quantum_mechanics
Perhaps some may say Everett’s Many Worlds in not absurd, if so, then in some other parallel universe, where Elvis happens to now be president of the United States, they actually do think that the Many Worlds conjecture is absurd! That type of 'flexible thinking' within science I find to be completely absurd! And that one 'Elvis' example from Many Worlds is just small potatoes to the levels of absurdity that we would actually witness in reality if Many Worlds were actually true.

Though Eugene Koonin is correct to recognize that the infinite probabilistic resource postulated in ‘Many Worlds’ does not absolutely preclude the sudden appearance of massive amounts of functional information on the earth, he is very incorrect to disregard the ‘Logos’ of John 1:1 needed to correctly specify the ‘precisely controlled mechanism of implementation’ for the massive amounts of complex functional and specified information witnessed abruptly and mysteriously appearing in the first life on earth, nor for the mysterious appearing of the subsequent 'sudden' appearances of life on earth. i.e. Koonin must sufficiently account for the 'cause' for the 'effect' he wants to explain. And as I have noted previously, Stephen Meyer clearly points out that the only known cause now in operation, sufficient to explain the generation of the massive amounts of functional information we find in life, is intelligence:

Stephen C. Meyer – What is the origin of the digital information found in DNA? – August 2010 - video
http://www.evolutionnews.org/2010/08/stephen_meyer_on_intelligent_d037271.html

Evolutionist Koonin's estimate of 1 in 10 followed by 1018 zeros, for the probability of the simplest self-replicating molecule 'randomly occurring', is a fantastically large number. The number, 10^1018, if written out in its entirety, would be a 1 with one-thousand-eighteen zeros following to the right! The universe itself is estimated to have only 1 with 80 zeros following to the right particles in it. This is clearly well beyond the 10^150 universal probability bound set by William Dembski and is thus clearly a irreducibly complex condition. Basically Koonin, in appealing to a never before observed 'materialistic miracle' from the 'Many Worlds' hypothesis, clearly illustrates that the materialistic argument essentially appears to be like this:
Premise One: No materialistic cause of specified complex information is known.
Conclusion: Therefore, it must arise from some unknown materialistic cause
On the other hand, Stephen Meyer describes the intelligent design argument as follows:
“Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
“Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
“Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”


There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs -- intelligent design. We know this from our uniform experience and from the design filter -- a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)

"Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent."
(Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)
Is intelligent design merely an "argument from ignorance?" (Dembski's Design Filter)
http://www.ideacenter.org/contentmgr/showdetails.php/id/1186

Stephen Meyer - The Scientific Basis for the Intelligent Design Inference - video
http://vimeo.com/32148403

Infographic - Intelligence is the most causually adequate explantion for irreducible complexity and specified complexity (functional information) in biochemistry
http://www.evolutionnews.org/2013/09/post_41077191.html

What Is the Theory of Intelligent Design? - Casey Luskin - August 10, 2013
http://www.evolutionnews.org/2013/08/what_is_the_the075281.html
Response to Darrel Falk’s Review of Signature in the Cell - Stephen Meyer
Excerpt: The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question.
http://www.signatureinthecell.com/responses/response-to-darrel-falk.php
Stephen Meyer's Rebuttal to Robert Asher's "You Don't Have A Mechanism" Argument - Jan. 2014
http://www.evolutionnews.org/2014/01/meyer_asher_rebuttal081161.html

Is There Evidence of Something Beyond Nature? - (Semiotic Information) - John Lennox - video
http://www.youtube.com/watch?v=F6rd4HEdffw

Alvin Plantinga on Being Created in God's Image - video
http://www.youtube.com/watch?v=hyrdicomWk8

Though purely material processes have NEVER shown the ability to produce ANY functional information whatsoever (Abel - Null Hypothesis), Darwinists are adamant that material processes produced more information, of a much higher level of integrated complexity than man can produce, than is contained in a very large library:
“a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong
http://www.uncommondescent.com/darwinism/media-mum-about-deranged-darwinist-gunman/#comment-363647

“Again, this is characteristic of all animal and plant cells. Each nucleus … contains a digitally coded database larger, in information content, than all 30 volumes of the Encyclopaedia Britannica put together. And this figure is for each cell, not all the cells of a body put together. … When you eat a steak, you are shredding the equivalent of more than 100 billion copies of the Encyclopaedia Britannica.”
(Dawkins R., “The Blind Watchmaker [1986], Penguin: London, 1991, reprint, pp.17-18. Emphasis in original)
http://www.uncommondescent.com/darwinism/media-mum-about-deranged-darwinist-gunman/#comment-363645
When faced with the staggering impossibilities of random material processes ever generating any functional information, Evolutionists will sometimes make the claim that infinite monkeys banging away on infinite typewriters could produce the entire works of Shakespeare. Well someone humorously put that 'hypothesis' to the test:
Monkey Theory Proven Wrong:
Excerpt: A group of faculty and students in the university’s media program left a computer in the monkey enclosure at Paignton Zoo in southwest England, home to six Sulawesi crested macaques. Then, they waited. At first, said researcher Mike Phillips, “the lead male got a stone and started bashing the hell out of it. “Another thing they were interested in was in defecating and urinating all over the keyboard,” added Phillips, who runs the university’s Institute of Digital Arts and Technologies. Eventually, monkeys Elmo, Gum, Heather, Holly, Mistletoe and Rowan produced five pages of text, composed primarily of the letter S. Later, the letters A, J, L and M crept in — not quite literature.
http://www.arn.org/docs2/news/monkeysandtypewriters051103.htm

The story of the Monkey Shakespeare Simulator Project
Excerpt: Starting with 100 virtual monkeys typing, and doubling the population every few days, it put together random strings of characters. It then checked them against the archived works of Shakespeare. Before it was scrapped, the site came up with 10^35 number of pages, all typed up. Any matches?
Not many. It matched two words, “now faire,” and a partial name from A Midsummer Night’s Dream, and three words and a comma, “Let fame, that,” from Love’s Labour’s Lost. The record, achieved suitably randomly at the beginning of the site’s run in 2004, was 23 characters long, including breaks and spaces.

http://io9.com/5809583/the-story-of-the-monkey-shakespeare-simulator-project
Can Monkeys Type Shakespeare? (Doing the math) - video
http://www.youtube.com/watch?v=MkEvzRMEP3s
Written by Chance?
Excerpt: "You might think that someone wrote this article. But of course, you would be mistaken. Articles are not written by people. They are the result of chance. Every intelligent person knows it. There might be some people who want you to think that articles are written by people. But this view is totally unscientific. After all, we cannot see the person who allegedly wrote the article. We cannot detect him or her in any way. The claim that this article has an author cannot be empirically verified, and therefore it must be rejected. All we have is the article itself, and we must find a scientific explanation for its origin. ,,,"
http://www.youroriginsmatter.com/conversations/view/written-by-chance/142
The following is a very interesting 'origin of first self-replicating molecule' interview with one of the top chemists in America today:

On The Origin Of Life And God - Henry F. Schaefer, III PhD. - video
http://www.metacafe.com/watch/4018204

Further comments:
Intelligent Design or Evolution? Stuart Pullen
The chemical origin of life is the most vexing problem for naturalistic theories of life's origins. Despite an intense 50 years of research, how life can arise from non-life through naturalistic processes is as much a mystery today as it was fifty years ago, if not more.
http://www.arn.org/arnproducts/php/book_show_item.php?id=106

If the evidence for God is so strong, why are so many smart people unconvinced?
Excerpt: “Many investigators feel uneasy about stating in public that the origin of life is a mystery, even though behind closed doors they freely admit that they are baffled.”
http://www.godevidence.com/2010/10/if-the-evidence-for-god-is-so-strong-why-are-so-many-smart-people-unconvinced/

When You Wish Upon a Star - May 14, 2012
Excerpt: "Didn't President Clinton announce in 1996 that a Martian meteorite recovered in Antarctica "speaks of the possibility of life" on Mars? (No, it turned out to be mineralic artifacts.) Wasn't some "alien" arsenic-based life discovered recently in Mono Lake, California? (No, it's a familiar proteobacterium struggling to survive in a toxic environment.) Didn't Craig Venter and his colleagues recently create a synthetic bacterial cell, "the first self-replicating species we've had on the planet whose parent is a computer"? (No, its parent is Mycoplasma mycoides and its genome was dutifully reconstructed through DNA synthesis and PCR amplification.)" - Dr. Gerald Joyce - a leading origin of life researcher
http://www.evolutionnews.org/2012/05/when_you_wish_u059591.html

Szostak on Abiogenesis: Just Add Water - Cornelius Hunter - Aug. 2009
Excerpt: "While Szostak and Ricardo may sound scientific with their summary of the abiogenesis research, the article is firmly planted in the non scientific evolution genre where evolution is dogmatically mandated to be a fact. Consequently, the bar is lowered dramatically as the silliest of stories pass as legitimate science."
http://darwins-god.blogspot.com/2009/08/szostak-on-abiogenesis-just-add-water.html
Along these lines of 'silliest of stories' passing for rigorous science in origin of life research:
Grandma Gets Sexy Idea for Origin of Life - August 2010
Excerpt: In the video clip, she suggested that it might be possible some day to get good evidence for her ideas on the origin of life, implying that evidence has not yet been a primary concern.
http://www.creationsafaris.com/crev201008.htm#20100807a

SETI Ignorance Gets Stronger - December 2010
Excerpt: Steve Benner, an origin of life researcher, “used the analogy of a steel chain with a tinfoil link to illustrate that the arsenate ion said to replace phosphate in the bacterium’s DNA forms bonds that are orders of magnitude less stable.”
http://www.creationsafaris.com/crev201012.htm#20101209a

Scientists say NASA's 'new arsenic form of life' was untrue - July 9, 2012
Excerpt: "Contrary to an original report, the new research clearly shows that the bacterium, GFAJ-1, cannot substitute arsenic for phosphorus to survive," said a statement by the US journal Science, a prestigious, peer-reviewed magazine.
http://phys.org/news/2012-07-scientists-nasa-arsenic-life-untrue.html

Study Confirms that Arsenic-Containing Bacteria Prefer Phosphorous - October 9, 2012
Excerpt: Furthermore, arsenic is substantially larger (on a molecular scale) than phosphorous, which would stress the three-dimensional structure of the DNA molecule as well as any associated bonding with other proteins.
Even if bacteria had incorporated arsenate into its DNA, something that was not definitively proved when the announcement was made, there is no reason to believe that this structure is as stable as its phosphate alternative, and certainly no reason to believe that it leads to protein translation.
Several scientists voiced their concern over this and other issues with the study. Casey Luskin documented them here (link at site).
Now, almost two years later, Nature confirms what most of us already figured was true: "'Arsenic-life' bacterium prefers phosphorous after all." This paper addresses one of the unconfirmed questions regarding this study: How do the bacteria know the difference between phosphate and arsenate, and do the bacteria prefer one over the other? Those questions have been laid to rest. Not only do the bacteria preferentially consume phosphate, but they are so desperate for the stuff that they will fish out the smallest bit of phosphate in a sea of arsenate.

http://www.evolutionnews.org/2012/10/latest_non-news065081.html

Pumice and the Origin of Life - October 17, 2011
Excerpt: However, the reactions required are not simple reactions, and the steps involved, even using a substrate such as pumice, are still too numerous and specific to have happened by chance. It appears highly unlikely that pumice is capable of solving the problem of the origin of life.
http://www.evolutionnews.org/2011/10/pumice_and_the_origin_of_life051861.html

'We are all Martians': Chemist's otherworldly claim stirs debate - Alan Boyle, Aug. 28, 2013
Excerpt: If left to themselves, adding energy to organic molecules just tends to turn them into tar or an oily substance. That's what Benner calls the "tar paradox": How could organic materials ever give rise to biopolymers like DNA?
"Certain elements seem able to control the propensity of organic materials to turn into tar, particularly boron and molybdenum, so we believe that minerals containing both were fundamental to life first starting," Benner said. Such minerals can't form easily in the presence of water, but the early Earth was thought to have been covered with water.,,,

http://www.nbcnews.com/science/we-are-all-martians-chemists-otherworldly-claim-stirs-debate-8C11026339

"In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously -- and every reason to believe that they cannot. The problem of achieving sufficient specificity, whether in consisting of or occurring within a water-based system, aqueous solution, or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible." Leslie Orgel, 1998
By the way, there is a one million dollar 'Origin-of-Life' prize being offered:
"The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life.
http://www.us.net/life/index.htm
To reiterate, the problem for the origin of life clearly turns out to be explaining where the information came from in the first place:
“The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”
Origin of life theorist Bernd-Olaf Kuppers in his book "Information and the Origin of Life".

Book Review - Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren't chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it's a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.

http://www.fourmilab.ch/documents/reading_list/indices/book_726.html

To clarify as to how the 500 bit universal limit is found for 'structured, functional information':

Dembski's original value for the universal probability bound is 1 in 10^150,

10^80, the number of elementary particles in the observable universe.
10^45, the maximum rate per second at which transitions in physical states can occur.
10^25, a billion times longer than the typical estimated age of the universe in seconds.

Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang.

How many bits would that be:

Pu = 10-150, so, -log2 Pu = 498.29 bits

Call it 500 bits (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity)

Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors
http://www.tbiomed.com/content/2/1/29
Arguing God from Teleology? (William Dembski) – video
http://www.youtube.com/watch?v=iGTOQ-fUNMY

Sequences Probability Calculator v.1.1
http://progettocosmo.altervista.org/spc.php
How to calculate Chi_500, a log-reduced, simplified form of the Dembski Chi-metric for CSI
Excerpt: Item 6 So, the idea of the Dembski metric in the end — debates about peculiarities in derivation notwithstanding — is that if the Hartley-Shannon- derived information measure for items from a hot or target zone in a field of possibilities is beyond 398 – 500 or so bits, it is so deeply isolated that a chance dominated process is maximally unlikely to find it, but of course intelligent agents routinely produce information beyond such a threshold.
http://www.uncommondescent.com/intelligent-design/how-to-calculate-chi_500-a-log-reduced-simplified-form-of-the-dembski-chi-metric-for-csi/

This short sentence, "The quick brown fox jumped over the lazy dog" is calculated by Winston Ewert, in this following video at the 10 minute mark, to contain 1000 bits of algorithmic specified complexity, and thus to exceed the Universal Probability Bound (UPB) of 500 bits set by Dr. Dembski
Proposed Information Metric: Conditional Kolmogorov Complexity - Winston Ewert - video
http://www.youtube.com/watch?v=fm3mm3ofAYU

Here are the slides of preceding video with the calculation of the information content of the preceding sentence on page 14
http://www.blythinstitute.org/images/data/attachments/0000/0037/present_info.pdf

Lack of Signal Is Not a Lack of Information - July 18, 2012
Excerpt: Putting it all together:
The NFL (No Free Lunch) Theorems show that evolution is stuck with a blind search. Information lights the path out of blind search; the more information, the brighter the light.
Complex specified information (CSI) exceeds the UPB, so in the evolutionary context a blind search is not an option.
Our uniform experience with CSI is that it always has an intelligent cause.
Evolution is disconfirmed by negative arguments (NFL theorems and the UPB). Intelligent design is confirmed by positive arguments (uniform experience and inference to the best explanation).

http://www.evolutionnews.org/2012/07/lack_of_signal062231.html

"Monkeys Typing Shakespeare" Simulation Illustrates Combinatorial Inflation Problem - October 2011
Excerpt: In other words, Darwinian evolution isn't going to be able to produce fundamentally new protein folds. In fact, it probably wouldn't even be able to produce a single 9-character string of nucleotides in DNA, if that string would not be retained by selection until all 9 nucleotides were in place.
http://www.evolutionnews.org/2011/10/monkeys_typing_shakespeare_sim051561.html

Dilbert - infinite monkeys - cartoon
http://dilbert.com/fast/2013-12-12/

Before They've Even Seen Stephen Meyer's New Book, Darwinists Waste No Time in Criticizing Darwin's Doubt - William A. Dembski - April 4, 2013
Excerpt: In the newer approach to conservation of information, the focus is not on drawing design inferences but on understanding search in general and how information facilitates successful search. The focus is therefore not so much on individual probabilities as on probability distributions and how they change as searches incorporate information. My universal probability bound of 1 in 10^150 (a perennial sticking point for Shallit and Felsenstein) therefore becomes irrelevant in the new form of conservation of information whereas in the earlier it was essential because there a certain probability threshold had to be attained before conservation of information could be said to apply. The new form is more powerful and conceptually elegant. Rather than lead to a design inference, it shows that accounting for the information required for successful search leads to a regress that only intensifies as one backtracks. It therefore suggests an ultimate source of information, which it can reasonably be argued is a designer. I explain all this in a nontechnical way in an article I posted at ENV a few months back titled "Conservation of Information Made Simple" (go here). ,,,
,,, Here are the two seminal papers on conservation of information that I've written with Robert Marks:
"The Search for a Search: Measuring the Information Cost of Higher-Level Search," Journal of Advanced Computational Intelligence and Intelligent Informatics 14(5) (2010): 475-486
"Conservation of Information in Search: Measuring the Cost of Success," IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, 5(5) (September 2009): 1051-1061
For other papers that Marks, his students, and I have done to extend the results in these papers, visit the publications page at www.evoinfo.org
http://www.evolutionnews.org/2013/04/before_theyve_e070821.html

Of Molecules and (Straw) Men: Stephen Meyer Responds to Dennis Venema's Review of Signature in the Cell - Stephen C. Meyer October 9, 2011
Excerpt of Conclusion: The origin-of-life scenarios that Venema cites as alternatives to intelligent design lack biochemical plausibility and do not account for the ultimate origin of biological information.
http://www.evolutionnews.org/2011/10/of_molecules_and_straw_men_a_r051601.html

Natural selection cannot explain the origin of life
Excerpt: “DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.”
Paul Davies
http://creation.com/ns-origin-of-life

“The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.”,,,"The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.”
Hubert P. Yockey: Information Theory, Evolution, and the Origin of Life, page 2 and 5

H.P. Yockey also notes in the Journal of Theoretical Biology:
It is important to understand that we are not reasoning by analogy. The sequence hypothesis applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical:
"Self Organization Origin of Life Scenarios and Information Theory," J. Theoret. Biol.

"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."
Norbert Weiner - MIT Mathematician - Father of Cybernetics

“One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin?
And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce.
In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires.
Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.”

-Dr. Stephen C. Meyer earned his Ph.D. in the History and Philosophy of science from Cambridge University for a dissertation on the history of origin-of-life biology and the methodology of the historical sciences.

Programming of Life - October 2010
Excerpt: "Evolutionary biologists have failed to realize that they work with two more or less incommensurable domains: that of information and that of matter... These two domains will never be brought together in any kind of the sense usually implied by the term ‘reductionism.'... Information doesn't have mass or charge or length in millimeters. Likewise, matter doesn't have bytes... This dearth of shared descriptors makes matter and information two separate domains of existence, which have to be discussed separately, in their own terms."
George Williams - Evolutionary Biologist
http://scienceintegrity.net/ProgrammingofLife.aspx
The simplest, non-parasitic, bacteria ever found on earth is constructed with over a million individual protein molecules divided into hundreds of different protein types. Protein molecules are made from one dimensional sequences of the 20 different L-amino acids that can be used as building blocks for proteins. (there are hundreds of amino acids found in nature, but only 20 are commonly used in life). These one dimensional sequences of amino acids fold into highly complex three-dimensional structures. The proteins vary in length of sequences of amino acids. The average sequence of a typical protein is about 300 to 400 amino acids long. Yet many crucial proteins are thousands of amino acids long. Titin, which helps in the contraction of striated muscle tissues, consists of 34,350 amino acids, and is the largest known protein. Some proteins are now shown to be absolutely irreplaceable in their specific biological/chemical reactions for the first cell:
Without enzyme, biological reaction essential to life takes 2.3 billion years: UNC study:
In 1995, Wolfenden reported that without a particular enzyme, a biological transformation he deemed “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years.“Now we’ve found a reaction that – again, in the absence of an enzyme – is almost 30 times slower than that,” Wolfenden said. “Its half-life – the time it takes for half the substance to be consumed – is 2.3 billion years, about half the age of the Earth. Enzymes can make that reaction happen in milliseconds.”
http://www.med.unc.edu/www/news/2008-news-archives/november/without-enzyme-biological-reaction-essential-to-life-takes-2-3-billion-years-unc-study/?searchterm=Wolfenden

"Phosphatase speeds up reactions vital for cell signalling by 10^21 times. Allows essential reactions to take place in a hundreth of a second; without it, it would take a trillion years!" Jonathan Sarfati
http://www.pnas.org/content/100/10/5607.abstract

Programming of Life - Proteins & Enzymes - video
http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/3/BOxR23EdG3s

Book Review: Creating Life in the Lab: How New discoveries in Synthetic Biology Make a Case for the Creator - Rich Deem - January 2011
Excerpt: Despite all this "intelligent design," the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, "is it reasonable to think that undirected evolutionary processes routinely accomplished this task?"
http://www.godandscience.org/evolution/creating_life_in_the_lab.html

Research group develops more efficient artificial enzyme - November 2011
Excerpt: Though the artificial enzyme is still many orders of magnitude less efficient than nature’s way of doing things, it is far more efficient than any other artificial process to date, a milestone that gives researchers hope that they will one day equal nature’s abilities.
http://www.physorg.com/news/2011-11-group-efficient-artificial-enzyme.html
When they try to heat solutions to get around these prohibitive reaction times they run into the competing problem of product stability:
Is the Origin of Life in Hot Water? - December 2010
Excerpt: Heating a reaction does nothing for product stability. Cooling a reaction makes the reaction rate problems worse.
http://www.evolutionnews.org/2010/12/is_the_origin_of_life_in_hot_w041311.html
To reiterate what was quoted before, amino acids don't even have a tendency to chemically bond with each other, despite over fifty years of experimentation trying to get the amino acids to bond naturally. The odds of just one protein of 150 amino acids, overcoming the barriers presented by chemical bonding and forming a functional protein spontaneously, have been calculated at less than 1 in 10^164 (Meyer, Signature In The Cell). On top of the fact that nature cannot 'naturally' produce proteins, the limit to man's ability to 'intelligently' form a single synthetic amino acid chain (a protein), using all his intelligence and lab equipment, is currently severely constrained to about 70-100 amino acids:
Peptide synthesis
"typically peptides and proteins in the range of 70~100 amino acids are pushing the limits of synthetic accessibility. Synthetic difficulty also is sequence dependent; typically amyloid peptides and proteins are difficult to make."(To make larger proteins requires “non-natural” peptide bonds - (Chemical Synthesis Of Proteins - 2005))
http://en.wikipedia.org/wiki/Peptide_synthesis
On top of that, Doug Axe has shown that only 1 in 10^77 of any proteins 'randomly' formed would perform any beneficial biological function. The rest of the sequences would be totally useless for any meaningful function in the cell. Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place.
Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
http://www.toriah.org/articles/axe-2004.pdf

Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe
http://www.biologicinstitute.org/post/19310918874/correcting-four-misconceptions-about-my-2004-article-in

ID Scientist Douglas Axe Responds to His Critics - June 2011 - Audio Podcast
http://intelligentdesign.podomatic.com/entry/2011-06-01T15_59_43-07_00

Doug Axe Knows His Work Better Than Steve Matheson
Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance.
http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.html
Evolution vs. Functional Proteins - Doug Axe - Video
http://www.metacafe.com/watch/4018222

Dennis Venema, a theistic evolutionist, had tried to challenge Doug Axe's work on the extreme rarity of functional proteins, and here is what one of the very papers said, that Venema tried to use to supposedly refute Axe:
Responding to Venema - Casey Luskin - October 2011
Excerpt: However, these experiments do not really model the evolution that occurs through gradual, step-by-step changes, with all intermediates being fully foldable proteins (Blanco et al., 1999). To create such an evolutionarily relevant path from all-a to all-b domains would be the next challenge for protein designers.
http://www.evolutionnews.org/2011/10/responding_to_venemas_response052061.html

Axe Diagram for finding a functional protein domain out of all sequence space:
The y-axis can be seen as representing enzyme activity, and the x-axis represents all possible amino acid sequences. Enzymes sit at the peak of their fitness landscapes (Point A). There are extremely high levels of complex and specified information in proteins--informational sequences which point to intelligent design.
http://www.evolutionnews.org/axediagram.jpg
And how do Darwinists deal with the astronomical improbabilities that are stacked against them for explaining the novel origination of even just one required protein by 'natural' means? At least as far as the public is concerned??? Well by deception of course!
Back to School Part VIII
Excerpt: Amazingly evolutionists think hemoglobin’s special amino acid sequence encoding for this machine is no different than any random list, such (as) a list of birthdays. To be sensible Johnson’s and Losos’ analogy would need the list of birthdays to provide something fantastic, such as the answers to the biology class final exam.
http://darwins-god.blogspot.com/2010/12/back-to-school-part-viii.html

Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact - Cornelius Hunter - July 2011
Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
http://darwins-god.blogspot.com/2011/07/response-to-comments-proteins-did-not.html

Here Are Those Two Protein Evolution Falsifications That Have Evolutionists Rewriting Their Script - Cornelius Hunter - March 2012
Excerpt: Several different studies indicate that, at a minimum, about 10^70 (a one followed by 70 zeros) evolutionary experiments would be needed to get close enough to a workable protein design before evolutionary mechanisms could take over and establish the protein in a population. For instance, one study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required. This requirement for 10^70 evolutionary experiments is far greater than what evolution could accomplish. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70. Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assume the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. Even more importantly, it assumes the pre existence of bacteria and, yes, proteins.
http://darwins-god.blogspot.com/2012/03/here-are-those-two-protein-evolution.html

Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Cornelius Hunter - Dec. 1, 2012
Excerpt: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21.
http://rsif.royalsocietypublishing.org/content/5/25/953.long
These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein.
http://www.ncbi.nlm.nih.gov/pubmed/2199970
And a similar result (10^65 attempts required) was obtained by comparing protein sequences.
http://www.sciencedirect.com/science/article/pii/0022519377900443
Another study found that 10^64 to 10^77 attempts are required.
http://www.ncbi.nlm.nih.gov/pubmed/15321723
And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000096
These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins.
http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354423575480#c6691708341503051454

Build me a protein – no guidance allowed! A response to Allan Miller and to Dryden, Thomson and White - May 5, 2013
Excerpt: But speculation is one thing; misinformation is another. Even though there are now several detailed online rebuttals of claims Dryden, Thomson and White’s claim that there would have been plenty of time for natural processes to hit upon a functional protein on the primordial Earth, the myth refuses to die.
http://www.uncommondescent.com/intelligent-design/build-me-a-protein-no-guidance-allowed-a-response-to-allan-miller-and-to-dryden-thomson-and-white/
As to defining information in proteins:
Fred Sanger, Protein Sequences and Evolution Versus Science - Are Proteins Random? Cornelius Hunter - November 2013
Excerpt: Standard tests of randomness show that English text, and protein sequences, are not random.,,,
http://darwins-god.blogspot.com/2013/11/fred-sanger-protein-sequences-and.html
Kirk Durston has done work on defining how much functional information resides in proteins:

Does God Exist? - Argument From Molecular Biology - Proteins - Kirk Durston - short video
http://www.metacafe.com/watch/4171853
Intelligent Design - Kirk Durston - Lecture video
http://vimeo.com/1775160
Measuring the functional sequence complexity of proteins - 2007: Kirk K Durston, David KY Chiu, David L Abel, Jack T Trevors
In this paper, we provide a method to measure functional sequence complexity (in proteins).
Conclusion: This method successfully distinguishes between order, randomness, and biological function (for proteins).

http://www.tbiomed.com/content/4/1/47/

A Scientific Method to Detect Intelligent Design in Biological Life – Kirk Durston – October 15, 2013
Excerpt: Intelligent Design in Biological life:
1. If an effect requires, encodes or produces statistically significant levels of functional information or functional complexity, it requires an intelligent mind to produce. (from above hypothesis)
2. Universal protein Ribosomal S12 requires (at) least 359 bits of functional information to encode.
3. Therefore, Ribosomal S12 required an intelligent mind to encode.

http://p2c.com/students/blogs/truthquest/2013/10/scientific-method-detect-intelligent-design-biological-life

Intelligent Design: Required by Biological Life? K.D. Kalinsky - Pg. 10 - 11
Case Three: an average 300 amino acid protein:
Excerpt: It is reasonable, therefore, to estimate the functional information required for the average 300 amino acid protein to be around 700 bits of information. I(Ex) > Inat and ID (Intelligent Design) is 10^155 times more probable than mindless natural processes to produce the average protein.
http://www.newscholars.com/papers/ID%20Web%20Article.pdf

"a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away."
Kirk Durston

Dr. Durston elaborates on how futile an evolutionary search is to find a single functional protein:
Excerpt: From this, we can come up with a very rough estimate for the total number of stable, folding 3D sequences in 300 residue sequence space … roughly 10^74 sequences that will give stable 3D folds (this is very rough, but it will illustrate my point and help one see why scientists don’t search for novel stable 3D folds from a library of random sequences). One might think that 10^75 sequences is an enormous number, however, it is miniscule in comparison with 20^300, which is the total number of sequences in 300 –residue sequence space. This is why the theory that an evolutionary search, even if it involved all the planets in all the galaxies of the known universe, is utterly implausible.
http://www.uncommondescent.com/biophysics/kirk-durston-a-common-either-or-mistake-both-darwinists-and-id-theorists-make/#comment-466489
Axe's work substantiates, and extends, previous work that was done at Massachusetts Institute of Technology (MIT):
Experimental Support for Regarding Functional Classes of Proteins to be Highly Isolated from Each Other: - Michael Behe
"From actual experimental results it can easily be calculated that the odds of finding a folded protein are about 1 in 10 to the 65 power (Sauer, MIT).,,, The odds of finding a marked grain of sand in the Sahara Desert three times in a row are about the same as finding one new functional protein structure. Rather than accept the result as a lucky coincidence, most people would be certain that the game had been fixed.”
Michael J. Behe, The Weekly Standard, June 7, 1999
http://www.arn.org/docs/behe/mb_smu1992.htm
Dr. Cornelius Hunter analyses one paper in which Darwinists tried to get around the extreme rarity of functional proteins being found by experimental results:
Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Dr. Cornelius Hunter - December 1, 2012
Excerpt: As for the fraction of protein sequence space that evolution is required to search to find native proteins, the Introduction of the paper merely refers to conjecture that only two types of amino acids are required (from 20), and on top of that only a subset of a protein’s amino acids even matter. They also refer to other conjectures that the required search space can be narrowed yet further. They conclude that the search space reduces dramatically.
This conjecture has no correspondence with reality, as indicated by the various experimental results that are available which are nowhere close to their optimistic conjectures. Likewise their estimate of the fraction of protein sequence space that evolution can feasibly search is equally off base.
So what (Darwinists) are doing is placing their lattice-based, back of the envelope, conjecture of the search space required over and above several detailed and experimental studies that all converge on the same neighborhood. (Given all that 'adjustment' their upper limit was still 10^43 and the lower limit was 10^21.)
Here's is their 'back of the envelope' Paper:
How much of protein sequence space has been explored by life on Earth? http://rsif.royalsocietypublishing.org/content/5/25/953.long

http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354427893142#c3593379630734118145
Even the lowest end estimate, for functional proteins given by evolutionists (1 in 10^12), is still very rare:
Fancy footwork in the sequence space shuffle - 2006
"Estimates for the density of functional proteins in sequence space range anywhere from 1 in 10^12 to 1 in 10^77. No matter how you slice it, proteins are rare. Useful ones are even more rare."
http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html
It is interesting to note that the 1 in 10^12 (trillion) estimate for functional proteins (Szostak), though still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario, was arrived at by an in-vitro (out of living organism) binding of ANY random proteins to the 'universal' ATP energy molecule.
How Proteins Evolved - Cornelius Hunter - December 2010
Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html
The entire episode of Szostak’s failed attempt to establish the legitimacy of the 1 in 10^12 functional protein number from a randomly generated library of proteins can be read here:
http://www.uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-2/#comment-358394

This following paper was the paper that put the final nail in the coffin for Szostak's work:
A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells - 2009
Excerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division."
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385

Strange Behavior: New Study Exposes Living Cells to Synthetic Protein - Dec. 27, 2012
Excerpt: ,,,"ATP is the energy currency of life," Chaput says. The phosphodiester bonds of ATP contain the energy necessary to drive reactions in living systems, giving up their stored energy when these bonds are chemically cleaved. The depletion of available intracellular ATP by DX binding disrupts normal metabolic activity in the cells, preventing them from dividing, (though they continue to grow).,,,
In the current study, E. coli cells exposed to DX transitioned into a filamentous form, which can occur naturally when such cells are subject to conditions of stress. The cells display low metabolic activity and limited cell division, presumably owing to their ATP-starved condition.
The study also examined the ability of E. coli to recover following DX exposure. The cells were found to enter a quiescent state known as viable but non-culturable (VBNC), meaning that they survived ATP sequestration and returned to their non-filamentous state after 48 hours, but lost their reproductive capacity.
Further, this condition was difficult to reverse and seems to involve a fundamental reprogramming of the cell.

http://www.sciencedaily.com/releases/2012/12/121227143001.htm

Protein Life Times: Just-Right Evidence for Design - Fazale Rana PhD. - biochemistry
Excerpt: Researchers learned that the amino acid sequences are exquisitely arranged to precisely balance the need for structural stability, while minimizing aggregation propensity.,,, Yet the optimization of proteins is not limited to their aggregation propensities. A cascade of optimization characterizes protein structure and function. In The Cell’s Design, I described a number of other ways that protein structure is optimized.
http://www.reasons.org/articles/protein-life-times-just-right-evidence-for-design
Here is a very interesting comment by Jack Szostak himself:
The Origin of Life on Earth
Excerpt: Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time.
It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago.

