Sunday, 2 August 2015

A criticism of Stephen Palmer's talks at the Coventry Creation Day - 10

Correcting Creationist Abuse of Probability

The special creationist abuse of the probability argument likewise is one that has been debunked ages ago. As molecular pharmacologist Ian Musgrave notes, special creationists who make this claim make the following major errors:
1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all. 
2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.  
3) They calculate the probability of sequential trials, rather than simultaneous trials. 
4) They misunderstand what is meant by a probability calculation.. 
5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences[1]
In short, they make the mistake of thinking that the first living cell emerged by pure random association of amino acids forming, something which as Musgrave reminds the creationists, ignores both the fact that the processes involved are not random, and the first living creatures would be far simpler than a modern cell, making the naïve creationist probability calculations meaningless.

This probability argument unsurprisingly is a complete misrepresentation of abiogenesis. It ignores the fact that the earliest form of life would have been far less complex than the simplest living cell currently alive today. It also makes the fundamental mistake of blindly applying probability laws to the interaction of molecules without understanding the specifics of how they interact. This argument is merely the classic special creationist abuse of “Borel’s Law”, which alleges that anything with odds of greater than one in 1050 is impossible. However, Borel himself was at pains to point out the fallacies in this argument:
In conclusion, I feel it is necessary to say a few words regarding a question that does not really come within the scope of this book, but that certain readers might nevertheless reproach me for having entirely neglected. I mean the problem of the appearance of life on our planet (and eventually on other planets in the universe) and the probability that this appearance may have been due to chance. If this problem seems to me to lie outside our subject, this is because the probability in question is too complex for us to be able to calculate its order of magnitude. It is on this point that I wish to make several explanatory comments. 
When we calculated the probability of reproducing by mere chance a work of literature, in one or more volumes, we certainly observed that, if this work was printed, it must have emanated from a human brain. Now the complexity of that brain must therefore have been even richer than the particular work to which it gave birth. Is it not possible to infer that the probability that this brain may have been produced by the blind forces of chance is even slighter than the probability of the typewriting miracle?

It is obviously the same as if we asked ourselves whether we could know if it was possible actually to create a human being by combining at random a certain number of simple bodies. But this is not the way that the problem of the origin of life presents itself: it is generally held that living beings are the result of a slow process of evolution, beginning with elementary organisms, and that this process of evolution involves certain properties of living matter that prevent us from asserting that the process was accomplished in accordance with the laws of chance.

Moreover, certain of these properties of living matter also belong to inanimate matter, when it takes certain forms, such as that of crystals. It does not seem possible to apply the laws of probability calculus to the phenomenon of the formation of a crystal in a more or less supersaturated solution. At least, it would not be possible to treat this as a problem of probability without taking account of certain properties of matter, properties that facilitate the formation of crystals and that we are certainly obliged to verify. We ought, it seems to me, to consider it likely that the formation of elementary living organisms, and the evolution of those organisms, are also governed by elementary properties of matter that we do not understand perfectly but whose existence we ought nevertheless admit.

Similar observations could be made regarding possible attempts to apply the probability calculus to cosmogonical problems. In this field, too, it does not seem that the conclusions we have could really be of great assistance.[2] (Emphasis mine)
No serious biologist believes that the first living cell emerged in one fell swoop. Rather, we are talking about an incremental process over time. Ian Musgrave neatly skewers this deeply mistaken view:
“…in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria…but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

The first "living things" could have been a single self replicating molecule, similar to the "self-replicating" peptide…or the self replicating hexanucleotide, or possibly an RNA polymerase that acts on itself. 

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle…No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747. Just to hammer this home, here is a simple comparison of the theory criticised by creationists, and the actual theory of abiogenesis. 

Note that the real theory has a number of small steps, and in fact I've left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap.[3] (Emphasis mine)

There is no 'edge to evolution' - the YEC argument from probability fails again

The same naive argument evolution denialists use in an attempt to refute abiogenesis also fails when they attempt to apply it to evolution, with the claim that 'random chance' has no creative power. This claim yet again reflects the gross ignorance of evolutionary biology given that evolution is anything but random. Mutation and drift may be random, but natural selection acting on random mutation is anything but random - selection by definition is the opposite of random.

