Darwin’s bluff

Many years ago, I learned about a game called The Fox and the Hound. It requires a pack of cards and a chessboard. The following rules are approximate from what I remember. The hound moves counter-clockwise in a square path circling around outside the four central squares. The fox moves in a random pattern determined by the suit that's drawn from the deck. Spades=North, Clubs=South, Hearts=West, Diamonds=East. The Fox starts in most northwest of the four center squares; the hound starts in the southeast corner of his path. If the fox and hound ever occupy the same square, the hound catches the fox. Now deal the fox five cards. The fox moves one square, then the (robot) hound moves a square. If the fox doesn't get caught after the fifth card, the fox keeps the "set" and gets dealt five more cards. If the fox gets caught, you discard the last set of five cards and start from the beginning. Eventually, the fox can go through an entire deck without being caught by the hound. It has learned or evolved to survive by incorporating information from its environment. There are numerous reasons why this is not a good model for evolution . . . but information is generated by the interaction between the rules and the foxes environment. -Q Querius

Eric Anderson #35 We agree cent percent. Reproduction provides more opportunities for variation. In this sense it seems to help evolution. But it is a double-edged sword. If there are fragile processes where evolutionist small variations may cause big catastrophes these are indeed the embryo developments, where all is critical and must be fine tuned. So, evolutionists who so much trust reproduction in their theory (as reproduction could save Darwinism from bankrupt and it cannot) are like men who horse a crocodile to get across a river. niwrad

Lincoln Phipps: I completely disagree with you. That artificial miniprotein folds, but it has no biochemical function, as far as I know. If you know differently, please explain. Moreover, if you hypothesize that it could be naturally selected, please explain in what way it could confer a reproductive advantage to some living being. Until then, I stick to what I have already said. gpuccio

niwrad @31: Yeah, it is hard to get people to carefully think through the issue of reproduction. Most people have heard so often throughout their lives, particularly those supporting the evolutionary storyline, about "differential reproduction" being a key to evolution that they just reflexively accept it as fact. The only way to break through that assumption is to try and get people to define -- not vaguely and generally, but to really lay out with precision -- what it is exactly that they think reproduction brings to the table. When we take time to do that, we realize the only thing it brings to the table is more opportunities for variation, meaning that it bumps up the probabilistic resources over time versus a non-reproducing organism that were to live for the same amount of time. Is bumping up the probabilistic resources important for the evolutionary story? Sure. So in that sense reproduction is critical to evolution. But we need to be very clear that it is not critical in the sense of either (i) either bringing something fundamentally new to the table or (ii) significantly changing the ultimate calculation. Eric Anderson

gpuccio, you cannot know that to say that it is "not enough (...) to be naturally selected". Firstly it has function and it persists. It is derived from a bigger naturally occurring protein but as it is smaller then this dramatically reduces the problem landscape for "random" processes by many orders of scale. In fact if this was a crypto problem then such a discovery of an intermediate solution would mean that cryto would be deemed to be crippled. What is in effect crippled is the ID claim that the difficulty is many orders as that's based on the size of modern proteins and is ignorant of possible pathways that reduce the big O time complexity. Trp-cage means that we can consider that ID argument to be unreasonable. It is early days but there is no reason why we would not see others and in fact there should be a reasonable pathway from small to larger proteins. That these small proteins may not exist today would be answered by examining the selective pressures on proteins for the past 3.5 billion years. That's going to take a while. Lincoln Phipps

Box (#21): You are absolutely right. Trp-cage is definitely a designed miniprotein. Its only function, as far as I know, is to be used as a model for protein folding studies. Not enough, I am afraid, to be naturally selected :) gpuccio

TSZ ilk are using animal camouflage as evidence for darwinian evolution! They are quite the bunch of cowardly equivocators... Joe

Eric Anderson #27

And, actually, reproduction isn’t even fundamental.