Dr. Jack Szostak - Nobel Laureate and leading Origin of Life researcher who, despite the evidence he sees first hand, still believes 'life' simply 'emerged' from molecules
http://www.scientificamerican.com/article.cfm?id=origin-of-life-on-earth
Further defence of Dr. Axe's work on the rarity of proteins:

Axe (2004) And The Evolution Of Protein Folds - March 2011
http://www.uncommondescent.com/intelligent-design/axe-2004-and-the-evolution-of-protein-folds/

On top of the fact that Origin of Life researcher Jack Szostak, and others, failed to generate any biologically relevant proteins, from a library of trillions of randomly generated proteins, proteins have now been shown to have a ‘Cruise Control’ mechanism, which works to ‘self-correct’ the integrity of the protein structure from any random mutations imposed on them.
Proteins with cruise control provide new perspective:
"A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order."
http://www.princeton.edu/main/news/archive/S22/60/95O56/
Cruise Control permeating the whole of the protein structure??? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced mathematical information must reside 'transcendentally' along the entirety of the protein structure, in order to achieve such control of the overall protein structure. This fact gives us clear evidence that there is far more functional information residing in proteins than meets the eye. Moreover this ‘oneness’ of cruise control, within the protein structure, can only be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism! For a sample of the equations that must be dealt with, to 'engineer' even a simple process control loop like cruise control for a single protein, please see this following site:
PID controller
A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal.
http://en.wikipedia.org/wiki/PID_controller
It is in realizing the staggering level of engineering that must be dealt with to achieve ‘cruise control’ for each individual protein, along the entirety of the protein structure, that it becomes apparent even Axe’s 1 in 10^77 estimate for rarity of finding specific functional proteins within sequence space is far, far too generous. In fact probabilities over various ‘specific’ configurations of material particles simply do not even apply, at all, since the ’cause’ of the non-local quantum information does not even reside within the material particles in the first place (i.e. falsification of local realism; Alain Aspect, Anton Zeilinger). Here is corroborating evidence that ‘protein specific’ quantum information/entanglement resides in functional proteins and DNA:
Quantum states in proteins and protein assemblies:
The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.
http://www.tony5m17h.net/SHJTQprotein.pdf

Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73
Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
http://www.scimednet.org/quantum-coherence-living-cells-and-protein/
In fact since quantum entanglement/information falsified reductive materialism/local realism in the first place (Alain Aspect; Anton Zeilinger) then finding quantum entanglement/information to be ‘protein specific’ is absolutely shattering to any rational hope that materialists had, in whatever slim probabilities there were for finding specific functional protein sequences by neo-Darwinian processes, since a ‘transcendent’, ‘non-local’, cause must be supplied which is specific to each unique protein structure. Reductive materialism, which is the basis of neo-Darwinian thought, is simply at a complete loss to supply such a ‘non-local’ transcendent cause, whereas Theism has always postulated such a transcendent, ‘non-local’, cause for life!
The following articles also show that the specific amino acid sequence of proteins is found to be 'context dependent';
Why Proteins Aren't Easily Recombined, Part 2 - Ann Gauger May 17, 2012
Excerpt: In other words, even if only 10% of non-matching residues were changed, the resulting hybrid enzyme no longer functioned. Why? Because the substitution of different amino acids into the existing protein structure destabilized the fold, even though those same amino acids worked well in another context. Thus, each protein's amino acid sequence works as a whole to help generate a proper stable fold, in a context-dependent fashion.
http://www.evolutionnews.org/2012/05/why_proteins_ar_1059771.html

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
Excerpt (Page 4): The Probabilities Get Worse
This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

The World’s Toughest Bacterium - 2002
Excerpt: Several recent studies of the bacterium's DNA repair pathway have focused on one protein that is now known to be essential for radiation resistance—the RecA protein.,,
"When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments," they write in Proceedings of the National Academy of Sciences. "RecA proteins may play role in finding overlapping fragments and splicing them together."

http://www.genomenewsnetwork.org/articles/07_02/deinococcus.shtml

Extreme Genome Repair - 20 March 2009
Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.
http://www.sciencedirect.com/science/article/pii/S0092867409002657
Though the authors of the ‘cruise control’ paper tried to put a evolution friendly spin on the ‘cruise control’ evidence, for finding such a highly advanced ‘Process Control Loop’ at such a base molecular level, (before natural selection even has a chance to select for any morphological novelty that a protein may have from ‘random’ mutations), the fact is that this strict limit to the variability of a protein, imposed by the quantum information of a protein to the protein’s specific function, is very much to be expected from a Intelligent Design/Genetic Entropy viewpoint, and this finding is in fact a very constraining thing to the amount of 'random' variation we should reasonably expect from any specific functional protein in the first place

Here are some more articles highlighting the extreme rarity of functional proteins:
Minimal Complexity Relegates Life Origin Models To Fanciful Speculation - Nov. 2009
Excerpt: Based on the structural requirements of enzyme activity Axe emphatically argued against a global-ascent model of the function landscape in which incremental improvements of an arbitrary starting sequence "lead to a globally optimal final sequence with reasonably high probability". For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10exp140 and 1 in 10exp164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids.
http://www.arn.org/blogs/index.php/2/2009/11/10/minimal_complexity_relegates_life_origin

The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010
Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin."
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1
The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio
http://intelligentdesign.podomatic.com/player/web/2010-05-03T11_09_03-07_00

On the Origin of Protein Folds - Jonathan M. - September 2012
http://www.uncommondescent.com/intelligent-design/on-the-origin-of-protein-folds/

A Response to Martin Poenie on Protein Evolution - Jonathan M. July 25, 2013
http://www.evolutionnews.org/2013/07/a_response_to_m074821.html

Here is a refutation of computer simulation of protein origination:

Why Skolnick and Gao (2013) Doesn’t Refute ID Research on the Origin of Proteins - Casey Luskin July 23, 2013
http://www.evolutionnews.org/2013/07/why_skolnick_an074761.html

The following site offers a short summary of the 'Darwinian shortcuts' that failed to overcome Axe's finding for the rarity of protein folds:
Shortcuts to new protein folds - October 2010
Excerpt: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends.
http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html

Conservation of Information Made Simple - William A. Dembski - August, 2012
Excerpt: Biological configuration spaces of possible genes and proteins, for instance, are immense, and finding a functional gene or protein in such spaces via blind search can be vastly more improbable than finding an arbitrary electron in the known physical universe. ,,,
,,,Given this background discussion and motivation, we are now in a position to give a reasonably precise formulation of conservation of information, namely: raising the probability of success of a search does nothing to make attaining the target easier, and may in fact make it more difficult, once the informational costs involved in raising the probability of success are taken into account. Search is costly, and the cost must be paid in terms of information. Searches achieve success not by creating information but by taking advantage of existing information. The information that leads to successful search admits no bargains, only apparent bargains that must be paid in full elsewhere.

http://www.evolutionnews.org/2012/08/conservation_of063671.html
Here are articles that clearly illustrate that the protein evidence, no matter how crushing to Darwinism, is always crammed into the Darwinian framework by Evolutionists:

The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study - Cornelius Hunter - January 2011
http://darwins-god.blogspot.com/2011/01/hierarchy-of-evolutionary-apologetics.html

Here is a critique of the failed attempt to evolve a 'fit' protein to replace a protein in a virus which had a gene knocked out:
New Genes: Putting the Theory Before the Evidence - January 2011
Excerpt: What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.
http://darwins-god.blogspot.com/2011/01/new-genes-putting-theory-before.html

Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact - Cornelius Hunter - July 2011
Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
The theory, even by the evolutionist’s own reckoning, is unworkable. Evolution fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 orders of magnitude. And that is conservative.

http://darwins-god.blogspot.com/2011/07/response-to-comments-proteins-did-not.html
Here is a fairly good defense of the rarity of protein folds, from a blogger called gpuccio, from the best Darwinian objections that could be mustered against it:
http://www.uncommondescent.com/darwinism/media-mum-about-deranged-darwinist-gunman/comment-page-5/#comment-363452
Signature In The Cell - Review
Excerpt: Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created.
http://www.fourmilab.ch/documents/reading_list/indices/book_726.html
Our most advanced supercomputers pale in comparison to this assumption, of a universe full of chemical laboratories, that has been generously granted to evolutionists for 'randomly' finding a functional protein in sequence space:
"SimCell," anyone?
"Unfortunately, Schulten's team won't be able to observe virtual protein synthesis in action. Even the fastest supercomputers can only depict such atomic complexity for a few dozen nanoseconds." - cool cellular animation videos on the site
http://whyfiles.org/shorties/230simcell/
Instead of us just looking at the probability of finding a single 'simple' functional protein molecule by chance, (a solar system full of blind men solving the Rubik’s Cube simultaneously (Hoyle), let’s also look at the complexity which goes into crafting the shape of just one protein molecule. Complexity will give us a better indication if a protein molecule is indeed the handi-work of an infinitely powerful Creator.
Francis Collins on Making Life
Excerpt: 'We are so woefully ignorant about how biology really works. We still don't understand how a particular DNA sequence—when we just stare at it—codes for a protein that has a particular function. We can't even figure out how that protein would fold—into what kind of three-dimensional shape. And I would defy anybody who is going to tell me that they could, from first principles, predict not only the shape of the protein but also what it does.' - Francis Collins - Former Director of the Human Genome Project
http://www.pbs.org/wgbh/nova/tech/collins-genome.html

Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator - Fazale Rana
Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”
http://www.amazon.com/gp/product/0801072093
Dr. Fuz Rana, at the 41:30 minute mark of the following video, speaks on the tremendous effort that went into building the preceding protein:

Science - Fuz Rana - Unbelievable? Conference 2013 - video
http://www.youtube.com/watch?v=-u34VJ8J5_c&list=PLS5E_VeVNzAstcmbIlygiEFir3tQtlWxx&index=8

Engineering principles, not Darwinian principles, lead to breakthrough in designing new proteins:
Computer-designed proteins recognize and bind small molecules - September 5, 2013
Excerpt: In conducting the study, the researchers learned general principles for engineering small molecule-binding proteins with strong attraction energies. Their findings open up the possibility that binding proteins could be created for many medical, industrial and environmental uses.,,,
The researchers adapted a computational tool called Rosetta developed in the Baker lab to craft new proteins that would bind the steroid digoxigenin, which is related to the heart-disease medication digoxin.,,,
After generating many designs for digoxigenin-binders on a computer, the researchers chose 17 to synthesize in a lab. Experimental tests led the researchers to hone in on the protein they called DIG10. Further observations revealed that the binding activities of this protein were indeed mediated by its computer-designed interface, just as the researchers had intended.
To upgrade their overall design methods, the researchers then used next-generation deep gene sequencing to probe the effect of each amino acid molecular building block on binding fitness. Using this method, they were able to discover how various engineered genetic variations affect the designed protein's binding capabilities. The binding fitness map gave the researchers ideas for enhancing the binding affinity of the designed protein to the picomolar level, tighter than the nano-level.,,,

http://phys.org/news/2013-09-computer-designed-proteins-small-molecules.html

The Challenge to Darwinism from a Single Remarkably Complex Enzyme - Ann Gauger - May 1, 2012
Excerpt: How does a neo-Darwinian process evolve an enzyme like this? Even if enzymes that carried out the various partial reactions could have evolved separately, the coordination and combining of those domains into one huge enzyme is a feat of engineering beyond anything we can do.
http://www.evolutionnews.org/2012/05/the_challenge_t059191.html
Computers trying the 'solve' protein folding give another compelling piece of evidence for the Intelligent Design of life;
Confronting Science’s Logical Limits - John L. Casti - 1996
Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard. http://www.cs.virginia.edu/~robins/Confronting_Sciences_Logical_Limits.pdf
In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, which was 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it was estimated to take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape.
"Blue Gene's final product, due in four or five years, will be able to "fold" a protein made of 300 amino acids, but that job will take an entire year of full-time computing." Paul Horn, senior vice president of IBM research, September 21, 2000
http://www.news.com/2100-1001-233954.html
Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule:

A Few Hundred Thousand Computers vs. A Single Protein Molecule - video
http://www.metacafe.com/watch/4018233
The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012
Excerpt: Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe.
http://www.evolutionnews.org/2012/10/a_revolutionary065521.html

Physicists Discover Quantum Law of Protein Folding – February 22, 2011
Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.

http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
Interestingly, there are some (perhaps many?) complex protein folding problems found by scientists that have still refused to be solved by the brute number crunching power of super-computers, but, 'surprisingly', these problems have been solved by the addition of 'human intuition';
So Much For Random Searches - PaV - September 2011
Excerpt: There’s an article in Discover Magazine about how gamers have been able to solve a problem in HIV research in only three weeks (!) that had remained outside of researcher’s powerful computer tools for years. This, until now, unsolvable problem gets solved because: "They used a wide range of strategies, they could pick the best places to begin, and they were better at long-term planning. Human intuition trumped mechanical number-crunching." Here’s what intelligent agents were able to do within the search space of possible solutions:,,, "until now, scientists have only been able to discern the structure of the two halves together. They have spent more than ten years trying to solve structure of a single isolated half, without any success. The Foldit players had no such problems. They came up with several answers, one of which was almost close to perfect. In a few days, Khatib had refined their solution to deduce the protein’s final structure, and he has already spotted features that could make attractive targets for new drugs." Thus,,
Random search by powerful computer: 10 years and No Success
Intelligent Agents guiding powerful computing: 3 weeks and Success.

http://www.uncommondescent.com/intelligent-design/so-much-for-random-searches/
Online Gamers Achieve First Crowd-Sourced Redesign of Protein - January 2012
http://www.scientificamerican.com/article.cfm?id=victory-for-crowdsourced-biomolecule2

As well, despite some very optimistic claims, it seems future 'quantum computers' will not fair much better in finding functional proteins in sequence space than even a idealized 'material' supercomputer of today can do:
The Limits of Quantum Computers – March 2008
Excerpt: "Quantum computers would be exceptionally fast at a few specific tasks, but it appears that for most problems they would outclass today’s computers only modestly. This realization may lead to a new fundamental physical principle"
http://www.scientificamerican.com/article.cfm?id=the-limits-of-quantum-computers

The Limits of Quantum Computers - Scott Aaronson - 2007
Excerpt: In the popular imagination, quantum computers would be almost magical devices, able to “solve impossible problems in an instant” by trying exponentially many solutions in parallel. In this talk, I’ll describe four results in quantum computing theory that directly challenge this view.,,, Second I’ll show that in the “black box” or “oracle” model that we know how to analyze, quantum computers could not solve NP-complete problems in polynomial time, even with the help of nonuniform “quantum advice states”,,,
http://www.springerlink.com/content/0662222330115207/
Here is Scott Aaronson's blog in which refutes recent claims that P=NP (Of note: if P were found to equal NP, then a million dollar prize would be awarded to the mathematician who provided the proof that NP problems could be solved in polynomial time):
Shtetl-Optimized
Excerpt: Quantum computers are not known to be able to solve NP-complete problems in polynomial time.
http://scottaaronson.com/blog/?p=456
Protein folding is found to be a 'intractable NP-complete problem' by several different methods. Thus protein folding will not be able to take advantage of any advances in speed that quantum computation may offer to any other problems of computation that may be solved in polynomial time:
Combinatorial Algorithms for Protein Folding in Lattice
Models: A Survey of Mathematical Results – 2009
Excerpt: Protein Folding: Computational Complexity
4.1
NP-completeness: from 10^300 to 2 Amino Acid Types
4.2
NP-completeness: Protein Folding in Ad-Hoc Models
4.3
NP-completeness: Protein Folding in the HP-Model

http://www.cs.brown.edu/~sorin/pdfs/pfoldingsurvey.pdf
Another factor severely complicating man's ability to properly mimic protein folding is that, much contrary to evolutionary thought, many proteins fold differently in different 'molecular' situations:
The Gene Myth, Part II - August 2010
Excerpt: the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.
http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html

Protein knots gain new evolutionary significance - June 2012
Excerpt: Relatively little is known about protein folding, the process by which a polypeptide chain with a specific sequence of amino acid chains forms the three-dimensional structures — their "native states" — required to become functional. How this process reproducibly achieves the required structure is the subject of intensive study. Even harder is understanding how this is accomplished for knotted proteins, where the chain loops around itself in entanglements of varying complexity; or the even rarer slipknotted proteins, where a loop is bound by another segment of the protein chain, similar to a shoelace bow. "
http://phys.org/news/2012-06-protein-gain-evolutionary-significance.html

A Knotty Puzzle - Ann Gauger PhD. - June 7, 2012
Excerpt: Let me untangle the rhetoric. The reason why knots in folded proteins are unlikely is because they are hard to achieve, without resulting in misfolded proteins, aggregation, and possible disease states. Even though it's unlikely they evolved -- let's make that highly unlikely -- we know knotted proteins must have evolved somehow, simply because they exist. And that's because design is "knot" an option.
http://www.evolutionnews.org/2012/06/a_knotty_puzzle060611.html

Duly Knotted: A (Billion Year) Problem for Evolution - June 2012
Excerpt: "Untangling Knots, Slipknots in Species Separated by a Billion Years of Evolution.",,, string of amino acids that can automatically fold itself into a slipknot,,, "The slipknot is surprisingly conserved across many different families, from different species: bacteria, yeast and even human," Sulkowska said.
http://www.evolutionnews.org/2012/06/a_knotty_proble061361.html

Acrobatic Protein Stars in Two Gymnastic Events - July 2012
Excerpt: "We showed that RfaH refolds, which is a big enough deal already. You would think this is impossible. That's what you're told in school," says Ohio State microbiologist Irina Artsimovitch,,, Though the process happens in seconds, Artsimovitch likened the refolding (of a single protein to a completely different fold pattern) to "having a knitted sweater that you rip out and then knit into a sweater with a different pattern."
http://www.evolutionnews.org/2012/07/acrobatic_prote_1062541.html
As a sidelight to the complexity found for folding any relatively short amino acid sequence into a 3-D protein, the complexity of computing the actions of even a simple atom, in detail, quickly exceeds the capacity of our most advanced supercomputers of today:
Delayed time zero in photoemission: New record in time measurement accuracy - June 2010
Excerpt: Although they could confirm the effect qualitatively using complicated computations, they came up with a time offset of only five attoseconds. The cause of this discrepancy may lie in the complexity of the neon atom, which consists, in addition to the nucleus, of ten electrons. "The computational effort required to model such a many-electron system exceeds the computational capacity of today's supercomputers," explains Yakovlev.
http://www.physorg.com/news196606514.html
Also of interest to the extreme difficultly man has in computing the folding of a protein within any reasonable amount of time, it seems water itself, (H2O), was 'designed' with protein folding in mind:
Protein Folding: One Picture Per Millisecond Illuminates The Process - 2008
Excerpt: The RUB-chemists initiated the folding process and then monitored the course of events. It turned out that within less than ten milliseconds, the motions of the water network were altered as well as the protein itself being restructured. “These two processes practically take place simultaneously“, Prof. Havenith-Newen states, “they are strongly correlated.“ These observations support the yet controversial suggestion that water plays a fundamental role in protein folding, and thus in protein function, and does not stay passive.
http://www.sciencedaily.com/releases/2008/08/080805075610.htm

Water Is 'Designer Fluid' That Helps Proteins Change Shape - 2008
Excerpt: "When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life."
http://www.sciencedaily.com/releases/2008/08/080806113314.htm

Water found to be an ideal lubricant for nanomachines - September 1, 2013
Excerpt: Researchers from the University of Amsterdam have discovered that machines just one molecule in size move far quicker if you add a 'lubricant' to their surroundings. To their surprise, water proved to be the best lubricant by far.
http://phys.org/news/2013-08-ideal-lubricant-nanomachines.html
Of related interest to water being a 'designer fluid':
DNA Sequence Reconstituted from Water Memory? - 2011
Water carrying only the electromagnetic signature of a DNA sequence can make a replica of the sequence out of simple building blocks, Nobel laureate HIV researcher shows.
Excerpt: When Noble laureate HIV researcher Luc Montagnier discovered that certain bacterial and viral DNA sequences dissolved in water causes electromagnetic signals to be emitted at high dilutions, that was bad enough. Now, new results from his lab appear to show that the DNA sequence itself could be reconstituted from the electromagnetic signal. That has so stunned the scientific community that one prominent supporter was nonetheless moved to remark: “Luc is either a genius or he is mad!” But some quantum physicists are taking that very seriously, and are linking Montagnier’s findings to decades of research demonstrating the sensitivity of organisms to extremely weak electromagnetic fields.
http://www.i-sis.org.uk/DNA_sequence_reconstituted_from_Water_Memory.php
As well, there are overlapping 'chaperone' systems insuring that proteins fold into the precisely correct shape:
(How do) Chaperone Proteins Know (how to fold other proteins)? - September 2012
Excerpt: Here are some of the neat features of Trigger Factor:
*Trigger Factor actually constrains protein folding more than the ribosome does. It doesn't just "get in the way" like the ribosome. It also regulates the folding.
*Trigger Factor's function is specific to the particular region of the amino acid chain. It does not just perform one function no matter what the composition of the amino acid chain. It changes based on the region of the chain it is working with.
*Trigger Factor also changes its activity based on where the protein is in the translation process.
*Trigger Factor's process depends on how the amino acid chain is bound to the ribosome, and can even unfold parts of the chain that were misfolded in the translation process.

An additional factor that regulates when amino acid chains fold into proteins is its distance from the ribosome (the place where the amino acid chain is made). The closer the chain is to the ribosome, the less room it has to fold into a three-dimensional protein. Trigger Factor works with this spatial hindrance, making an interesting and complex regulation system.
Trigger Factor is only called into the game once the amino acid chain is a certain length (around 100 amino acids long) and when the chain has certain features, such as hydrophobicity. As the authors state it, Trigger Factor keeps the protein from folding into its three-dimensional structure until the amino acid chain has all of the information it needs to fold properly:
In summary, we show that the ribosome and TF each uniquely affect the folding landscape of nascent polypeptides to prevent or reverse early misfolds as long as important folding information is still missing and the nascent chain is not released from the ribosome.
So we have a protein that is able to perform various functions that inhibit or slow protein folding until the amino acid has the right chemical information for folding to occur.
This does not solve the riddle about proteins being made from proteins (otherwise known as the chicken-and-the-egg problem). It actually adds another twist to the riddle: How does one protein know how much information a completely different protein needs to fold into a three dimensional structure? How does a protein evolve the ability to "know" how to respond to specific translational circumstances as Trigger Factor does?

http://www.evolutionnews.org/2012/09/what_chaperone063951.html

Cell Machinery Untangles Misfolded Proteins - April 2, 2013
Excerpt: biologist Helen R. Saibil, provides a model diagram of this "highly dynamic" machine and descriptions of what the parts do. There are channels, toggles, linkers, mobile lids, and dockers. One of the primary parts looks like a stack of 3-tiered rings with a channel down the middle. The other part looks a little like Pac-man, biting down on a "hot spot" on the side of the rings, accompanied by other moving parts. Each of the primary parts is further composed of several protein domains. Multiple ATP "energy pellets" power the operation at three locations.
The cell first has to identify the misfolded aggregate, find a loose end, and feed it into a slot on the side-mounted machine. The docking point acts as a regulator that can reprogram the side-mounted machine according to the stage of the operation. Once threaded into the right position, the loose end is fed into the central channel of the three-tiered machine, so that untangling can proceed. The untangled polypeptide exiting the central channel can then be refolded by other chaperone machines at the ready.
Only dim details of this operation are understood so far. The "mechanism" by which the strand is "handed over" from one domain to the other is "unclear," Saibil writes. It's also not clear how the tangled mess of peptide pictured in the model diagram can avoid snags as it passes through the machinery. Yet it works. Rightly, Dr. Saibil praises "the remarkable ability of cells to reverse protein aggregation."

http://www.evolutionnews.org/2013/04/cell_machinery070411.html

Proteins Fold Who Knows How - July 2010
Excerpt: New work published in Cell shows that this “chaperone” device speeds up the proper folding of the polypeptide when it otherwise might get stuck on a “kinetic trap.” A German team likened the assistance to narrowing the entropic funnel. “The capacity to rescue proteins from such folding traps may explain the uniquely essential role of chaperonin cages within the cellular chaperone network,” they said. GroEL+GroES therefore “rescues” protein that otherwise might misfold and cause damage to the cell.,,, “In contrast to all other components of this chaperone network, the chaperonin, GroEL, and its cofactor, GroES, are uniquely essential, forming a specialized nano-compartment for single protein molecules to fold in isolation.”
http://www.creationsafaris.com/crev201007.htm#20100709a

Nature Review Article Yields Unpleasant Data For Darwinism - August 2011
Excerpt: The number of possible shapes that a protein can fold into is very high and folding reactions are very complex, involving the co-operation of many weak, non-covalent interactions. A high percentage of proteins do not fold automatically into the required shape and are at risk of aberrant folding and aggregation. As the abstract to this paper states: “To avoid these dangers, cells invest in a complex network of molecular chaperones, which are ingenious mechanisms to prevent aggregation and promote efficient folding.”
http://www.uncommondescent.com/intelligent-design/nature-review-article-yields-unpleasant-data-for-darwinism/
In real life, the protein folds into its final shape in a fraction of a second! The Blue Gene computer would have to operate at least 33 million times faster to accomplish what the protein does in a fraction of a second. This is the complexity found for folding JUST ONE relatively short 'simple' existing protein molecule. Yet, evolution must account for the origination, and organization, of far, far, more than just one relatively short specifically sequenced protein molecule:
A New Guide to Exploring the Protein Universe
"It is estimated, based on the total number of known life forms on Earth, that there are some 50 billion different types of proteins in existence today, and it is possible that the protein universe could hold many trillions more."
Lynn Yarris - 2005
http://www.lbl.gov/Science-Articles/Archive/sabl/2005/March/02-protein-universe.html
Shoot, no one even really has a firm clue as to exactly how many different proteins reside in a single cell much less all of life;
Go to the Cell, Thou Sluggard - March 2011
Excerpt: Calculations indicate that each human cell contains roughly a billion protein molecules.,,, These proteins have a kind of address label, a signal sequence, that specifies what place inside or outside the cell they need to be transported to. This transport must function flawlessly if order is to be maintained in the cell,
http://www.creationsafaris.com/crev201103.htm#20110302a
Even the most generous of protein classifications, 'folds and superfamilies' yields several thousand completely unique proteins:
SCOP (Structural Classification of Proteins) site - gpuccio
Excerpt: However we group the proteome, we have at present at least 1000 different fundamental folds, 2000 “a little less fundamentally different” folds (the superfamilies), and 6000 totally unrelated groups of primary sequences.
http://www.uncommondescent.com/intelligent-design/uh-oh-is-he-going-to-get-gould-ed/#comment-367564
What makes matters much worse for the materialist is that he will try to assert that existing functional proteins of one structure can easily mutate into other functional proteins, of a completely different structure or function, by pure chance. Yet once again the empirical evidence betrays the materialist. The proteins that are found in life are shown to be highly constrained in their ability to evolve into other proteins:

Collected notes on the severe limits found for the ability of proteins to ‘randomly’ evolve to new functions, for new binding sites, for new domain-domain interactions, and for new ORFan genes/proteins:
https://docs.google.com/document/d/11VRNz03ox-vXauBTVonqmRM7amD5CbUWwu6wxr2ABr4/edit

Dr. Axe challenges a Darwinist to create a single new gene by Darwinian processes:
Show Me: A Challenge for Martin Poenie - Douglas Axe August 16, 2013
Excerpt: Poenie want to be free to appeal to evolutionary processes for explaining past events without shouldering any responsibility for demonstrating that these processes actually work in the present. That clearly isn't valid. Unless we want to rewrite the rules of science, we have to assume that what doesn't work didn't work.
It isn't valid to think that evolution did create new enzymes if it hasn't been demonstrated that it can create new enzymes. And if Poenie really thinks this has been done, then I'd like to present him with an opportunity to prove it. He says, "Recombination can do all the things that Axe thinks are impossible." Can it really? Please show me, Martin!
I'll send you a strain of E. coli that lacks the bioF gene, and you show me how recombination, or any other natural process operating in that strain, can create a new gene that does the job of bioF within a few billion years.

http://www.evolutionnews.org/2013/08/a_challenge_for075611.html

Belgian Waffle - Douglas Axe - January 18, 2013
Excerpt:,, an article from Ghent University in Belgium claims a recent scientific paper has rescued evolutionary theory by solving the problem of evolutionary innovation.,,,
Here's the concession:
"An important unanswered question in Darwin's theory of evolution is how new characteristics seem to appear out of nowhere."
Hmmm. Yes, I can see how this could be a problem for a theory of biological origins.,,
,,,here's the plain statement:
"The preduplication [i.e., ancestral] ancMalS enzyme was multifunctional and already contained the different activities found in the postduplication [i.e., evolved] enzymes, albeit at a lower level."
So, all we have here is a demonstration of what we already knew -- that evolution can adjust somewhat the relative preferences enzymes show for the molecules they already work on. Those aren't new activities, though, and this isn't a new result either.
What would be really new and welcome would be for evolutionary biologists to begin taking the word new seriously.

http://www.evolutionnews.org/2013/01/belgian_waffle068421.html
The main claims, used by Darwinists for saying that proteins have been shown to have evolved into new functions, are debunked here:

Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013
http://www.evolutionnews.org/2013/08/hopeless_matzke075631.html
Following the Evidence Where It Leads: Observations on Dembski's Exchange with Shapiro - Ann Gauger - January 2012
Excerpt: So far, our research indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure.
http://www.evolutionnews.org/2012/01/observations_re055171.html

Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009
Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.

http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html

Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009
Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html

Wheel of Fortune: New Work by Thornton's Group Supports Time-Asymmetric Dollo's Law - Michael Behe - October 5, 2011
Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection.
http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html

To Traverse a Maze, It Helps to Have a Mind - Michael Behe - November 7, 2012
Excerpt: Although the printed paper itself and an accompanying commentary by Elizabeth Pennisi (about the supposed evolution of a single gene/enzyme) paint the results as an advance in understanding evolution, that's so only if evolution has eyes and a mind like a kid solving a maze. The investigators' exceptionally intelligent manipulations are relegated to the online supplemental materials.
http://www.evolutionnews.org/2012/11/to_traverse_a_m_1066201.html

Stability effects of mutations and protein evolvability. October 2009
Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
http://www.ncbi.nlm.nih.gov/pubmed/19765975

The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway - Ann K. Gauger and Douglas D. Axe - April 2011
Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1

When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide

"Biologist Douglas Axe on Evolution's (non) Ability to Produce New (Protein) Functions " - video
Quote: It turns out once you get above the number six [changes in amino acids] -- and even at lower numbers actually -- but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
http://intelligentdesign.podomatic.com/entry/2012-10-15T16_05_14-07_00
Doug Axe PhD. on the Rarity and 'non-Evolvability' of Functional Proteins - video (notes in video description)
http://www.metacafe.com/watch/9243592/

Can Even One Polymer Become a Protein in 13 billion Years? – Dr. Douglas Axe, Biologic Institute - June 20, 2013 - audio
http://radiomaria.us/discoveringintelligentdesign/2013/06/20/june-20-2013-can-even-one-polymer-become-a-protein-in-13-billion-years-dr-douglas-axe-biologic-institute/
Corticosteroid Receptors in Vertebrates: Luck or Design? - Ann Gauger - October 11, 2011
Excerpt: if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start.
http://www.evolutionnews.org/2011/10/luck_or_design051801.html

“Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

"A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble."
Problems in Protein Evolution:
http://www.cs.unc.edu/~plaisted/ce/blocked.html

Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors - Doug Axe
Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.
http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/AxeProteinEvolution.pdf

Darwin's God: Post Synaptic Proteins Intolerant of Change - December 2010
Excerpt: Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change.
http://darwins-god.blogspot.com/2010/12/post-synaptic-proteins-intolerant-of.html
As well, the 'errors/mutations' that are found to 'naturally' occur in protein sequences are found to be 'designed errors':
Cells Defend Themselves from Viruses, Bacteria With Armor of Protein Errors - Nov. 2009
Excerpt: These "regulated errors" comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed,
http://www.sciencedaily.com/releases/2009/11/091125134701.htm
There are even 'protein police':

GATA-1: A Protein That Regulates Proteins - Feb. 2010
http://darwins-god.blogspot.com/2010/02/gata-1-protein-that-regulates-proteins.html
Heat shock proteins:
Excerpt: They play an important role in protein-protein interactions such as folding and assisting in the establishment of proper protein conformation (shape) and prevention of unwanted protein aggregation.
http://en.wikipedia.org/wiki/Heat_shock_protein
This following paper, and audio interview, shows that there is a severe 'fitness cost' for cells to carry 'transitional' proteins that have not achieved full functionality yet:
Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - May 2010
Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2
Testing Evolution in the Lab With Biologic Institute's Ann Gauger - audio
http://www.idthefuture.com/2010/05/testing_evolution_in_the_lab_w.html

In fact the Ribosome, which makes the myriad of different, yet specific, types of proteins found in life, is found to be severely intolerant to any random mutations occurring to proteins.
The Ribosome: Perfectionist Protein-maker Trashes Errors
Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.
http://www.sciencedaily.com/releases/2009/01/090107134529.htm
And exactly how is the evolution new life forms suppose to 'randomly' occur if it is prevented from 'randomly' occurring to the proteins in the first place?

As well, the 'protein factory' of the ribosome, which is the only known machine in the universe capable of making proteins of any significant length, is far more complicated than first thought:
Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service
Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.”
http://creationsafaris.com/crev200910.htm#20091010a
As well, The Ribosome of the cell is found to be very similar to a CPU in a electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012
David J D’Onofrio1*, David L Abel2* and Donald E Johnson3
Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,,
An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,,
The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm.
It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive.

http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf

LIFE: WHAT A CONCEPT!
Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be?
George Church
http://www.edge.org/documents/life/church_index.html
Of note, although the ribosome is present in all life, it is not uniform across all life:
Ribosome
Excerpt: Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA.
http://en.wikipedia.org/wiki/Ribosome

Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013
Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell.
"The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,,
,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,,

http://www.sciencedaily.com/releases/2013/07/130718130617.htm
Moreover, scientists are finding many protein complexes are extremely intolerant to any random mutations:
Warning: Do NOT Mutate This Protein Complex: - June 2009
Excerpt: In each cell of your body there is a complex of 8 or more proteins bound together called the BBSome. This protein complex, discovered in 2007, should not be disturbed. Here’s what happens when it mutates: “A homozygous mutation in any BBSome subunit (except BBIP10) will make you blind, obese and deaf, will obliterate your sense of smell, will make you grow extra digits and toes and cause your kidneys to fail.”... the BBSome is “highly conserved” (i.e., unevolved) in all ciliated organisms from single-celled green algae to humans,..."
http://www.creationsafaris.com/crev200906.htm#20090630a
Which begs the question, "If this complex of 8 proteins which is found throughout life, is severely intolerant to any mutations happening to it now, how in the world did it come to be in the first photosynthetic life in the first place?

Even if evolution somehow managed to overcome these impossible hurdles for generating novel proteins by totally natural means, evolution would still face the monumental hurdles of generating complimentary protein/protein binding sites, in which the novel proteins would actually interact with each other in order to accomplish the specific tasks needed in a cell (it is estimated that there are least 10,000 different types of protein-protein binding sites in a 'simple' cell; Behe: Edge Of Evolution).

What does the recent hard evidence say about novel protein-protein binding site generation?
Protein-Protein Interactions (PPI) Fine-Tune the Case for Intelligent Design - Article with video - April 2011
Excerpt: The most recent work by the Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also carefully designed.
http://www.reasons.org/protein-protein-interactions-fine-tune-case-intelligent-design

"The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable."
Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")
Intelligent Design and the Edge of Evolution – Dr. Michael Behe - summer 2013 - audio
http://radiomaria.us/discoveringintelligentdesign/2013/06/13/june-13-2013-intelligent-design-and-the-edge-of-evolution-dr-michael-behe/

The Sheer Lack Of Evidence For Macro Evolution - William Lane Craig - video
http://www.metacafe.com/watch/4023134
Nature Paper,, Finds Darwinian Processes Lacking - Michael Behe - Oct. 2009
Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
http://www.evolutionnews.org/2009/10/nature_paper_finally_reaches_t.html
So, how many protein-protein binding sites are found in life?

Dr. Behe, on the important Table 7.1 on page 143 of his book 'Edge Of Evolution', finds that a typical cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites in a multicellular creature is,,,
Largest-Ever Map of Plant Protein Interactions - July 2011
Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker.
http://www.sciencedaily.com/releases/2011/07/110728144936.htm
So taking into account that they only covered 2%, of the full protein-protein "interactome", then that gives us a number, for different protein-protein interactions, of 310,000. Thus, from my very rough 'back of the envelope' calculations, we find that this is at least 30 times higher than Dr. Behe's estimate of 10,000 different protein-protein binding sites for a typical single cell (Page 143; Edge of Evolution; Behe). Therefore, at least at first glance from my rough calculations, it certainly seems to be a gargantuan step that evolution must somehow make, by purely unguided processes, to go from a single cell to a multi-cellular creature. To illustrate just how difficult of a step it is, the order of difficulty, of developing a single protein-protein binding site, is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

Dr. Behe's empirical research agrees with what is found if scientists try to purposely design a protein-protein binding site:
Viral-Binding Protein Design Makes the Case for Intelligent Design! - Fazale Rana - June 2011
Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:
"...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2"
If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?
In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise.

http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool

Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012
Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder.
http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.html
Moreover, there is, 'surprisingly', found to be 'rather low' conservation of Domain-Domain Interactions occurring in Protein-Protein interactions:
A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms
Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,,
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005096

What Evidence Is There for the Homology of Protein-Protein Interactions? - 2012
Excerpt: Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care…
Conclusion excerpt: Using this framework, we are able to estimate interactome sizes with a method that is different from others in the literature.
Our estimates for the fraction of conserved interactions are very low for definitions of homology that are often associated with the transfer of functional annotations across species. We emphasise that our results will be overestimates due to the preferential investigation of homologous proteins in multiple species.,,,
We urge extreme caution in interpreting interactions transferred across species unless the definition of homology employed is a strict one, and we believe that interactome incompleteness is not solely responsible for the lack of observed conservation of interactions.

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002645
Two Domain Protein - video (several binding sites required)
http://www.facebook.com/photo.php?v=421708024519477

As if, the probability of finding a novel protein by neo-Darwinian processes were not already overwhelmingly difficult, it is now found that amino acid positions in a protein are interdependent to other amino acid positions, thus exponentially exasperating the problem for neo-Darwinists:
(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012
Excerpt (Page 4): The Probabilities Get Worse
This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.

http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

And here is the paper from Durston and company:

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring - Kirk K Durston, David KY Chiu, Andrew KC Wong and Gary CL Li - 2012
Results
The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.
Conclusions
Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

http://bsb.eurasipjournals.com/content/2012/1/8

Why Proteins (Protein Domains) Aren't Easily Recombined - Ann Gauger - May 2012
Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
http://www.biologicinstitute.org/post/22595615671/why-proteins-arent-easily-recombined

"Why Proteins Aren't Easily Recombined, Part 2" - Ann Gauger - May 2012
Excerpt: "So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required."
http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2

Design by Any Other Name - April 9, 2013
Excerpt: One reason for Endy's team's success is the way that they have approached biological systems. Rather than in terms of modular pieces, they took a more integrated approach.,,,
Darwinism assumes that organisms are built from the bottom-up, where complexity comes from the incorporation of additional components via chance and selection pressure. An engineering perspective assumes that biological systems are built from the top-down.
In other words, the end function is already in mind when the biological system is constructed. Because of this, the system functions as a cohesive whole, rather than as modular components. Furthermore, and as (the success of) Endy's group in particular points out, the parts of the biological systems are not interchangeable like Lego blocks. They have specific functions.
Evolutionary theory says that trial and error lead to the biological structures that we see today. But this same trial-and-error method does not work in the laboratory setting, so why should we assume that it worked in nature?

http://www.evolutionnews.org/2013/04/design_by_any_o070891.html
Moreover, it is interesting to note that many (most?) proteins are now found to be multifunctional depending on what overall context (or cell type) that the protein happens to be involved in. Thus, the sheer brick wall that Darwinian processes face in finding ANY novel functional protein to perform any specific single task in a cell is only exponentially exasperated by the fact that many proteins are multifunctional and, serendipitously, perform several different 'context dependent' tasks within the cell:
Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:
Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.
http://www.sciencedaily.com/releases/2008/11/081102134623.htm

Genes Code For Many Layers of Information - They May Have Just Discovered Another - Cornelius Hunter - January 21, 2013
Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms."
http://darwins-god.blogspot.com/2013/01/genes-code-for-many-layers-of.html
http://www.fasebj.org/content/23/7/2022.full

Explaining how a protein can perform multiple roles - Cell Biology - December 18, 2009
Excerpt: It’s been known for more than a decade that some cell proteins can carry out multiple functions. For example, it was discovered in 1999 that the protein TyrRS (explained shortly) participated not only in the building of enzymes, but also could function to stimulate the growth of blood vessels. Discovering that the same protein could perform very different roles opened one of the great new chapters in molecular biology.
http://scitechstory.com/2009/12/18/explaining-how-a-protein-can-perform-multiple-roles/

Epigenetics and the “Piano” Metaphor – January 2012
Excerpt: And this is only the construction of proteins we’re talking about. It leaves out of the picture entirely the higher-level components — tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players.
http://www.evolutionnews.org/2012/01/epigenetics_and054731.html

What Do Organisms Mean? Stephen L. Talbott – Winter 2011
Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,,
http://www.thenewatlantis.com/publications/what-do-organisms-mean
As well, RNA, which codes for the proteins at the ribosome, is found to be intolerant to 'random mutations':
Molecular Typesetting: How Errors Are Corrected (In RNA) While Proteins Are Being Built
Excerpt: Ensuring that proteins are built correctly is essential to the proper functioning of our bodies,,,“Scientists have been puzzled as to how this process makes so few mistakes.,,,“In fact, there is more than one identified mechanism for ensuring that genetic code is copied correctly."
http://www.sciencedaily.com/releases/2009/06/090623090157.htm

The cell has elaborate ways to safeguard its genetic library by repairing DNA, but now scientists are finding the same enzymes can also repair RNA. RNA methylation damage can be repaired by the same AlkB enzyme that repairs DNA. This is surprising because RNA and proteins were considered more expendable than DNA. (Creation-Evolution Headlines - Feb. 2003)

RNA: Protein Regulators Are Themselves Regulated
“What was formerly conceived of as a direct, straightforward pathway is gradually turning out to be a dense network of regulatory mechanisms: genes are not simply translated into proteins via mRNA (messenger RNA). MicroRNAs control the translation of mRNAs (messenger RNAs) into proteins, and proteins in turn regulate the microRNAs at various levels.”
http://www.sciencedaily.com/releases/2009/09/090910084147.htm

Researchers Uncover New Kink In Gene Control: - Oct. 2009
Excerpt: a collaborative effort,, has uncovered more than 300 proteins that appear to control genes, a newly discovered function for all of these proteins previously known to play other roles in cells.,,,The team suspects that many more proteins encoded by the human genome might also be moonlighting to control genes,,,
http://www.sciencedaily.com/releases/2009/10/091029125536.htm
On top of these monumental problems, for just finding any one specific functional protein, or for just finding any protein/protein binding sites, or for accounting for multiple layers of error correction that prevent evolution from happening to proteins in the first place, a materialist must still account for how the DNA code came about in any origin of life scenario he puts forth. These following videos and articles highlight the 'DNA problem':

Programming of Life - DNA - video
http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/7/O4GV1xI-DSQ
A New Design Argument - Charles Thaxton
Excerpt: "There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology."
http://www.arn.org/docs/thaxton/ct_newdesign3198.htm
Here are some quotes by leading Darwinists on the fact that DNA contains information
"All of life depends on the accurate transmission of information."
Miroslav Radman and Robert Wagner, “The High Fidelity of DNA Duplication,” Scientific American 259 (August 1988): 42, 40-46.

