First off I must apologize for doing another post on a subject that’s been done to death around here, but I’ve been meaning to make a post about this for a while but other stuff kept coming up. Anyway, things have quietened down at work where I now only have to maintain some cell cultures, so I have a bit of time duing the christmas holiday.
My post, which is a repost of something I also brought up in a thread on Larry Moran’s sandwalk blog, is about a chapter in Stephen Meyer’s book Darwin’s Doubt and what I can, if I’m being generous, only attribute to extremely shoddy scholarship.
Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:
“Axe had a key insight that animated the development of his experimental program. He wanted to focus on the problem of the origin of new protein folds and the genetic information necessary to produce them as a critical test of the neo-Darwinian mechanism. Proteins comprise at least three distinct levels of structure:4 primary, secondary, and tertiary, the latter corresponding to a protein fold. The specific sequence of amino acids in a protein or polypeptide chain make up its primary structure. The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures (see Fig. 10.2).
Axe knew that as new life-forms arose during the history of life—in events such as the Cambrian explosion—many new proteins must also have arisen. New animals typically have new organs and cell types, and new cell types often call for new proteins to service them. In some cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins. But more often, proteins capable of performing new functions require new folds to perform these functions. That means that explosions of new life-forms must have involved bursts of new protein folds as well.”
In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiates that the cambrian diversification, or indeed any kind of speciation, or the that new cells types or organs, requires new protein folds. ZERO. Not one single reference that supports these claims. At first It reads like what I quote above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that attepts to address how hard it is to evolve new folds(and that work has it’s own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.
Meyer mentions Ohno:
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life such as sponges or one-celled organisms. Thus, Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds.”
No reference is given here either. The claim is simply made initially, so it’s hard to check. Is Meyer and Axe willing to bet that a preceding evolutionary history of, for example, Lysyl oxidase cannot be found in structure and sequence of related molecules? That there ARE no related molecules? Is that his claim? That the Cambrian explosion required tonnes of bona fide Orphan proteins with no preceding history? Where are the references that support this? Did Meyer or Axe look for homologues of Lysyl Oxidase and found none?
It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”
Well, much later in the same chapter, Meyer finally references Ohno:
“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21”
What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.”
What does that reference say? Let’s look:
“Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the
mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”
The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.
Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:
“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”
Where does he get this? His ass, that’s where.