Exactly. Notice that at TSZ Lizzie Liddle's main objection to my poker analogy is it would miss reproduction. Reproduction or non reproduction the fact is that between small variations and large hierarchical functional bio-systems there are countless abysses of evolutionary impossibility. That is what my analogy shows with the abysmal differences between the dealt molecules of cards and complete playable poker hands. N.B. For Lizzie Liddle. Your defense of Darwinism is brave and pathetic. Unfortunately, when the defense of a theory by means of a dialectically gifted person like you is ineffective that means the theory is fully bogus. Differently, when a theory is sound as the ID one, also for a dialectically bare person like me it is easy and fun to defend it. niwrad

Eric Anderson @ 27 mentioned

The only reason reproduction is necessary is because organisms don’t live forever.

But part of the original amoeba is still alive today! And what does it have to say for itself after 3 billion years of life? ;-) -Q Querius

Joe, that sums up the basics of Darwinism pretty well. Dang. Why didn't you tell me sooner? I could have saved myself 600+ pages of wading through The Origin! :) Eric Anderson

Accumulations of stuff happening: Somethings unspecified happened some point in time. Somethings didn't work and were eliminated. Somethings were eliminated enmass. Somethings worked, accumulated and here we are Joe

Joe: And, actually, reproduction isn't even fundamental. The only reason reproduction is necessary is because organisms don't live forever. To see what I mean, as an interesting thought experiment consider a single-celled organism that were to live for 100M years. What kinds of changes would we expect it to experience during its lifetime? How would we expect it to change? Would we expect it to turn into a different kind of creature over that time period, and if not, why not? Once we have taken time to thoughtfully consider the above questions, we realize that the only thing reproduction does is provide additional opportunities for variation (due to copying mistakes, swaps, etc.). But reproduction doesn't fundamentally alter anything about the evolutionary storyline: (mostly unspecified) random changes occur in an organism, and over time they add up to wonderful new biological features, including whole new body plans and different organisms. No, the real thing that is fundamental to evolutionary theory is: Stuff Happens. Eric Anderson

Lizzie sez that the fundamentals of evolutionism are reproduction and variation. Those are the same fundamentals as Intelligent Design Evolution and Baraminology. Joe

Mr. Phipps, Stepping past your gross oversimplification of the problem that the rarity of functional proteins presents to neo-Darwinian conjectures for a moment, I noticed that you were trying to 'bridge a gap', find stepping stones if you will, to fill in the astronomical chasm between functional islands in sequence space for functional proteins, to say the chasm is not unbridgeable, but that is only one part of the problem. Even if your conjecture were true, which I don't buy for a moment, but even if your conjecture were true for stepping stones to fully functional proteins, there is another astronomical chasm that you seem to have neglected to take into consideration. That is the chasm of coordinating all the proteins into a functional whole, a functioning self-replicating organism: 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/ 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) “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) 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 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 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 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/ bornagain77

Little Lizzie Liddle has taken excxeption to thois OP and spews:

I suggest that a first step for ID supporters is to learn what Darwinian evolution actually is – build some proper models, vary some parameters – and feel the power.

LoL! The sad part is that Lizzie doesn't even know what darwinian evolution actually is. If she did she would know that it doesn't have any power at all. Joe

The ID claim is that there is this gap that can’t be bridged through the random walk and natural selection. But we do know of small natural proteins like Trp-cage (20 residues) and also man-made ones like CLN025 (10 residues). So that gap really isn’t there except as our ignorance. Is there a full suite of functional miniproteins ? The ID stance is no whereas the honest stance is that we do not know for sure but there are some.

My apologies, Phipps. I did indeed misunderstand you. It's worse than I thought. You're claiming that if a suite of miniproteins comes together like popcorn on a string - Shazam! - we've got ourselves a functional protein. Aside from your vivid imagination, is there a possible pathway to which you can point us? Maybe reverse engineer an existing protein to see how many Trp-cages result. "whereas the honest stance is that we do not know" Interesting how Darwinists conveniently appeal to their own ignorance except when it comes to their metaphysical certainty of methodological naturalism and the falsehood of ID. RexTugwell

Lincoln Phipps you claim:

All the life on Earth is also the result of 3.5 billion years of evolution. It is unreasonable to think that the proteins we see today existed with LUCA and it is unreasonable to think that what polypeptides were in LUCA (as proteins) are here now.