"[The information in a DNA cell] if written out would fill a thousand 600-page books."
Rick Gore, “The Awesome Worlds Within a Cell,” National Geographic (September 1976): 360, 354-95

"And at this point, strangely enough, the discovery of DNA, which is so widely thought to prove that life is mere chemistry, provides the missing link for proving the contrary. That the formation of a DNA molecule is embodied in the morphology of the corresponding offspring, assures us of the fact that this morphology is not the product of a chemical equilibration, but is designed by other than chemical forces."
Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical and Engineering News 45 (August 1967): 66, 55-66

"Information theory can be applied to any situation involving messages. It follows therefore that the language of life, the genetic code written along the lengths of DNA molecules, in groups of three coding for the various twenty-two amino acids of proteins, can also be expressed in terms of a given amount of information."
Edmund Jack Ambrose, The Nature and Origin of the Biological World (New York: Halsted Press, 1982), 125.
Even the United States Supreme Court has weighed in on the 'information issue'.
United States Supreme Court Holds that Life is Based on Information - December 21, 2013
,," Sequences of DNA nucleotides contain the information necessary to create strings of amino acids, which in turn are used in the body to build proteins.”,,
Association for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2111 (2013)
http://www.uncommondescent.com/intelligent-design/united-states-supreme-court-holds-that-life-is-based-on-information/

The "Wow! signal" of the terrestrial genetic code - March 2013
Excerpt: Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality,,,
http://gencodesignal.org/

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005
Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.”
http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc

Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005
“The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” Let me provide the unstated conclusion: But they don’t.
http://www.uncommondescent.com/intelligent-design/living-things-machines-and-intelligent-design-part-two-of-a-response-to-the-smithy/#comment-353336
The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video
http://www.metacafe.com/watch/4060532

Information (in DNA and functional proteins) Proves God - video
http://www.youtube.com/watch?v=PYSmV2FlHDw

Codes and Axioms are always the result of mental intention, not material processes
https://docs.google.com/document/pub?id=1PrE2Syt5SJUxeh2YBBBWrrPailC3uTFMdqPMFrzvwDY
Assessing the "Algorithmic Origin of Life" (Paul Davies' Recent Paper) - December 18, 2012
Excerpt: It is the functionality of the expressed RNAs and proteins that is biologically important. Functionality, however, is not a local property of a molecule. It is defined only relationally, in a global context, which includes networks of relations among many sub-elements,,
One is therefore left to conclude that the most important features of biological information (i.e. functionality) are decisively nonlocal. Biologically functional information is therefore not an additional quality, like electric charge, painted onto matter and passed on like a token. It is of course instantiated in biochemical structures, but one cannot point to any specific structure in isolation and say "Aha! Biological information is here!",,,
,,,For example, mechanical stresses on a cell may affect gene expression. Mechanotransduction, electrical transduction and chemical signal transduction -- all well-studied biological processes -- constitute examples of what philosophers term "top-down causation", where the system as a whole exerts causal control over a subsystem (e.g. a gene) via a set of time-dependent constraints.

http://www.evolutionnews.org/2012/12/assessing_the_a067541.html
A.E. Wilder Smith, DNA, Cactus, and Von Neumann Machines - John MacArthur - audio
http://www.vimeo.com/11341080

Interestingly, Erwin Schrödinger predicted that molecular life was information based 10 years before the discovery of DNA by Watson and Crick:
Passing the baton of life - from Schrödinger to Venter - July 2012
Excerpt: A decade after Schrödinger was awarded the Nobel Prize for his work on atomic theory, the Austrian physicist was serving as the first director of the school of theoretical physics at the newly established Dublin Institute of Advanced Studies. At a public lecture in February, 1943, he turned his attention to the physical nature of the gene. Little was understood about the composition of genes at that stage, but Schrödinger proposed that a gene could be thought of as an 'aperiodic crystal'.
That proved to be a key insight, said Luke O'Neill, professor of biochemistry ,, "The gene had to be stable, so it had to be a crystal, and it had to have information so it was aperiodic," he explained.
"Equally important, Schrödinger also discussed the possibility of a genetic code, stating the concept in clear physical terms."

http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html
Information - The Utter Demise Of Darwinian Evolution - video
http://www.metacafe.com/watch/4914327
"Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent." (Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

"A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107."
(The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)
Biological Information — What is It? - published online May 2013 -
Werner Gitt 1*, Robert Compton 2 and Jorge Fernandez 3
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0001

Dr. Werner Gitt, starting around the 2:00 minute mark of the following video, touches on how using the infinite regress argument from information confirms Theism:

Dr.Werner Gitt Ph.D."In The Beginning was Information" Part 3 of 3 - video
http://www.youtube.com/watch?v=kWZpG0ye8KI

Evolution Impossible! - The Insurmountable 'Information Problem' - video
http://www.youtube.com/watch?v=uIae8PPg-fE
The Digital Code of DNA - 2003 - Leroy Hood & David Galas
Excerpt: The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science.
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html
The Digital Code of DNA and the Unimagined Complexity of a ‘Simple’ Bacteria – Rabbi Moshe Averick – video (Notes in Description)
http://vimeo.com/35730736
Upright Biped Replies to Dr. Moran on “Information” - December 2011
Excerpt: 'a fair reading suggests that the information transfer in the genome shouldn’t be expected to adhere to the qualities of other forms of information transfer. But as it turns out, it faithfully follows the same physical dynamics as any other form of recorded information.'
http://www.uncommondescent.com/intelligent-design/upright-biped-replies-to-dr-moran-on-information/
Even the leading "New Atheist" in the world, Richard Dawkins, agrees that DNA functions exactly like digital code:

Richard Dawkins Opens Mouth; Inserts Foot - video
http://www.evolutionnews.org/2010/06/richard_dawkins_opens_mouth_in035861.html#more
Venter: Life Is Robotic Software - July 15, 2012
Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter.
http://crev.info/2012/07/life-is-robotic-software/
The operating system of life - animated protein robots - video
https://www.youtube.com/watch?v=JufLDxmCwB0

i.e. DNA functions exactly as a 'devised code':
Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177)

With New Research, the Genetic Code Looks More and More Like a Deliberate Choice - July 11, 2012
Excerpt: Even though the natural genetic code is "conserved through all of life," experiments such as these show that other codes are possible. If natural DNA were the only solution to the problems posed by biological information storage and retrieval, it might be argued that nature had to converge on it. But the researchers concluded that natural DNA does not represent a one-and-only solution. Though they don't say this, it surely gives more the appearance of a deliberate choice.
http://www.evolutionnews.org/2012/07/with_new_resear061911.html

A Critique of Douglas Theobald’s - “29 Evidences for Macroevolution” by Ashby Camp
Excerpt: There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature.
- Biophysicist Cornelius G. Hunter
http://www.trueorigin.org/theobald1b.asp

Ode to the Code - Brian Hayes
The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we'll never see again in the modern world.
https://www.americanscientist.org/issues/pub/ode-to-the-code/4
Evolutionists have long argued that the genetic code is universal for all lifeforms, and maintain that that fact is strong evidence for evolution from a universal common anscestor, yet it appears they were wrong once again:

Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! - video
Quote: "I think the tree of life is an artifact of some early scientific studies that aren't really holding up.,, So there is not a tree of life. In fact from our deep sequencing of organisms in the ocean, out of, now we have about 60 million different unique gene sets, we found 12 that look like a very, very deep branching—perhaps fourth domain of life. "
- Dr. Craig Venter, American Biologist involved in sequencing the human genome
http://www.youtube.com/watch?v=MXrYhINutuI
http://darwins-god.blogspot.com/2013/03/a-common-code-surely-that-means-theyre.html
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011
Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal:
"The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10)
OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.

http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
As well there was a ‘optimality’ found for the 20 amino acid set used in the 'standard' Genetic code when the set was compared to 1 million randomly generated alternative amino acid sets;
Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011
Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof."
http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html

Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement – 2009
Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics.
http://pre.aps.org/abstract/PRE/v79/i6/e060901

The Finely Tuned Genetic Code - Jonathan M. - November 2011
Excerpt: Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: "why is the genetic code the way it is and how did it come to be?," that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. - Eugene Koonin and Artem Novozhilov
http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html

"The more we learn about the chemical basis of life and the intricacy of the genetic code, the more unbelievable the standard historical account becomes."
- Thomas Nagel - "Mind & Cosmos"
Moreover the first DNA code of life on earth had to be at least as complex as the current DNA code found in life:

Shannon Information - Channel Capacity - Perry Marshall - video
http://www.metacafe.com/watch/5457552/
“Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
Donald E. Johnson – Bioinformatics: The Information in Life

Deciphering Design in the Genetic Code - Fazale Rana
Excerpt: Sixty-four codons make up the genetic code. Because the genetic code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.,,,
Genetic code rules incorporate a design that allows the cell to avoid the harmful effects of substitution mutations. For example, six codons encode the amino acid leucine (Leu). If at a particular amino acid position in a polypeptide, Leu is encoded by 5′ (pronounced five prime, a marker indicating the beginning of the codon). CUU, substitution mutations in the 3′ position from U to C, A, or G produce three new codons, 5′ CUC, 5′ CUA, and 5′ CUG, all of which code for Leu. The net effect produces no change in the amino acid sequence of the polypeptide. For this scenario, the cell successfully avoids the negative effects of a substitution mutation.
Likewise, a change of C in the 5′ position to a U generates a new codon, 5′UUU, that specifies phenylalanine, an amino acid with similar physical and chemical properties to Leu. A change of C to an A or to a G produces codons that code for isoleucine and valine, respectively. These two amino acids also possess chemical and physical properties similar to leucine. Qualitatively, the genetic code appears constructed to minimize errors that result from substitution mutations.,,,
The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution.18 Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of 10^18 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.

http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code

“The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.”
Fazale Rana - From page 175; 'The Cell’s Design'
http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code
Here is a comment on a study of a 'putative primitive' amino acid set;
http://www.uncommondescent.com/intelligent-design/the-first-gene-an-information-theory-look-at-the-origin-of-life/comment-page-1/#comment-409611

DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video
http://www.metacafe.com/watch/4491422
Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010
Excerpt: It appears then, that the genetic code has been put together in view of minimizing not just the occurence of amino acid substitution mutations, but also the detrimental effects that would result when amino acid substitution mutations do occur.
http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html
Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, of how a specific amino acid is spelled, is far greater than had at first been thought:
Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010
Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,,
http://www.creationsafaris.com/crev201009.htm#20100919a

'Snooze Button' On Biological Clocks Improves Cell Adaptability - Feb. 17, 2013
Excerpt: Like many written languages, the genetic code is filled with synonyms: differently spelled "words" that have the same or very similar meanings. For a long time, biologists thought that these synonyms, called synonymous codons, were in fact interchangeable. Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes,,
http://www.sciencedaily.com/releases/2013/02/130217134246.htm

A New Study Adds Further Depth to the Information Story - JonathanM - March 2012
Excerpt: The conventional genetic code involves 20 different amino acids, which map to 64 different triplets of nucleotides called codons. Since there are many more codons than amino acids, this means that there is an element of redundancy because amino acids can be specified by multiple codons. As I noted before, this redundancy allows the genetic code to be exquisitely fine-tuned to minimize error. The paper explains that "redundancy in the genetic code allows the same protein to be translated at different rates." In other words, even so-called silent substitutions (that is, those mutations that exchange a nucleotide for another without changing the amino acid specified by the codon) can have an impact on the rate of translation of the protein product.
http://www.evolutionnews.org/2012/03/new_study_adds058051.html

A hidden genetic code: Researchers identify key differences in seemingly synonymous parts of the structure - January 21, 2013
Excerpt: (In the Genetic Code) there are 64 possible ways to combine four bases into groups of three, called codons, the translation process uses only 20 amino acids. To account for the difference, multiple codons translate to the same amino acid. Leucine, for example, can be encoded in six ways. Scientists, however, have long speculated whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Harvard researchers have deciphered that second code,,,
Under some stressful conditions, the researchers found, certain sequences manufacture proteins efficiently, while others—which are ostensibly identical—produce almost none. "It's really quite remarkable, because it's a very simple mechanism," Subramaniam said. "Many researchers have tried to determine whether using different codons affects protein levels, but no one had thought that maybe you need to look at it under the right conditions to see this.",,,
While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological failsafe, allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources.

http://phys.org/news/2013-01-hidden-genetic-code-key-differences.html

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. - Jan 2013
Excerpt: Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides.,,,
Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles.

http://www.ncbi.nlm.nih.gov/pubmed/23293005

Here is commentary on the severe constraint that the preceding finding places on Darwinian evolution:
http://www.uncommondescent.com/intelligent-design/here-is-that-new-paper-on-synonymous-nucleotides/#comment-444834

Synonymous (“Silent”) Mutations in Health, Disease, and Personalized Medicine: Review - 2012
Excerpt: In contrast, a synonymous mutation does not delete or substitute one amino acid for another; thus the protein produced by both the normal gene and the mutant have the identical amino acid sequence. However, it can reduce the amount of a specific protein the cell makes or cause the structure of the protein to be distorted in a manner that disrupts its functioning in the body.,,,
The CBER authors compiled a list of synonymous mutations that are linked to almost fifty diseases, including diabetes, a blood clotting disorder called hemophilia B, cervical cancer, and cystic fibrosis.

http://www.fda.gov/BiologicsBloodVaccines/ScienceResearch/ucm271385.htm

Here is How Genes Are Exquisitely Timed - Cornelius Hunter - December 28, 2012
Excerpt: The new research helps to elucidate for which genes RNA polymerase is paused, and how this pausing regulation of RNA polymerase varies over time and between tissues.
It is yet another mechanism in the fantastically complex gene regulation.

http://darwins-god.blogspot.com/2012/12/here-is-how-genes-are-exquisitely-timed.html

The coding system used for living beings is optimal from an engineering standpoint.
Werner Gitt - In The Beginning Was Information - p. 95
Collective evolution and the genetic code - 2006:
Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.
http://www.pnas.org/content/103/28/10696.full

Time mag: (Another) Second Code Uncovered Inside the DNA -- Scientists have discovered a second code hidden within the DNA, written on top of the other. - December 2013
http://science.time.com/2013/12/13/second-code-uncovered-inside-the-dna/
To get a sense of the breath-taking complexity this represents, watch this video of J.S. Bach's "Crab canon." It was composed to be played backwards and forwards at the same time, and then with one part flipped upside down on the music stand.
http://www.openculture.com/2013/02/the_genius_of_js_bachs_crab_canon_visualized_on_a_mobius_strip.html

Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection - Casey Luskin - December 20, 2013
Excerpt: In fact, one commentator observed that on the same analysis, codons may have more than two uses: "By this logic one could coin the term "trion" by pointing out that histone binding is also independently affected by A-C-T-G letter frequencies within protein-coding stretches of DNA."
But this isn't the first time that scientists have discovered multiple codes in biology. Earlier this year I discussed research that found an analog code in the DNA that helps regulate gene expression, in addition to the digital code that encodes primary protein sequence. In other cases, multiple proteins are encoded by the same gene! And then of course there's the splicing code, which helps control how RNAs transcribed from genes are spliced together in different ways to construct different proteins (see here and here).
It boggles the mind to think about how such "codes within codes" could evolve by random mutation and natural selection. But now it turns out that evidence of different functions for synonymous codons could threaten many standard methods used to infer selection in the first place,,,

http://www.evolutionnews.org/2013/12/codes_within_co080381.html

The genetic code is nearly optimal for allowing additional information within protein-coding sequences - Shalev Itzkovitz and Uri Alon - 2006
Excerpt: Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes.
http://genome.cshlp.org/content/17/4/405.full

DNA as Poetry: Multiple Messages in a Single Sequence - James Shapiro - 2012
Excerpt: Another question is harder to answer: How do multiple messages come to be inscribed in a single sequence in the course of evolution? This is an evolutionary mystery, especially when the second message has a complex structure. My own particular intellectual headache comes from structures called "shufflons" found in some bacteria that use them to diversify extracellular protein structures. Variability in surface proteins is advantageous in extending the range of specific cell-cell attachments for transfer of DNA and other macromolecules.
In a shufflon, the coding sequence contains two or more copies of the intricate signals required for a DNA rearrangement process known as "site-specific recombination." When a coding region carrying two or more recombination sites undergoes an inversion, the protein sequence changes because there is now a new string of triplet codons between the recombining sites. Some shufflons have up to seven different recombination sites embedded in the coding sequence. These structures are theoretically capable of generating over 100 different protein-coding DNA sequences (33 of which have actually been isolated from one shufflon).
Such remarkable protein diversifying systems in bacterial genomes pose a mystery. How do the recombination sites evolve within sequences encoding functional proteins? It does not make sense to argue that each one evolved by selection operating a few nucleotides at a time; there is no benefit until at least two complete recombination signals are present. Moreover, known mechanisms for duplicating and inserting copies of a complex DNA signal at multiple locations generally disrupt coding capacity. Further, as in mammalian dual-coding regions, we do not understand how both strands evolve simultaneously to encode functional protein segments.
At a time when we pride ourselves for being able to read DNA sequences with increasing speed, it is salutary to keep in mind that we are still far from knowing how to interpret the complex overlapping meanings contained in the genomic texts we store in our databases. DNA, like poetry, often has to be read in several ways.

http://www.huffingtonpost.com/james-a-shapiro/dna-as-poetry-multiple-me_b_1229190.html

The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy - 2005

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

The multiple codes of nucleotide sequences. Trifonov EN. - 1989
Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code).
http://www.ncbi.nlm.nih.gov/pubmed/2673451

Multiple genetic codes
Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code.
Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins:,,

chromatin code (Trifonov 1980)
RNA-to-protein translation code (triplet code)
framing code (Trifonov 1987)
translation pausing code (Makhoul & Trifonov 2002) protein folding code (Berezovsky, Grosberg & Trifonov 2000)
fast adaptation codes (Trifonov 1989)
binary code (Trifonov 2006)
genome segmentation code (Kolker & Trifonov 1995)

The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered.

http://en.wikipedia.org/wiki/Edward_Trifonov#Multiple_genetic_codes
Seems some heavy hitters are citing Trifonov as well, i.e. Zimmer, Koonin, Szostak, etc..
citations:
http://en.wikipedia.org/wiki/Edward_Trifonov#Citations
here is a mp3 audio of Trifonov from 2010 in which he makes reference of up to '13 codes' in the genome:

One spectacular case of code crowding - Edward N. Trifonov - 2010
http://bio.natur.cuni.cz/~flegr/ctvrtky/audio/2010Z_01a_Trifonov.mp3
Q&A
http://bio.natur.cuni.cz/~flegr/ctvrtky/audio/2010Z_01b_Trifonov.mp3

At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:

Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video
https://vimeo.com/81930637

In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

Concluding powerpoint of the lecture (at the 1 hour mark):
"Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages."
Edward N. Trifonov - 2010

Trifanov EN - Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. - 1997
Excerpt: The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages.
http://www.garfield.library.upenn.edu/histcomp/alberts_na-auth-citing/node/6766.html
Codes of biosequences - E. N. Trifonov - 2007
http://is.muni.cz/el/1431/jaro2007/Bi_IB8/Codes_of_biosequences.pdf
Multiple levels of meaning in DNA sequences, and one more. - Trifonov EN, Volkovich Z, Frenkel ZM. - 2012
Excerpt: If we define a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology, then there are multiple genetic codes. Sequences involved in these codes overlap and, thus, both interact with and constrain each other, such as for the triplet code, the intron-splicing code, the code for amphipathic alpha helices, and the chromatin code. Nucleosomes preferentially are located at the ends of exons, thus protecting splice junctions, with the N9 positions of guanines of the GT and AG junctions oriented toward the histones.,,
http://www.ncbi.nlm.nih.gov/pubmed/22954214

Circular RNAs: A Hidden, Parallel Universe - Cornelius Hunter PhD. - March 2, 2013
Excerpt: Recall that protein-coding genes, in addition to coding for an incredible protein machine, may also contain several more layers of information encoding signals for the transcript (mRNA) stability, mRNA editing, DNA copy error correction, the speed of translation, the protein’s three-dimensional protein structure, the stability of that structure, the multiple functions of the protein, interactions of the protein with other proteins, instructions for transport, avoiding an amyloid state, any other genes that overlap with the gene, and controlling tRNA selection which can help to respond to different environmental conditions.
That is a tall order and now we have yet another layer of information for which genes much encode: circular RNA macromolecules which just happen to interact with microRNA and which just happen to be expressed at the right time, because if they are expressed at the wrong time you don’t have a normal brain. And amazingly, in protein-coding genes, circular RNA macromolecules may be encoded both in the antisense strand and in the sense strand. In fact numerous circular RNAs form by head-to-tail splicing of exons.,,,

http://darwins-god.blogspot.com/2013/03/circular-rnas-hidden-parallel-universe.html

How the Cell Exploits Genetic Code Degeneracy - January 7, 2013
Excerpt: This implies that degenerate systems provide a way to encode extra information; indeed, quantum computing and steganography exploit this capacity.
http://www.evolutionnews.org/2013/01/how_the_cell_ex068101.html

"In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
Donald E. Johnson – Programming of Life – pg.51 - 2010

DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011
Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
http://www.sciencedaily.com/releases/2011/01/110128104244.htm

Smallest, fastest-known RNA switches provide new drug targets - October 7, 2012
Excerpt: While RNA's switching function has been well-documented, Hashim Al-Hashimi and his U-M colleagues report online Oct. 7 in the journal Nature a new class of switches that are significantly smaller and orders of magnitude faster than the other known class of RNA switches. Al-Hashimi calls these short-lived structures, which were detected using a new imaging technique developed in his laboratory, micro-switches. "We're finally able to zoom in on these rare, alternative forms of RNA that exist for just a split second and then are gone," said Al-Hashimi, the Robert L. Kuczkowski Professor of Chemistry and Biophysics. "These things are so difficult to see because they exist for roughly 1 percent of the time and for only a microsecond to a millisecond."
http://phys.org/news/2012-10-smallest-fastest-known-rna-drug.html

Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011
Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer."
http://www.evolutionnews.org/2011/09/ends_and_means050391.html

Histone Inspectors: Codes and More Codes - Cornelius Hunter - March 2010
Excerpt: By now most people know about the DNA code. A DNA strand consists of a sequence of molecules, or letters, that encodes for proteins. Many people do not realize, however, that there are additional, more nuanced, codes associated with the DNA.
http://darwins-god.blogspot.com/2010/03/histone-inspectors-codes-and-more-codes.html

Four More DNA Bases? - August 2011
Excerpt: As technology allows us to delve ever deeper into the inner workings of the cell, we continue to find layer-upon-layer of complexity. DNA, in particular, is an incredibly complex information-bearing molecule that bears the hallmarks of design.
http://www.evolutionnews.org/2011/08/four_more_dna_bases049091.html

New technique reveals unseen information in DNA code - May 17, 2012
Excerpt: Imagine reading an entire book, but then realizing that your glasses did not allow you to distinguish "g" from "q." What details did you miss? Geneticists faced a similar problem with the recent discovery of a "sixth nucleotide" in the DNA alphabet.,,, Two modifications of cytosine, one of the four bases that make up DNA, look almost the same but mean different things.,,,
http://phys.org/news/2012-05-technique-reveals-unseen-dna-code.html
Besides multiple layers of 'classical information' embedded in overlapping layers throughout the DNA, there has now been discovered another layer of 'quantum information' embedded throughout the DNA:

Quantum Information In DNA - short video
http://www.metacafe.com/watch/5936605/
Human DNA is like a computer program but far, far more advanced than any software we've ever created.
Bill Gates, The Road Ahead, 1996, p. 188
How DNA Killed Evolutionism pt 1 of 4 - video
http://www.youtube.com/watch?v=35fulERIUnU&list=PL935140E53256839D&index=1&feature=plcp

The Coding Found In DNA Surpasses Man's Ability To Code - Stephen Meyer - video
http://www.metacafe.com/watch/4050638

Stephen Meyer - Excerpted Clip of CBN interview on problems of Craig Venter's Synthetic Life - DNA - Complexity Of The Cell - Layered Information - video
http://www.metacafe.com/watch/4798685

Evolution of Synthetic DNA (turns out to support Intelligent Design) - Fazale Rana PhD. - podcast (starts to get interesting around the 20 minute mark)
http://www.reasons.org/podcasts/science-news-flash/evolution-of-synthetic-dna
Synthetic Genetics Is ID, not Darwinism - May 1, 2012
Excerpt: The researchers' bullish sentence, "Thus heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage" is a colossal non sequitur. They didn't see any evolution of information. They simply imagined it.
http://www.evolutionnews.org/2012/05/synthetic_genet059111.html
Genetic Entropy - Dr. John Sanford - Evolution vs. Reality (Super Programming in the Genome that 'dwarfs' our computer programs) - video
http://vimeo.com/35088933

DNA - Evolution Vs. Polyfuctionality - video
http://www.metacafe.com/watch/4614519/

DNA - Poly-Functional Complexity equals Poly-Constrained Complexity
http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ
"applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It's just not going to work."
- David Berlinski

Do you believe Richard Dawkins exists?
Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.
http://creation.com/does-dawkins-exist
Information Storage in DNA by Wyss Institute - video
https://vimeo.com/47615970
Quote from preceding video:
"The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA."
Sriram Kosuri PhD. - Wyss Institute

Storing information in DNA - Test-tube data - Jan 26th 2013
Excerpt: Dr Goldman’s new scheme is significant in several ways. He and his team have managed to set a record (739.3 kilobytes) for the amount of unique information encoded. But it has been designed to do far more than that. It should, think the researchers, be easily capable of swallowing the roughly 3 zettabytes (a zettabyte is one billion trillion or 10²¹ bytes) of digital data thought presently to exist in the world and still have room for plenty more.
http://www.economist.com/news/science-and-technology/21570671-archives-could-last-thousands-years-when-stored-dna-instead-magnetic

Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA - January 29, 2013
Excerpt: Gigabytes have become commonplace, and now we're warming up to terabytes. Ready for petabytes? That's a thousand terabytes and a million gigabytes. It's the new lingo that will migrate from geek to street, if DNA hard drives become a reality.,,,
Last year, researchers led by bioengineers Sriram Kosuri and George Church of Harvard Medical School reported that they stored a copy of one of Church's books in DNA, among other things, at a density of about 700 terabits per gram, more than six orders of magnitude more dense than conventional data storage on a computer hard disk. Now, researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they've improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,,
This is truly a profound achievement of human intelligent design. Why wouldn't the same be true of natural DNA? ,,,
There's far more information in our DNA than the UK team embedded in theirs -- layers and layers of coding that regulate gene expression and respond interactively to signals in a vast network of complex feedback loops. It's a whole system of information. To clinch the comparison, natural DNA also has elaborate error correction, proofreading and repair systems that can copy all that information with extremely high fidelity.
As the Shakespearean sonnets in DNA point to intelligent design, the functional information in natural DNA points to intelligent design. It would be foolish to ascribe the superior information to blind, unguided processes.

http://www.evolutionnews.org/2013/01/how_do_you_peta068641.html

Applied Intelligent Design: Storing Information on DNA - JonathanM - January 25, 2013
Excerpt: One naturally wonders whether the clear intelligent design implications of this project crossed the minds of the paper's authors. In terms of efficiency, DNA far surpasses any current manmade technology and can last for thousands of years. To get a handle on this, consider that 1 petabyte is equivalent to 1 million gigabytes of information storage. This paper reports an information storage density of 2.2 petabytes per gram.
http://www.evolutionnews.org/2013/01/applied_intelli068631.html

Harvard cracks DNA storage, crams 700 terabytes of data into a single gram - Sebastian Anthony - August 17, 2012
Excerpt: A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.,,, Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored.
http://www.extremetech.com/extreme/134672-harvard-cracks-dna-storage-crams-700-terabytes-of-data-into-a-single-gram

Craig Venter's Genetic Typo - 3/14/2011
Excerpt: In order to distinguish their synthetic DNA from that naturally present in the bacterium, Venter’s team coded several famous quotes into their DNA, including one from James Joyce’s A Portrait of the Artist of a Young Man: “To live, to err, to fall, to triumph, to recreate life out of life.”
After announcing their work, Venter explained, his team received a cease and desist letter from Joyce’s estate, saying that he’d used the Irish writer’s work without permission. ”We thought it fell under fair use,” said Venter.

http://www.forbes.com/sites/davidewalt/2011/03/14/craig-venters-genetic-typo/

Scientists have successfully encoded MP3s, Shakespeare's sonnets, and research papers onto strands of the double helix molecules. - January 28, 2013
Excerpt: Scientists from the European Bioinformatics Institute in the UK have successfully stored and retrieved large amounts of data using DNA. Shakespeare’s 154 sonnets, an MP3 of Martin Luther King’s “I have a dream” speech, and the research paper that first described the double helical nature of DNA, were all encoded into a strand of DNA. Vast quantities of information could be written into DNA; 2.2 petabytes per gram. This could be archived for tens of thousands of years and retrieved with 100% accuracy.
http://www.psfk.com/2013/01/encode-dna-information.html#!qvUMj

DNA: The Ultimate Hard Drive - Science Magazine, August-16-2012
Excerpt: "When it comes to storing information, hard drives don't hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare."
http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html

DNA Stores Data More Efficiently than Anything We've Created - Casey Luskin - August 29, 2012
Excerpt: Nothing made by humans can approach these kind of specs. Who would have thought that DNA can store data more efficiently than anything we've created. But DNA wasn't designed -- right?
http://www.evolutionnews.org/2012/08/who_would_have_063701.html

Harvard Scientists Write the Book on Intelligent Design—in DNA - Dr. Fazale Rana - September 10, 2012
Excerpt: One gram of DNA can hold up to 455 exabytes (one exabyte equals 10^18 bytes). In comparison, a CD-ROM holds about 700 million (7 x 10^8) bytes of data. (One gram of DNA holds the equivalent amount of data as 600 billion CD-ROMs. Assuming a typical book requires 1 megabyte of data-storage capacity, then one gram of DNA could harbor 455 trillion books.)
http://www.reasons.org/articles/harvard-scientists-write-the-book-on-intelligent-design-in-dna

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA - January 2013
Excerpt: Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11875.html
Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area:
Welcome to CoSBi - (Computational and Systems Biology)
Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. (Of note the preceding header has now been removed from the site)
http://www.cosbi.eu/index.php/component/content/article/171

DNA Computer
Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours.
http://www.tech-faq.com/dna-computer.html

Biochemical Turing Machines “Reboot” the Watchmaker Argument - Fazale Rana - July 2012
Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.
http://stevebrownetc.com/2012/07/02/biochemical-turing-machines-%E2%80%9Creboot%E2%80%9D-the-watchmaker-argument/

Engineers design cells that can compute logarithms, divide and take square roots - May 15, 2013
Excerpt: The circuits perform those calculations in an analog fashion by exploiting natural biochemical functions that are already present in the cell rather than by reinventing them with digital logic, thus making them more efficient than the digital circuits pursued by most synthetic biologists,,,
Sarpeshkar has previously identified thermodynamic similarities between analog transistor circuits and the chemical circuits that take place inside cells. In 2011, he took advantage of those similarities to model biological interactions between DNA and proteins in an electronic circuit, using only eight transistors.,,,
In the new Nature paper, Sarpeshkar, Lu and colleagues have done the reverse—mapping analog electronic circuits onto cells.

http://phys.org/news/2013-05-analog-circuits-cells-logarithms-square.html

Introducing "Bi-Fi": The Biological Internet - October 3, 2012
Excerpt: They already achieved 5 petabits per cubic millimeter! That's 1,000 terabits of data -- nearly twice the entire volume of digital records at the Library of Congress1 -- in a cube the size of the space between your thumb and forefinger when you hold them slightly apart.2
There are more reasons they think DNA storage is the wave of the future: "DNA is particularly suitable for immutable, high-latency, sequential access applications such as archival storage. Density, stability, and energy efficiency are all potential advantages of DNA storage, although costs and times for writing and reading are currently impractical for all but century-scale archives. However, the costs of DNA synthesis and sequencing have been dropping at exponential rates of 5- and 12-fold per year, respectively--much faster than electronic media at 1.6-fold per year. Hand-held, single-molecule DNA sequencers are becoming available and would vastly simplify reading DNA-encoded information."
Hand-held? You mean your smartphone might read and write documents in DNA? Why not? Well, if DNA is the ideal storage medium, how about using it for the Internet? In fact, "Bi-Fi: The Biological Internet" is in development at Stanford School of Medicine. (links provided at site)

http://www.evolutionnews.org/2012/10/introducing_bi-064781.html

Biological Computer: Stanford Researchers Discover Genetic Transistors That Turn Cells Into Computers - March 29, 2013 (w/video)
Excerpt: This isn't to say that highly functional biological computers will arrive in short order, but we should certainly begin to see simple biological sensors that measure and record changes in a cell’s environment. Stanford has contributed the...gate design to the public domain, which should allow other research institutes, such as Harvard's Wyss Institute, to also begin work on the first biological computer.
http://www.huffingtonpost.com/2013/03/29/biological-computer_n_2981753.html
How DNA Compares To Human Language - Perry Marshall - video
http://www.metacafe.com/watch/4298072

Understanding ENCODE - Sept. 2012 - gene regulation is similar to adding punctuation and spacing to a paragraph of written text - video
http://www.youtube.com/watch?v=yjpW30z-SB8

I like the analogy in the preceding video of comparing the genetic text in the DNA to the written text of humans, but I would hold that the regulation of genes they have uncovered by the ENCODE project, thus far, is much better to be compared to constructing entire paragraphs, whole cloth, complete with punctuation and spelling, from a dictionary of a very basic set of 23,000 'gene words'. That extended analogy would be much more realistic to what ENCODE has actually found in the genome!

Yet the DNA code is not even reducible to the laws of physics or chemistry:
British Geneticist Robert Saunders Leaves a Highly Prejudiced Signature in His Review of “Signature in the Cell” - April 2012
Excerpt: Meyer points out a rather astonishing fact – about which there is no scientific controversy – regarding the arrangements of the nucleobases in DNA. There are absolutely no chemical affinities or preferences for which nucleobases bond with any particular phosphate and sugar molecule. The N-glycosidic bond works equally well with (A), (T), (G), or (C). And secondly, there are also no chemical bonds in the vertical axis between the nucleobases. What this means is that there are no forces of physical/chemical attraction and no chemical or physical law that dictates the order of the nucleobases; they can be arranged in a nearly infinite amount of different sequences.
http://www.algemeiner.com/2012/04/04/british-geneticist-robert-saunders-leaves-a-highly-prejudiced-signature-in-his-review-of-signature-in-the-cell/

The Origin of Life and The Suppression of Truth
Excerpt: 'Many claims have been made that nucleotides of DNA have been produced in such “spark and soup” experiments. However, after a careful review of the scientific literature, evolutionist Robert Shapiro stated that the nucleotides of DNA and RNA, "….have never been reported in any amount in such sources, yet a mythology has emerged that maintains the opposite….I have seen several statements in scientific sources which claim that proteins and nucleic acids themselves have been prepared… These errors reflect the operation of an entire belief system… The facts do not support his belief…Such thoughts may be comforting, but they run far ahead of any experimental validation."
http://the_wordbride.tripod.com/origin.html

Life’s Irreducible Structure
Excerpt: “Mechanisms, whether man-made or morphological, are boundary conditions harnessing the laws of inanimate nature, being themselves irreducible to those laws. The pattern of organic bases in DNA which functions as a genetic code is a boundary condition irreducible to physics and chemistry." Michael Polanyi - Hungarian polymath - 1968 - Science (Vol. 160. no. 3834, pp. 1308 – 1312)

“an attempt to explain the formation of the genetic code from the chemical components of DNA… is comparable to the assumption that the text of a book originates from the paper molecules on which the sentences appear, and not from any external source of information.”
Dr. Wilder-Smith

The Capabilities of Chaos and Complexity - David L. Abel - 2009
Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
http://www.mdpi.com/1422-0067/10/1/247/pdf
i.e. There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequence of nucleotides to exist as they do. In fact as far as the foundational laws of the universe are concerned the DNA molecule doesn’t even have to exist at all.
Judge Rules DNA is Unique (and not patentable) Because it Carries Functional Information - March 2010
“Today the idea that DNA carries genetic information in its long chain of nucleotides is so fundamental to biological thought that it is sometimes difficult to realize the enormous intellectual gap that it filled.... DNA is relatively inert chemically.”
http://www.uncommondescent.com/intelligent-design/judge-rules-dna-is-unique-because-it-carries-information/
Stephen Meyer is interviewed about the "information problem" in DNA, Signature in the Cell - video
http://downloads.cbn.com/cbnnewsplayer/cbnplayer.swf?aid=8497

The DNA Enigma - The Ultimate Chicken and Egg Problem - Chris Ashcraft - video
http://www.metacafe.com/watch/5542033/

The DNA Enigma - Where Did The Information Come From? - Stephen C. Meyer - video
http://www.metacafe.com/watch/4125886

Signature In The Cell - Stephen Meyer - e-book
http://intelligentdesignscience.files.wordpress.com/2012/07/signature-in-the-cell.pdf

Believing Life's 'Signature in the Cell' an Interview with Stephen Meyer - CBN video
http://www.evolutionnews.org/2010/06/believing_lifes_signature_in_t035911.html
Every Bit Digital DNA’s Programming Really Bugs Some ID Critics - March 2010
Excerpt: In 2003 renowned biologist Leroy Hood and biotech guru David Galas authored a review article in the world’s leading scientific journal, Nature, titled, “The digital code of DNA.”,,, MIT Professor of Mechanical Engineering Seth Lloyd (no friend of ID) likewise eloquently explains why DNA has a “digital” nature: "It’s been known since the structure of DNA was elucidated that DNA is very digital. There are four possible base pairs per site, two bits per site, three and a half billion sites, seven billion bits of information in the human DNA. There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins."
http://www.salvomag.com/new/articles/salvo12/12luskin2.php

ID Vindicated - August 17, 2012
Excerpt: Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing.
http://www.uncommondescent.com/intelligent-design/id-vindicated/

Stephen C. Meyer - Signature In The Cell:
"DNA functions like a software program," "We know from experience that software comes from programmers. Information--whether inscribed in hieroglyphics, written in a book or encoded in a radio signal--always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source."
http://www.evolutionnews.org/2009/07/leading_advocate_of_intelligen.html
Extreme Software Design In Cells - Stephen Meyer - video
http://www.metacafe.com/watch/5495397/
The handwriting in our DNA - December 27, 2013
Excerpt: Stephen C. Meyer,, told cnsnews.com the story of a former Microsoft software engineer:
"He walks into my office one day, throws a book down on the table. It's called Design Patterns -- standard textbook for computer design engineers -- and he says, 'I get the eerie feeling, when I'm looking at what's going on in the cell, that's somebody's figured this out before us.' And I said, 'What do you mean?' And he says, 'Well, it's the design patterns,' and then he points to the book. . . . 'We've got design logic for processing information, for doing error correction, for doing distributed data retrieval and reassembly, and for hierarchical organization -- we've got files within folders, like on your desktop, you know, in the hierarchical filing system.' And he says, 'All those design patterns are inside the cell, except they're using a design logic that's like an 8.0, 9.0, 10.0 version of ours. It's the same basic logic, but it's more elegantly executed,' and he says, 'It gives me an eerie feeling.'"

http://www.newsday.com/opinion/oped/o-reilly-the-handwriting-in-our-dna-1.6683000
DNA - The Genetic Code - Optimization, Error Minimization & Parallel Codes - Fazale Rana - video
http://www.metacafe.com/watch/4491422/

As well as coding optimization, DNA is also optimized to prevent damage from light:
DNA Optimized for Photostability
Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage.
http://www.reasons.org/dna-soaks-suns-rays
The materialist must also account for the overriding complex architectural organization of DNA:

DNA Wrapping (Histone Protein Wrapping to Cell Division)- video
http://www.youtube.com/watch?v=gbSIBhFwQ4s

DNA - Replication, Wrapping & Mitosis - video
http://vimeo.com/33882804

Unwinding the Double Helix: Meet DNA Helicase - Jonathan M. February 20, 2013 - article with video
Excerpt: With a rotational speed of up to 10,000 rotations per minute, the helicase rivals the rotational speed of jet engine turbines.
http://www.evolutionnews.org/2013/02/unwinding_the_d_1069371.html

Four-strand DNA structure found in cells Unusual nucleic-acid structure may have role in regulating some genes. - Alison Abbott - 20 January 2013 - with picture
http://www.nature.com/news/four-strand-dna-structure-found-in-cells-1.12253
'Quadruple helix' DNA discovered in human cells - January 20, 2013
Excerpt: In 1953, Cambridge researchers Watson and Crick published a paper describing the interweaving 'double helix' DNA structure - the chemical code for all life. Now, in the year of that scientific landmark's 60th Anniversary, Cambridge researchers have published a paper proving that four-stranded 'quadruple helix' DNA structures - known as G-quadruplexes - also exist within the human genome.,,,
Physical studies over the last couple of decades had shown that quadruplex DNA can form in vitro - in the 'test tube', but the structure was considered to be a curiosity rather than a feature found in nature. The researchers now know for the first time that they actually form in the DNA of human cells.
"This research further highlights the potential for exploiting these unusual DNA structures to beat cancer –,,,
"It's been sixty years since its structure was solved but work like this shows us that the story of DNA continues to twist and turn.",,,
While quadruplex DNA is found fairly consistently throughout the genome of human cells and their division cycles, a marked increase was shown when the fluorescent staining grew more intense during the 's-phase' - the point in a cell cycle where DNA replicates before the cell divides.,,,
It's a philosophical question as to whether they are there by design or not - but they exist and nature has to deal with them.,,,
"The 'quadruple helix' DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark."

http://phys.org/news/2013-01-quadruple-helix-dna-human-cells.html

Another Remarkable DNA Rescuing Machine (Elucidated) -June 4, 2013
Excerpt: Some of these are composed of four strands that form stable structures called G-quadruplexes or G4s, so named because they tend to be rich in guanine. They are not uncommon,,,,
,,there is a machine that can unwind these G4s quickly and efficiently. Called Pif1 helicase, it is conserved from bacteria to humans.,,,
Pif1 is “highly conserved, from bacteria to humans,

(Thus, at least to me, suggesting important functionality for G4s though precisely what that functionality may be is not known yet).
http://www.evolutionnews.org/2013/06/another_remarka072811.html

Dr. Jerry Bergman, "Divine Engineering: Unraveling DNA's Design":
The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million.
http://www.harunyahya.com/books/darwinism/if_darwin_had_known/if_darwin_had_known06.php#dipnot

DNA Packaging: Nucleosomes and Chromatin
each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth's equator 2.5 million times! How is this possible?
http://www.nature.com/scitable/topicpage/DNA-Packaging-Nucleosomes-and-Chromatin-310
This is interesting. Euler's formula (the most famous of all formulas), when plotted in 3D, results in the fundamental geometry of DNA: a helix!