YEC often invoke the eye as an example of something 'too complex to evolve' but as Nilsson and Pelger note in their model of eye evolution, selection acting on a light sensing patch is more than capable of evolving a functioning eye in a few hundred thousand years:
Because eyes cannot evolve on their own, our calculations do not say how long it actually took for eyes to evolve in the various animal groups. However, the estimate demonstrates that eye evolution would be extremely fast if selection for eye geometry and optical structures imposed the only limit. This implies that eyes can be expected to respond very rapidly to evolutionary changes in the lifestyle of a species. Such potentially rapid evolution suggests that the eye design of a species says little about its phylogenetic re-lationship, but much about its need for vision. It follows that the many primitive eye designs of recent animals may be perfectly adequate, and simply reflect the animal's present requirements. In this context it is obvious that the eye was never a real threat to Darwin's theory of evolution. [4] (Emphasis mine)
Eight years after Darwin's Black Box, Behe and physicist David Snoke published a paper in the journal Protein Science in which they attempted to justify their claim that Darwinian evolution could not "account for the evolution of complex biochemical systems." [5] Far from sealing the fate of evolution, as some special creationists claimed, the paper was widely savaged, with the paper by respected geneticist Michael Lynch:
In summary, the conclusions derived from the current study are based on a model that is quite restrictive with respect to the requirements for the establishment of new protein functions, and this very likely has led to order-of-magnitude underestimates of the rate of origin of new gene functions following duplication. Yet, the probabilities of neofunctionalization reported here are already much greater than those suggested by Behe and Snoke. Thus, it is clear that conventional population-genetic principles embedded within a Darwinian framework of descent with modification are fully adequate to explain the origin of complex protein functions[6] (Emphasis mine)
pointing out the considerably flaws in the Behe and Snoke paper, while the Panda's Thumb article by molecular pharmacologist Ian Musgrave, molecular biologist Steve Reuland, and computational evolutionary geneticist Reed Cartwright: 
We began this essay with a quotation from Behe complaining that a paper describing an evolutionary simulation (Lenski et al. 2003) had “precious little real biology” in it. What we see here is that Behe and Snoke’s paper is acutely vulnerable to the same criticism. A theoretical model is useful to the extent that it accurately represents or appropriately idealizes the processes that occur in the phenomenon being studied. Although it is worthwhile to investigate the importance of neutral drift, Behe and Snoke have in our opinion over-simplified the process, resulting in questionable conclusions. 
Their assumptions bias their results towards more pessimistic numbers. The worst assumption is that only one target sequence can be hit to produce a new function. This is probably false under all circumstances. The notion that a newly arisen duplicate will remain selectively neutral until the modern function is firmly in place is also probably false as a general rule. Their assumption that 70% of all amino acid substitutions will destroy a protein’s function is much too high. And finally, we have shown that their flagship example does not require a large multi-residue change before being selectable. 
And ironically, despite these faulty assumptions, Behe and Snoke show that the probability of small multi-residue features evolving is extremely high, given the types of organisms that Behe and Snoke’s model applies to. When we use more realistic assumptions, though many bad ones still remain, we find that the evolution of multi-residue features is quite likely, even when there are smaller populations and larger changes involved. In fact, the times required are within the estimated divergence times gleaned from the fossil record. We can therefore say, with confidence, that the evolution of novel genes via multi-residue changes is not problematic for evolutionary theory as currently understood. [7] (Emphasis mine)
likewise reiterating the fundamental flaws with the ID argument against evolution.

Despite the poor review this argument received, Behe expanded on this theme in his follow-up book The Edge of Evolution: The Search for the Limits of Darwinism, which while conceding the reality of common descent asserted that Darwinian evolution was incapable of producing the diversity of life we see today. Unsurprisingly, given the poor reception of his previous book and the paper co-authored with Snoke, The Edge of Evolution was critically slated. It's fatal flaws, as evolutioanry geneticist and developmental biologist Sean Carroll pointed out in his book review for Science was:
...minimizing the power of natural selection to act cumulatively as traits or molecules evolve stepwise from one state to another via intermediates. Behe states correctly that in most species two adaptive mutations occurring instantaneously at two specific sites in one gene are very unlikely and that functional changes in proteins often involve two or more sites. But it is a non sequitur to leap to the conclusion, as Behe does, that such multiple-amino acid replacements therefore can't happen. Multiple replacements can accumulate when each single amino acid replacement affects performance, however slightly, because selection can act on each replacement individually and the changes can be made sequentially.

Behe begrudgingly allows that only “rarely, several mutations can sequentially add to each other to improve an organism's chances of survival.” Rarely? This, of course, is the everyday stuff of evolution. Examples of cumulative selection changing multiple sites in evolving proteins include tetrodotoxin resistance in snakes, the tuning of color vision in animals, cefotaxime antibiotic resistance in bacteria, and pyrimethamine resistance in malarial parasites—a notable omission given Behe's extensive discussion of malarial drugresistance. 