That's what you believe but we can never seem to catch evolution in the act of evolving anything,,,

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 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 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/

So I find your belief in evolution unreasonable! bornagain77

LP #19 :But we do know of small natural proteins like Trp-cage (20 residues) and also man-made ones like CLN025 (10 residues).

Aren't they both (CLN025 AND Trp-cage) synthetic peptides? If so, is there a biological function? Box

PaV,

Surely, one of these trillions upon trillions of organisms, and millions upon millions of species would have turned up the residues.

according to GOLD - http://www.genomesonline.org/cgi-bin/GOLD/index.cgi?page_requested=Complete+Genome+Projects there are, Archaeal: 277 Bacterial: 11777 Eukaryal: 312 species sequenced. So a tiny fraction of life. All the life on Earth is also the result of 3.5 billion years of evolution. It is unreasonable to think that the proteins we see today existed with LUCA and it is unreasonable to think that what polypeptides were in LUCA (as proteins) are here now. Lincoln Phipps

RexTugwell,

If a suite of functional polypeptides of say 10 residues exists then the probability of natural occurrence increases dramatically i.e. it doesn’t need a God to magic up the sequences. That humans have made at least one such miniprotein shows that the claims about the 300 residues is a bluff.

Do I understand you correctly, Lincoln Phipps? Are you saying that since humans made 10 residue proteins therefore there’s a known pathway to functional 300 residue proteins? How about 30,000 residues in the Titan protein? Still a bluff?

as you can see above, no you did not understand me correctly. I said "If a suite ..." I did not say that there was. The ID claim is that there is this gap that can't be bridged through the random walk and natural selection. But we do know of small natural proteins like Trp-cage (20 residues) and also man-made ones like CLN025 (10 residues). So that gap really isn't there except as our ignorance. Is there a full suite of functional miniproteins ? The ID stance is no whereas the honest stance is that we do not know for sure but there are some. As for titin it isn't really 30,000 residues but many copies of the same protein domains. That's not going to help you very much. http://www.lincolnphipps.org/sound-bites/improbability-of-large-proteins/ Again it is ID that is bluffing and it's been called out with protein. Lincoln Phipps

Lincoln Ph:

The problem bornagain77 is that no one knows if there is a gap in functionality from a few residues to the many residue proteins we see in life today.

I suspect we do know this. That is, if you have to ask the question of whether or not these residues do, in fact, exist, then very likely the don't exist. Why? The sheer probabilities involved. How many species are there that exist? How many examinations of said species have been conducted? And we run into certain protein sequences and not others. Surely, one of these trillions upon trillions of organisms, and millions upon millions of species would have turned up the residues. Your argument, Lincoln, amounts to the very argument that Darwin made regarding the fossil record: it's imperfect; we haven't STUDIED IT ENOUGH! And, now, 150 years later, with fossils being investigated from all over the earth, the same "imperfection" still exists. The Cambrian Explosion is still a problem. Why should any of this be different for the "proteinome"? PaV

LP:

why do you restrict your god from choosing the fundamental parameters of this universe so that life could form spontaneously ?

There isn't any evidence that life could form spontaneously. And there isn't any evidence that blind and undirected chemical processes can construct a protein from scratch. Joe