The following images show the graph of the complex exponential function, complex exponential function, e^{ix}, by plotting the Taylor series of e^{ix} in the 3D complex space (a helix)
http://www.songho.ca/math/euler/euler.html

It turns out that DNA is also optimized for 'maximally dense packing' as well:
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009
Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
http://www.sciencemag.org/cgi/content/abstract/326/5950/289

3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009
Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
http://www.sciencedaily.com/releases/2009/10/091008142957.htm

Genetics Is Too Complex for Evolutionists to Fake It Anymore - April 30, 2013
Excerpt: Using the same amount of space, DNA can store 140,000 times more data than iron (III) oxide molecules, which stores information on computer hard drives.
http://www.evolutionnews.org/2013/04/genetics_is_too071621.html

Biochemical Turing Machines “Reboot” the Watchmaker Argument - Fazale Rana - July 2012
Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.
http://stevebrownetc.com/2012/07/02/biochemical-turing-machines-%E2%80%9Creboot%E2%80%9D-the-watchmaker-argument/

Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009
Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
http://www.sciencedaily.com/releases/2009/12/091215160649.htm
Although evolution depends on 'mutations/errors' to DNA to make evolution plausible, there are multiple layers of error correction in the cell to protect against any "random changes" to DNA from happening in the first place:
The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011
Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation."
http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic
Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution)
http://www.youtube.com/watch?v=dzh6Ct5cg1o
The Darwinism contradiction of repair systems
Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
http://www.uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/

Repair mechanisms in DNA include:

A proofreading system that catches almost all errors
A mismatch repair system to back up the proofreading system
Photoreactivation (light repair)
Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
Base excision repair
Nucleotide excision repair
Double-strand DNA break repair
Recombination repair
Error-prone bypass

http://www.newgeology.us/presentation32.html

Scientists Decipher Missing Piece Of First-responder DNA Repair Machine - Oct. 2009
Excerpt: The first-responder machine, a protein complex called Mre11-Rad50-Nbs1 (or MRN for short), homes in on the gravest kind of breaks in which both strands of a DNA double helix are cut. It then stops the cell from dividing and launches an error-free DNA repair process called homologous recombination, which replaces defective genes.
http://www.sciencedaily.com/releases/2009/10/091001164106.htm

A Look at the Quality Control System in the Protein Factory - JonathanM - March 2012
Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.
http://www.evolutionnews.org/2012/03/a_look_at_the_q057791.html

Molecular Machines Are Amazing Alone, but When They Cooperate -- Wow! - January 14, 2014
Excerpt: RNA polymerase -- the machine that translates DNA into RNA -- is the star player. It patrols the DNA like an automated inspector on train tracks. When it encounters a break, it stops and waits. The problem is, when it stops, it stalls over the break, preventing repair machines from reaching it. Not to worry. Everything is under control.
In the new study, the NYU School of Medicine researchers reveal how another enzyme called UvrD helicase acts like a train engine to pull the RNA polymerase backwards and expose the broken DNA so a repair crew can get to work....
The study by Dr. Nudler's group and colleagues in Russia used a battery of biochemical and genetic experiments to directly link UvrD to RNA polymerase and to demonstrate that UvrD's pulling activity is essential for DNA repair. The lab results also suggest that UvrD relies on a second factor, called NusA, to help it pull RNA polymerase backwards. Those two partners then recruit a repair crew of other proteins to patch up the exposed DNA tracks before the train-like polymerase continues on its way.

http://www.evolutionnews.org/2014/01/molecular_machi_3081111.html

Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010
Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.

NP-hard problem - Examples
http://en.wikipedia.org/wiki/NP-hard#Examples
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013
Excerpt: quantum computing is, "in some cases, really, really fast."
McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "travelling salesperson" problem that's been a foundation of theoretical computing for decades.,,,
"This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory."

http://www.sciencedaily.com/releases/2013/05/130508122828.htm
Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA;

Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
http://www.metacafe.com/watch/5936605/
Is DNA a quantum computer? Stuart Hameroff
Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,,
http://www.quantumconsciousness.org/dnaquantumcomputer1.htm
Of related interest:

Can Quantum Mechanics Play a Role in DNA Damage Detection? (Short answer; YES!) – video - as well at about 27 Minute mark in the video - Fröhlich Condensation and Quantum Consciousness
http://www.scivee.tv/node/25476

Electric (Quantum) DNA repair - video
http://www.youtube.com/watch?feature=player_embedded&v=60tqaKyzHxs#!
Researchers discover how key enzyme repairs sun-damaged DNA - July 2010
Excerpt: Ohio State University physicist and chemist Dongping Zhong and his colleagues describe how they were able to observe the enzyme, called photolyase, inject a single electron and proton into an injured strand of DNA. The two subatomic particles healed the damage in a few billionths of a second. "It sounds simple, but those two atomic particles actually initiated a very complex series of chemical reactions," said Zhong,,, "It all happened very fast, and the timing had to be just right."
http://www.physorg.com/news199111045.html

DNA 'molecular scissors' discovered - July 2010
Excerpt: ' We discovered a new protein, FAN1, which is essential for the repair of DNA breaks and other types of DNA damage.
http://www.physorg.com/news197902053.html

More DNA Repair Wonders Found - October 2010
Excerpt: This specialized enzyme may attract other repair enzymes to the site, and “speeds up the process by about 100 times.” The enzyme “uses several rod-like helical structures... to grab hold of DNA.”,,, On another DNA-repair front, today’s Nature described a “protein giant” named BRCA2 that is critically involved in DNA repair, specifically targeting the dangerous double-stranded breaks that can lead to serious health consequences
http://www.creationsafaris.com/crev201010.htm#20101007a

Protein Researchers Unravel the Molecular Dance of DNA Repair - March 2012
Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, "We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications," Petra Beli says.
"This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works."
The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways.

http://www.sciencedaily.com/releases/2012/03/120315123022.htm

Safeguarding genome integrity through extraordinary DNA repair - April, 2011
Excerpt: Unlike euchromatin, where most of an organism’s genes reside and where most DNA consists of long, unrepetitive sequences of base pairs, DNA in heterochromatin consists mostly of short repeated sequences that don’t code for proteins; indeed, heterochromatin was long regarded as containing mostly “junk” DNA.
Heterochromatin is now known to be anything but junk, playing a crucial role in organizing chromosomes and maintaining their integrity during cell division. It is concentrated near centromeres, where chromatids are in closest contact, which are required to transmit chromosomes from one generation to the next. Maintaining heterochromatin structure is necessary to the normal growth and functions of cells and organisms.

http://phys.org/news/2011-04-safeguarding-genome-extraordinary-dna.html

Extreme Genome Repair - 20 March 2009
Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.
http://www.sciencedirect.com/science/article/pii/S0092867409002657

RNA: From Messenger to Guardian of Genome Integrity - (May 2012)
Excerpt: For decades the scientific community has attributed a role to RNA that is subordinate to that of DNA: the functional processes of expression of genetic information into proteins. With some known exceptions, such as the classes of tRNA and rRNA involved in the synthesis of proteins, RNA molecules were considered "fleeting" messengers necessary to carry genetic instructions from the nucleus, site of the genome, to the cytoplasm where proteins, the scaffolding of living organisms, are produced.
In recent years, this simplistic view has given way to an increasingly complex scenario, with the identification of new RNA classes involved in numerous cellular events.
One in particular, however, had never been identified or described to date: it is DDRNA, a class of non protein-coding RNAs that are generated every time the genome is damaged. They originate from the same sequence of DNA damaged and have the essential task of launching the molecular alarms through which the cell detects the problem and resolves it by repairing the damage.

http://www.sciencedaily.com/releases/2012/05/120523161323.htm

‘How good would each typists have to be, in order to match the DNA’s performance? The answer is almost too ludicrous to express. For what it is worth, every typists would have to have an error rate of about one in a trillion; that is, he would have to be accurate enough to make only a single error in typing the Bible 250,000 times at a stretch.
Richard Dawkins - The Blind Watchmaker - Page 123-124
Proof reading of DNA polymerase (Reduces error rate to 1 in 100 million) - video
http://www.youtube.com/watch?v=YcNhuYh34P4
Evolutionists Caught Again—But They Still Believe - Dr. Cornelius Hunter - May 2012
Excerpt: As a new paper now explains, under evolution we must believe that mutations rates have been “evolutionarily optimized.” That is, evolution is now so brilliant that it created the means to not only control, but to optimize the actual mutation rates.,,, (Here is how they put their findings)
"Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.,, Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.,, Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.,, Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. ,, The findings have important implications for our understanding of evolution and the control of mutations.,,"
Dr. Hunter Comments: "These findings have important implications for our understanding of evolution? Well sure, if by that they mean how absurd are evolution truth claims."

http://darwins-god.blogspot.com/2012/05/evolutionists-caught-againbut-they.html
This is simply unreal! It turns out that finding out that random mutations/variations are not truly random does not bother committed Darwinists in the least as to questioning whether their theory is true or not:
Fully Random Mutations - Kevin Kelly - Jan. 2014
Excerpt: What is commonly called "random mutation" does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.,,,
Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.,,,
,,,the lack of direct evidence for actual random mutations has now reached a stage where the idea needs to be retired. There are several related reasons why this unsubstantiated idea continues to be repeated without evidence. The first is fear that non-random mutations would be misunderstood and twisted by creationists,,,

http://www.edge.org/responses/what-scientific-idea-is-ready-for-retirement
Moreover, the protein machinery that replicates DNA is found to be vastly different in even the most ancient of different single celled organisms:
Did DNA replication evolve twice independently? - Koonin
Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus.
http://nar.oxfordjournals.org/cgi/content/full/27/17/3389
Problems of the RNA World - Did DNA Evolve Twice? - Dr. Fazale Rana - video
http://www.metacafe.com/watch/4564682

There simply is no smooth 'gradual transition' to be found between these most ancient of life forms as this following articles and videos clearly point out:
Oops, Evolution Forgot About the Eukaryotes - February 14, 2013
Excerpt: How about this 1998 paper in which the evolutionists admit that “One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve.” Evolution omitted how eukaryotes could emerge and evolve? That would be like physics omitting gravity, politics omitting elections or baseball omitting homeruns. Yet this paper came more than a century after evolutionists began insisting that it is beyond all reasonable doubt that the species, and that would be all the species, arose spontaneously.
http://darwins-god.blogspot.com/2013/02/oops-evolution-forgot-about-eukaryotes.html

Was our oldest ancestor a proton-powered rock?
Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,... Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria and the archaea).
http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html?page=1

Bacterial Cell Division and Peptidoglycan Synthesis: An Evolutionary Enigma - April 3, 2013
Excerpt: In eukaryotes, cell division occurs by either meiosis (sex cells) or mitosis (somatic cells). Bacteria, however, undergo neither of those processes (they are asexual and contain no membrane-enclosed organelles or nuclei). Bacterial cell division occurs by a process known as binary fission. Rod-shaped bacteria (e.g. Escherichia coli or Salmonella typhimurium) elongate to twice their original length. This is followed by invagination of the cell membrane, and the formation of a septal ring in the middle (Vicente et al., 2006; Weiss, 2004). The elongated bacterial cell splits down the middle, forming two daughter cells. ,,,
Now, here's the conundrum. Consider the following two observations: (1) Critical to the elongation process is the severing of the peptidoglycan cell wall by the autolysins. (2) Critical to cell viability is the re-synthesis of the peptidoglycan cell wall. This has to be done in a coordinated fashion. Breaking of the cell wall can serve no adaptive utility until a mechanism has arisen for the simultaneous integration of peptidoglycan precursors. Indeed, without the latter mechanism, the cell is rendered non-viable. This is a classic example of what one might describe as an irreducibly complex system.

http://www.evolutionnews.org/2013/04/bacterial_cell070681.html
An overview of the system hierarchy of a bacterial cell is picked up around the 41:00 minute mark of the following video:

The Systems Architecture of a Bacterial Cell Cycle with Lucy Shapiro - video
http://www.youtube.com/watch?&v=8qiwOxVf1T4#t=2489s

How the Eukaryotic Cell Cycle Is Controlled - Jonathan M. - June 17, 2013 - with two videos
http://www.evolutionnews.org/2013/06/how_the_eukaryo073371.html

An enormous gap exists between prokaryote cells and eukaryote cells. A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP (energy).
http://www.trueorigin.org/atp.asp

The ATP Synthase Enzyme - exquisite motor necessary for first life - video
http://www.youtube.com/watch?v=W3KxU63gcF4

Mitochondria - Molecular Machine - Powerhouse Of The Cell - video
http://www.metacafe.com/watch/5510941/

On The Non-Evidence For The Endosymbiotic Origin Of The Mitochondria - March 2011
http://www.uncommondescent.com/intelligent-design/on-the-non-evidence-for-the-endosymbiotic-origin-of-the-mitochondria/
On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story
Jonathan M. - January 10, 2012
Excerpt: While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to -- at the very least -- give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist -- and justifiably gives one cause for skepticism.
http://www.evolutionnews.org/2012/01/on_the_origin_o054891.html

Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010
Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote.
http://www.creationsafaris.com/crev201007.htm#20100712b

Bacterial Protein Acetylation: The Dawning of a New Age - July 2012
Excerpt: Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely.
http://darwins-god.blogspot.com/2012/07/bacterial-protein-acetylation-dawning.html

Even the Cell's (RNA) Shredder Looks Designed - February 14, 2013
Excerpt: They have established that this machine is irreducibly complex in eukaryotes. Does it have any evolutionary precursors?
Quote: "The RNA-binding and threading mechanism used by the exosome in eukaryotes is very similar to that of the exosome in bacteria and archaebacteria that the researchers had structurally characterized in earlier studies. "Although the chemistry of the shredding reaction in eukaryotes is very different from that used in bacteria and archaebacteria, the channeling mechanism of the exosome is conserved, and conceptually similar to the channeling mechanism used by the proteasome, a complex for shredding proteins," says Elena Conti.,,,
With this description in mind, several problems become apparent for evolutionary explanations of these machines. First of all, they are already present in bacteria and archaebacteria, presumably the simplest living things. Moreover, the bacterial exosome is chemically different but structurally similar. This means the design is "conserved" but not the ancestry. Then there is another chemically different but structurally similar machine in eukaryotes: the proteasome.
These machines all appear to be irreducibly complex. They are composed of multiple parts, each essential for function. They are also essential for life: the article says that "unwanted accumulation of RNAs can be damaging to the cell" and that these complex machines have multiple functions. In addition to shredding excess RNAs, the exosome "processes certain RNA molecules into their mature form." Since all living things rely on DNA translation via RNA molecules (messenger RNAs and transfer RNAs), it is difficult to imagine any putative ancestor getting by without functional exosomes from the very beginning. Maybe that's why the article did not even mention evolution.

http://www.evolutionnews.org/2013/02/even_the_cells_1068921.html
Materialism simply has no credible answer for how this extreme level of complexity 'accidentally' arose in the first living cell, nor how this extreme integrated complexity found in life randomly evolved to the next 'simple' step of life.

Even more problematic for evolutionists, than the unexplained gap between prokaryote and eukaryote cells, is that even within the 'bacterial world' there are found to be enormous unexplained gaps of completely unique genes within each different type of bacteria which has had its DNA sequenced:

ORFan Genes Challenge Common Descent – Paul Nelson – video with references
http://www.vimeo.com/17135166

Because of these insurmountable problems, for generating novel functional proteins, or meaningful DNA, or any meaningfully functional information whatsoever, materialists are trying real hard to sell the 'RNA World' to the general public. Yet, we have absolutely no compelling reason to believe that a hypothetical 'RNA World' will ever start magically generating the massive amounts of complex functional information required for the first life. Here is a sampling of many critiques against the RNA world hypothesis:
Paul Davies on the RNA-world or what he calls “digital-first” scenarios:
Excerpt: “For example, much of the information digitally stored in DNA must be first transcribed and translated before it becomes algorithmically meaningful in the context of the cell where it is then processed as analog information through protein interaction networks. Focusing strictly on digital storage therefore neglects this critical aspect of how biological information is processed. As we discuss below, due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it.”
“Although trivial self-replicators can undergo Darwinian evolution [23, 24], the lack of separation between algorithm and implementation implies that mono-molecular systems are divided from known life by a logical and organizational chasm that cannot be crossed by mere complexification of passive hardware. In that respect we regard the case of the RNA world as currently understood as falling short of being truly living.”

http://arxiv.org/abs/1207.4803

RNA world: Chemists Propose a Seemingly Unlikely Environment for the Origin of Life - February 27, 2013
Excerpt: Benner and his colleagues consider three major problems with the RNA-world model:
*The "asphalt problem": Organic reactions often produce unreactive byproducts. These byproducts are a mixture of pieces of the product or polymerization of the product, but are chemically insignificant and otherwise unpromising. Hence the metaphor of "asphalt." Typically, avoiding the production of such byproducts requires very specific and controlled conditions, or post-reaction purification steps.
*The "water problem": Many of the bonds in RNA will undergo hydrolysis. This occurs when water reacts with the bond, causing it to break apart. In a lab, the problem is easily addressed by using a different solvent. However, the environment of the early Earth could not draw on the resource of various organic solvents.
*The "impossible bond problem": The authors refer here to the difficulty in forming certain bonds in RNA. Usually this follows from thermodynamic issues that prohibit bonds from spontaneously forming.
Conspicuously missing from the authors' list of critiques are the "chirality problem" and the "information problem." Later in the paper, however, they concede that their model does not solve the enigma of chirality, and they allude to a potential "fatal flaw" in their proposition, namely that the kinds of RNA molecules that catalyze the destruction of RNA are more likely to emerge than RNA molecules that catalyze the synthesis of RNA. -

http://www.evolutionnews.org/2013/02/death_valley_da068661.html

Three subsets of sequence complexity and their relevance to biopolymeric information - David L Abel and Jack T Trevors:
Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction...No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization...It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.
http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf

Origin of Life: Claiming Something for Almost Nothing (RNA)
Excerpt: Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.” But does this (laboratory) work support a naturalistic origin of life? A key question is whether a (self-replicating) molecule could form under plausible prebiotic conditions. Here’s how the paper described their work in the lab to get this (precursor) molecule:,,(several 'unnatural' complex steps of laboratory work are listed)
http://www.creationsafaris.com/crev201003.htm#20100302a

Chemists Seek Possible Precursor to RNA - February 5, 2014
Excerpt: In the modern cell, cooking up an RNA molecule is a complex process involving multiple enzymes that link a sugar (ribose) to one of four nucleobases — chemical letters that make up the genetic code and come in the flavors guanine, adenine, uracil and cytosine — and a phosphate, which provides the backbone of the structure. Another enzyme ties together repeating units of each of these three components into the long chain of RNA.
But in the pre-biotic Earth, there were no enzymes. So how could the first RNA molecules have formed? According to the RNA world hypothesis, RNA spontaneously came together through geochemical processes. Scientists studying the origins of life have spent the past 40 years trying to figure out exactly how this could have happened, analyzing the likely chemical components of early Earth and devising chemical reactions to bring them together. “The chemistry of making RNA is so difficult that it’s hard to imagine that you could have a one-pot reaction, where molecules come together and spontaneously make this complex molecule,” Hud said.
Scientists have been able to produce a few of these components without enzymes. In 2009, Sutherland and collaborators showed for the first time that they could synthesize one of the basic units of RNA from scratch. They argue RNA could have formed this way in nature, but Hud and Freeland say the precise chemical conditions and steps required for the reaction would have been unlikely to occur in the chaotic chemical cauldron of prebiotic Earth.

https://www.simonsfoundation.org/quanta/20140205-chemists-pursue-possible-precursor-to-rna/
Doug Axe humorously dismantled one of the latest ploys by materialists to oversell their meager evidence for a "self-replicating RNA molecule" in this following article:
Biologic Institute Announces First Self-Replicating Motor Vehicle - Doug Axe -
Excerpt: "So, advertising this as “self-replication” is a bit like advertising something as “free” when the actual deal is 1 free for every 1,600 purchased. It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off. That makes the real deal more like n free for every 1,600 n purchased, with the caveats that n must be a very large number and that full payment must be made in advance."
http://www.biologicinstitute.org/post/19309047110/biologic-institute-announces-first-self-replicating

Origin of life researchers say they are one step closer to RNA world - January 17, 2014
Excerpt: "Holliger lab,, made an RNA molecule that is able to accurately copy RNA sequences that are longer than itself – more than 200 building blocks long"
Informed sources note that the molecule can replicate other template RNAs if it is given activated nucleotides, the right buffer, and other advantages.

http://www.uncommondescent.com/intelligent-design/origin-of-life-researchers-say-they-are-one-step-closer-to-rna-world/
Dr. Stephen Meyer: Chemistry/RNA World/crystal formation can't explain genetic information - video
Excerpt 5:00 minute mark: "If there is no chemical interaction here (in the DNA molecule) you can't invoke chemistry to explain sequencing"
http://www.youtube.com/watch?v=yLeWh8Df3k8

Stephen Meyer points out that intelligence design was clearly required for even this meager result that Dr. Axe spoke about:
Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved - Stephen C. Meyer
Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises.
http://www.evolutionnews.org//2009/06/biological_information_the_puz.html
Stephen Meyer Responds to Fletcher in Times Literary Supplement - Jan. 2010
Excerpt: everything we know about RNA catalysts, including those with partial self-copying capacity, shows that the function of these molecules depends upon the precise arrangement of their information-carrying constituents (i.e., their nucleotide bases). Functional RNA catalysts arise only once RNA bases are specifically-arranged into information-rich sequences—that is, function arises after, not before, the information problem has been solved.
http://www.evolutionnews.org/2010/01/stephen_meyer_responds_to_flet.html

Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?
Stephen C. Meyer and Paul A. Nelson
Excerpt: Although Yarus et al. claim that the DRT model undermines an intelligent design explanation for the origin of the genetic code, the model’s many shortcomings in fact illustrate the insufficiency of undirected chemistry to construct the semantic system represented by the code we see today.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.2/BIO-C.2011.2
Ann Gauger offers a easy to understand outline of Meyer and Nelson's preceding paper:
In BIO-Complexity, Meyer and Nelson Debunk DRT - Ann Gauger
Excerpt: While DNA carries information necessary to build cells, it performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins, which then can carry out the various chemical and structural functions of life. But there is no direct way to convert a given DNA sequence into a protein sequence -- no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.
That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form.,,, The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. As it stands now, you need the machinery that translates DNA into protein in order to make the very same machinery that translates DNA into protein.,,, There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.

http://www.evolutionnews.org/2011/08/in_bio-complexity_meyer_and_ne050041.html
Materialists have not even created all 4 'letters' of RNA by natural means:
Response to Darrel Falk’s Review of Signature in the Cell - Stephen Meyer - Jan. 2010
Excerpt: Sutherland’s work only partially addresses the first and least severe of these difficulties: the problem of generating the constituent building blocks or monomers in plausible pre-biotic conditions. It does not address the more severe problem of explaining how the bases in nucleic acids (either DNA or RNA) acquired their specific information-rich arrangements.
http://www.signatureinthecell.com/responses/response-to-darrel-falk.php

Stirring the Soup - May 2009
"essentially, the scientists have succeeded in creating a couple of letters of the biological alphabet (in a "thermodynamically uphill" environment). What they need to do now is create the remaining letters, and then show how these letters were able to attach themselves together to form long chains of RNA, and arrange themselves in a specific order to encode information for creating specific proteins, and instructions to assemble the proteins into cells, tissues, organs, systems, and finally, complete phenotypes."
Uncommon Descent - C Bass:
http://www.uncommondescent.com/intelligent-design/stirring-the-soup/#comments

Scientists Say Intelligent Designer Needed for Origin of Life Chemistry
Excerpt: Organic chemist Dr. Charles Garner recently noted in private correspondence that "while this work helps one imagine how RNA might form, it does nothing to address the information content of RNA. So, yes, there was a lot of guidance by an intelligent chemist." Sutherland's research produced only 2 of the 4 RNA nucleobases, and Dr. Garner also explained why, as is often the case, "the basic chemistry itself also required the hand of an intelligent chemist." http://www.evolutionnews.org/2009/07/scientists_say_intelligent_des.html#more

Meyer Responds to Stephen Fletcher - Stephen Meyer - March 2010
Excerpt: Nevertheless, this work does nothing to address the much more acute problem of explaining how the nucleotide bases in DNA or RNA acquired their specific information-rich arrangements, which is the central topic of my book (Signature In The Cell). In effect, the Powner (Sutherland) study helps explain the origin of the “letters” in the genetic text, but not their specific arrangement into functional “words” or “sentences.”
http://www.evolutionnews.org/2010/03/meyer_responds_to_stephen_flet.html

Deflating the synthetic proofs of the RNA World - David Tyler - August 2011
Excerpt: There may be a consensus about the RNA World, but it is not a consensus based on evidence. The approach is supported by synthetic proofs drawn from unrealistic laboratory experiments, showing all the signs of a dogmatism that pastes its ideas on to nature.
http://www.arn.org/blogs/index.php/literature/2011/08/04/deflating_the_synthetic_proofs_of_the_rn
Here are some more critiques of the 'RNA World' scenario:

Did Life Begin in an RNA World?
http://www.creationsafaris.com/crev0702.htm#abiogenesis62

Self Replication and Perpetual Motion - The Second Law's Take On The RNA World
http://theory-of-evolution.net/chap10/self-replicating-RNA-perpetual-motion-4.php

Of related note:

Unlocking the Mysteries of Extracellular RNA Communication - video
http://www.youtube.com/watch?feature=player_embedded&v=XHqNS4M-_IY
Chemistry by Chance: A Formula for Non-Life by Charles McCombs, Ph.D.
Excerpt: The following eight obstacles in chemistry ensure that life by chance is untenable.
1. The Problem of Unreactivity
2. The Problem of Ionization
3. The Problem of Mass Action
4. The Problem of Reactivity
5. The Problem of Selectivity
6. The Problem of Solubility
7. The Problem of Sugar
8. The Problem of Chirality
The chemical control needed for the formation of a specific sequence in a polymer chain is just not possible through random chance. The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size.

http://www.icr.org/article/chemistry-by-chance-formula-for-non-life/
The RNA World: A Critique - Gordon Mills and Dean Kenyon:
http://www.arn.org/docs/odesign/od171/ribo171.htm
OOL (Origin Of Life) on the Rocks:
Excerpt: Robert Shapiro, a senior prize-winning chemist, cancer researcher, emeritus professor and author of books in the field, debunks the Miller experiment, the RNA World and other popular experiments as unrealistic dead ends.
http://www.creationsafaris.com/crev200702.htm#20070215a

Libby Anne: Portrait of an atheist feminist - V.J. Torley - November 8, 2012
Excerpt: the late Professor Robert Shapiro (1935-2011) explained why he found the RNA world hypothesis incredible:
" …[S]uppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback – and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself – appearing on the Earth."

www.uncommondescent.com/intelligent-design/libby-anne-portrait-of-an-atheist-feminist/
Life What A Concept! - Robert Shapiro – video
http://www.youtube.com/watch?&v=ku9wUbbPVYg#!
Professor Robert Shapiro~ quote from preceding video
“I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.
I’m always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself — appearing on the Earth.”

Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic: Origins, a Skeptic’s Guide to the Creation of Life on Earth and Planetary Dreams.
Top Ten Most Cited Chemist in the world wants to understand evolution but can’t – James Tour, Phd. – video
http://www.youtube.com/watch?v=WCyAOCesHv0
New Scientist Weighs in on the Origin of Life - Jonathan M. - August 17, 2011
Excerpt: To conclude, Michael Marshall's New Scientist article does not even come close to demonstrating the feasibility of the RNA world hypothesis, much less the origin of the sequence-specific information necessary for even the simplest of biological systems.
http://www.evolutionnews.org/2011/08/new_scientist_weighs_in_on_ori049621.html

The Origin of Life: An RNA World? - Jonathan M. - August 22, 2011 (Refutation of Nick Matzke)
Excerpt Summary & Conclusion
We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don't know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses.

http://www.evolutionnews.org/2011/08/the_rna_world_a_response_to_ni049871.html

Origin of Life: Claiming Something for Almost Nothing - March 2010
Excerpt: A look through the paper, however, shows complex lab procedures that are hard to justify in nature. (intelligence is required for even this meager step),,, the problem of sequencing the nucleotides – the key question – has not been addressed. Where did the genetic code come from? One ribozyme is not a code.
http://www.creationsafaris.com/crev201003.htm#20100302a

Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010
Excerpt: As Stephen Meyer has comprehensively documented in his book, Signature in the Cell, the RNA-world hypothesis is fraught with problems, quite apart from those pertaining to the origin of information. For example, the formation of the first RNA molecule would have required the prior emergence of smaller constituent molecules, including ribose sugar, phosphate molecules, and the four RNA nucleotide bases. However, it turns out that both synthesizing and maintaining these essential RNA building blocks -- especially ribose -- and the nucleotide bases is a very difficult task under origin-of-life conditions.
http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html

An Evolutionist Just Gave Up On a Fundamental Just-So Story (And Then Made Up Another to Replace it) - March 2012
Excerpt: "I'm convinced that the RNA world (hypothesis) is not correct," Caetano-Anollés said. "That world of nucleic acids could not have existed if not tethered to proteins.",, The ribosome is a "ribonucleoprotein machine," a complex that can have as many as 80 proteins interacting with multiple RNA molecules,,,, Furthermore, "you can't get RNA to perform the molecular function of protein synthesis that is necessary for the cell by itself."… It appears the basic building blocks of the machinery of the cell have always been the same from the beginning of life to the present:
http://darwins-god.blogspot.com/2012/03/evolutionist-just-gave-up-on.html

The RNA world hypothesis: the worst theory for the early evolution of life (except for all the others) - July 2012
Excerpt: "The RNA World scenario is bad as a scientific hypothesis" - Eugene Koonin
“The RNA world hypothesis has been reduced by ritual abuse to something like a creationist mantra” - Charles Kurland
"I view it as little more than a popular fantasy." - Charles Carter
http://www.biology-direct.com/content/pdf/1745-6150-7-23.pdf

Rabbi nails it: Origin of life theory is a demolition derby - October 13, 2013
Excerpt: The history of scientific endeavor to discover a naturalistic origin of life reads like a laboratory version of a demolition derby. A researcher roars into the arena to propose a new theory and is summarily rammed and demolished by another theory driven by its respective theoretician who in turn is rammed and demolished by the next eager contestant. A few examples for the uninitiated reader:,,,
http://www.uncommondescent.com/intelligent-design/rabbi-nails-it-origin-of-life-theory-is-a-demolition-derby/#comment-476506

New findings challenge assumptions about origins of life - September 13, 2013
Excerpt: But for the hypothesis to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. That's a hard sell; scientists calculate that it would take much longer than the age of the universe for randomly generated RNA molecules to evolve sufficiently to achieve the modern level of sophistication. Given Earth's age of 4.5 billion years, living systems run entirely by RNA could not have reproduced and evolved either fast or accurately enough to give rise to the vast biological complexity on Earth today.
"The RNA world hypothesis is extremely unlikely," said Carter. "It would take forever."
Moreover, there's no proof that such ribozymes even existed billions of years ago. To buttress the RNA World hypothesis, scientists use 21st century technology to create ribozymes that serve as catalysts. "But most of those synthetic ribozymes," Carter said, "bear little resemblance to anything anyone has ever isolated from a living system.",,,
The (current) study leaves open the question of exactly how those primitive systems managed to replicate themselves—something neither the RNA World hypothesis nor the Peptide-RNA World theory can yet explain.

http://phys.org/news/2013-09-assumptions-life.html
Since the RNA-World has so many insurmountable problems, some evolutionists have tried the 'metabolism first' scenario to try get past the gargantuan probabilistic hurdles facing the origin of life 'problem'. But yet again the evolutionists have failed miserably:
Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life - Dec. 2009
Excerpt: we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations).
http://www.pnas.org/content/107/4/1470
A realistic look at the preceding paper is found here:
Metabolism-First Origin of Life Won’t Work
Excerpt: "“We do not know how the transition to digitally encoded information has happened in the originally inanimate world; that is, we do not know where the RNA world might have come from,"
http://www.creationsafaris.com/crev201001.htm#20100105a
Douglas Axe also comments on the results of the preceding study here:
Explaining Life by Explaining it Away — February 6th, 2010 by Douglas Axe
Excerpt: Think of it this way. If no conceivable mixture of small molecules provides even a faint hope for the emergence of metabolism catalyzed by genetically encoded enzymes, then whatever these mixtures may or may not do, they can’t explain life as we see it. And as the evidence now stands, one would be hard pressed to argue that there is even a faint hope.
http://biologicinstitute.org/2010/02/06/explaining-life-by-explaining-it-away/
Other leading researchers find the metabolism first scenario wholly implausible:
“Pigs don’t fly”
Excerpt: One of the most devastating critiques of the new “metabolism first” approaches to the origin of life was leveled two years ago by Leslie Orgel right before he died (Nov. 2007)
http://www.creationsafaris.com/crev200801.htm#20080126a
Even leading 'new atheist' Richard Dawkins admits no one has a clue how the first living cell 'evolved':
Leading Darwinist Richard Dawkins Dodges Debates, Refuses to Defend Evolution - Stephen Meyer
"(Richard) Dawkins says that there is no evidence for intelligent design in life, and yet he also acknowledges that neither he nor anyone else has an evolutionary explanation for the origin of the first living cell. We know now even the simplest forms of life are chock-full of digital code, complex information processing systems and other exquisite forms of nanotechnology."
http://www.discovery.org/a/12801
In realizing the staggering impossibilities presented for any conceivable origin of life scenario, some materialists, including Francis Crick the co-discover of the DNA helix, have, in my opinion, completely left the field of experimental biology and suggested pan-spermia, the theory pre-biotic amino acids, or life itself, came to earth from outer-space on comets, or even delivered by UFO's, to account for this sudden appearance of life on earth.