Behe seems to lack any appreciation of the quantitative dimensions of molecular and trait evolution. He appears to think of the functional features of proteins in qualitative terms, as if binding or catalysis were all or nothing rather than a broad spectrum of affinities or rates. Therefore, he does not grasp the fundamental reality of a mutational path that proteins follow in evolving new properties. 

This lack of quantitative thinking underlies a second, fatal blunder resulting from the mistaken assumptions Behe makes about protein interactions. The author has long been concerned about protein complexes and how they could or, rather, could not evolve. He argues that the generation of a single new protein-protein binding site is extremely improbable and that complexes of just three different proteins “are beyond the edge of evolution.” But Behe bases his arguments on unfounded requirements for protein interactions. He insists, based on consideration of just one type of protein structure (the combining sites of antibodies), that five or six positions must change at once in order to make a good fit between proteins—and, therefore, good fits are impossible to evolve. An immense body of experimental data directly refutes this claim.There are dozens of well-studied families of cellular proteins (kinases, phosphatases, proteases, adaptor proteins, sumoylation enzymes, etc.) that recognize short linear peptide motifs in which only two or three amino acid residues are critical for functional activity. Thousands of such reversible interactions establish the protein networks that govern cellular physiology. 

Very simple calculations indicate how easily such motifs evolve at random. If one assumes an average length of 400 amino acids for proteins and equal abundance of all amino acids, any given two-amino acid motif is likely to occur at random in every protein in a cell. (There are 399 dipeptide motifs in a 400-amino acid protein and 20 × 20 = 400 possible dipeptide motifs.) Any specific three-amino acid motif will occur once at random in every 20 proteins and any four-amino acid motif will occur once in every 400 proteins. That means that, without any new mutations or natural selection, many sequences that are identical or close matches to many interaction motifs already exist. New motifs can arise readily at random, and any weak interaction can easily evolve, via random mutation and natural selection, to become a strong interaction. Furthermore, any pair of interacting proteins can readily recruit a third protein, and so forth, to form larger complexes. Indeed, it has been demonstrated that new protein interactions and protein networks can evolve fairly rapidly and are thus well within the limits of evolution. 

Is it possible that Behe does not know this body of data? Or does he just choose to ignore it? Behe has quite a record of declaring what is impossible and of disregarding the scientific literature, and he has clearly not learned any lessons from some earlier gaffes. He has again gone “public” with assertions without the benefit (or wisdom) of first testing their strength before qualified experts. [8]
Damning as Carroll's criticism are, his most important point is in the final paragraph quoted above. Behe's arguments are made in defiance of the established scientific literature, do not represent solid, peer-reviewed arguments that have survived the test of time, and when they are made on arguments that have made it into the peer-reviewed literature, they have been solidly criticised and dismissed. This is characteristic of how special creationist and intelligent design advocates operate. They bypass the peer-reviewed literature and peddle snake oil to the masses, rather than offer an argument that has been scrutinised by the mainstream scientific community, subjected to scrutiny, and come out unscathed. What they are doing is not science, but Christian apologetics, and pretty shabby apologetics at that. It is disappointing that our community uncritically appeals to these arguments rather than recognising the fact that as they have not been subjected to proper scrutiny they are worthless.

Of all the special creationist arguments, the argument from probability, while appearing to be the most impressive is by far the easiest to dismiss once one recognises that the special creationist is criticising a straw man.

[1] Musgrave I “Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations” TalkOrigins Archive.
[2] Borel E “Probability and Certainty” (1963: Dover) p 124-126. Cited in Stockwell J “Borel's Law and the Origin of Many Creationist Probability Assertions
[3] Musgrave, op cit
[4] Nilsson D, Pelger S "A Pessimistic Estimate of the Time Required for an Eye to Evolve" Proc. R. Soc. Lond. B (1994) 256:53-58
[5] Behe M.J., Snoke D.W. "Simulating evolution by gene duplication of protein features that require multiple amino acid residues." Protein Sci. (2004) 13:2651-64.
[6] Lynch M "Simple evolutionary pathways to complex proteins" Protein Sci. (2005) 14: 2217–2225
[7] Musgrave, I.F., Reuland S., Cartwright R.A. "Theory is as Theory Does." Panda's Thumb October 11, 2004.
[8] Carroll S.B. "Books: God as Genetic Engineer" Science (2007) 316:1427-1428