Mr. Phipp's as to "it is more useful to the other side" Buddy, this ain't one side vs. the other side. This is about getting to the truth! and even if we bend over backwards and give Darwinian processes ever benefit of a doubt, with the most optimistic number available for rarity of functional proteins (1 in 10^12), this is the absurd scenario we end up with: 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 Moreover, even that 1 in 10^12 man-made protein failed to be incorporated into life, 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 footnote as to the denialism Darwinists employ when faced with these facts: 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 bornagain77

bornagain77, no, Axe's work is considered to be of limited use here. As for your use of Yockey, he too seems to just want the mathematics to fail and not discover how-it-happened. The Dryden, Thomson, White paper isn't what you think it is as it is showing how the complexity is reduced (it is more useful to the other side). Sure in absence of a comprehensive theory on how proteins fold you could cherry-pick a number out of context but that gap in our knowledge remains. Now a problem for you: why do you restrict your god from choosing the fundamental parameters of this universe so that life could form spontaneously ? In the end that is your story isn't it ? You are actually making a claim as to how your god made life i.e. you are saying that god made life some way else and it was not through setting up chemicals so that proteins formed spontaneously through a natural process. Are there any other things you think your god can't do ? Lincoln Phipps

If a suite of functional polypeptides of say 10 residues exists then the probability of natural occurrence increases dramatically i.e. it doesn’t need a God to magic up the sequences. That humans have made at least one such miniprotein shows that the claims about the 300 residues is a bluff.

Do I understand you correctly, Lincoln Phipps? Are you saying that since humans made 10 residue proteins therefore there's a known pathway to functional 300 residue proteins? How about 30,000 residues in the Titan protein? Still a bluff? RexTugwell

Lincoln Phipps, actually the work of Dr. Axe focused on the rarity of protein domain folds. Which, as far as I know, is the smallest unit of 'supposedly' (neglecting the princess and the pea paradox) selectable functionality in a given protein structure. Domains have limits on size http://en.wikipedia.org/wiki/Protein_domain#Domains_have_limits_on_size Perhaps you would like to take the issue up with Dr. Axe or any number of other scientists who have worked in this area? 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 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 bornagain77

This is a discussion of the science of protein origin. Why bring God or religion into it. Someone above was talking about different fallacies of reasoning. Sounds like a desperate measure to me. jerry

Thanks Barry at #8. You are right, really “Sometimes ‘nothing’ is a real cool hand.” In fact Darwin's bluff has deceived a lot of people for 150+ years (not all people though). The power of bluff! But bluff is not eternal (only Truth is such). The ID movement has called Darwin's bluff. Its time is over. niwrad

Again the argument comes down to origin of a new functional protein. Actually to the origin of thousands of functional proteins. If Durston and Axe are correct or even close to correct there is not enough universes in the multiverse for one let alone the thousand of proteins to arise. If proteins have arisen by natural means and this means Axe and Durston are incorrect, the evidence will be in the various genomes of species in the world. Why, because there should be forensic evidence in the genomes for this process in progress. It doesn't happen quickly but over thousands or millions of generations of a species and it should leave a trail. Remember these sequences are not discarded because they are not selected. That is the essential point of genes forming by natural processes. They must build slowly till the sequence can produce a functional protein. It will then be selected. For example, What separates species A from species B (both are assumed to have a recent common ancestor) is that A has a gene that produces a protein that is different from species B which does not have this gene in completed form. But species B should have some of the genomic elements similar to the gene in species A but this sequence in species B did not end up as a gene that when transcribed provides a functional protein as it did in species A. If no such sequence exists, then the gene in species A did not arise by natural means. This would represent proof for either the Darwinian hypothesis or the ID hypothesis depending on what is found. In other words every gene producing a functional protein must have incomplete genomic sequence in other similar organisms. jerry

I see bornagain77 hasn't understood the problem. Using the trick of copy+pasting the probability of an arbitrary residue length they then assume that means whatever god or supernature they are selling is true. If it's a Muslim then that usually means Allah, if it's a Fundamental Christian then that means God and so on through thousands of religions. With ID then bets are off as ID can be anything from a cargo-cult-science veneer over classical creationism or it can be some atheistic interpretation. Not all Christians though reject evolution. European Catholics, Protestants and Anglicans seem happy with the science of Evolution. The problem bornagain77 is that no one knows if there is a gap in functionality from a few residues to the many residue proteins we see in life today. If a suite of functional polypeptides of say 10 residues exists then the probability of natural occurrence increases dramatically i.e. it doesn't need a God to magic up the sequences. That humans have made at least one such miniprotein shows that the claims about the 300 residues is a bluff. Lincoln Phipps