Richard Dawkins Vs. Ben Stein - The UFO Interview - video
http://www.metacafe.com/watch/4134259

The panspermia hypothesis, which is really born out of sheer desperation rather than any sound reason on the materialist part, has several problems. One problem is astronomers, using spectral analysis, have not found any vast reservoirs of biological molecules anywhere they have looked in the universe (Ross; Creation as Science). Another problem is, even if comets were nothing but pre-biotic amino acid snowballs, how are the amino acids going to molecularly survive the furnace-like temperatures generated when the comet crashes into the earth, or assemble themselves into proteins once they land?
Botching Evolutionary Science - Casey Luskin - April 2009
Excerpt: Of course, the textbook makes no mention of studies which have shown that such impacts would likely vaporize organic molecules carried to earth. (See Edward Anders. “Pre-biotic organic matter from comets and asteroids.” Nature, Vol. 342:255-257 (1989).
http://www.evolutionnews.org/2010/04/the_biggest_problem_in_asking.html#more
Nor is there any 'prebiotic' chemical signature on the early earth:

Dr. Hugh Ross - Origin Of Life Paradox (No prebiotic chemical signatures)- video
http://www.metacafe.com/watch/4012696

Of note to 'prebiotic' chemistry:
How Life May Have First Emerged On Earth: Foldable Proteins in a High-Salt Environment - Apr. 4, 2013
Excerpt: Today the human body uses 20 common amino acids to make all its proteins. Ten of those (are synthesized by molecular machines) through biosynthetic pathways,,,. (The other) Ten -- the 'prebiotic' set -- can be made by chemical reactions without requiring any living system or biosynthetic pathway.
http://www.sciencedaily.com/releases/2013/04/130405064027.htm
Dr. Hugh Ross has surmised delivery of organic molecules by meteorites or comets has now effectively been ruled out because of the homochirality problem of finding only the 'left handed' amino acids needed to build life in the universe somewhere:
"Circularly polarized UV light only produces a 17% excess (of R or L-amino-acids) and such selective destruction of organics require monochromatic light (monochromatic light isn’t known to occur naturally anywhere in the universe). So directed panspermia (life delivered by UFO's) is their last resort." Hugh Ross
I would like to reiterate, materialism postulated a very simple first cell, yet the simplest cell scientists have been able to find on earth, which can't even be seen with the naked eye, is vastly more complex than any machine man has ever made through concerted effort. This is especially true since a cell can self-replicate with seeming ease whereas a machine cannot. This following site has a interactive graph that lets people look into this 'invisible' world of microbes:

CELL TO CARBON ATOM - SIZE AND SCALE - Interactive Graph - Move cursor at the bottom of graph to the right to reduce the size:
http://learn.genetics.utah.edu/content/begin/cells/scale/

The Cell As Revealed By The Electron-Microscope – video
http://www.metacafe.com/watch/5766297/

Diatoms – photos
https://docs.google.com/document/d/1gfH7WuD87e863tx-ICudApYGCWK9gvj0cd2ldmpYpyQ/edit

Here is a neat little video clip that I wish was a bit longer (they say a longer one is in the works):

The Flow – Resonance Film – video
Description: The Flow, from inside a cell, looks at the supervening layers of reality that we can observe, from quarks to nucleons to atoms and beyond. The deeper we go into the foundations of reality the more it loses its form, eventually becoming a pure mathematical conception.
http://vimeo.com/groups/7286/videos/25430131

The smallest cyano-bacterium known to science has hundreds of millions of individual atomic molecules (not counting water molecules), divided into nearly a thousand completely distinct atomic molecule types; and a genome (DNA sequence) of 1.8 million bits, with over a million individual protein molecules which are sub-divided into hundreds of distinct protein classes.
The physics of going viral: Researchers measure the rate of DNA transfer from viruses to bacteria - June 27, 2012
Excerpt: E. coli cells contain roughly 3 million proteins within a box that is roughly one micron (1,000 nanometers) on each side. Less than 10 nanometers separate each protein from its neighbors. "There's no room for anything else," Phillips says. "These cells are really crowded."
http://phys.org/news/2012-06-physics-viral-dna-viruses-bacteria.html
Once again, the integrated complexity found in the simplest bacterium known to science easily outclasses the integrated complexity of any machine man has ever made. These following articles and videos make this point clear:
James Shapiro on “dangerous oversimplifications” about the cell - August 6, 2013
Excerpt: "Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function.
Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4]."

http://www.uncommondescent.com/news/james-shapiro-on-dangerous-oversimplifications-about-the-cell/

"The manuals needed for building the entire space shuttle and all its components and all its support systems would be truly enormous! Yet the specified complexity (information) of even the simplest form of life - a bacterium - is arguably as great as that of the space shuttle."
J.C. Sanford - Geneticist - Genetic Entropy and the Mystery Of the Genome

'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica."Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894
Ben Stein - EXPELLED - The Staggering Complexity Of The Cell - video
http://www.metacafe.com/watch/4227700
“Although the tiniest living things known to science, bacterial cells, are incredibly small (10^-12 grams), each is a veritable micro-miniaturized factory containing thousands of elegantly designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world”. Michael Denton, "Evolution: A Theory in Crisis," 1986, p. 250.

The Cell as a Collection of Protein Machines
"We have always underestimated cells. Undoubtedly we still do today,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each which is composed of a set of large protein machines."
Bruce Alberts: Former President, National Academy of Sciences;
http://www.imbb.forth.gr/people/aeconomou/documents/Alberts98.pdf

The operating system of life - animated protein robots - video
https://www.youtube.com/watch?v=JufLDxmCwB0

Problems with the Metaphor of a Cell as "Machine" - July 2012
Excerpt: Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life.
Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others.
Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,,

http://www.evolutionnews.org/2012/07/problems_with_t062691.html

Passing the baton of life - from Schrödinger to Venter - July 2012
Excerpt: "All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to design new DNA software." - Craig Venter
http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html
The (Simple?) Cell - Chuck Missler - video
http://www.youtube.com/watch?v=n8Qo3SuhtaY

The Cell - A World Of Complexity Darwin Never Dreamed Of - Donald E. Johnson - video
http://www.metacafe.com/watch/4139390

Bioinformatics: The Information in Life - Donald Johnson - video
http://vimeo.com/11314902

On this episode of ID the Future, Casey Luskin interviews Dr. Donald E. Johnson about his 2010 book, Programming of Life, which compares the workings of biology to a computer.

Programming of Life - February 2012 - podcast
http://intelligentdesign.podomatic.com/entry/2012-02-17T13_29_15-08_00

Here is the video that goes with the 'Programming Of Life' book:

Programming of Life - video
http://www.youtube.com/watch?v=k6iWX9nGocg&feature=list_related&playnext=1&list=SPAFDF33F11E2FB840

Here is Dr. Johnson's Home Page;

Science Integrity - Exposing Unsubstantiated Science Claims
http://scienceintegrity.net/default.aspx

On a slide in the preceding video, entitled 'Information Systems In Life', Dr. Johnson points out that:

* the genetic system is a pre-existing operating system;
* the specific genetic program (genome) is an application;
* the native language has codon-based encryption system;
* the codes are read by enzyme computers with their own operating system;
* each enzyme’s output is to another operating system in a ribosome;
* codes are decrypted and output to tRNA computers;
* each codon-specified amino acid is transported to a protein construction site; and
* in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

Cells Are Like Robust Computational Systems, - June 2009
Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail."
http://www.sciencedaily.com/releases/2009/06/090616103205.htm

Nanoelectronic Transistor Combined With Biological Machine Could Lead To Better Electronics: - Aug. 2009
Excerpt: While modern communication devices rely on electric fields and currents to carry the flow of information, biological systems are much more complex. They use an arsenal of membrane receptors, channels and pumps to control signal transduction that is unmatched by even the most powerful computers.
http://www.sciencedaily.com/releases/2009/08/090811091834.htm

Paramecium caudatum can communicate with neighbors using a non-molecular method, probably photons. The cell populations were separated either with glass allowing photon transmission from 340 nm to longer waves, or quartz being transmittable from 150 nm, i.e. from UVlight to longer waves. Energy uptake, cell division rate and growth correlation were influenced.
http://en.wikipedia.org/wiki/Paramecium_caudatum

Systems biology: Untangling the protein web - July 2009
Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening."
http://www.nature.com/nature/journal/v460/n7253/full/460415a.html
The following impressive videos highlight some of the innovative techniques that are being employed to visualize, in 3D, some of these very complex interactions happening in a cell:

SPARKYT3DHD - video
https://www.youtube.com/watch?v=UsoQNq1kadc

(3D representation of) YEAST PROTEIN INTERACTION NETWORK HD - video
http://www.youtube.com/watch?feature=player_detailpage&v=iO0XqEslL7Q#t=206s

Here is an excellent article, from ENV, that shows it is impossible, due to polyfuctionality, to ever completely understand living organisms in a bottom up manner much less explain their origination in such a bottom up manner:
"Complexity Brake" Defies Evolution - August 2012
Excerpt: "This is bad news. Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology speeds up by an order of magnitude each year.",,,
Even with shortcuts like averaging, "any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system," Koch said. "It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner." He described the concept of the Complexity Brake:,,,
"Allen and Greaves recently introduced the metaphor of a "complexity brake" for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.",,,
Why can't we use the same principles that describe technological systems? Koch explained that in an airplane or computer, the parts are "purposefully built in such a manner to limit the interactions among the parts to a small number." The limited interactome of human-designed systems avoids the complexity brake. "None of this is true for nervous systems.",,,

to read more go here:
http://www.evolutionnews.org/2012/08/complexity_brak062961.html

Simulations reveal new information about the gateway to the cell nucleus
Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,"...
http://www.psc.edu/science/2006/schulten/

Mathematicians find solution to biological building block puzzle – July 31, 2012
Excerpt: Professor Gorban said: “We have shown that what appeared to be very different mechanisms are in fact manifestations of one relatively simple biochemical reaction, but taking place in various contexts. “Our model proposes that microRNA performs many actions simultaneously to the protein development, basically acting to get the job done (regulating the speed of protein production) in a stable and efficient way, given whatever conditions the experiment is occurring in.
http://phys.org/news/2012-07-mathematicians-solution-biological-block-puzzle.html
Here’s an Incredible Electronic Version of the Biochemical Pathways Chart
http://darwins-god.blogspot.com/2012/04/heres-incredible-electronic-version-of.html

Here is a better website for glimpsing some of the staggering complexity of the Biochemical Pathways of a 'simple' cell!

ExPASy - Biochemical Pathways - interactive schematic
http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl

I showed that particular biochemical pathway chart to a Darwinist once when he asked me for ANY evidence of intelligent design in biology. His response upon seeing it was something along the lines of, ‘Just because it is horrendously complex does not prove it was designed.’. ,,, Well maybe so, but such ‘horrendous complexity’ certainly does not give comfort to the notion that such ‘horrendous complexity’ can be the accumulation of random genetic accidents either!

Here is a ‘horrendously complex’ metabolic pathway chart:

Map Of Major Metabolic Pathways In A Cell - Diagram
http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf

Part of the ‘horrendous complexity’ inherent in metabolic pathways is gone over here:

The 10 Step Glycolysis Pathway In ATP Production: An Overview – video
http://www.youtube.com/watch?v=8Kn6BVGqKd8

At the 6:00 minute mark of the following video, Chris Ashcraft, PhD – molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production:

Evolution vs ATP Synthase – Molecular Machine – video
http://www.metacafe.com/watch/4012706

Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways - Cornelius Hunter - July 2011
http://darwins-god.blogspot.com/2011/07/glycolysis-and-citric-acid-cycle.html

Moreover, the ATP molecular machine (which is found at the bottom of the metabolic pathway chart) is found to be 100% efficient:
Thermodynamic efficiency and mechanochemical coupling of F1-ATPase – 2011
Excerpt: F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,,
Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase.

http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1
As well the cell is found to be optimal in its metabolic efficiency:
Metabolism: A Cascade of Design - 2009
Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized.
http://www.reasons.org/metabolism-cascade-design

Making the Case for Intelligent Design More Robust - 2010
Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites.
http://www.reasons.org/making-case-intelligent-design-more-robust

Optimal Design of Metabolism - Dr. Fazale Rana - July 2012
Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition.
http://www.reasons.org/articles/the-optimal-design-of-metabolism

Life Leads the Way to Invention - Feb. 2010
Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.
http://creationsafaris.com/crev201002.htm#20100226a
In fact, optimal metabolism is found to be 'strikingly similar' across all life domains, thus strongly suggesting that all life on earth was Intelligently Designed with maximal efficiency in mind instead of reflecting a pattern of more or less random distribution that would be expected if Darwinism had occurred:
Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum
Excerpt: Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet—from bacteria to elephants, and algae to sapling trees—we show that metabolism displays a striking degree of homeostasis across all of life.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572558/
Such 100% efficiency and optimality being found in molecular biology is hard (impossible?) to explain on Darwinism given what was revealed in this following paper:
Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration
An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,,
By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales.

http://phys.org/news/2014-02-evolutionary-important-success.html
This following headline sums up the preceding study very nicely:

Fittest Can’t Survive If They Never Arrive – February 7, 2014
http://crev.info/2014/02/fittest-cant-survive-if-they-never-arrive/

Moreover, as if that were not ‘horrendously’ bad enough for Darwinists, metabolic pathways are found to operate on ‘Quarter Power Scaling’. i.e. Metabolic Pathways operate as if they were ‘four-dimensional’
Kleiber’s law
Excerpt: Kleiber’s law,[1] named after Max Kleiber’s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the 3/4 power of the animal’s mass.
http://en.wikipedia.org/wiki/Kleiber%27s_law
4-Dimensional 'Quarter Power Scaling' In Biology – video
http://www.metacafe.com/w/5964041/
The predominance of quarter-power (4-D) scaling in biology
Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form:

Y = Yo M^b,

where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent.
A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling.

http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf
Jerry Fodor and Massimo Piatelli-Palmarini put the problem that Quarter Power Scaling presents to Darwinism this way:
“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.”
Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79
i.e. The reason why ’4-Dimensional’ metabolic pathways are impossible for Darwinism to explain is that Natural Selection operates on the 3-Dimensional phenotypes of an organism. ’4-Dimensional’ metabolic pathways are simply ‘invisible’ to natural selection. The fact that 4-Dimensional things are completely invisible to 3-Dimensional things is best illustrated by ‘flatland’:

Flatland – 3D to 4D shift – Carl Sagan – video
http://www.youtube.com/watch?v=UnURElCzGc0

Also of interest is that the integrated coding between the DNA, RNA and Proteins of the cell apparently seem to be ingeniously programmed along the very stringent guidelines laid out by Landauer’s principle, by Charles Bennett from IBM of Quantum Teleportation fame, for ‘reversible computation’ in order to achieve such amazing energy/metabolic efficiency.
Logical Reversibility of Computation* - C. H. Bennett - 1973
Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,,
http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html

Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003
Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,,
http://www.sciencedirect.com/science/article/pii/S135521980300039X

Logically and Physically Reversible Natural Computing: A Tutorial - 2013
Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years.
http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20
The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day:
Reversible computing
Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally.
http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing
Related note:
The unavoidable cost of computation revealed - Physicists have proved that forgetting (erasure of information) is the undoing of Maxwell’s demon. - Philip Ball - 07 March 2012
Excerpt: To test the principle, the researchers created a simple two-state bit: a single microscopic silica bead held in a ‘light trap’ by a laser beam. The trap contains two ‘valleys’ where the particle can rest, one representing a 1 and the other a 0. It could jump between the two if the energy ‘hill’ separating them is not too high.,,,
By monitoring the position and speed of the particle during a cycle of switching and resetting the bit, they could calculate how much energy was dissipated. Landauer’s limit applies only when the resetting is done infinitely slowly, and Lutz and colleagues found that, as they used longer switching cycles, the dissipation got smaller, heading towards a plateau equal to the amount predicted by Landauer.,,,
More practically, Landauer’s principle implies a limit on how low the energy dissipation — and thus consumption — of a computer can be. “Heat dissipation in computer chips is one of the major problems hindering their miniaturization,” says Lutz.,,,
Meanwhile, in fledgling quantum computers, which exploit the rules of quantum physics to achieve greater processing power, this limitation is already being confronted. “Logic processing in quantum computers already is well within the Landauer regime,” says physicist Seth Lloyd of the Massachusetts Institute of Technology in Cambridge. “One has to worry about Landauer's principle all the time.”

http://www.nature.com/news/the-unavoidable-cost-of-computation-revealed-1.10186
Further quotes on the unmatched complexity of the cell:
How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002
Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.
- Paul Davies
http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk

“Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours"
Michael Denton PhD. Evolution: A Theory In Crisis pg. 329

"To grasp the reality of life as it has been revealed by molecular biology, we must first magnify a cell a thousand million times until it is 20 kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would see then would be an object of unparalleled complexity,...we would find ourselves in a world of supreme technology and bewildering complexity."
Michael Denton PhD., Evolution: A Theory In Crisis, pg.328

Building a Cell: Staggering Complexity: - Feb. 2010
Excerpt: “All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 10^9 base pairs) of DNA when each cell divides,” “,,,the segregation machinery must function with far greater accuracy than man-made machines and with an exquisitely soft touch to prevent the DNA strands from breaking.” Bloom and Joglekar talked “machine language” over and over. The cell has specialized machines for all kinds of tasks: segregation machines, packaging machines, elaborate machines, streamlined machines, protein translocation machines, DNA-processing machines, DNA-translocation machines, robust macromolecular machines, accurate machines, ratchets, translocation pumps, mitotic spindles, DNA springs, coupling devices, and more. The authors struggle to “understand how these remarkable machines function with such exquisite accuracy.”
http://www.creationsafaris.com/crev201002.htm#20100202a

A very compelling part of a cumulative body of evidence - September 4, 2013
"The more I come to terms with the sheer engineering prowess of the cell, the more I am becoming convinced that the argument from biological design is perhaps the single most powerful argument for God's existence -- I now consider it to be stronger than even the cosmological and teleological arguments. It seems to be a rather under-used apologetic, however, particularly in Christian-atheist debates. ID as a scientific proposition, of course, doesn't necessitate God as designer. But it is certainly a very compelling part of a cumulative body of evidence for theism. Catching just a glimpse of the beauty and sophistication of the cell should be enough to render absolutely anyone without excuse."
—Jonathan McLatchie
Here is a good article that came out in GN magazine in Nov. 2009:
10 Ways Darwin Got It Wrong
Excerpt: As molecular biologist Jonathan Wells and mathematician William Dembski point out: “It’s true that eukaryotic cells are the most complicated cells we know. But the simplest life forms we know, the prokaryotic cells (such as bacteria, which lack a nucleus), are themselves immensely complex.,,, There is no evidence whatsoever of earlier, more primitive life forms from which prokaryotes might have evolved” (How to Be an Intellectually Fulfilled Atheist (or Not), 2008, p. 4). These authors then mention what these two types of cells share in terms of complexity:

• Information processing, storage and retrieval.
• Artificial languages and their decoding systems.
• Error detection, correction and proofreading devices for quality control.
• Digital data-embedding technology.
• Transportation and distribution systems.
• Automated parcel addressing (similar to zip codes and UPS labels).
• Assembly processes employing pre-fabrication and modular construction.
• Self-reproducing robotic manufacturing plants.
So it turns out that cells are far more complex and sophisticated than Darwin could have conceived of. How did mere chance produce this, when even human planning and engineering cannot?

http://www.gnmagazine.org/issues/gn85/10-ways-darwin-wrong.htm

"(Although atheists accuse Theists of making extraordinary claims) The truly extraordinary claim — indeed, the wildly and irresponsibly outrageous claim — is that a highly scalable, massively parallel system architecture incorporating a 4-bit digital coding system and a super-dense, information-rich, three-dimensional, multi-layered, multi-directional database structure with storage, retrieval and translation mechanisms, utilizing file allocation, concatenation and bit-parity algorithms, operating subject to software protocol hierarchies could all come about through a long series of accidental particle collisions. That is beyond extraordinary. It is preposterous. It is laughable."
http://www.uncommondescent.com/intelligent-design/naturalism-intelligent-design-and-extraordinary-claims-part-ii/

Need for Speed: Molecular Ticket Determines RNA’s Destination and Speed Inside Egg Cell - March 2012
Excerpt: Like any law-abiding train passenger, a molecule called oskar RNA carries a stamped ticket detailing its destination and form of transport, scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have found. They show that for this molecule, moving in the right direction isn't enough: speed is of the essence.
http://www.sciencedaily.com/releases/2012/03/120318144021.htm

2013 Nobel Prize for intracellular transport networks - October 7, 2013
Excerpt: Each cell is a factory that produces and exports molecules. For instance, insulin is manufactured and released into the blood and chemical signals called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles. The three Nobel Laureates have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell.... In a large and busy port, systems are required to ensure that the correct cargo is shipped to the correct destination at the right time. The cell, with its different compartments called organelles, faces a similar problem: cells produce molecules such as hormones, neurotransmitters, cytokines and enzymes that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Timing and location are everything. Miniature bubble-like vesicles, surrounded by membranes, shuttle the cargo between organelles or fuse with the outer membrane of the cell and release their cargo to the outside. This is of major importance, as it triggers nerve activation in the case of transmitter substances, or controls metabolism in the case of hormones. How do these vesicles know where and when to deliver their cargo?
http://www.uncommondescent.com/origin-of-life/2013-nobel-prize-for-intracellular-transport-networks/

Cellular Traffic Control System Research Earns the Nobel Prize - Keeps Activities Inside Cells From Descending Into Chaos - Cornelius Hunter - December 22, 2013
Excerpt: ,,,here is how the Nobel Prize press release describes the work:

“Through their discoveries, Rothman, Schekman and Südhof have revealed the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders.
Without this wonderfully precise organization, the cell would lapse into chaos.”

,,,Not surprisingly there is no scientific explanation for how such a traffic control system evolved.

http://darwins-god.blogspot.com/2013/12/cellular-traffic-control-system.html
Vesicles can be seen, as they are visualized by researchers, in this semi-famous Harvard (XVIVO) video:

The Inner Life of a Cell – video (page down just a bit to view the video)
http://www.studiodaily.com/2006/07/cellular-visions-the-inner-life-of-a-cell/

Here is a User’s guide to the video:
vesicles screenshot comment: The enormous organelle the stalwart kinesin guy is carrying is a vesicle filled with proteins destined for the outside, perhaps in response to the signal that the cell had received a while back. The vesicle itself has membrane proteins studding its surface. If you look closely in this sequence, you see hundreds of fellow kinesin proteins hauling their own burdens along the microtubule highways.
http://sparkleberrysprings.com/innerlifeofcell.html

There simply is no "simple life" on earth as materialism had presumed - even the well known single celled amoeba has the complexity of the city of New York and reproduces that complexity in only 20 minutes.

Programming of Life - Biological Computers - video
http://www.youtube.com/watch?v=hRooe6ehrPs

Dr. Fazale (Fuz) Rana discusses the beauty and elegance of biochemistry - video
http://www.youtube.com/watch?v=_zxYPO62Ygc

Here are some fairly simple overviews of the cell:

How the Body Works: The Cell - video
http://www.youtube.com/watch?v=NiiLS_ovLwM

Programming of Life - Eukaryotic Cell - video
http://www.youtube.com/user/Programmingoflife#p/c/6/WVCwDOMCpXY

Wonders of the Cell - 2008 - Christopher Wayne Ashcraft - video
http://www.youtube.com/watch?v=bfoRTMmoxzo
Primary Cilium As Cellular 'GPS System' Crucial To Wound Repair
Excerpt: The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.
"What we are dealing with is a physiological analogy to the GPS system with a coupled autopilot that coordinates air traffic or tankers on open sea,"

http://www.sciencedaily.com/releases/2008/12/081217190330.htm

Learning from Bacteria about Social Networking (Information Processing) - video
Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers.
http://www.youtube.com/watch?v=yJpi8SnFXHs

Researchers study code that allows bacteria to either bet on the present or travel in time - April 22, 2013
Excerpt: Experimental studies have revealed dozens of regulatory genes, signaling proteins and other genetic tools that cells use to gather information and communicate with one another.,,,
Each bacterium in the colony communicates via chemical "tweets" and performs a sophisticated decision-making process using a specialized complex gene network comprised of many genes connected via complex circuitry.,,,
"The ingenuity is that at each oscillation the cell also sends 'chemical tweets' to inform the other cells about its stress and attempt to escape,",,, "The tweets sent by others help regulate the circuits of their neighbors and guarantee that no more than a specific fraction of cells within the colony will enter into competence."

http://phys.org/news/2013-04-code-bacteria.html

Wetware: A Computer in Every Living Cell - book - Dennis Bray
Description - In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties.
http://www.amazon.com/dp/0300167849

Dennis Bray - Amazon Description of Author
Dennis Bray is an active emeritus professor at University of Cambridge. His group is also part of the Oxford Centre for Integrative Systems Biology. After a first career in Neurobiology, working on cell growth and movement, Dennis Bray moved in Cambridge to develop computational models of cell signaling, in particular in relation to bacterial chemotaxis. On November 3, 2006, he was awarded the Microsoft European Science Award for his work on chemotaxis of E. coli.
Mere Biochemistry: Cell Division Involves Thousands of Complex, Interacting Parts - September 2010
http://www.creationsafaris.com/crev201009.htm#20100925a

Astonishingly, actual motors, which far surpass man-made motors in 'engineering parameters', are now being found inside 'simple cells'.

Articles and Videos on Molecular Motors
http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en

Michael Behe - Life Reeks Of Design - 2010 - video
http://www.metacafe.com/watch/5066181
Macroevolution, Good Science, and Redeeming Mathematics - Kate Deddens - February 2012
Excerpted quote: As obviously designed as a spaceship or a computer…Evolutionary biologists have been able to pretend to know how complex biological systems originated only because they treated them as black boxes. Now that biochemists have opened the black boxes and see what is inside, they know the Darwinian theory is just a story, not a scientific explanation…
(Phillip E. Johnson, Defeating Darwinism, Downers Grove, IL: InterVarsity Press, 1997, 77-78.)
http://www.classicalconversations.com/easyblog/entry/macroevolution-good-science-and-redeeming-mathematics.html
And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.
"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject."
James Shapiro, molecular biologist, National Review, Sept. 16, 1996
The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,
‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,
Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,
,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
*Professor Emeritus of Biochemistry, Colorado State University, USA
Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
http://www.metacafe.com/watch/5302950/
EVOLUTIONARY JUST-SO STORIES
Excerpt: ,,,The term “just-so story” was popularized by Rudyard Kipling’s 1902 book by that title which contained fictional stories for children. Kipling says the camel got his hump as a punishment for refusing to work, the leopard’s spots were painted on him by an Ethiopian, and the kangaroo got its powerful hind legs after being chased all day by a dingo.
Kipling’s just-so stories are as scientific as the Darwinian accounts of how the amoeba became a man.
Lacking real scientific evidence for their theory, evolutionists have used the just-so story to great effect. Backed by impressive scientific credentials, the Darwinian just-so story has the aura of respectability.
Biologist Michael Behe observes:
“Some evolutionary biologists--like Richard Dawkins--have fertile imaginations. Given a starting point, they almost always can spin a story to get to any biological structure you wish” (Darwin’s Black Box).,,,

http://www.wayoflife.org/database/evolutionary_just_so_stories.html
"Grand Darwinian claims rest on undisciplined imagination"
Dr. Michael Behe - 29:24 mark of following video
http://www.youtube.com/watch?feature=player_detailpage&v=s6XAXjiyRfM#t=1762s
Molecular Machines: - Michael J. Behe
Excerpt: JME is a journal that was begun specifically to deal with the topic of how evolution occurs on the molecular level. It has high scientific standards, and is edited by prominent figures in the field.,,,
In the past ten years JME has published 886 papers. Of these, 95 discussed the chemical synthesis of molecules thought to be necessary for the origin of life, 44 proposed mathematical models to improve sequence analysis, 20 concerned the evolutionary implications of current structures, and 719 were analyses of protein or polynucleotide sequences. here were zero papers discussing detailed models for intermediates in the development of complex biomolecular structures. This is not a peculiarity of JME. No papers are to be found that discuss detailed models for intermediates in the development of complex biomolecular structures in the Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology or, to my knowledge, any journal whatsoever.

http://www.arn.org/docs/behe/mb_mm92496.htm

“The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.”
David Ray Griffin - retired professor of philosophy of religion and theology

Calling Nick Matzke's literature bluff on molecular machines - DonaldM UD blogger - April 2013
Excerpt: So now, 10 years later in 2006 Matzke and Pallen come along with this review article. The interesting thing about this article is that, despite all the hand waving claims about all these dozens if not hundreds of peer reviewed research studies showing how evolution built a flagellum, Matzke and Pallen didn’t have a single such reference in their bibliography. Nor did they reference any such study in the article. Rather, the article went into great lengths to explain how a researcher might go about conducting a study to show how evolution could have produced the system. Well, if all those articles and studies were already there, why not just point them all out? In shorty, the entire article was a tacit admission that Behe had been right all along.
Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.
Matzke will not answer the question because there is no answer he can give…no peer reviewed research study he can reference, other than the usual literature bluffing he’s done in the past.

http://www.uncommondescent.com/irreducible-complexity/andre-asks-an-excellent-question-regarding-dna-as-a-part-of-an-in-cell-irreducibly-complex-communication-system/#comment-453291

More Irreducible Complexity Is Found in Flagellar Assembly - September 24, 2013
Concluding Statement: Eleven years is a lot of time to refute the claims about flagellar assembly made in Unlocking the Mystery of Life, if they were vulnerable to falsification. Instead, higher resolution studies confirm them. Not only that, research into the precision assembly of flagella is provoking more investigation of the assembly of other molecular machines. It's a measure of the robustness of a scientific theory when increasing data strengthen its tenets over time and motivate further research. Irreducible complexity lives! -
http://www.evolutionnews.org/2013/09/more_irreducibl077051.html
Dr. Behe, in an inappropriately named lecture, gives a talk on Intelligent Design in this following video (Of note, the last half of the video, at the 2:22:25 hour and minute mark of the video, is a Q&A session that gets into some of the interesting technical details of his defense of Irreducible Complexity of the Blood Clotting cascade from some high level criticisms)

Theistic Evolution - Michael Behe - video
http://www.youtube.com/watch?v=r4dpVpS38Cc

of related note to the fact that Darwinists have ZERO empirical evidence of Darwinian processes EVER producing a molecular machine, here are several examples that intelligence can do as such:

(Man-Made) DNA nanorobot – video
https://vimeo.com/36880067

Making Structures with DNA "Building Blocks" - Wyss institute - video
https://vimeo.com/68254051

Roomy cages built from DNA could one day deliver drugs, devices - March 13, 2014
http://www.sciencedaily.com/releases/2014/03/140313142716.htm

Programmable glue made of DNA directs tiny gel bricks to self-assemble - Sept. 9, 2013
http://phys.org/news/2013-09-programmable-dna-tiny-gel-bricks.html

Whether Lab or Cell, (If it's a molecular machine) It's Design - podcast
http://intelligentdesign.podomatic.com/entry/2013-01-25T15_53_41-08_00

Examples of molecular machines (molecular switches (or shuttles) and molecular motors) - Synthetic (Made By Chemists)
http://en.wikipedia.org/wiki/Molecular_machine#Examples_of_molecular_machines

Also of note, Dr. James Tour, who, in my honest opinion, currently builds the most sophisticated man-made molecular machines in the world,,,

Science & Faith — Dr. James Tour – video (At the two minute mark of the following video, you can see a nano-car that was built by Dr. James Tour’s team)
https://www.youtube.com/watch?v=pR4QhNFTtyw

,,will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:
“I build molecules for a living, I can’t begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God."
James Tour – one of the leading nano-tech engineers in the world - Strobel, Lee (2000), The Case For Faith, p. 111
Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video
https://www.youtube.com/watch?v=JB7t2_Ph-ck

What I find particularly persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the 'near optimal' capacities allowed in any physical system:
William Bialek - Professor Of Physics - Princeton University:
Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,,"
http://www.princeton.edu/~wbialek/wbialek.html
More Perfect Than We Imagined: A Physicist's View - William Bialek - video (particularly part 7)
http://fora.tv/2010/11/03/More_Perfect_Than_We_Imagined_A_Physicists_View
"Organisms are not cobbled together as a series of adequate compromises but are close to optimality. Examples of supposedly “poor design” often turn out to be “very well engineered indeed”. Simon Conway Morris
http://darwins-god.blogspot.com/2012/04/even-evolutionists-admit-its-mess.html

Physicists Finding Perfection… in Biology — June 1st, 2009 by Biologic Staff
Excerpt: "biological processes tend to be optimal in cases where this can be tested."
http://biologicinstitute.org/2009/06/01/physicists-finding-perfection-in-biology/
Also of note: There is a fairly substantial economic payoff to be had for presupposing superior 'Intelligent Design' in life, as is testified to by the burgeoning field of Biomimicry:

Biomimicry - Superior Designs That Were Found In Life
http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfNDBkZ3Nwcnd0Yw&hl=en

From 3.8 to .6 billion years ago photosynthetic bacteria, and sulfate-reducing reducing bacteria, dominated the geologic and fossil record (that’s over 80% of the entire time life has existed on earth). The geologic and fossil record also reveals, during this time, a large portion of these very first bacterial life-forms lived in irreducibly complex, symbiotic, mutually beneficial, colonies called Stromatolites. Stromatolites are rock like structures the photo-synthetic bacteria built up over many years, much like coral reefs are slowly built up over many years by the tiny creatures called corals. Although Stromatolites are not nearly as widespread as they once were, they are still around today in a few sparse places like Shark’s Bay Australia.

Michael Denton - Stromatolites Are Extremely Ancient - video
http://www.metacafe.com/watch/4023098

Shark's Bay - Modern Stromatolites - Pictures
http://seapics.com/feature-subject/marine-invertebrates/stromatolite-pictures.html

Ancient Microorganisms Helped Build 3.4-billion-year-old Stromatolite Rock Structures
http://www.sciencedaily.com/releases/2009/07/090716141221.htm

Both the oldest Stromatolite fossils, and the oldest bacterium fossils, found on earth demonstrate an extreme conservation of morphology which, very contrary to evolutionary thought, simply means they have not changed and look very similar to Stromatolites and bacteria of today.
Odd Geometry of Bacteria May Provide New Way to Study Earth's Oldest Fossils - May 2010
Excerpt: Known as stromatolites, the layered rock formations are considered to be the oldest fossils on Earth.,,,That the spacing pattern corresponds to the mats' metabolic period -- and is also seen in ancient rocks -- shows that the same basic physical processes of diffusion and competition seen today were happening billions of years ago,,,
http://www.sciencedaily.com/releases/2010/05/100517152520.htm

3.5 billion-year-old ecosystem found - November 12, 2013
Excerpt: "Mound-like deposits created by ancient bacteria, called stromatolites, and microfossils of bacteria have previously been discovered in this region. However, a phenomenon called microbially induced sedimentary structures, or MISS, had not previously been seen in rocks of this great age."
MISS were created by microbial mats as the microbial communities responded to changes in physical sediment dynamics, Professor Wacey said.
"A common example would be the binding together of sediment grains by microbes to prevent their erosion by water currents," he said. "The significance of MISS is that they not only demonstrate the presence of life, but also the presence of whole microbial ecosystems that could co-ordinate with one another to respond to changes in their environment.",,,
The team described the various MISS from the ancient coastal flats preserved in the Dresser Formation and found close similarities in both form and preservation style to MISS in younger rocks.

http://www.sciencealert.com.au/news/20131211-25003.html

Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13
Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages.
http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1

Scientists find signs of life in Australia dating back 3.48 billion years - Thu November 14, 2013
Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”... “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,”
http://www.cnn.com/2013/11/13/world/asia/australia-ancient-life/

Everything new is old again: Photosynthesis from 3.3 billion years ago - July 2011
Excerpt: The most direct evidence yet for ancient photosynthesis has been uncovered in a fossil of a matted carpet of microbes that lived on a beach 3.3 billion years ago.
http://www.uncommondescent.com/darwinism/everything-new-is-old-again-photosynthesis-from-3-3-billion-years-ago/

AMBER: THE LOOKING GLASS INTO THE PAST:
Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html

Static evolution: is pond scum the same now as billions of years ago?
Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found;
http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330
Bacteria: Fossil Record - Ancient Compared to Modern - Picture
http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html

This following study reveals that enzymes were complex from the get-go
Enzymes Complex from the Get-go
Excerpt: “Given the ancient origin of the reconstructed thioredoxin enzymes (a vital enzyme found in all living cells), with some of them predating the buildup of atmospheric oxygen, we expected their catalytic chemistry to be simple," said Fernandez. "Instead we found that enzymes that existed in the Precambrian era up to four billion years ago possessed many of the same chemical mechanisms observed in their modern-day relatives.”,, Further examination of the ancient enzymes revealed some striking features: The enzymes were highly resistant to temperature and were active in more acidic conditions. The findings suggest that the species hosting these ancient enzymes thrived in very hot environments that since then have progressively cooled down, and that they lived in oceans that were more acidic than today.
http://www.uncommondescent.com/intelligent-design/enzymes-complex-from-the-get-go/
Contrary to what materialism would expect, these very first photosynthetic bacteria found in the fossil record, and by chemical analysis of the geological record, are shown to have been preparing the earth for more advanced life to appear from the very start of their existence by producing the necessary oxygen for higher life-forms to exist, and by reducing the greenhouse gases of earth’s early atmosphere. Photosynthetic bacteria slowly removed the carbon dioxide, and built the oxygen up, in the earth’s atmosphere primarily by this following photosynthetic chemical reaction:

6H2O + 6CO2 ----------> C6H12O6+ 6O2

The above chemical equation translates as:

Six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar plus six molecules of oxygen

Interestingly, the gradual removal of greenhouse gases corresponded to the gradual 15% increase of light and heat coming from the sun during that time (Ross; Creation as Science). This 'lucky' correspondence of the slow increase of heat from the sun with the same perfectly timed slow removal of greenhouse gases from the earth’s atmosphere was necessary to keep the earth from cascading into either a 'greenhouse earth' or 'snowball earth'.
Why Didn't Early Earth Freeze? The Mystery Deepens - April 2010
Excerpt: The results were "very surprising," Rosing says. As to the question of what kept the planet warm instead of CO2, he says his research points to two possibilities. First, Earth's land masses were much smaller billions of years ago, meaning that the oceans, which generally are darker than continents, could absorb more of the sun's heat. Second, because life was brand new, organisms were manufacturing little of the gases that help clouds form. So, more sunlight reached the surface.,, There are bound to be other factors, Rosing says. "I think that our paper is just one link in a long chain of further refinements of our understanding of the early Earth and of the dynamics of our planet."
http://news.sciencemag.org/sciencenow/2010/03/why-didnt-early-earth-freeze-the.html
This following paper offers methane gas as a possible contributing solution to the faint sun paradox:

Methane-Based Greenhouse and Anti-Greenhouse Events Led to Stable Archean Climate
http://earthobservatory.nasa.gov/Newsroom/view.php?id=22846

This following paper shows that the Earth's early atmosphere would have been stripped away by the sun if it had not been finely tuned:
Earth’s Primordial Atmosphere Must Be Fine-Tuned - Hugh Ross
Excerpt: The team then produced calculations demonstrating that the only reasonable scenario for explaining why the Sun’s radiation did not remove Earth’s primordial atmosphere was that the early Earth’s atmosphere was at least a hundred times richer in carbon dioxide.
http://www.reasons.org/earths-primordial-atmosphere-must-be-fine-tuned
Thus following study shows that the buildup of oxygen in the atmosphere was more gradual than previously thought;
Rise of Atmospheric Oxygen More Complicated (Gradual) Than Previously Thought - December 2011
Excerpt: Oxygen levels gradually crossed the low atmospheric oxygen threshold for pyrite -- an iron sulfur mineral -- oxidation by 2,500 million years ago and the loss of any mass-independently fractionated sulfur by 2,400 million years ago. Then oxygen levels rose at an ever-increasing rate through the Paleoproterozoic, achieving about 1 percent of the present atmospheric level.,, Initially, any oxygen in the atmosphere, produced by the photosynthesis of single-celled organisms, was used up when sulfur, iron and other elements oxidized. When sufficient oxygen accumulated in the atmosphere, it permeated the groundwater and began oxidizing buried organic material, oxidizing carbon to create carbon dioxide.
http://www.sciencedaily.com/releases/2011/12/111201142754.htm
More interesting still, the byproducts of the complex biogeochemical processes involved in the oxygen production by these early bacteria are (red banded) iron formations, limestone, marble, gypsum, phosphates, sand, and to a lesser extent, coal, oil and natural gas (note; though some coal, oil and natural gas deposits are from this early era of bacterial life, most coal, oil and natural gas deposits originated on earth after the Cambrian explosion of higher life forms some 540 million years ago). The resources produced by these early photosynthetic bacteria are very useful, one could even very well say 'necessary', for the technologically advanced civilizations of humans today to exist.

