Tuesday, November 08, 2005

More scientific iconoclasm

I am writing with reference to: Chen et al. 1997. “Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish.” Proc. Natl. Acad. Sci. USA 94.
Here is a link to the full paper, and this is the abstract.
Freezing avoidance conferred by different types of antifreeze proteins in various polar and subpolar fishes represents a remarkable example of cold adaptation, but how these unique proteins arose is unknown. We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process by which this occurred through characterization and analyses of notothenioid AFGP and trypsinogen genes. The primordial AFGP gene apparently arose through recruitment of the 5 and 3 ends of an ancestral trypsinogen gene, which provided the secretory signal and the 3 untranslated region, respectively, plus de novo amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor to create a new protein coding region for the repetitive tripeptide backbone of the antifreeze protein. The small sequence divergence (4-7%) between notothenioid AFGP and trypsinogen genes indicates that the transformation of the proteinase gene into the novel ice-binding protein gene occurred quite recently, about 5-14 million years ago (mya), which is highly consistent with the estimated times of the freezing of the Antarctic Ocean at 10-14 mya, and of the main phyletic divergence of the AFGP-bearing notothenioid families at 7-15 mya. The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly.

Firstly, I would like to say that this is a good paper. It is well-researched; the paper itself doesn’t make too strong claims for itself; and it is an example of exactly the sort of paper that darwinism needs to present if it is to move from the realm of story-telling to being on a solid scientific footing.
What I do not agree with, however, is the iconic status that this paper has in the darwinist community. Like the Avida paper that I discuss below, this paper crops up over and over again as a demonstration of how darwinism can – nay, has – solved all the problems that challenge it.

For example: it is cited here in a comment on a post by William Dembski; it is presented here on the NAS website as a “cool tale in molecular evolution”; and it is effectively the framework of one of the objections to the Meyer paper that Panda’s Thumb are reacting against to in Meyer’s Hopeless Monster.

If AFGPs arose in this way, this is a significant example of new – and highly useful – functionality arising. However, let’s think about the evolutionary process that has taken place, if this account of how AFGPs appeared is correct.

Firstly, presumably (since the trypsinogen gene continues to be used by the organism) the gene was duplicated. In organismal terms, this is a necessary first step; however, it is basically an evolutionarily neutral step. Then, a large section of the functional part of the trypsinogen gene was deleted – again, following duplication, this is a neutral step. Then comes the insertion or deletion of a couple of nucleotides to induce a frame shift within the gene that has lost its original functionality. This is analogous to where the computer model, Avida, mutates the genomes of its digital organisms. These are the evolutionarily significant steps. Then, having established the AFGP functionality, it was amplified. Once the functionality is there, it is possible to select for increased expression of the functionality. The significant step, then – to establish the functionality – requires only a couple of changes. Of course, the first neutral steps were significant in terms of evolution – but the likelihood is that these don’t provide anything that can be selected for.

It is significant that, even in this simple example of a beneficial process, all of the “difficult” evolution has happened elsewhere. The 5’ sequence of 67 nucleotides and the 3’ sequence of a couple of hundred nucleotides, is preserved in the AFGP gene from the trypsinogen gene. The 1.7 kbp insert in the AFGP gene is irrelevant to the gene. The spacer sequence is almost identical to an existing sequence that has undergone a frameshift. The backbone sequence has also been recruited from an already specified sequence. And the gene is highly repetitive, containing tens of copies of functionally identical sub-genes.

The fish breeding mechanism is also significant. The fish certainly aren’t sexually mature for many years. My reference books didn’t provide a definitive answer on this, but is it the case that these fish breed in the conventional fishy way – by mixing milt and roe? So many thousands of baby fish are released – presumably fully biochemically functional – but without the investment of huge amounts of energetic resources on the part of the parents. The significance of this is that this means of reproduction gives many opportunities for “beneficial mutations” to be present - and also tested - in every generation (compare mammals with litters or calves, birds or amphibians with a clutch of eggs). Furthermore, with sexual reproduction (compare bacteria) it is possible for beneficial mutations to spread through the population, rather than simply following one genetic line. This form of reproduction provides about the best possible framework within the animal kingdom for evolution.

So to summarize: this papers provides a coherent explanation of how the AFGP functionality might appear, and this is a significant evolutionary change. However, it is a long way removed from the appearance of complex polypeptides, and it is an evolutionary change that takes place in the reproductive environment which is most suited to evolution. Also, it is not a complicated evolutionary step – most of the complex evolution has already taken place elsewhere, and to use the analogy of “climbing Mount Improbable”, this evolutionary step represents climbing onto the trig point at the top of the mountain once the mountain itself has already been scaled. So it is presumptuous to argue – as many darwinists seem to think – that this paper suggests that darwinist explanations of all biological features are just around the corner.