Great post niwrad. So the Darwinian hand is "nothing." Yet Darwinians, like our friend Lincoln, cling to it tenaciously. I guess they agree with Luke (from one of the best movies of all time, Cool Hand Luke): "Sometimes 'nothing' is a real cool hand." :-) Barry Arrington

A few notes of related interest:, Considering nobody has ever seen a single gene, or even a single novel protein domain, arise by purely gradual evolutionary processes,,

"Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way. - Doug Axe PhD. Nothing In Molecular Biology Is Gradual - Doug Axe PhD. http://www.metacafe.com/watch/5347797/

,,,It is interesting to see the numbers that scientists get when they try to figure out what it would take for evolutionary processes produce a protein domain:

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 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 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 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 "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. https://uncommondescent.com/biophysics/kirk-durston-a-common-either-or-mistake-both-darwinists-and-id-theorists-make/#comment-466489 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/

But finding a functional protein is not the worse job that Darwinian processes have failed to give a coherent explanation for. The worse job that Darwinian processes have failed to give a coherent explanation for is how do all these trillions upon trillions of proteins know how to cohere their actions into a 'oneness'?

HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling... and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells,,,, http://www.netfuture.org/2012/May1012_184.html#2 ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681

bornagain77

Natural select is truly a tautology and worthless as a scientific concept. Jeff M

@Lincoln Phipps #1

But we humans do not know the relative strengths of all combinations of residues from small sized polypeptides to any lengths. We probably will never know this for many years yet and at best all we would do is know the probability of what is functional.

That lack of knowledge doesn't seem to have stopped neo-Darwinians from asserting that heritable alternations of DNA are "random", aimless, independent of future fitness. Without knowing the transition probabilities in the combinatorial space and distribution of fitness in that space (and no one knows either since even the transition probabilities in the space of all configurations requires at least a quantum mechanical treatment of large DNA molecules, or likely of the entire biochemical network of a cell, any of which is far beyond the present computational technology), any assertions on the nature and origin of the observed DNA alternations, random/aimless or intelligently guided, are equally a bluff. Hence, in the claimed neo-Darwinian mechanism "random mutation" for the origin of evolutionary novelty, the attribute "random" (or aimless) of the observed mutations is purely a gratuitous, parasitic ideological/theological add on, without basis in scientific facts. nightlight

Earth to Lincoln Phipps- There isn't any valid hypotheses wrt unguided evolution. ASlso there isn't any "evolution vs ID"- perhaps YOU should learn books as it is all there... Joe

niwad, all that Darwin has said is what he has had published. You should learn to read books as it is all there. The OP's analogy is bust. Live with that and move on. Lincoln Phipps

#1 Lincoln Phipps' bluff = Darwin's bluff niwrad

Argument from false analogy and ignorance as the relative strengths of poker hands are predefined and known. But we humans do not know the relative strengths of all combinations of residues from small sized polypeptides to any lengths. We probably will never know this for many years yet and at best all we would do is know the probability of what is functional. Neither do ID supporters know this and if they don't know this then they certainly can't start claiming to know that functionality is absent for smaller numbers of residues unless they brute-force work this out (or use pseudo-random trials). But given that mini-proteins of a small number of residues do have functionality (and fold) then there doesn't seem to be a irreducible gap. That a certain set of proteins are found in modern life does not follow that this set was in place since the dawn of life of Earth. As smaller mini-proteins have functionality (i.e. it still is a winning poker hand) then the opening argument seems to be defeated. For evolution to stay valid the hypothesis is that there will be a continuum of functional proteins from small numbers of residues through to modern life. That humans have found some just means Evolution verses ID debate will be filling in the gaps in residue counts and understanding what functionality happens so it is a good bet that such a hypothesis would stay on the table. Lincoln Phipps