The following video, at the 2:45 minute mark, is good for showing the history of banded iron formations in the geologic record and shows that banded iron formations go back as far as 3.8 billion years ago, although Dr. Newman, in the video, believes banded iron formations 'may' have been formed abiotically.

Exploring the deep connection between bacteria and rocks - Dianne Newman - MIT lecture video
http://video.mit.edu/watch/from-rocks-to-genes-and-back-stories-about-the-evolution-of-photosynthesis-9299/

The following study shows that the oldest banded iron formations, contrary to Dr. Newman's belief that they may have formed abiotically, were actually formed biotically:
Iron in Primeval Seas Rusted by Bacteria - Apr. 23, 2013
Excerpt: The oldest known iron ores were deposited in the Precambrian period and are up to four billion years old (the Earth itself is estimated to be about 4.6 billion years old). ,,,
This research not only provides the first clear evidence that microorganisms were directly involved in the deposition of Earth's oldest iron formations; it also indicates that large populations of oxygen-producing cyanobacteria were at work in the shallow areas of the ancient oceans, while deeper water still reached by the light (the photic zone) tended to be populated by anoxyenic or micro-aerophilic iron-oxidizing bacteria which formed the iron deposits.,,,

http://www.sciencedaily.com/releases/2013/04/130423110750.htm
Further notes along this line
Ancient Microbes Responsible for Breathing Life Into Ocean 'Deserts' - August 2010
Excerpt: Brian Kendall and Ariel Anbar, together with colleagues at other institutions, show that "oxygen oases" in the surface ocean were sites of significant oxygen production long before the breathing gas began to accumulate in the atmosphere..,, What Kendall discovered was a unique relationship of high rhenium and low molybdenum enrichments in the samples from South Africa, pointing to the presence of dissolved oxygen on the seafloor itself.,,, "It was especially satisfying to see two different geochemical methods -- rhenium and molybdenum abundances and Fe chemistry -- independently tell the same story," Kendall noted. Evidence that the atmosphere contained at most minute amounts of oxygen came from measurements of the relative abundances of sulfur (S) isotopes.
http://www.sciencedaily.com/releases/2010/08/100823113436.htm

Breathing new life into Earth: New research shows evidence of early oxygen on our planet - August 2011
Excerpt: Waldbauer and Summons surmise that oxygen production and consumption may have occurred in the oceans for hundreds of millions of years before the atmosphere saw even a trace of the gas. They say that in all likelihood, cyanobacteria, blue-green algae living at the ocean surface, evolved the ability to produce O2 via sunlight in a process known as oxygenic photosynthesis. But instead of building up in the oceans and then seeping into the atmosphere, O2 may have been rapidly consumed by early aerobic organisms. Large oceanic and atmospheric sinks, such as iron and sulfide spewing out of subsea volcanoes, likely consumed whatever O2 was left over.
http://www.physorg.com/news/2011-08-life-earth-evidence-early-oxygen.html

Large Bacterial Population Colonized Land 2.75 Billion Years Ago (Sep. 24, 2012)
Excerpt: new research,, suggests that early microbes might have been widespread on land, producing oxygen and weathering pyrite, an iron sulfide mineral, which released sulfur and molybdenum into the oceans.,,
"This shows that life didn't just exist in a few little places on land. It was important on a global scale because it was enhancing the flow of sulfate from land into the ocean,"
"It supports the theory that oxygen was being produced for several hundred million years before the Great Oxidation Event. It just took time for it to reach higher concentrations in the atmosphere," Stüeken said.

http://www.sciencedaily.com/releases/2012/09/120924101741.htm

Early life built Earth's continents - 25 November 2013
Excerpt: Norm Sleep, a geophysicist at Stanford University, California, however, says the model fits with what we know about the evolution of Earth, and says the process it describes is backed by indirect evidence of life in early subducted rocks. In particular, the presence of aluminium oxide in continental granite is an indication that life was eroding land and dumping sediment into subduction zones, he says. Such oxides comes from clay, which is mostly produced by the biological weathering of rock.
http://www.newscientist.com/article/mg22029443.100-early-life-built-earths-continents.html#.UpPUDeL4Lmt
New Paper states atmospheric oxygen was present on Earth much earlier than Darwinists were forced to presuppose
Oxygen, the Scourge of Evolution - Oct. 10, 2013
Excerpt: The scourge of evolution has re-emerged−this time with renewed vengeance. Scientists have long known that extremely low levels of free-oxygen [< 10^-5] atmosphere on early Earth is critical for any viable origin of life model of evolution.,,,
(New) Scientific Evidence for Early Earth Free-Oxygen Theory
An international research team led by Sean Crowe (of) University of Southern Denmark in September (2013) published in the journal Nature a paper re-establishing the presence of atmospheric oxygen on early Earth. The team representing the nations of Denmark, South Africa, and Germany discovered oxygen to exceed 30-times beyond the critical concentration of < 10^-5.

http://www.darwinthenandnow.com/2013/10/oxygen-the-scourge-of-evolution-4/
These following articles explore some of the other complex geochemical processes that are also involved in the forming of the red banded iron, and other precious ore, formations on the ancient earth.
Banded Rocks Reveal Early Earth Conditions, Changes
Excerpt: Called banded iron formations or BIFs, these ancient rocks formed between 3.8 and 1.7 billion years ago at what was then the bottom of the ocean. The stripes represent alternating layers of silica-rich chert and iron-rich minerals like hematite and magnetite. First mined as a major iron source for modern industrialization, BIFs are also a rich source of information about the geochemical conditions that existed on Earth when the rocks were made.
http://www.sciencedaily.com/releases/2009/10/091011184428.htm

Rich Ore Deposits Linked to Ancient Atmosphere - Nov. 2009
Excerpt: Much of our planet's mineral wealth was deposited billions of years ago when Earth's chemical cycles were different from today's.
http://www.sciencedaily.com/releases/2009/11/091119193640.htm
Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, other types of bacteria were also producing their own natural resources which would be very useful to modern man. Some types of bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, various types of bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms.
Bacterial Heavy Metal Detoxification and Resistance Systems:
Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.,, Recombinant DNA analysis has been applied to mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper resistance systems.
http://www.springerlink.com/content/u1t281704577v8t3/
http://www.int-res.com/articles/meps/26/m026p203.pdf

The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals.
http://www.goldschmidt2009.org/abstracts/finalPDFs/A1161.pdf

Similar organisms deal with life in the extreme differently, research finds - September 24, 2012
Excerpt: One single-celled organism from a hot spring near Mount Vesuvius in Italy fights uranium toxicity directly – by eating the heavy metal and acquiring energy from it. Another single-celled organism that lives on a "smoldering heap" near an abandoned uranium mine in Germany overcomes uranium toxicity indirectly – essentially shutting down its cellular processes to induce a type of cellular coma when toxic levels of uranium are present in its environment. Interestingly, these very different responses to environmental stress come from two organisms that are 99.99 percent genetically identical.
http://phys.org/news/2012-09-similar-life-extreme-differently.html

Researchers Identify Mysterious Life Forms in the Extreme Deep Sea
Excerpt: Xenophyophores are noteworthy for their size, with individual cells often exceeding 10 centimeters (4 inches), their extreme abundance on the seafloor and their role as hosts for a variety of organisms.,,, The researchers spotted the life forms at depths up to 10,641 meters (6.6 miles) within the Sirena Deep of the Mariana Trench.,,, Scientists say xenophyophores are the largest individual cells in existence. Recent studies indicate that by trapping particles from the water, xenophyophores can concentrate high levels of lead, uranium and mercury,,,
http://www.sciencedaily.com/releases/2011/10/111024165037.htm
Here are a couple of sites showing the crucial link of a minimal levels of metals to biological life:

Transitional Metals And Cytochrome C oxidase - Michael Denton - Nature's Destiny
http://books.google.com/books?id=CdYpDRY0Z6oC&pg=PA203&lpg
Proteins prove their metal - July 2010
Excerpt: ‘Nearly half of all enzymes require metals to function in catalysing biological reactions,’ Kylie Vincent, of Oxford University’s Department of Chemistry tells us. ‘Both the metal and the surrounding protein are crucial in tuning the reactivity of metal catalytic centres in enzymes.' These ‘metal centres’ are hives of industry at a microscopic scale, with metals often held in a special protein environment where they may be assembled into intricate clusters inside proteins.
http://www.physorg.com/news197728929.html

Your Copper Pipes - November 2011
Excerpt: In the fascinating field of ‘metals in biology’, by virtue of direct interactions with amino acid side-chains within polypeptide chains, metals play unique and critical roles in biology, promoting structures and chemistries that would not otherwise be available to proteins alone.,,, ATP7A is also important for the delivery of copper to nascent proteins in the Golgi apparatus. In mammals, ATP7A is expressed in many tissues except the liver,
http://crev.info/content/111108-your_copper_pipes
As well, in conjunction with bacteria, geological processes helped detoxify the earth of dangerous levels of metal:
Unexpected allies help bacteria clean uranium from groundwater - March 8, 2013
Excerpt: Since 2009, SLAC scientist John Bargar has led a team using synchrotron-based X-ray techniques to study bacteria that help clean uranium from groundwater in a process called bioremediation. Their initial goal was to discover how the bacteria do it and determine the best way to help, but during the course of their research the team made an even more important discovery: "Nature" thinks bigger than that.
The researchers discovered that bacteria don't necessarily go straight for the uranium, as was often thought to be the case. The bacteria make their own, even tinier allies – nanoparticles of a common mineral called iron sulfide. Then, working together, the bacteria and the iron sulfide grab molecules of a highly soluble form of uranium known as U(VI), or hexavalent uranium, and transform them into U(IV), a less-soluble form that's much less likely to spread through the water table. According to Barger, this newly discovered partnership may be the basis of a global geochemical process that forms deposits of uranium ore.,,
Discovering that bacteria work together with minerals to transform uranium was a surprise, said Bargar.,,,
But as a scientist, he appreciates the glimpse he's been given into "Nature's" abilities to multitask. "Originally we wanted to see what happened to uranium and how it could help bioremediation technology to be successful," he said. "But scientifically the results are much deeper than that." And since their original hypothesis focused on bacteria alone, it's a little humbling, too.

http://phys.org/news/2013-03-unexpected-allies-bacteria-uranium-groundwater.html

The Concentration of Metals for Humanity's Benefit:
Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth's crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth's crust strongly suggests supernatural design.
http://www.reasons.org/TheConcentrationofMetalsforHumanitysBenefit
And on top of the fact that poisonous heavy metals on the primordial earth were brought into 'life-enabling' balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent 'Big Bang of life' there afterwards.
Newly Discovered Bacterium Forms Intracellular Minerals - May 11, 2012
Excerpt: A new species of photosynthetic bacterium has come to light: it is able to control the formation of minerals (calcium, magnesium, barium and strontium carbonates) within its own organism. ,, carbonate rocks that date back some 3.5 billion years and are among the earliest traces of life on Earth.
(Calcium carbonate, of which chalk, limestone and marble are made, also makes up corals, shells of snails and other animals, and stromatolites. Strontium Carbonate is used in Ceramics, Pyrotechnics, Electronics and metallurgy. Barium carbonate is widely used in the ceramics industry as an ingredient in glazes. It acts as a flux, a matting and crystallizing agent and combines with certain colouring oxides to produce unique colours not easily attainable by other means. In the brick, tile, earthenware and pottery industries barium carbonate is added to clays to precipitate soluble salts. Magnesium carbonate also has several important uses for man.)
http://www.sciencedaily.com/releases/2012/05/120511101352.htm

The Creation of Minerals:
Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.
http://www.reasons.org/The-Creation-of-Minerals

"Today there are about 4,400 known minerals - more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms"
- Bob Hazen - Smithsonian - Oct. 2010, pg. 54

Ancient Minerals: Which Gave Rise to Life? - Nov. 25, 2013
Excerpt: Carnegie's Robert Hazen compiled a list of every plausible mineral species on the Hadean Earth and concludes that no more than 420 different minerals -- about 8 percent of the nearly 5,000 species found on Earth today -- would have been present at or near Earth's surface.
By contrast, thousands of mineral species known today are the direct result of growth by living organisms, such as shells and bones, as well as life's chemical byproducts, such as oxygen from photosynthesis. In addition, hundreds of other minerals that incorporate relatively rare elements such as lithium, beryllium, and molybdenum appear to have taken a billion years or more to first appear because it is difficult to concentrate these elements sufficiently to form new minerals. So those slow-forming minerals are also excluded from the time of life's origins.

http://www.sciencedaily.com/releases/2013/11/131125164814.htm
To put it mildly, this minimization of poisonous elements, and 'explosion' of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that 'just so happens' to be of great benefit to modern man.

Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced 'space-age' technology of modern civilization.

Metallurgy
http://en.wikipedia.org/wiki/Metallurgy

also of note to Metallurgy:
The Fine-Tuning for Discoverability - Robin Collins - March 22, 2014
Excerpt: Examples of fine - tuning for discoverability.
,,A small increase in α (fine structure constant) would have resulted in all open wood fires going out; yet harnessing fire was essential to the development of civilization, technology, and science - e.g., the forging of metals.,,,
Going in the other direction, if α (fine structure constant) were decreased, light microscopes would have proportionality less resolving power without the size of living cells or other microscopic objects changing.,,, Thus, it is quite amazing that the resolving power of light microscopes goes down to that of the smallest cell (0.2 microns), but no further. If it had less resolving power, some cells could not be observed alive. The fine - structure constant, therefore, is just small enough to allow for open wood fires and just large enough for the light microscope to be able to see all living cells.

http://home.messiah.edu/~rcollins/Fine-tuning/Greer-Heard%20Forum%20paper%20draft%20for%20posting.pdf
Minerals and Their Uses
http://www.scienceviews.com/geology/minerals.html

Mineral Uses In Industry
http://www.peterharben.com/industrial_minerals_uses.htm

Mineral
http://en.wikipedia.org/wiki/Mineral

Inventions: Elements and Compounds - video
http://videos.howstuffworks.com/hsw/20809-invention-elements-and-compounds-video.htm
Bombardment Makes Civilization Possible
What is the common thread among the following items: pacemakers, spark plugs, fountain pens and compass bearings? Give up? All of them currently use (or used in early versions) the two densest elements, osmium and iridium. These two elements play important roles in technological advancements. However, if certain special events hadn't occurred early in Earth's history, no osmium or iridium would exist near the planet's surface.
http://www.reasons.org/BombardmentMakesCivilizationPossible
As well, many types of bacteria in earth's early history lived in what are called cryptogamic colonies on the earth's primeval continents. These colonies dramatically transformed the primeval land into stable nutrient filled soils which were receptive for future advanced vegetation to appear.
Land organisms from Cambrian found in soil layer under the soil - November 2011
Excerpt: Other evidence of life on land includes quilted spheroids (Erytholus globosus gen. et sp. nov.) and thallose impressions (Farghera sp. indet.), which may have been slime moulds and lichens, respectively. These distinctive fossils in Cambrian palaeosols represent communities comparable with modern biological soil crusts.
http://www.uncommondescent.com/cambrian-explosion/land-organisms-from-cambrian-found-in-soil-layer-under-the-soil/

Cryptobiotic Soils: Holding the Place in Place
Excerpt: Cryptobiotic soil crusts, consisting of soil cyanobacteria, lichens and mosses, play an important ecological roles,,, Cryptobiotic crusts increase the stability of otherwise easily eroded soils, increase water infiltration in regions that receive little precipitation, and increase fertility in soils often limited in essential nutrients such as nitrogen and carbon (Harper and Marble, 1988; Johansen, 1993; Metting, 1991; Belnap and Gardner, 1993; Belnap, 1994; Williams et al., 1995).
http://geochange.er.usgs.gov/sw/impacts/biology/crypto/

Bacterial 'Ropes' Tie Down Shifting Southwest
Excerpt: In the desert, the initial stabilization of topsoil by rope-builders promotes colonization by a multitude of other microbes. From their interwoven relationships arise complex communities known as "biological soil crusts," important ecological components in the fertility and sustainability of arid ecosystems.
http://www.sciencedaily.com/releases/2009/11/091116203140.htm

CRYPTOBIOTIC SOIL -
Excerpt: When moistened, cyanobacteria become active, moving through the soil and leaving a trail of sticky material behind. The sheath material sticks to surfaces such as rock or soil particles, forming an intricate web of fibers throughout the soil. In this way, loose soil particles are joined together, and an otherwise unstable surface becomes very resistant to both wind and water erosion.
http://www.toddshikingguide.com/FloraFauna/Other2.htm
Along this line of thought is the 'lignin enigma'
The Lignin Enigma By Ann Gauger - July 2012
Excerpt: Why should such an abundant resource go unexploited? Darwinian evolution has apparently failed to evolve “a relatively modest innovation—growth on lignin”—over 400 million years, even though many other spectacular innovations—nodulation (a symbiotic relationship between plants and bacteria that permits the fixation of nitrogen), symbiotic pollination systems (between plants, hummingbirds, and bees), and the appearance of carnivorous plants—all appeared during the same time period, and complex biochemical pathways such as C4 photosynthesis have apparently evolved independently many times.
How can one mechanism [Darwinism] have been at the same time so effective and so ineffective? That tension vanishes completely when the design perspective is adopted. Terrestrial animal life is crucially dependent on terrestrial plant life, which is crucially dependent on soil, which is crucially dependent on the gradual photo- and biodegradation of lignin. Fungi accomplish the biodegradation, and the surprising fact that it costs them energy to do so keeps the process gradual. The peculiar properties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem.

http://www.biologicinstitute.org/post/26379997641/the-lignin-enigma

Doug Axe: Lignin & the Coherent Design of the Ecosystem - podcast
Excerpt: Lignin provides a paradoxical case for the Darwinian method of evolution, but fits perfectly into a design oriented scientific paradigm. Thirty percent of non-fossil organic carbon on the planet is lignin, so in a Darwinian world, something should have developed the ability to consume lignin--but it hasn't. Lignin binds together and protects plant cellulose, which is vital to all types of large plant life; "The peculiar properties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem of our planet."
http://www.idthefuture.com/2012/08/doug_axe_lignin_the_coherent_d.html
Lignin—Designed Randomness Matti Leisola, Ossi Pastinen, and Douglas D. Axe - 2012
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2012.3/BIO-C.2012.3

Darwinists tried, and failed, to overturn the Lignin egnigma:

Lignin: The Enigma Remains - Ann Gauger - July 2012
http://www.evolutionnews.org/2012/07/lignin_the_enig_2061821.html

This paper reveals the ‘horrendously complex’ way in which lignin is biosynthesized (please see paper to see the graph of the ‘horrendously complex’ biosynthetic pathway),,,
Lignin breakthroughs serve as GPS for plant research - March 11, 2014
Excerpt: Lignin, an important and complex polymer responsible for plant growth and development, provides mechanical strength and water transport that enables some trees to grow 100 meters tall.,,,
This work in the new area of plant systems biology, integrating biology, chemistry and engineering, sets a new standard for understanding any complex biological feature in the future.,,,
Over many years of intensive research, the interdisciplinary team led by Chiang purified 21 pathway enzymes and analyzed 189 different parameters related to lignin formation. With help from engineering colleagues Cranos Williams and Joel Ducoste, the team developed models that predict how pathway enzymes affect lignin content and composition.

http://phys.org/news/2014-03-lignin-breakthroughs-gps.html
Yet, despite the fact that Darwinian evolution was somehow super genius enough to construct a biosynthetic pathway for lignin, that took years of intensive research by a interdisciplinary team to get a basic understanding of, Darwinian evolution is somehow too dumb to figure out the much easier biosynthetic pathway of how to tap lignin as an energy source?
“nothing in evolution makes sense in the light of biology”
—Duane T. Gish, biochemist
Moreover, worms, in addition to their critical role for soil aeration, are also found to detoxify the soils of poisonous heavy metals:
The worm that turned on heavy metal - December 2010
Excerpt: The team has carried out two feasibility studies on the use of worms in treating waste. The team first used compost produced by worms, vermicompost, as a successful adsorbent substrate for remediation of wastewater contaminated with the metals nickel, chromium, vanadium and lead. The second used earthworms directly for remediation of arsenic and mercury present in landfill soils and demonstrated an efficiency of 42 to 72% in approximately two weeks for arsenic removal and 7.5 to 30.2% for mercury removal in the same time period.
http://www.physorg.com/news/2010-12-worm-heavy-metal.html
Materialism simply has no coherent answers for why these different bacterial types, biogeochemical processes, and worms etc.., would start working in precise concert with each other preparing the earth for future life to appear from the very start of their first appearance on earth.

Since oxygen readily reacts and bonds with many of the solid elements making up the earth itself, and since the slow process of tectonic activity controls the turnover of the earth's crust, it took photosynthetic bacteria a few billion years before the earth’s crust was saturated with enough oxygen to allow a sufficient level of oxygen to be built up in the atmosphere as to allow higher life:
Earth’s Oxygen: A Mystery Easy to Take for Granted - October 3, 2013
Excerpt: But the oxygen disappeared almost as soon as it was formed.
That’s because oxygen is an enormously friendly element, forming bonds with a wide range of molecules. It attached to the iron in rocks, for example, creating rust. It joined with the hydrogen spewed out from volcanoes to form hydrogen peroxide and other compounds. Our planet, in other words, was a giant oxygen vacuum in its early years.

http://www.nytimes.com/2013/10/03/science/earths-oxygen-a-mystery-easy-to-take-for-granted.html?ref=scienceandtechnology&_r=1&
At about the 9:30 minute mark of the following video Dr Paul Falkowski relates how we were able to learn that the atmosphere was starting to be oxygenated 2.3 billion years ago (Isotopic Fractionation of sulfur implies that ozone was in the atmosphere 2.3 billion years ago)

Climate Change and the Oceans Dr Paul Falkowski - video
http://rmcp.dcollege.net/playlists/16624/193512.html
New Wrinkle In Ancient Ocean Chemistry - Oct. 2009
Excerpt: "Our data point to oxygen-producing photosynthesis long before concentrations of oxygen in the atmosphere were even a tiny fraction of what they are today, suggesting that oxygen-consuming chemical reactions were offsetting much of the production,"
http://www.sciencedaily.com/releases/2009/10/091029141217.htm

Increases in Oxygen Prepare Earth for Complex Life
Excerpt: We at RTB argue that any mechanism exhibiting complex, integrated actions that bring about a specified outcome is designed. Studies of Earth’s history reveal highly orchestrated interplay between astronomical, geological, biological, atmospheric, and chemical processes that transform the planet from an uninhabitable wasteland to a place teeming with advanced life. The implications of design are overwhelming.
http://www.reasons.org/increases-oxygen-prepare-earth-complex-life
As well, Erosion and plate tectonics are also shown to be finely-tuned and thus tied to the 'terra forming', intelligent design, perspective in this following paper:
The origin of complex life as a mining operation: Rob Sheldon’s thought experiment - March 13, 2014
Excerpt: You (and many others) have mentioned the necessity of oxygen to permit most of the body plans of the Cambrian in the first place. That is, if there isn’t much oxygen around, there’s no need for lungs, for gills etc. The unmentioned point, is that the oxygen was the result of algae, toiling away for millennia without any appreciation, without any audience, turning sunlight and carbon dioxide and water into oxygen.
What this paper is saying is that there was a necessary precursor, even less loved than algae, called cyanobacteria (aka pond scum) that weren’t quite as prolific as algae, but had this remarkable ability to convert N2 into NH3 into amines, to take an inert gas out of the atmosphere and make it water soluble. This is critical for proteins since every amino acid in a protein has an amine. No nitrogen fixation, no life.
But oh, is it difficult. N2 is enormously stable, which is why nitroglycerine wants to become N2 at the slightest provocation. It takes a lot of energy and clever enzymes, working in the total absence of oxygen, to make NH3.
What I had not realized, was that the enzymes that cyanobacteria need require vanadium and molybdenum, two transition metals that are not exactly common in the ocean. But wait, glaciers grind down mountains and dump the tailings in the ocean–a perfect mining operation. And the whole earth was covered in glaciers for 200 million years before the Cambrian Explosion. It all comes down to timing.
And I thought ice ages were a waste of time.

http://www.uncommondescent.com/intelligent-design/the-origin-of-complex-life-as-a-mining-operation-rob-sheldons-thought-experiment/

Evidence of Early Plate Tectonics
Excerpt: Plate tectonics plays a critical role in keeping the Earth’s temperature constant during the Sun’s significant brightness changes. Almost four billion years ago, the Sun was 30 percent dimmer than it is today, and it has steadily increased its light output over the intervening period. This steady increase would have boiled Earth’s oceans away without plate tectonics moderating the greenhouse gas content of the atmosphere.
http://www.reasons.org/evidence-early-plate-tectonics

The Goldilocks principle: New hypothesis explains Earth's continued habitability - March 19, 2014
Excerpt: Researchers from USC and Nanjing University in China have documented evidence suggesting that part of the reason that the Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator – the geologic cycles that churn up the planet's rocky surface.
Scientists have long known that "fresh" rock pushed to the surface via mountain formation effectively acts as a kind of sponge, soaking up the greenhouse gas CO2. Left unchecked, however, that process would simply deplete atmospheric CO2 levels to a point that would plunge the Earth into an eternal winter within a few million years during the formation of large mountain ranges like the Himalayas – which has clearly not happened.
And while volcanoes have long been pointed to as a source of carbon dioxide, alone they cannot balance out the excess uptake of carbon dioxide by large mountain ranges. Instead, it turns out that "fresh" rock exposed by uplift also emits carbon through a chemical weathering process, which replenishes the atmospheric carbon dioxide at a comparable rate.
"Our presence on Earth is dependent upon this carbon cycle. This is why life is able to survive,
"
http://phys.org/news/2014-03-goldilocks-principle-hypothesis-earth-habitability.html
Once sufficient oxygenation of the earth's mantle and atmosphere was finally accomplished, higher life forms could finally be introduced on earth. Moreover, scientists find the rise in oxygen percentages in the geologic record to correspond exactly to the sudden appearance of large animals in the fossil record that depend on those particular percentages of oxygen to be present. The geologic record shows a 10% oxygen level at the time of the Cambrian explosion of higher life-forms in the fossil record some 540 million years ago. The geologic record also shows a strange and very quick rise from the 17% oxygen level, of 50 million years ago, to a 23% oxygen level 40 million years ago (Falkowski 2005, 2008). This strange rise in oxygen levels corresponds exactly to the abrupt appearance of large mammals in the fossil record who depend on those high oxygen levels. Interestingly, for the last 10 million years the oxygen percentage has been holding steady around 21%. 21% happens to be a 'very comfortable' percentage for humans to exist. If the oxygen level was only a few percentage lower, large mammals would become severely hampered in their ability to metabolize energy; if only a few percentage higher, there would be uncontrollable outbreaks of fire across the land (Denton; Nature's Destiny).

Composition Of Atmosphere - Pie Chart and Percentages:
http://www.ux1.eiu.edu/~cfjps/1400/FIG01_010.JPG
http://www.ux1.eiu.edu/~cfjps/1400/TBL01_0T2.JPG

Because of this basic chemical requirement of complex photosynthetic bacterial life establishing and helping maintain the proper oxygen levels necessary for higher life forms on any earth-like planet, this gives us further reason to strongly believe the earth is extremely unique in its ability to support intelligent life in this universe. What is more remarkable is that this balance for the atmosphere is maintained through complex symbiotic relationships with other bacteria, all of which are intertwined in very complex geochemical processes. This is irreducible complexity stacked on top of irreducible complexity!!! All of these studies of early life, and processes, on early earth fall directly in line with the anthropic hypothesis and have no rational explanation, from any materialistic theory based on blind chance, as to why all the first types of bacterial life found in the fossil record would suddenly, from the very start of their appearance on earth, start working in precise harmony with each other, and with geology, to prepare the earth for future life to appear. Nor can materialism explain why once these complex bacterial-geological processes had helped prepare the earth for higher life forms, they continue to work in precise harmony with each other to help maintain the proper balanced conditions that are of primary benefit for the higher life that is above them:
The Microbial Engines That Drive Earth’s Biogeochemical Cycles - Falkowski 2008
Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.
- Paul G. Falkowski - Professor Geological Sciences - Rutgers
http://www.genetics.iastate.edu/delong1.pdf
Biologically mediated cycles for hydrogen, carbon, nitrogen, oxygen, sulfur, and iron - image of interdependent 'biogeochemical' web
http://www.sciencemag.org/content/320/5879/1034/F2.large.jpg

Moreover, the overall principle of long term balanced symbiosis, which is in fact what we have with the overall long term biogeochemical cycles of the earth, is a very anti-random chance fact which pervades the entire ecology of our planet and points powerfully to the intentional craftsmanship of a Designer:

Interestingly, when Dr. Hugh Ross factors in the probability for 'simple' bacterial life randomly happening in this universe, which is necessary for more advanced life to exist on any planet in the first place, the probability for a planet which can host life explodes into gargantuan proportions:
Does the Probability for ETI = 1?
Excerpt: In another book I wrote with Fuz, Who Was Adam?, we describe calculations done by evolutionary biologist Francisco Ayala and by astrophysicists John Barrow, Brandon Carter, and Frank Tipler for the probability that a bacterium would evolve under ideal natural conditions—given the presumption that the mechanisms for natural biological evolution are both effective and rapid. They determine that probability to be no more than 10-24,000,000.
The bottom line is that rather than the probability for extraterrestrial intelligent life being 1 as Aczel claims, very conservatively from a naturalistic perspective it is much less than 10^500 + 22 -1054 -100,000,000,000 -24,000,000. That is, it is less than 10-100,024,000,532. In longhand notation it would be 0.00 … 001 with 100,024,000,531 zeros (100 billion, 24 million, 5 hundred and thirty-one zeros) between the decimal point and the 1. That longhand notation of the probability would fill over 20,000 complete Bibles. (As far as scientific calculations are concerned, determining how close a probability is to zero, only Penrose's 1 in 10^10^123 calculation, for the initial phase-space of the universe, is closer)

http://www.reasons.org/does-probability-eti-1
Dr. Ross points out that the extremely long amount of time it took to prepare a suitable place for humans to exist in this universe, for the relatively short period of time that we can exist on this planet, is actually a point of evidence that argues strongly for Theism:
Anthropic Principle: A Precise Plan for Humanity By Hugh Ross
Excerpt: Brandon Carter, the British mathematician who coined the term “anthropic principle” (1974), noted the strange inequity of a universe that spends about 15 billion years “preparing” for the existence of a creature that has the potential to survive no more than 10 million years (optimistically).,, Carter and (later) astrophysicists John Barrow and Frank Tipler demonstrated that the inequality exists for virtually any conceivable intelligent species under any conceivable life-support conditions. Roughly 15 billion years represents a minimum preparation time for advanced life: 11 billion toward formation of a stable planetary system, one with the right chemical and physical conditions for primitive life, and four billion more years toward preparation of a planet within that system, one richly layered with the biodeposits necessary for civilized intelligent life. Even this long time and convergence of “just right” conditions reflect miraculous efficiency.
Moreover the physical and biological conditions necessary to support an intelligent civilized species do not last indefinitely. They are subject to continuous change: the Sun continues to brighten, Earth’s rotation period lengthens, Earth’s plate tectonic activity declines, and Earth’s atmospheric composition varies. In just 10 million years or less, Earth will lose its ability to sustain human life. In fact, this estimate of the human habitability time window may be grossly optimistic. In all likelihood, a nearby supernova eruption, a climatic perturbation, a social or environmental upheaval, or the genetic accumulation of negative mutations will doom the species to extinction sometime sooner than twenty thousand years from now.

http://christiangodblog.blogspot.com/2006_12_01_archive.html
As a Christian, I like the metaphor of 'preparing for a wedding' that Dr. Ross uses in the following video to illustrate the disparity that 'The Anthropic Inequality' presents in terms of time:

Hugh Ross - The Anthropic Principle and The Anthropic Inequality - video
http://www.metacafe.com/watch/8494065/

At least one secular scientist is far more pessimistic about the 'natural' future lifespan of the human race than 20,000 years:

Humans will be extinct in 100 years says eminent scientist - June 2010
http://www.physorg.com/news196489543.html

Related note:
The Place of Life and Man in Nature: Defending the Anthropocentric Thesis – Michael J. Denton – February 25, 2013
Summary (page 11)
Many of the properties of the key members of Henderson’s vital ensemble —water, oxygen, CO2, HCO3 —are in several instances fit specifically for warm-blooded, air-breathing organisms such as ourselves. These include the thermal properties of water, its low viscosity, the gaseous nature of oxygen and CO2 at ambient temperatures, the inertness of oxygen at ambient temperatures, and the bicarbonate buffer, with its anomalous pKa value and the elegant means of acid-base regulation it provides for air-breathing organisms. Some of their properties are irrelevant to other classes of organisms or even maladaptive. It is very hard to believe there could be a similar suite of fitness for advanced carbon-based life forms. If carbon-based life is all there is, as seems likely, then the design of any active complex terrestrial being would have to closely resemble our own. Indeed the suite of properties of water, oxygen, and CO2 together impose such severe constraints on the design and functioning of the respiratory and cardiovascular systems that their design, even down to the details of capillary and alveolar structure can be inferred from first principles. For complex beings of high metabolic rate, the designs actualized in complex Terran forms are all that can be. There are no alternative physiological designs in the domain of carbon-based life that can achieve the high metabolic activity manifest in man and other higher organisms.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.1/BIO-C.2013.1
In fact, bacteria could very well be helping to keep our atmosphere 'in balance' as well:
Bugs in the Atmosphere: Significant Microorganism Populations Found in Middle and Upper Troposphere - Jan. 28, 2013
Excerpt: In what is believed to be the first study of its kind, researchers used genomic techniques to document the presence of significant numbers of living microorganisms -- principally bacteria -- in the middle and upper troposphere, that section of the atmosphere approximately four to six miles above Earth's surface.
Whether the microorganisms routinely inhabit this portion of the atmosphere -- perhaps living on carbon compounds also found there -- or whether they were simply lofted there from Earth's surface isn't yet known.

http://www.sciencedaily.com/releases/2013/01/130128151912.htm
Of related interest, microbes deep in the earth's crust are found to be surprisingly similar all over the world:
Collecting Census Data On Microbial Denizens of Hardened Rocks Dec. 9, 2013
Excerpt: What they're finding is that, even miles deep and halfway across the globe, many of these (microbial)communities are somehow quite similar.
The results,,, suggest that these communities may be connected,,,
he said. "we're seeing the same types of organisms everywhere we look."
Schrenk leads a team,, studying samples from deep underground in California, Finland and from mine shafts in South Africa. The scientists also collect microbes from the deepest hydrothermal vents in the Caribbean Ocean.
"It's easy to understand how birds or fish might be similar oceans apart," Schrenk said. "But it challenges the imagination to think of nearly identical microbes 16,000 kilometers apart from each other in the cracks of hard rock at extreme depths, pressures and temperatures."
"Integrating this region into existing models of global biogeochemistry and gaining better understanding into how deep rock-hosted organisms contribute or mitigate greenhouse gases (and toxic metals) could help us unlock puzzles surrounding modern-day Earth, ancient Earth,,,

http://www.sciencedaily.com/releases/2013/12/131209124115.htm
Needless to say, that finding is not what evolution would have predicted:

Of somewhat related interest to this topic, it is found that colonies of bacteria have some very mysterious ways of communicating essential information very quickly amongst themselves:
Electrical Communication in Bacteria - August 2010
Excerpt: These responses occurred too quickly for any sort of chemical exchange or molecular process such as osmosis, says Nielsen. The most plausible option, his team reports in the 25 February issue of Nature, is that the bacteria are somehow communicating electrically by transmitting electrons back and forth. How exactly they do this is unclear,
http://www.uncommondescent.com/intelligent-design/electrical-communication-in-bacteria/comment-page-1/#comment-361367

Electric Bugs: New Microbe Forms Living, Deep-Sea Power Cables - Oct. 24, 2012
Excerpt: The world's deep seafloors are dark and airless places, but vast swaths may pulse gently with energy conducted through a type of newly discovered bacteria that forms living electrical cables.
The bacteria were first detected in 2010 by researchers perplexed at chemical fluctuations in sediments from the bottom of Aarhus Bay in Denmark. Almost instantaneously linking changing oxygen levels in water with reactions in mud nearly an inch below, the fluctuations occurred too fast to be explained by chemistry.
Only an electrical signal made sense -- but no known bacteria could transmit electricity across such comparatively vast distances. Were bacteria the size of humans, the signals would be making a journey 12 miles long.,,,
Seen through an electron microscope, the Desulfobulbaceae -- the researchers haven't yet given them a genus or species name -- appear in blue. They link end-to-end, forming filaments nearly an inch in length.,,,
In just one teaspoon of mud, the researchers found a full half-mile of Desulfobulbaceae cable, and it's not just a Danish phenomenon. Nielsen said other researchers have sent him samples from seafloors around the world, including Tokyo Bay. It's possible that, at the microbial level, the deep seafloor is humming with current.
With so much electricity being transferred, are other organisms tapping the lines? Might the Desulfobulbaceae be a power source for entire as-yet-unappreciated deep-sea microbial ecologies, which in turn shape some of the planet's fundamental biogeochemical processes? That's "an interesting possibility," said Nielsen,,
,,the Desulfobulbaceae are definitely breaking down iron sulfides and carbonates in deeper sediment, while generating iron oxide and magnesium calcite at the surface, Nielsen said. The latter are important compounds for life in the oceans above, and ultimately on land. If the new Desulfobulbaceae are as widespread and populous as they seem, they could be an important component of life's deep-time cycles.

http://www.wired.com/wiredscience/2012/10/bacteria-electric-wires/?pid=5171&viewall=true
The principle of symbiosis of the entire ecology of the planet simply does not fit within a materialistic framework:

Intelligent Design - Symbiosis and the Golden Ratio - video
http://www.metacafe.com/watch/4669633

God's Creation - Symbiotic (Cooperative) Relationships - video
http://www.metacafe.com/watch/4023110
The Life and Death of Oxygen - 2008
Excerpt: “The balance between burial of organic matter and its oxidation appears to have been tightly controlled over the past 500 million years.” “The presence of O2 in the atmosphere requires an imbalance between oxygenic photosynthesis and aerobic respiration on time scales of millions of years hence, to generate an oxidized atmosphere, more organic matter must be buried (by tectonic activity) than respired.” - Paul Falkowski
http://www.creationsafaris.com/crev200810.htm#20081024a
Ocean carbon (CO2) sink more complex than first realized:
New discovery of how carbon is stored in the Southern Ocean - July 29, 2012
Excerpt: The Southern Ocean is an important carbon sink in the world – around 40% of the annual global CO2 emissions absorbed by the world's oceans enter through this region.,,,
"The Southern Ocean is a large window by which the atmosphere connects to the interior of the ocean below. Until now we didn't know exactly the physical processes of how carbon ends up being stored deep in the ocean. It's the combination of winds, currents and eddies that create these carbon-capturing pathways drawing waters down into the deep ocean from the ocean surface.

http://phys.org/news/2012-07-discovery-carbon-southern-ocean.html
The Oxygen and Carbon Dioxide Cycle - video
http://videos.howstuffworks.com/hsw/7942-abiotic-factors-the-oxygen-carbon-dioxide-cycle-video.htm

This following article and video clearly indicate that the life sustaining balanced symbiosis of the atmosphere is far more robust, as to tolerating man's industrial activities, than Global Warming alarmist would have us believe:
Earth's Capacity To Absorb CO2 Much Greater Than Expected: Nov. 2009
Excerpt: New data show that the balance between the airborne and the absorbed fraction of carbon dioxide has stayed approximately constant since 1850, despite emissions of carbon dioxide having risen from about 2 billion tons a year in 1850 to 35 billion tons a year now. This suggests that terrestrial ecosystems and the oceans have a much greater capacity to absorb CO2 than had been previously expected.
http://www.sciencedaily.com/releases/2009/11/091110141842.htm
Also of note; Sometimes evolutionists will point to the Rubisco Enzyme as an example of 'bad design', but it turns out the Rubisco Enzyme is indeed optimal for the purpose to which it was created for. Namely providing feedback to rising CO2 in the atmosphere:
Rubisco is not an example of unintelligent design - David Tyler
Excerpt: Rubisco's ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco's ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth's ecology,,
http://www.arn.org/blogs/index.php/literature/2010/01/21/rubisco_is_not_an_example_of_unintellige
Global Warming? - A Really Inconvenient Truth!
http://www.youtube.com/watch?v=dAd1b1s9ulg

Global Warming Apocalypse? No! - video
http://www.youtube.com/watch?v=eu1cjp3hYcg

Evidence against Global warming:
https://docs.google.com/document/d/1Udkc8g7rA_QgIqIxkND4wrS-3IXUDATuWwzMkW_AJn8/edit

Of related interest, trees help regulate global temperature
Spring May Come Earlier to North American Forests, Increasing Uptake of Carbon Dioxide - Jan. 29, 2013
Excerpt: — Trees in the con­ti­nen­tal U.S. could send out new spring leaves up to 17 days ear­lier in the com­ing cen­tury than they did before global tem­per­a­tures started to rise, accord­ing to a new study by Prince­ton Uni­ver­sity researchers. These climate-driven changes could lead to changes in the com­po­si­tion of north­east­ern forests and give a boost to their abil­ity to take up car­bon dioxide.,,,
The date of bud­burst affects how much car­bon diox­ide is taken up each year, yet most cli­mate mod­els have used overly sim­plis­tic schemes for rep­re­sent­ing spring bud­burst,

http://www.sciencedaily.com/releases/2013/01/130129171427.htm
In further related note, several different types of bacteria are found to be integral for the nitrogen fixation cycle required for plants:

nitrogen fixation - illustration
http://www.bio.miami.edu/dana/pix/nitrogencycle.gif

nitrogen fixation - video:
http://www.youtube.com/watch?v=GVbHIR2xZ0E

Just how crucial, and finely tuned, the nitrogen cycle is is revealed by this following study:
Engineering and Science Magazine - Caltech - March 2010
Excerpt: “Without these microbes, the planet would run out of biologically available nitrogen in less than a month,” Realizations like this are stimulating a flourishing field of “geobiology” – the study of relationships between life and the earth. One member of the Caltech team commented, “If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt.” Microbes are key players in earth’s nutrient cycles. Dr. Orphan added, “...every fifth breath you take, thank a microbe.”
http://www.creationsafaris.com/crev201003.htm#20100316a

Planet's Nitrogen Cycle Overturned - Oct. 2009
Excerpt: "Ammonia is a waste product that can be toxic to animals.,,, archaea can scavenge nitrogen-containing ammonia in the most barren environments of the deep sea, solving a long-running mystery of how the microorganisms can survive in that environment. Archaea therefore not only play a role, but are central to the planetary nitrogen cycles on which all life depends.,,,the organism can survive on a mere whiff of ammonia – 10 nanomolar concentration, equivalent to a teaspoon of ammonia salt in 10 million gallons of water."
http://www.sciencedaily.com/releases/2009/09/090930132656.htm

Novel Nitrogen Uptake Design - Oct. 2009
Excerpt: The exceptionality of the snow roots and their nitrogen-capturing machinery, their extraordinarily complex designs, and their optimal efficiency qualifies them as evidence, not for evolution, but rather for supernatural design.
http://www.reasons.org/NovelNitrogenUptakeDesign

Arbuscular Mycorrhizal Fungi Design
Excerpt: The mutual relationship between vascular plants (flowering plants) and arbuscular mycorrihizal fungi (AMF) is the most prevalent known plant symbiosis. Vascular plants provide sites all along their root systems where colonies of AMF can assemble and feed on the nutrients supplied by the plants. In return, the AMF supply phosphorus, nitrogen, and carbon in molecular forms that the vascular plants can readily assimilate. The (overwhelming) challenge for evolutionary models is how to explain by natural means the simultaneous appearance of both vascular plants and AMF.
http://www.reasons.org/ArbuscularMycorrhizalFungiDesign2

Roots and Microbes: Bringing a Complex Underground Ecology Into the Lab - August 2012
Excerpt: As many as 120 different types of bacteria might reside inside the root of a single plant, Dangl says, and the composition of that community is distinct from the microbial population in the local soil. "We want to know the molecular rules that guide the assembly of a community of microbes on the roots that helps a plant grow. Ecologists see this as a 120-variable problem.
http://www.sciencedaily.com/releases/2012/08/120801132440.htm
Some Trees 'Farm' Bacteria to Help Supply Nutrients - July 2010
http://www.sciencedaily.com/releases/2010/07/100729172332.htm

In fact, it seems, in conjunction with the long term terraforming of the earth to make it habitable for people to live (Hugh Ross), and also in conjunction with the privileged planet principle (Denton, Gonzalez), it seems the earth truly is ‘robustly designed’ with us ‘messy’ humans in mind to a certain extent:
Global Nitrogen Availability Consistent for Past 500 Years Linked to Carbon Levels - Mar. 21, 2013
Excerpt: "Our best idea is that the nitrogen and carbon cycles were linked tightly back then and they are linked tightly today," McLauchlan said. "Humans are now manipulating both nitrogen and carbon at the same time, which means that there is no net effect on the biosphere.",,,
http://www.sciencedaily.com/releases/2013/03/130321105100.htm
As a side note to this 'robustness' that the ecology haves towards tolerating man's 'messy' presence, recently bacteria surprised scientists by their ability to quickly detoxify the millions of barrels of oil spilled in the Gulf of Mexico:
Mighty oil-eating microbes help clean up the Gulf - July 2010
Excerpt: Where is all the oil? Nearly two weeks after BP finally capped the biggest oil spill in U.S. history, the oil slicks that once spread across thousands of miles of the Gulf of Mexico have largely disappeared. Nor has much oil washed up on the sandy beaches and marshes along the Louisiana coast.,,, The lesson from past spills is that the lion’s share of the cleanup work is done by nature in the form of oil-eating bacteria and fungi. (Thank God)
http://news.yahoo.com/s/ynews_excl/ynews_excl_sc3270

Deepwater Oil Plume in Gulf Degraded by Microbes, Study Shows
Excerpt: An intensive study by scientists with the Lawrence Berkeley National Laboratory (Berkeley Lab) found that microbial activity degrades oil much faster than anticipated. This degradation appears to take place without a significant level of oxygen depletion.
http://www.sciencedaily.com/releases/2010/08/100824132349.htm

Methane Gas Concentrations in Gulf of Mexico Quickly Returned to Near-Normal Levels, Surprising Researchers - January 2011
Excerpt: Calling the results "extremely surprising", researchers report that methane gas concentrations in the Gulf of Mexico have returned to near normal levels only months after a massive release occurred following the Deepwater Horizon oil rig explosion.
http://www.sciencedaily.com/releases/2011/01/110106145436.htm

Microbes Consumed Oil in Gulf Slick at Unexpected Rates, Study Finds - August 2011
Excerpt: "Our study shows that the dynamic microbial community of the Gulf of Mexico supported remarkable rates of oil respiration, despite a dearth of dissolved nutrients," the researchers said. Edwards added that the results suggest "that microbes had the metabolic potential to break down a large portion of hydrocarbons and keep up with the flow rate from the wellhead."
http://www.sciencedaily.com/releases/2011/08/110801111752.htm

At Least 200,000 Tons of Oil and Gas from Deepwater Horizon Spill Consumed by Gulf Bacteria - Sept. 11, 2012
Excerpt: Researchers from the University of Rochester and Texas A&M University have found that, over a period of five months following the disastrous 2010
Deepwater Horizon explosion and oil spill, naturally-occurring bacteria that exist in the Gulf of Mexico consumed and removed at least 200,000 tons of oil and natural gas that spewed into the deep Gulf from the ruptured well head.

http://www.sciencedaily.com/releases/2012/09/120911125315.htm
In fact, humans ‘getting in the way’ to try to help clean up the oil spill only made the situation worse:
Gulf of Mexico Clean-Up Makes 2010 Spill 52-Times More Toxic; Mixing Oil With Dispersant Increased Toxicity to Ecosystems - (Nov. 30, 2012)
Excerpt: If the 4.9 million barrels of oil that spilled into the Gulf of Mexico during the 2010 Deep Water Horizon spill was a ecological disaster, the two million gallons of dispersant used to clean it up apparently made it even worse -- 52-times more toxic.,,,
The study found that mixing the dispersant with oil increased toxicity of the mixture up to 52-fold over the oil alone. In toxicity tests in the lab, the mixture's effects increased mortality of rotifers, a microscopic grazing animal at the base of the Gulf's food web.,,,
"Perhaps we should allow the oil to naturally disperse. It might take longer, but it would have less toxic impact on marine ecosystems."

http://www.sciencedaily.com/releases/2012/11/121130110518.htm
Moral of the story? Seems that other than man cleaning up animals covered with oil, and making minor clean up efforts on shore lines, that man only gets in God's way as to helping 'nature' restore the ecosystem to its pristine state following a major oil spill by dumping man-made dispersants into the ocean to try to break up the oil.
Moreover, besides cleaning our oils spills up better than we can, it is also good to remember that bacteria created oil in the first place:
Algae to crude oil: Million-year natural process takes minutes in the lab - Dec 18, 2013
Excerpt: Engineers have created a continuous chemical process that produces useful crude oil minutes after they pour in harvested algae – a verdant green paste with the consistency of pea soup.,,,
In the PNNL process, a slurry of wet algae is pumped into the front end of a chemical reactor. Once the system is up and running, out comes crude oil in less than an hour, along with water and a byproduct stream of material containing phosphorus that can be recycled to grow more algae.

http://phys.org/news/2013-12-algae-crude-oil-million-year-natural.html
Man has only recently caught on to harnessing the ancient detoxification ability of bacteria to cleanup his own accidental toxic spills, as well as his toxic waste, from industry:

What is Bioremediation? - video
http://www.youtube.com/watch?v=pSpjRPWYJPg
The World’s Toughest Bacterium - 2002
Deinococcus radiodurans may be a tool for cleaning up toxic waste and more
Excerpt: An efficient system for repairing DNA is what makes the microbe so tough. High doses of radiation shatter the D. radiodurans genome, but the organism stitches the fragments back together, sometimes in just a few hours. The repaired genome appears to be as good as new.
"The organism can put its genome back together with absolute fidelity," says Claire M. Fraser, of The Institute for Genome Research (TIGR) in Rockville, Maryland. She was the leader of the TIGR team that sequenced D. radiodurans in 1999.
"I was pretty much blown away by it," says John Battista, a microbiologist at Louisiana State University in Baton Rouge, recalling his introduction to the bacterium in 1988.

http://www.genomenewsnetwork.org/articles/07_02/deinococcus.shtml

Metal-mining bacteria are green chemists - Sept. 2010
Excerpt: Microbes could soon be used to convert metallic wastes into high-value catalysts for generating clean energy, say scientists writing in the September issue of Microbiology.
http://www.physorg.com/news202618665.html
Further note:

Arsenic removal: research on bioremediation using arsenite-eating bacteria
http://www.uncommondescent.com/intelligent-design/alien-life/#comment-368346

Besides degrading heavy metals, bacteria are now being harnessed to degrade styrofoam and plastic as well:
High school girl discovers Styrofoam-eating bacterium - June 2009
Excerpt: Tseng I-Ching swept the world's largest science fair in the Peoples Choice Category at the Intel International Science & Engineering Fair (ISEF) for her discovery of a polystyrene-decomposing bacterium derived from mealworm beetles.
I-Ching vivisected more than 500 mealworm beetles to isolate the single bacterium that allows the mealworm to digest one of the most troublesome forms of waste on the planet — Styrofoam.

http://www.mnn.com/green-tech/research-innovations/blogs/high-school-girl-discovers-styrofoam-eating-bacterium

Boy discovers microbe that eats plastic - PhDs have been searching for a solution to the plastic waste problem, and this 16-year-old finds the answer. - Jun 12, 2009
Excerpt: Plastic, one of the most indestructible of manufactured materials, does in fact eventually decompose. It takes 1,000 years but decompose it does, which means there must be microorganisms out there to do the decomposing.,,,, Could those microorganisms be bred to do the job faster? That was Daniel's question, and he put to the test with a very simple and clever process of immersing ground plastic in a yeast solution that encourages microbial growth, and then isolating the most productive organisms.
The preliminary results were encouraging, so he kept at it, selecting out the most effective strains and interbreeding them. After several weeks of tweaking and optimizing temperatures Burd was achieved a 43 percent degradation of plastic in six weeks, an almost inconceivable accomplishment.
NOTE: One of our readers pointed out a very interesting study in 2004 at the University of Wisconsin that isolated a fungus capable of biodegrading phenol-formaldehyde polymers previously thought to be non-biodegradable. Phenol polymers are produced at an annual rate of 2.2 million metric tons per year in the United States for many industrial and commercial applications including durable plastics.

http://www.mnn.com/green-tech/research-innovations/blogs/boy-discovers-microbe-that-eats-plastic#
Two young scientists break down plastics with bacteria - video
http://www.youtube.com/watch?v=ay-y3tSYGYw

Of related note to bacteria helping clean up after 'messy' humans, some materialists believe they have conclusive proof for evolution because bacteria can quickly adapt to detoxify new man-made materials, such as nylon, even though it is, once again, just a minor variation within kind, i.e. though the bacteria adapt they still do not demonstrate a gain in fitness over the parent strain once the nylon is consumed (Genetic Entropy). I’m not nearly as impressed with their 'stunning proof' as they think I should be. In fact recent research has shown the correct explanation for the nylon-eating enzyme, produced on the plasmids, seems to be a special mechanism which recombines parts of the genes in the plasmids in a way that is non-random. This is shown by the absence of stop codons, which would be generated if the variation were truly random. The 'clockwork' repeatability of the adaptation clearly indicates a designed mechanism that fits perfectly within the limited 'variation within kind' model of Theism, and stays well within the principle of Genetic Entropy since the parent strain is still more fit for survival once the nylon is consumed from the environment. (Answers In Genesis)

Nylon Eating Bacteria: NOT NEW INFORMATION - video
http://www.youtube.com/watch?v=wkNmfA09cGg
The three-dimensional structure of nylon hydrolase and the mechanism of nylon-6 hydrolysis - Seiji Negoro - Dec. 2011
SUMMARY: We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 Å-resolution. This enzyme is a member of the N-terminal nucleophile (N-tn) hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct.
We observed four identical heterodimers (27kDa+9kDa), which resulted from the autoprocessing of the precursor protein (36kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr267 of the 9kDa-subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked (greek symbols) core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T m=52°C, enhanced the protein thermostability by 36°C (T m=88° C), whereas a single mutation (G111S or L137A) decreased the stability by approximately 10°C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon-cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60°C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.

http://www.jbc.org/content/early/2011/12/19/jbc.M111.321992.full.pdf

Nylon Degradation – Analysis of Genetic Entropy
Excerpt: At the phenotypic level, the appearance of nylon degrading bacteria would seem to involve “evolution” of new enzymes and transport systems. However, further molecular analysis of the bacterial transformation reveals mutations resulting in degeneration of pre-existing systems. The most studied of the nylon degrading bacteria is Arthrobacter sp. K172 (formerly Flavobacterium sp.70). This bacterium employs three enzymes for nylon degradation, EI (NylA), EII (NylB), and EIII (NylC), which are found on the plasmid, pOAD2.71, 72 EI and EIII (also NylC in Agromyces sp.) have been initially characterized.73, 72 They apparently hydrolyze the cyclic forms of some nylons, which provides a linear substrate for EII. However, no detailed analysis of the mutational changes of EI or EIII has yet been performed.
The mutational changes of EII (6-aminohexanoatedimer hydrolase) have been characterized in detail. This analysis suggests that point mutations in a carboxyesterase gene lead to amino acid substitutions in the enzyme’s catalytic cleft. This altered the enzyme’s substrate specificity sufficiently that it could also hydrolyze linear nylon oligomers.74, 75 Yet, the EII enzyme still possesses the esterase function of the parent esterase. Thus, the mutational alteration results in a reduction of the parent enzyme’s specificity (Figure 4). This enables it to hydrolyze a wider range of oligomers that include nylon oligomers.76
Nonetheless, reduced specificity of a pre-existing enzyme is biochemically degenerative to the enzyme,77, 78 even if it provides a presumed phenotypic benefit. The “beneficial” phenotype of nylon degradation requires the a priori existence of the enzyme and its specificity. Its degeneration is not a mechanism that accounts for the origin of either the enzyme or its specificity.,,,

http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria

Why Scientists Should NOT Dismiss Intelligent Design - William Dembski
Excerpt: "the nylonase enzyme seems “pre-designed” in the sense that the original DNA sequence was preadapted for frame-shift mutations to occur without destroying the protein-coding potential of the original gene. Indeed, this protein sequence seems designed to be specifically adaptable to novel functions."
http://www.uncommondescent.com/evolution/why-scientists-should-not-dismiss-intelligent-design/
Though Darwinists love to claim this as a 'new' protein. The simple fact is that is the same exact enzyme/protein, esterase, with only a minor variation on its previous enzymatic activity:
“Mutational analysis of 6-aminohexanoate-dimer hydrolase:
Relationship between nylon oligomer hydrolytic and esterolytic activities”
Excerpt: “Based upon the following findings, we propose that the nylon oligomer hydrolase has newly evolved through amino acid substitutions in the catalytic cleft of a pre-existing esterase with the b-lactamase-fold”.
Taku Ohkia, Yoshiaki Wakitania, Masahiro Takeoa, Kengo Yasuhiraa, Naoki Shibatab,
Yoshiki Higuchib, Seiji Negoroa FEBS Letters 580 (2006) 5054–5058
http://www.uncommondescent.com/intelligent-design/intelligent-design-and-the-demarcation-problem/comment-page-12/#comment-362219
Even Wikipedia as of January 2014, which is notorious for its bias against Intelligent Design, admits that nylonase 'most probably developed as a single-step mutation', thus the adaptation is well within what Dr. Behe has set for the 'Edge of Evolution':
Nylon-eating bacteria - Jan. 2014
Excerpt: There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation.
http://en.wikipedia.org/wiki/Nylon-eating_bacteria#Role_in_evolution_teaching
Though it is impossible to reconstruct the DNA of the earliest bacteria fossils, scientists find in the fossil record, and compare them to their descendants of today, there are many ancient bacteria spores recovered and 'revived' from salt crystals and amber crystals which have been compared to their living descendants of today. Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many evolutionary scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence.
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes:
“Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637
Evolutionists were so disbelieving at this stunning lack of change, far less change than was expected from the neo-Darwinian view, that they insisted the stunning similarity was due to modern contamination in Vreeland's experiment. Yet the following study laid that objection to rest by verifying that Dr. Vreeland's methodology for extracting ancient DNA was solid and was not introducing contamination because the DNA sequences this time around were completely unique:
World’s Oldest Known DNA Discovered (419 million years old) - Dec. 2009
Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated. Not so this time around. A team of researchers led by Jong Soo Park of Dalhousie University in Halifax, Canada, found six segments of identical DNA that have never been seen before by science. “We went back and collected DNA sequences from all known halophilic bacteria and compared them to what we had,” Russell Vreeland of West Chester University in Pennsylvania said. “These six pieces were unique",,,
http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html
These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland's work:
“Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
http://www.physicsforums.com/showthread.php?t=281961

Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,(thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution's 'genetic drift' theory requires.)
http://www.sciencemag.org/cgi/content/abstract/268/5213/1060
30-Million-Year Sleep: Germ Is Declared Alive
http://query.nytimes.com/gst/fullpage.html?res=990CEFD61439F93AA25756C0A963958260&sec=&spon=&pagewanted=2

Dr. Cano's work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated:
“After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber."
http://www.uncommondescent.com/intelligent-design/reductionist-predictions-always-fail/comment-page-3/#comment-357693
In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' I had asked him about:
Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.":
Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki
Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

This following experiment is very interesting in how it confirmed the preceding observation of genetic entropy for modern bacteria:
Giving Ancient Life Another Chance to Evolve: Scientists Place 500-Million-Year-Old Gene in Modern Organism - July 11, 2012
Excerpt: After achieving the difficult task of placing the ancient gene in the correct chromosomal order and position in place of the modern gene within E. coli, Kaçar produced eight identical bacterial strains and allowed "ancient life" to re-evolve. This chimeric bacteria composed of both modern and ancient genes survived, but grew about two times slower than its counterpart composed of only modern genes.
"The altered organism wasn't as healthy or fit as its modern-day version, at least initially," said Gaucher, "and this created a perfect scenario that would allow the altered organism to adapt and become more fit as it accumulated mutations with each passing day."
The growth rate eventually increased and, after the first 500 generations, the scientists sequenced the genomes of all eight lineages to determine how the bacteria adapted. Not only did the fitness levels increase to nearly modern-day levels, but also some of the altered lineages actually became healthier than their modern counterpart.
When the researchers looked closer, they noticed that every EF-Tu gene did not accumulate mutations. Instead, the modern proteins that interact with the ancient EF-Tu inside of the bacteria had mutated and these mutations were responsible for the rapid adaptation that increased the bacteria's fitness. In short, the ancient gene has not yet mutated to become more similar to its modern form, but rather, the bacteria found a new evolutionary trajectory to adapt.

http://www.sciencedaily.com/releases/2012/07/120711100726.htm
Now the burning question that Darwinists will never ask is, of course, why are the modern genes adjusting to the information that the ancient 500 million year old gene had provided to the bacteria, to increase the fitness of the bacteria, instead of the other way around??? This evidence clearly is evidence of Genetic Entropy (deterioration) of the genes of modern bacteria since the modern strains of bacteria only 'regained' fitness once 'non-deteriorated' ancient genetic information was added to the genome of the bacteria.

This following study concurs:
Professor's hypothesis may be game changer for evolutionary theory - April 2012
Excerpt: "According to the hypothesis, evolution pushes microorganisms to lose essential functions when there is another species around to perform them. This idea counters popular evolutionary thinking that living organisms evolve by adding genes rather than discarding them.,,
"A common assumption about evolution is that it is directed toward increasing complexity," said Erik Zinser, associate professor of microbiology. "But we know from analysis of microbial genomes that some lineages trend toward decreasing complexity, exhibiting a net loss of genes relative to their ancestor."

http://www.physorg.com/news/2012-04-professor-hypothesis-game-changer-evolutionary.html
Related note:
If genetic entropy is true, why do bacteria still exist? by Robert Carter - October 2012
Excerpt: It is sufficient to say, however, that bacteria, of all the life forms on Earth, are the best candidates for surviving the effects of GE (Genetic Entropy) over the long term. Their simpler genomes, high population sizes, short generation times, and lower overall mutation rates combine to make them the most resistant to extinction.
http://creation.com/genetic-entropy-and-simple-organisms
Here is a revisit to the video of the 'Fitness Test' that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria:

Is Antibiotic Resistance evidence for evolution? - 'Fitness Test' - video
http://www.metacafe.com/watch/3995248

Moreover, according to prevailing evolutionary dogma, there 'HAS' to be 'major genetic drift' to the DNA of modern bacteria from 250 million years ago, even though the morphology (shape) of the bacteria can be expected to remain exactly the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, has also severely weakened the 'genetic drift' argument of evolutionists:
The consequences of genetic drift for bacterial genome complexity - Howard Ochman - 2009
Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
http://genome.cshlp.org/content/early/2009/06/05/gr.091785.109
I find it interesting that the materialistic theory of evolution expects there to be a significant amount of genetic drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the atheistic materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis.

Many times a materialist will offer what he considers conclusive proof for evolution by showing bacteria that have become resistant to a certain antibiotic such as penicillin. Yet upon close inspection, once again this 'conclusive proof' dissolves away. All observed instances of 'beneficial' adaptations of bacteria to new antibiotics have been shown to be the result of degradation of preexisting molecular abilities:

List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
http://www.trueorigin.org/bacteria01.asp

Moreover it is shown that nothing new has evolved since ancient bacteria have the very same ability to developed resistance to antibiotics as modern strains do:

Antibiotic resistance is ancient - September 2011
http://www.nature.com/nature/journal/v477/n7365/full/nature10388.html?WT.ec_id=NATURE-20110922

Evolution - Tested And Falsified - Don Patton - video
http://www.metacafe.com/watch/4036803

The following is a reflection on the true implications of the 'evolution' of bacteria becoming resistant to multiple antibiotics that has many people concerned as to its danger:
Superbugs not super after all
Excerpt: It is precisely because the mutations which give rise to resistance are in some form or another defects, that so-called supergerms are not really ‘super’ at all—they are actually rather ‘wimpy’ compared to their close cousins.
http://creation.com/superbugs-not-super-after-all

French Volcanic Clay Kills Antibiotic-Resistant MRSA Superbug
Excerpt: I've heard of some people being told to "go roll around in the dirt" to get rid of their MRSA, and I've heard some reports of that working. I believe the effect was in "normalizing" their resident bacteria living on their skin. Just like in our digestive system, bacteria live in balance. Put more of the "good" guys in, and that will support your body being in balance.
http://staph-infection-resources.blogspot.com/2008/04/french-volcanic-clay-kills-antibiotic.html

MRSA - Supergerms Do they prove evolution?
In places that are exposed to dirt from the street—such as your house—the supergerms are kept in their place not by powerful drugs and poisons but by competition with other germs. And their resistance genes are diluted by genes of the susceptible or non-resistant germs of the same species rather than being concentrated by selective breeding. That is why most non-hospital infections respond readily to antibiotics—the drug kills most of the germs, the body takes care of the rest. If it were not so, the so called supergerms would escape from hospitals and sweep the world.
http://www.answersingenesis.org/creation/v11/i2/supergerms.asp
Are You Too Clean? - New Studies Suggest Getting A Little Dirty May Be Just What The Doctor Ordered - December 2010
http://www.creationsafaris.com/crev201012.htm#20101208a

For materialists to conclusively prove evolution they would have to violate the principle of Genetic Entropy by clearly demonstrating a gain of functional information bits (Fits) over the parent species (Abel - Null-Hypothesis) in the fitness test which I've listed previously. Materialists have not done so, nor will they ever. The staggering interrelated complexity for the integrated whole of a distinct 'kind' of life-form simply will not allow the generation of complex functional information above the parent species to happen in its genome by chance alone. (Sanford, Genetic Entropy 2005)

This following site highlights the problem that the integrated complexity of a genome presents for Neo-Darwinism mechanism of random mutation:

Poly-Functional Complexity equals Poly-Constrained Complexity
http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ

This following quote reiterates the principle that material processes cannot generate functional information:
“There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.
Change is not enough -- it is the type of change that matters - video
http://www.youtube.com/watch?v=JaCEgJbc1iY

In fact it is now strongly suspected that all changes in the genome, which are deemed to be 'beneficial', are now found to be 'designed' changes that still stay within the overriding principle of Genetic Entropy:
Revisiting The Central Dogma (Of Evolution) In The 21st Century - James Shapiro - 2008
Excerpt: Genetic change is almost always the result of cellular action on the genome (not replication errors). (of interest - 12 methods of 'epigenetic' information transfer in the cell are noted in the paper)
http://www.uncommondescent.com/intelligent-design/central-dogma-revisited/

Scientists Discover What Makes The Same Type Of Cells Different - Oct. 2009
Excerpt: Until now, cell variability was simply called “noise”, implying statistical random distribution. However, the results of the study now show that the different reactions are not random, but that certain causes (environmental clues) lead to predictable distribution patterns,,,
http://www.sciencedaily.com/releases/2009/09/090911204217.htm

Bacteria 'Invest' (Designed) Wisely to Survive Uncertain Times, Scientists Report - Dec. 2009
Excerpt: Essentially, variability of bacterial cells appears to match the variability in the environment, thereby increasing the chances of bacterial survival,
http://www.sciencedaily.com/releases/2009/11/091102112102.htm

De Novo Genes: - Cornelius Hunter - Nov. 2009
Excerpt: Cells have remarkable adaptation capabilities. They can precisely adjust which segments of the genome are copied for use in the cell. They can edit and regulate those DNA copies according to their needs. And they can even modify the DNA itself, such as with adaptive mutations,,,,One apparent de novo gene is T-urf13 which was found in certain varieties of corn.
http://darwins-god.blogspot.com/2009/11/de-novo-genes-evolutionary-explanation.html

The secrets of intelligence lie within a single cell - April 2010
Excerpt: Yet something amazing is happening here: because the damage to the Antithamnion filament is unforeseeable, the organism faces a situation for which it has not been able to adapt, and is therefore unable to call upon inbuilt responses. It has to use some sort of problem-solving ingenuity instead.
http://www.newscientist.com/article/mg20627571.100-the-secrets-of-intelligence-lie-within-a-single-cell.html
This overriding truth of never being able to violate the Genetic Entropy of poly-constrained information by natural means applies to the 'non-living realm' of viruses, such as bird flu and HIV, as well:
Ryan Lucas Kitner, Ph.D. 2006. - Bird Flu
Excerpt: influenza viruses do possess a certain degree of variability; however, the amount of genetic information which a virus can carry is vastly limited, and so are the changes which can be made to its genome before it can no longer function.
http://www.answersingenesis.org/articles/aid/v1/n1/has-it-evolved
As well, the virus is far more complex than many people have ever imagined, as this following video clearly points out:

Virus - Assembly Of A Nano-Machine - video
http://www.metacafe.com/watch/4023122

Though most people think of viruses as being very harmful to humans, the fact is that the Bacteriophage (Bacteria Eater) virus, in the preceding video, is actually a very beneficial virus to man.
Bacteriophage
Excerpt: Bacteriophages are among the most common biological entities on Earth,,,They have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe.[5] They are seen as a possible therapy against multi drug resistant strains of many bacteria.,,,development of phage therapy was largely abandoned in the West, but continued throughout 1940s in the former Soviet Union for treating bacterial infections, with widespread use including the soldiers in the Red Army—much of the literature was published in Russian or Georgian, and unavailable for many years in the West. Their use has continued since the end of the Cold War in Georgia and elsewhere in Eastern Europe.,,,In August, 2006 the United States Food and Drug Administration (FDA) approved using bacteriophages on cheese to kill the Listeria monocytogenes bacteria, giving them GRAS status (Generally Recognized As Safe).[10] In July 2007, the same bacteriophages were approved for use on all food products.[11] Government agencies in the West have for several years been looking to Georgia and the Former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, e.g., Anthrax, Botulism.
http://en.wikipedia.org/wiki/Bacteriophage

(Bacteriophage) Viruses in the gut protect from infection - 20 May 2013
Excerpt: Barr and his colleagues,, show that animal mucus — whether from humans, fish or corals — is loaded with bacteria-killing viruses called phages. These protect their hosts from infection by destroying incoming bacteria. In return, the phages are exposed to a steady torrent of microbes in which to reproduce. “It’s a unique form of symbiosis, between animals and viruses,” says Rotem Sorek, a microbial geneticist ,,
“It’s groundbreaking,” adds Frederic Bushman, a microbiologist ,, “The idea that phage can be viewed as part of the innate immune system is original and exciting.

http://www.nature.com/news/viruses-in-the-gut-protect-from-infection-1.13023

Viruses: A Pirate Phage Commandeers the Immune System of Bacteria - Feb. 27, 2013
Excerpt: The study provides the first evidence that this type of virus, the bacteriophage ("phage" for short), can acquire a wholly functional and adaptive immune system.
The phage used the stolen immune system to disable -- and thus overcome -- the cholera bacteria's defense system against phages. Therefore, the phage can kill the cholera bacteria and multiply to produce more phage offspring, which can then kill more cholera bacteria. The study has dramatic implications for phage therapy,,,

http://www.sciencedaily.com/releases/2013/02/130227134334.htm

Giant Viruses Undermine Common Ancestry - March 6, 2014
Excerpt: "We thought it was a property of viruses that they pack DNA extremely tightly into the smallest particle possible, but this guy is 150 times less compacted than any bacteriophage [viruses that infect bacteria]. We don’t understand anything anymore!”,,,
“There is a mechanism of permanent creation going on in amoeba producing a new repertoire of viruses and predisposing giant viruses to become pathogens once they specialise”, Raoult said.
He said the mechanism was not foreseen by Charles Darwin’s theory that life comes from a common ancestor. “The idea of a common ancestor makes no sense in the light of viruses,” he said. “That was Darwin’s idea, but he was clearly wrong.”

http://www.uncommondescent.com/evolution/biggest-virus-ever-we-dont-understand-anything-anymore/
Michael Behe defends the one 'overlooked' protein/protein binding site generated by the HIV virus, that Abbie Smith and Ian Musgrave had found, by pointing out it is well within the 2 binding site limit he set in "The Edge Of Evolution" on this following site:
Response to Ian Musgrave's "Open Letter to Dr. Michael Behe," Part 4
"Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane --- not something to crow about after 10^20 replications and a greatly enhanced mutation rate."
http://behe.uncommondescent.com/2007/11/response-to-ian-musgraves-open-letter-to-dr-michael-behe-part-5/
An information-gaining mutation in HIV? NO!
http://creation.com/an-information-gaining-mutation-in-hiv

In fact, I followed this debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were 'crowing' about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a 'leaky cell membrane' in binding site complexity. Thus the 'evolution' of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined for millions of years, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive. The logic of this is nicely summed up here:
Richard Dawkins interview with a 'Darwinian' physician goes off track - video
Excerpt: "I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly -- a few hours sometimes, they can reproduce themselves -- that they can evolve very, very quickly. And we're stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?"
http://www.evolutionnews.org/2012/07/video_to_dawkin062031.html
i.e. Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction be realistically 'selected' for? Any other function besides reproduction, such as sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would slow down successful reproduction. Indeed, instead of eating us, time after time these different types of microbial life are found to be helping us in essential ways that have nothing to do with their ability to successfully reproduce,,,
NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012
Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival.
http://www.nih.gov/news/health/jun2012/nhgri-13.htm

We are living in a bacterial world, and it's impacting us more than previously thought - February 15, 2013
Excerpt: We often associate bacteria with disease-causing "germs" or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,,
I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens."

http://phys.org/news/2013-02-bacterial-world-impacting-previously-thought.html#ajTabs

Forcing bacteria to 'evolve' turns helpful bacteria into pathogenic bacteria:
From friend to foe: How benign bacteria evolve to virulent pathogens, December 12, 2013
Excerpt: "Bacteria can evolve rapidly to adapt to environmental change. When the "environment" is the immune response of an infected host, this evolution can turn harmless bacteria into life-threatening pathogens. ...It is thought that many strains of E. coli that cause disease in humans evolved from commensal strains."
http://medicalxpress.com/news/2013-12-friend-foe-benign-bacteria-evolve.html

The Microbial Engines That Drive Earth’s Biogeochemical Cycles - Falkowski 2008
Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. -
Paul G. Falkowski - Professor Geological Sciences - Rutgers
http://www.genetics.iastate.edu/delong1.pdf
Sometimes materialists, instead of conceding the fact that pathogens do not present any evidence for 'vertical' Darwinian evolution, will complain that a 'loving' God would not make pathogens. Yet there is very good reason to believe that pathogens were originally created 'non-pathogenic':
Setting a Molecular Clock for Malaria Parasites - July 8, 2010
Excerpt: The ancestors of humans acquired the parasite 2.5 million years ago.
"Malaria parasites undoubtedly were relatively benign for most of that history (in humans), becoming a major disease only after the origins of agriculture and dense human populations," said Ricklefs.

http://www.nsf.gov/news/news_summ.jsp?cntn_id=117259

"the AIDS virus originated relatively recently, as a mutation from SIV, the simian immuno-deficiency virus. According to Wikipedia, this virus was also benign in its original form:.. Unlike HIV-1 and HIV-2 infections in humans, SIV infections in their natural hosts appear in many cases to be non-pathogenic. Extensive studies in sooty mangabeys have established that SIVsmm infection does not cause any disease in these animals, despite high levels of circulating virus."
http://www.uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/#comment-448372
Dr. Meyer makes a interesting comment here about simple self-replicating molecules which got simpler very quickly by neo-Darwinian processes;
In a classic experiment, Spiegelman in 1967 showed what happens to a molecular replicating system in a test tube, without any cellular organization around it. … these initial templates did not stay the same; they were not accurately copied. They got shorter and shorter until they reached the minimal size compatible with the sequence retaining self-copying properties. And as they got shorter, the copying process went faster. - Stephen Meyer - The Nature of Nature: Examining the Role of Naturalism in Science (Wilmington, DE: ISI Books, 2011), p. 313–18.
This following link has a nice overview of the classic self-replicating experiment in 1967 by Spiegelman in which the self-replicating RNA molecule got simpler and simpler in an artificial environment,(i.e. from 4500 nucleotides to the 220 nucleotide ‘Spiegelman’s monster’), instead of evolving any new complexity that might have led to self sustaining capability;

Origins of Life – Freeman Dyson – page 75
http://books.google.com/books?id=aQ75QhwpXoEC&pg=PA75#v=onepage&q&f=false

Here is a defence of Dr. Behe's binding site limit from the T-urf13 gene/protein that was argued, by Darwinists, to be a 'new' gene/protein that refuted Behe's limit:

How Arthur Hunt Fails To Refute Behe (T-URF13)- Jonathan M - February 2011
http://www.uncommondescent.com/intelligent-design/on-the-non-evolution-of-irreducible-complexity-how-arthur-hunt-fails-to-refute-behe/#comment-373010
On the non-evolution of Irreducible Complexity – How Arthur Hunt Fails To Refute Behe
Excerpt: furthermore, T-urf 13 involves a kind of degradation of maize. In the case of the Texas maize–hence the T—the T-urf 13 was located by researchers because it was there that the toxin that decimated the corn grown in Texas in the late 60′s attached itself. So the “manufacturing” of this “de novo” gene proved to make the maize less fit. This is in keeping with Behe’s latest findings.
http://www.uncommondescent.com/intelligent-design/on-the-non-evolution-of-irreducible-complexity-how-arthur-hunt-fails-to-refute-behe/comment-page-3/#comment-373178
Moreover, TURF-13 is a constitutively transcribed mitochondrial gene that is derived from two already existing genes.
Genetic and molecular basis of cytoplasmic male sterility in maize - 2007
Excerpt page 51: The specific virulence of B. maydis towards CMS-T maize was found to be due to mitochondrial gene Turf 13, which is also responsible for the CMS phenotype in CMS-T. It is a constitutively transcribed gene which produces a 13 kd polypetide (Williams et al., 1992). Such a polypeptide is not found in CMS -S, CMS -C or normal maize cytoplasm. Turf 13 is a chimeric region gene which is a recombination product of 5’ region of the atp 6 gene and 3’ region of the 265 ribosomal gene (rrn 26). Its transcription is presumably under the control of the atp 6 promoter (Stamper et al., 1987). It is located in 3547-nucleotide mt DNA sequence that contains two open reading frames, one coding for urf 13 and the other for orf 221, which codes for a 25 kd polypeptide consisting of 221 amino acids and is 77 nucleotides downstream of urf 13 (Levings, 1990). The orf 221 encodes a membrane bound protein that has been identified as ATP4 (Heazlewood et al., 2003).
http://agrobiol.sggw.waw.pl/~cbcs/articles/CBCS_2_1_7.pdf
I would also like to point out scientists have never changed any one type of single cell organism, bacteria, or virus, into any other type of single cell organism, bacteria, or virus, despite years of exhaustive experimentation trying to change them. In fact, it is commonly known the further scientists deviate any particular single cell organism, bacteria, or virus, type from its original state, the more unfit for survival the manipulated population will quickly become (Genetic Entropy). As former president of the French Academy of Sciences Pierre P. Grasse has stated:
“What is the use of their unceasing mutations, if they do not change? In sum, the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect.”
As well, to reiterate what was said in another article I listed previously, bacteria that are resistant to multiple antibiotics (MRSA) are actually superwimps instead of supergerms. This is because the multiple deleterious mutations they have incurred, from their interaction with different antibiotics, make them dramatically less fit for survival in the wild than their non-mutated cousins:
Superbugs not super after all
Excerpt: It is precisely because the mutations which give rise to resistance are in some form or another defects, that so-called supergerms are not really ‘super’ at all—they are actually rather ‘wimpy’ compared to their close cousins. When I was finally discharged from hospital, I still had a strain of supergerm colonizing my body. Nothing had been able to get rid of it, after months in hospital. However, I was told that all I had to do on going home was to ‘get outdoors a lot, occasionally even roll in the dirt, and wait.’ In less than two weeks of this advice, the supergerms were gone. Why? The reason is that supergerms are actually defective in other ways, as explained. Therefore, when they are forced to compete with the ordinary bacteria which normally thrive on our skin, they do not have a chance. They thrive in hospital because all the antibiotics and antiseptics being used there keep wiping out the ordinary bacteria which would normally outcompete, wipe out and otherwise keep in check these ‘superwimps’.
http://creation.com/superbugs-not-super-after-all
NDM-1 Superbug the Result of Bad Policies, Not Compelling Evidence for Evolution's Creative Powers - Sept. 2010
http://www.evolutionnews.org/2010/09/ndm-1_superbug_the_result_of_b038021.html

'Random mutations', though touted as this great engine of creativity by evolutionists, are in fact a pitiful mechanism to explain the generation of the functional information that we find in life, as this following references show:
Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010
Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html
Random Mutations Destroy Information - Perry Marshall - video
http://www.metacafe.com/watch/4023143
Random Mutations and the Heroics of Evolution
Excerpt: A child once informed his friends his toy bulldozer could dig all the way through the Earth. But wasn’t the Earth too big? No, look at the Grand Canyon—it is proof of what such small shovels can do. Such childish logic, amazingly, shows up repeatedly in evolutionary “theory.”
http://darwins-god.blogspot.com/2010/07/random-mutations-and-heroics-of.html

Michael Behe's Blog - October 2007
Excerpt: As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems.
http://behe.uncommondescent.com/page/6/
Blink and You'll Miss It: Jerry Coyne Turns His Attention to the "Engine of Evolution" (Lenski, Lynch, Hall, Antibiotic resistance, Insecticide resistance) - December 7, 2012
http://www.evolutionnews.org/2012/12/blink_and_youll2067161.html

Materialists simply do not have any evidence for the truly 'beneficial' mutations they need to make evolution work. The following site has numerous quotes, studies and videos which reveal the overwhelmingly negative mutation rate which has been found in life:

Mutation Studies, Videos, And Quotes
http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjZjZnM5M21mZg

It is also interesting to note that scientists have actually used a mechanism of 'excessive mutations' to help humans in their fight against pathogenic viruses, as the following articles clearly point out:
GM Crops May Face Genetic Meltdown
Excerpt: Error catastrophe occurs when high mutation rates give rise to so many deleterious mutations that they make the population go extinct. For example, foot and mouth disease virus treated with mutagens (base analogues fluorouracil and azacytidine) eventually become extinct [1]. Polio virus treated with the mutagenic drug ribavirin similarly went extinct [2].
http://www.i-sis.org.uk/meltdown.php

Quasispecies Theory and the Behavior of RNA Viruses - July 2010
Excerpt: Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. ,,, it has been termed “mutational meltdown.” It is now clear that many RNA viruses replicate near the error threshold. Early studies with VSV showed that chemical mutagens generally reduced viral infectivity, and studies with poliovirus clearly demonstrated that mutagenic nucleoside analogs push viral populations to extinction [40]–[43]. The effect is dramatic—a 4-fold increase in mutation rate resulted in a 95% reduction in viral titer.,,, While mutation-independent activities have also been identified, it is clear that APOBEC-mediated lethal mutagenesis is a critical cellular defense against RNA viruses. The fact that these pathogens replicate close to the error threshold makes them particularly sensitive to slight increases in mutational load.,,,
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1001005#ppat-1001005-g003
In fact, trying to narrow down an actual hard number for the truly beneficial mutation rate, that would actually explain the massively integrated machine-like complexity of proteins we find in life, is what Dr. Behe did in this following book:

"The Edge of Evolution: The Search for the Limits of Darwinism"
http://www.amazon.com/Edge-Evolution-Search-Limits-Darwinism/dp/0743296206

What are the Limits of Darwinism? A Presentation by Dr. Michael Behe at the University of Toronto - November 15th, 2012 - video
http://www.youtube.com/watch?v=V_XN8s-zXx4

Here is a in-depth interview with biologist Michael Behe on the theory of Intelligent Design from Nov. 2013.

Michael Behe: Intelligent Design - video - Nov. 2013
http://www.youtube.com/watch?v=H9SmPNQrQHE

The Edge Of Evolution - Michael Behe - Video Lecture
http://www.c-spanvideo.org/program/199326-1

The Edge of Evolution (Michael Behe) - radio interview
http://www.youtube.com/watch?v=eP0LN63b8qY

Sites which responded to the criticisms of "The Edge' are listed in the preceding video's description:
A review of The Edge of Evolution: The Search for the Limits of Darwinism
The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have "invented" little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
http://creation.com/review-michael-behe-edge-of-evolution

Graph - Behe comes to the conclusion that the edge of Darwinian evolution for a vertebrate lies somewhere between the level of species and class. That is, evolution cannot explain the categories above this level. Interestingly, creationist biologist Frank Marsh proposed in 1976 that the created kinds (baramins) were often at the level of genus or family, although sometimes at the level of order.
(Figure 10.1, p. 218 - Edge Of Evolution).
http://creation.com/images/journal_of_creation/vol22/6472chart-lge.jpg
Dr. Behe states in The Edge of Evolution on page 135:
"Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite."

"The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable."
- Michael Behe - The Edge of Evolution - page 146
Behe's Proposed "Edge Of Evolution" (2 Mutation Limit) Vindicated In New Study On Insects - July 2012
http://www.uncommondescent.com/intelligent-design/was-michael-behe-right/

Where's the substantiating evidence for neo-Darwinism?
https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

To illustrate just how difficult of a step it is, the order of difficulty, of developing a single protein-protein binding site, is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.
Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe - Oct. 2009
Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
http://www.evolutionnews.org/2009/10/richard_dawkins_the_greatest_s.html

Antimalarial drug resistance - Nicholas J. White 1,2
Excerpt: Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14). This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10^20 parasite multiplications. The single point mutations in the gene encoding cytochrome b (cytB), which confer atovaquone resistance, or in the gene encoding dihydrofolate reductase (dhfr), which confer pyrimethamine resistance, have a per-parasite probability of arising de novo of approximately 1 in 10^12 parasite multiplications (5). To put this in context, an adult with approximately 2% parasitemia has 10^12 parasites in his or her body. But in the laboratory, much higher mutation rates thane 1 in every 10^12 are recorded (12).
http://www.jci.org/articles/view/21682
The Sheer Lack Of Evidence For Macro Evolution - William Lane Craig - video
http://www.metacafe.com/watch/4023134/

An Atheist Interviews Michael Behe About "The Edge Of Evolution" - video
http://www.in.com/videos/watchvideo-bloggingheads-interview-with-michael-behe-4734623.html

Thus, the actual rate for 'truly' beneficial mutations, which would account for the staggering machine-like complexity we see in life, is far in excess of one-hundred-billion-billion mutational events. So the one in a thousand, to one in a million, number for 'truly' beneficial mutations is actually far, far, too generous for an estimate for evolutionists to use as an estimate in their 'hypothetical' calculations for beneficial mutations.

In fact, from consistent findings such as these, it is increasingly apparent the principle of Genetic Entropy is the overriding foundational rule for all of biology, with no exceptions at all, and belief in 'truly' beneficial mutations is nothing more than wishful speculation on the materialist part which has no foundation in empirical science whatsoever.

Evolution vs. Genetic Entropy - video
http://www.metacafe.com/watch/4028086

The following article has a simple example of how Genetic Entropy plays out, even allowing that some mutations might truly be slightly beneficial in the molecular sense as far as molecular functionality is concerned:
Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information
Excerpt: Even if there were several possible pathways by which to construct a gain-of-FCT mutation, or several possible kinds of adaptive gain-of-FCT features, the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.
(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

The sort of loss-of-function examples seen in the Lenski's LTEE (Long Term Evolution Experiment) will never show that natural selection can increase high CSI. To understand why, imagine the following hypothetical situation.

Consider an imaginary order of insects, the Evolutionoptera. Let’s say there are 1 million species of Evolutionoptera, but ecologists find that the extinction rate among Evolutionoptera is 1000 species per millennium. The speciation rate (the rate at which new species arise) during the same period is 1 new species per 1000 years. At these rates, every thousand years 1000 species of Evolutionoptera will die off, while one new species will develop–a net loss of 999 species. If these processes continue, in 1,000,001 years there will be no species of Evolutionoptera left on earth.

http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html

More Darwinian Degradation: Much Ado about Yeast - Michael Behe - January 2012
Excerpt: "It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis. The authors did not analyze the genetic changes that occurred in the cells, but I strongly suspect that if and when they do, they'll discover that functioning genes or regulatory regions were broken or degraded. This would be just one more example of evolution by loss of pre-existing systems, at which we already knew that Darwinian processes excel. The apparently insurmountable problem for Darwinism is to build new systems."
http://www.evolutionnews.org/2012/01/more_darwinian055511.html
The foundational overriding principle, in life sciences, for explaining the sub-speciation of all species from any particular initial parent species that was designed is Genetic Entropy. Genetic Entropy, a rule which draws its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks, Abel), and the principle can be stated something like this:
"All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome."
Genetic Entropy also fits very well with the theological question that many children ask their teachers, 'Why would a loving God allow pathogenic viruses and bacteria to exist?'
What about parasites? - September 2010
Excerpt: these parasites must have been benign and beneficial in their original form. Perhaps some were independent and free-living, and others had beneficial symbiotic relationships with animals or humans. ,,,These once-harmless creatures degenerated, and became parasitic and harmful.
http://creation.com/what-about-parasites
The following shows that we can actually watch the 'final act' of Genetic Entropy, 'mutational meltdown', in the laboratory for small asexual populations (bacteria, yeast, etc.):
The Mutational Meltdown in Asexual Populations - Lynch
Excerpt: Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown,,,
http://www.oxfordjournals.org/our_journals/jhered/freepdf/84-339.pdf
These following articles refute Richard E. Lenski's 'supposed evolution' of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli from his 'Long Term Evolution Experiment' (LTEE) which has been going on since 1988:
Multiple Mutations Needed for E. Coli - Michael Behe
Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell.
http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/

Rose-Colored Glasses: Lenski, Citrate, and BioLogos - Michael Behe - November 13, 2012
Excerpt: Readers of my posts know that I'm a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,,
In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient -- that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism.

http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html

Innovation or Renovation? By Ann Gauger - Sept. 24, 2012
Excerpt: But how significant was this innovation (citrate; Lenski)? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions.
After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter.

http://www.biologicinstitute.org/post/32246480851/innovation-or-renovation?og=1

Michael Behe's Quarterly Review of Biology Paper Critiques Richard Lenski's E. Coli Evolution Experiments - December 2010
Excerpt: After reviewing the results of Lenski's research, Behe concludes that the observed adaptive mutations all entail either loss or modification--but not gain--of Functional Coding ElemenTs (FCTs)
http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html

Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information - September 2011
Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski's research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.
(Michael J. Behe, "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution'," Quarterly Review of Biology, Vol. 85(4) (December, 2010).)
http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html

Lenski's e-coli - Analysis of Genetic Entropy
Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.
http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria

Genetic Entropy Confirmed (in Lenski's e-coli) - June 2011
Excerpt: No increases in adaptation or fitness were observed, and no explanation was offered for how neo-Darwinism could overcome the downward trend in fitness.
http://crev.info/content/110605-genetic_entropy_confirmed

Mutations : when benefits level off - June 2011 - (Lenski's e-coli after 50,000 generations)
Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
http://www2.cnrs.fr/en/1867.htm?theme1=7

New Research on Epistatic Interactions Shows "Overwhelmingly Negative" Fitness Costs and Limits to Evolution - Casey Luskin June 8, 2011
Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn't run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
http://www.evolutionnews.org/2011/06/new_research_on_epistatic_inte047151.html
The preceding experiment was interesting, for they found, after 50,000 generations of e-coli which is equivalent to about 1,000,000 years of 'supposed' human evolution, only 5 'beneficial' mutations. Moreover, these 5 'beneficial' mutations were found to interfere with each other when they were combined in the ancestral population. Needless to say, this is far, far short of the functional complexity we find in life that neo-Darwinism is required to explain the origination of. Even more problematic for neo-Darwinism is when we realize that Michael Behe showed that the 'beneficial' mutations were actually loss or modification of function mutations. i.e. The individual 'beneficial' mutations were never shown to be in the process of building functional complexity at the molecular level in the first place!

Moreover, Lenski's work has also shown that 'convergent evolution' is impossible because his work has shown that evolution is 'historically contingent'. This following video and article make this point clear:

Lenski's Citrate E-Coli - Disproof of Convergent Evolution - Fazale Rana - video (the disproof of convergence starts at the 2:45 minute mark of the video)
http://www.metacafe.com/watch/4564682
The Long Term Evolution Experiment - Analysis
Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth.
http://www.scienceagainstevolution.org/v12i11f.htm
The loss of 'convergent evolution', as a argument for molecular sequence similarity in widely divergent species, is a major blow to neo-Darwinian story telling:
Implications of Genetic Convergent Evolution for Common Descent - Casey Luskin - Sept. 2010
Excerpt: When building evolutionary trees, evolutionists assume that functional genetic similarity is the result of inheritance from a common ancestor. Except for when it isn't. And when the data doesn't fit their assumptions, evolutionists explain it away as the result of "convergence." Using this methodology, one can explain virtually any dataset. Is there a way to falsify common descent, even in the face of convergent genetic similarity? If convergent genetic evolution is common, how does one know if their tree is based upon homologous sequences or convergent ones? Critics like me see the logic underlying evolutionary trees to be methodologically inconsistent, unpersuasive, and ultimately arbitrary.
http://www.evolutionnews.org/2010/09/implications_of_genetic_conver037841.html

Origin of Hemoglobins: A Repeated Problem for Biological Evolution - 2010
Excerpt: When analyzed from an evolutionary perspective, it appears as if the hemoglobins originated independently in jawless vertebrates and jawed vertebrates.,,, This result fits awkwardly within the evolutionary framework. It also contradicts the results of the Long-term Experimental Evolution (LTEE; Lenski) study, which demonstrated that microevolutionary biochemical changes are historically contingent.
http://www.reasons.org/origin-hemoglobins-repeated-problem-biological-evolution

Convergence: Evidence for a Single Creator - Fazale Rana
Excerpt: When critically assessed, the evolutionary paradigm is found to be woefully inadequate when accounting for all the facets of biological convergence. On the other hand, biological convergence is readily explained by an origins model that evokes a single Creator (reusing optimal designs).
http://www.reasons.org/convergence-evidence-single-creator

Frequent and widespread parallel evolution of protein sequences - 2008
Excerpt: To quantify the extent and type of homoplasy among evolving proteins, we used phylogenetic methodology to analyze 8 genome-scale data matrices from clades of different evolutionary depths that span the eukaryotic tree of life. We found that the frequency of homoplastic amino acid substitutions in eukaryotic proteins was more than 2-fold higher than expected under neutral models of protein evolution.
http://www.ncbi.nlm.nih.gov/pubmed/18583353

Adaptive molecular convergence - Molecular evolution versus molecular phylogenetics - 2010
Excerpt: Contrary to these expectations, in a recent study we showed that widespread convergent molecular evolution occurred at an unprecedented scale across key parts of mitochondrial proteins in snakes and a distantly related group of lizards (agamids).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881246/

Bernard d'Abrera on Butterfly Mimicry and the Faith of the Evolutionist - October 2011
Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe (science) that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible.
http://www.evolutionnews.org/2011/10/in_this_excerpt_from_the051571.html

Getting Crushed: Evolutionists Are Now Saying That Some Species Have a Reputation For “Doing Things Their Own Way” - Cornelius Hunter - 2012
Excerpt: This fundamental tenet of evolutionary thought—that evolution is a fact—is utterly at odds with the evidence. It is in spite of the evidence, not because of the evidence. This is because evolution is not about the evidence. Evolution is not about an objective analysis of the biology. You see, evolution is not science, it is dogma.
http://darwins-god.blogspot.com/2012/04/getting-crushed-evolutionists-are-now.html?spref=fb
Here's a figure showing bats and dolphins group together on the same tree based on Prestin sequence comparisons.
http://sphotos.xx.fbcdn.net/hphotos-ash3/580955_215152708593734_182588468516825_355811_30197372_n.jpg

Lenski's work also conforms to the extreme limit found for just two 'coordinated' mutations conferring any 'evolutionary benefit';

Michael Behe on the most recent Richard Lenski “evolvability” paper - April 2011
http://www.uncommondescent.com/irreducible-complexity/michael-behe-on-the-most-recent-richard-lenski-%E2%80%9Cevolvability%E2%80%9D-paper/
More from Lenski's Lab, Still Spinning Furiously - Michael Behe - January, 2012
Excerpt: So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.
http://www.evolutionnews.org/2012/01/more_from_lensk055751.html
Even more crushing evidence can be gleaned from Lenski's long term evolution experiment on E-coli. Upon even closer inspection, it seems Lenski's 'cuddled' E. coli are actually headed for genetic meltdown instead of evolving into something, anything, better.
New Work by Richard Lenski:
Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal.
http://www.evolutionnews.org/2009/10/new_work_by_richard_lenski.html

Lenski's Long-Term Evolution Experiment: 25 Years and Counting - Michael Behe - November 21, 2013
Excerpt: Twenty-five years later the culture -- a cumulative total of trillions of cells -- has been going for an astounding 58,000 generations and counting. As the article points out, that's equivalent to a million years in the lineage of a large animal such as humans.,,,
,,,its mutation rate has increased some 150-fold. As Lenski's work showed, that's due to a mutation (dubbed mutT) that degrades an enzyme that rids the cell of damaged guanine nucleotides, preventing their misincorporation into DNA. Loss of function of a second enzyme (MutY), which removes mispaired bases from DNA, also increases the mutation rate when it occurs by itself. However, when the two mutations, mutT and mutY, occur together, the mutation rate decreases by half of what it is in the presence of mutT alone -- that is, it is 75-fold greater than the unmutated case.
Lenski is an optimistic man, and always accentuates the positive. In the paper on mutT and mutY, the stress is on how the bacterium has improved with the second mutation. Heavily unemphasized is the ominous fact that one loss of function mutation is "improved" by another loss of function mutation -- by degrading a second gene. Anyone who is interested in long-term evolution should see this as a baleful portent for any theory of evolution that relies exclusively on blind, undirected processes.

http://www.evolutionnews.org/2013/11/richard_lenskis079401.html
Sometimes a materialist will say, "gene duplication is the real engine of evolution" which generates the new functional information in molecular biology. Yet they simply don't have any evidence to support that assertion:

Gene Duplication Quotes and Papers
https://docs.google.com/document/d/1u-mn_eUVxx5aSv_iz6xkRXbqJri_ZxJLY2Q9Hx02-X4/edit?hl=en_US
Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
"Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use."
http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge.html

Again I would like to emphasize, I’m not arguing Darwinism cannot make complex functional systems, the data on malaria, and the other examples, are a observation that it does not. In science observation beats theory all the time. So Professor (Richard) Dawkins can speculate about what he thinks Darwinian processes could do, but in nature Darwinian processes have not been shown to do anything in particular.
Michael Behe - 46 minute mark of video lecture on 'The Edge of Evolution' for C-SPAN
http://www.uncommondescent.com/intelligent-design/michael-behe-lecture-recommend/comment-page-1/#comment-361037

Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution” - Michael J. Behe - December 2010
Excerpt: In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.
http://www.journals.uchicago.edu/doi/abs/10.1086/656902

A Critique of Douglas Theobald’s - “29 Evidences for Macroevolution”
Excerpt: "The study of bacteria has been profoundly at the center of studies of mutations. This is because they reproduce rapidly, producing large populations and large numbers of mutants. They are also easily maintained and their environments are easily manipulated in the laboratory. Despite all their advantages, never has there arisen in a colony of bacteria a bacterium with a primitive nucleus. Never has a bacterium in a colony of bacteria been observed to make a simple multicellular formation. Although hundreds of strains and varieties of Escherichia coli have been formed, it is still Escherichia coli and easily identifiable as such." (Lester and Bohlin, 88.)
http://www.trueorigin.org/theobald1f.asp

Mike Behe on a new journal paper admitting that Darwinian evolution 'can’t do' complex systems - August 2011
Excerpt: 'I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. - Michael Behe
http://www.uncommondescent.com/evolution/mike-behe-on-a-new-journal-paper-admitting-that-darwinian-evolution-can%E2%80%99t-do-really-complex-systems/
The following experiment recently confirmed the severe limit for evolution found by Dr Behe:
Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010
Excerpt: When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2/BIO-C.2010.2

Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
http://www.discovery.org/a/9951

Epistasis between Beneficial Mutations - July 2011
Excerpt: We found that epistatic interactions between beneficial mutations were all antagonistic—the effects of the double mutations were less than the sums of the effects of their component single mutations. We found a number of cases of decompensatory interactions, an extreme form of antagonistic epistasis in which the second mutation is actually deleterious in the presence of the first. In the vast majority of cases, recombination uniting two beneficial mutations into the same genome would not be favored by selection, as the recombinant could not outcompete its constituent single mutations.
http://www.uncommondescent.com/epigenetics/darwins-beneficial-mutations-do-not-benefit-each-other/
Behe and Snoke go even further, addressing the severe problems with the Gene Duplication scenario in this following study:
Simulating evolution by gene duplication of protein features that require multiple amino acid residues: Michael J. Behe and David W. Snoke
Excerpt: The fact that very large population sizes—10^9 or greater—are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2286568
Interestingly Fred Hoyle arrived at the same conclusion, of a 2 amino acid limit, years earlier from a 'mathematical' angle:
http://www.uncommondescent.com/intelligent-design/uh-oh-is-he-going-to-get-gould-ed/comment-page-3/#comment-367658
The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations - Douglas D. Axe* - December 2010
quote of note: ,, the most significant implication comes not from how the two cases contrast but rather how they cohere—both showing severe limitations to complex adaptation. To appreciate this, consider the tremendous number of cells needed to achieve adaptations of such limited complexity. As a basis for calculation, we have assumed a bacterial population that maintained an effective size of 10^9 individuals through 10^3 generations each year for billions of years. This amounts to well over a billion trillion (10^21) opportunities (in the form of individuals whose lines were not destined to expire imminently) for evolutionary experimentation. Yet what these enormous resources are expected to have accomplished, in terms of combined base changes, can be counted on the fingers.
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.4/BIO-C.2010.4

The GS (genetic selection) Principle – David L. Abel – 2009
Excerpt: No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”
http://www.bioscience.org/2009/v14/af/3426/fulltext.htm
This following paper clearly reveals that there is a 'cost' to duplicate genes that further precludes the scenario from being plausible:
Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model
Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/content/vp471464014664w8/
This recent paper also found the gene duplication scenario to be highly implausible:
The Extinction Dynamics of Bacterial Pseudogenes - Kuo and Ochman - August 2010
Excerpt: "Because all bacterial groups, as well as those Archaea examined, display a mutational pattern that is biased towards deletions and their haploid genomes would be more susceptible to dominant-negative effects that pseudogenes might impart, it is likely that the process of adaptive removal of pseudogenes is pervasive among prokaryotes."
http://www.evolutionnews.org/2010/08/on_reductive_evolution_and_the037581.html
Many times evolutionists are very deceptive in saying that evolutionary processes can generate functional information, as with the duplicate gene scenario, when in fact no one has ever experimentally demonstrated a gain in functional information, above a parent species, that would violate the principle of genetic entropy. These following articles reveal some of the many elaborate ploys evolutionists have used in the past to try to deceive, yes deceive!, the public into thinking evolutionary processes can easily generate functional information:

Assessing the NCSE’s Citation Bluffs on the Evolution of New Genetic Information - Feb. 2010
http://www.evolutionnews.org/2010/02/assessing_the_ncses_citation_b.html

Casey Luskin, in response to a comment from Nick Matzke claiming that there are many examples of neo-Darwinian processes creating functional information in life, points out the 'scientifically' vacuous nature of the vast majority of neo-Darwinian claims for the origin of new biological information here:
Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information - September 2011
Excerpt: many papers which Nick (Matzke) would probably claim show the “origin of new genetic information” invoked natural selection, but then:
did not identify a stepwise mutational pathway,
did not identify what advantages might be gained at each step
did not calculate the plausibility of this pathway evolving under known population sizes, mutation rates, and other relevant probabilistic resources, and in many cases
DID NOT EVEN KNOW THE FUNCTION OF THE GENE, AND THUS HAD NO IDEA WHAT FUNCTION WAS BEING SELECTED FOR
Is it persuasive to invoke natural selection as the cause of new genetic information when you don’t even know what function is being selected? This is why I said that in many cases, natural selection is used as a “magic wand.” It’s just asserted, even though no one really knows what was going on.

http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html#comment-11290411
How to Play the Gene Evolution Game - Casey Luskin - Feb. 2010
http://www.evolutionnews.org/2010/02/how_to_play_the_gene_evolution.html

The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information - Casey Luskin - March 2010
http://www.discovery.org/a/14251

To answer our fourth question (What evidence is found for the appearance of all species of life on earth, and is man the last species to appear on earth?) we come to the evidence found for the amazing variety of complex life on earth.
Explaining Innovation By Ann Gauger - June 13, 2013
Excerpt: It is widely believed that the first cells were much simpler than cells today. Estimates for the size of the smallest possible genome range from 250 to 400 genes. This hypothetical minimal genome would have included the genes necessary for cell division, replication, transcription, and translation, but not the genes necessary for making amino acids, nucleotides, vitamins, and many other metabolites, because it is also widely assumed that at least in the beginning, cells would have acquired these metabolites from the environment. So even if granted the existence of a first minimal cell, the challenge remains to explain how subsequent cells might have evolved the ability to make things like amino acids and vitamins for themselves, as nutrients disappeared. In a recently published open access paper called, “Explaining Metabolic Innovation: Neo-Darwinism versus Design,” Doug Axe and I reviewed how well neo-Darwinism has met this challenge.,,,
,,,Summary: What’s needed to explain metabolic innovation is foresight, investment, reapplication of old concepts as well as development of new ones, and the purposeful top-down organization of parts to serve the function of the whole. Not the kind of thing an unintelligent process can deliver, is it?

http://www.biologicinstitute.org/post/52887834874/explaining-innovation
There simply isn't any evidence in the fossil record indicating that single cells ever formed anything other than 'simple aggregates':
"We go from single cell protozoa. which would be ameoba and things like that. Then you get into some that are a little bit bigger, still single cell, and then you get aggregates, they're still individual cells that aggregate together. They don't seem to have much in the way of cooperation,,, but when you really talk about a functioning organism, that has more than just one type of cell, you are talking about a sponge and you can have hundreds, thousands, tens of thousands of cells. So we don't really have organisms that function with say two different types of cells, but there is only five total. We don't have anything like that."
- Dr. Raymond G. Bohlin - quote taken from 31:00 minute mark of this following video
Natural Limits to Biological Change 2/2 - video
http://www.youtube.com/watch?v=vo3OKSGeFRQ

From one cell to many: How did multicellularity evolve? January 25, 2014
Excerpt: Indeed, no matter how it is defined, scientists agree that multicellularity has occurred multiple times across many clades. Defined in the loosest sense, as an aggregation of cells, multicellularity has evolved in at least 25 lineages. However, even when defined more strictly -- requiring that cells be connected, communicate, and cooperate in some fashion or another -- it has still notably evolved once in animals, three times in fungi, six times in algae, and multiple times in bacteria.,,,
http://www.sciencedaily.com/releases/2014/01/140125172414.htm
So evolution now did it 25 times somehow?
That Conference On The Evolution of Multicellularity Revealed The Usual Problems - Cornelius Hunter - December 25, 2013
Excerpt: "The emergence of multicellular animals or metazoans from their single-celled ancestors is one of the most important evolutionary transitions in the history of life. However, little is known about how this transition took place.",,,
"That is nowhere more true than with the miracle of multicellularity which, if evolution is true, must have independently evolved more than, err, twenty-five times."

http://darwins-god.blogspot.com/2013/12/that-conference-on-evolution-of.html

Challenging Fossil of a Little Fish
Excerpt: “I think this is a major mystery in paleontology,” said Chen. “Before the Cambrian, we should see a number of steps: differentiation of cells, differentiation of tissue, of dorsal and ventral, right and left. But we don’t have strong evidence for any of these.” Taiwanese biologist Li was also direct: “No evolution theory can explain these kinds of phenomena.”
http://www.fredheeren.com/boston.htm
Nor does the experimental evidence suggest that such a transition from single cell aggregates to multicellular organisms is possible. To highlight the monumental problem that Darwinian processes face in going from a single cell to a multicellular creature,,,
"The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable."
Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")
And yet, Dr. Behe, on the important Table 7.1 on page 143 of Edge Of Evolution, finds that a typical cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites in a multicellular creature is,,,
Largest-Ever Map of Plant Protein Interactions - July 2011
Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker.
http://www.sciencedaily.com/releases/2011/07/110728144936.htm
So taking into account that they only covered 2%, of the full protein-protein "interactome", then that gives us a number, for different protein-protein interactions, of 310,000. Thus, from my very rough 'back of the envelope' calculations, we find that this is at least 30 times higher than Dr. Behe's estimate of 10,000 different protein-protein binding sites for a typical single cell (Page 143; Edge of Evolution; Behe). Therefore, at least at first glance from my rough calculations, it certainly appears to be a impossible step that evolution cannot make, by purely unguided processes, to go from a single cell to a multi-cellular creature.

Further experimental work agrees with this conclusion:
More Darwinian Degradation - M. Behe - January 2012
Excerpt: Recently a paper appeared by Ratcliff et al. (2012) entitled “Experimental evolution of mulitcellularity” and received a fair amount of press attention, including a story in the New York Times.,,, It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis.
http://behe.uncommondescent.com/2012/01/more-darwinian-degradation/
Indeed the ‘social networks’ of bacteria are very sophisticated and certainly defy any coherent explanation from the simplistic reductive (i.e. bottom up) materialistic narrative of neo-Darwinism:
Learning from Bacteria about Social Networks - video
Description: Bacteria do not store genetically all the information required to respond efficiently to all possible environmental conditions. Instead, to solve new encountered problems (challenges) posed by the environment, they first assess the problem via collective sensing, then recall stored information of past experience and finally execute distributed information processing of the 109-12 bacteria in the colony,,, I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers.
http://www.youtube.com/watch?v=yJpi8SnFXHs
In fact Dr. Stephen Meyer's, who wrote "Signature In The Cell", next book is going to be on the sheer impossibility of neo-Darwinian processes to explain the origination of 'Body-Plan information' from single cells to multicellular organisms in the Cambrian Explosion:

Here is a sneak peek at his forthcoming book:

Dr. Stephen Meyer: Why Are We Still Debating Darwin? pt. 2 - podcast
http://intelligentdesign.podomatic.com/entry/2012-05-23T13_26_22-07_00
The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer - 2004
Excerpt: "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion."
http://eyedesignbook.com/ch6/eyech6-append-d.html
Stephen Meyer - Functional Proteins And Information For Body Plans - video
http://www.metacafe.com/watch/4050681

Moreover there another whole level of information on a cell's surface that is scarcely understood at all, much less understood to a DNA information theoretic basis:

Glycan Carbohydrate Molecules - A Whole New Level Of Scarcely Understood Information on The Surface of Cells
https://docs.google.com/document/d/1bO5txsOPde3BEPjOqcUNjL0mllfEc894LkDY5YFpJCA/edit

Of note:
New Way to Look at Dawn of Life: Focus Shifts from 'Hardware' to 'Software' - Dec. 12, 2012
Excerpt: By addressing the causal role of information directly, many of the baffling qualities of life are explained."
The authors expect that, by re-shaping the conceptual landscape in this fundamental way, not just the origin of life, but other major transitions will be explained, for example, the leap from single cells to multi-cellularity.

http://www.sciencedaily.com/releases/2012/12/121212205918.htm
This following article from Dr. Jonathan Wells is interesting for, as well as answering why things go in a general 'evolutionary' order, from simpler life forms to more complex life forms, this following article gets pretty close to answering my question as to when God forms a human soul.
Why Does the History of Life Give the Appearance of Evolution? - Jonathan Wells - February 21, 2013
Excerpt: Fossil evidence suggests that life on earth originated about three and a half billion years ago, starting with prokaryotes (single-celled organisms without nuclei, such as bacteria). Much later came eukaryotes (cells with nuclei), which included algae and single-celled animals (protozoa). Multicellular marine animals appeared long after that. Then came land plants, amphibians, reptiles, mammals, primates, and finally humans. Not only did living things appear in a certain order, but in some cases they also had features intermediate between organisms that preceded them and those that followed them. Kenneth R. Miller challenges critics of Darwinism to explain why we find "one organism after another in places and in sequences... that clearly give the appearance of evolution."

The answer is found in various religious traditions, especially Christianity. "Far from denying life's progression, tradition provides a reason for it," wrote Huston Smith in 1976. "Earth mirrors heaven. But mirrors, as we have noted, invert. The consequence here is that that which is first in the ontological order appears last in the temporal order." Smith explained: "In the celestial realm the species are never absent; their essential forms or archetypes reside there from an endless beginning. As earth ripens to receive them, each in its turn drops to the terrestrial plane." But "first a viable habitat must be devised, hence the inorganic universe is matured to a point where life can be sustained. And when living beings do arrive, they do so in a vaguely ascending order that passes from relatively undifferentiated organisms... to ones that are more complex." Thus "man, who is first in the order of worth on the terrestrial plane, will be last in the order of his appearance."

http://www.evolutionnews.org/2013/02/why_does_the_hi069451.html
The reason why I had/have a hard time figuring out specifically 'when' God creates a human soul is because sequential, temporal, time, as we understand it here on earth, loses any point of reference in the higher, eternal, dimensions:
The 'Top Down' Theistic Structure Of The Universe and Of The Human Body
Excerpt: “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass.”
Richard Swenson – More Than Meets The Eye, Chpt. 12
https://docs.google.com/document/d/1NhA4hiQnYiyCTiqG5GelcSJjy69e1DT3OHpqlx6rACs/edit

Psalm 139:16
You saw me before I was born. Every day of my life was recorded in your book. Every moment was laid out before a single day had passed.
The following site goes into the Cambrian Explosion thru the Refutation Of Human Evolution
http://lettherebelight-77.blogspot.com/2010/08/corrected-link.html

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