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Does Gene Duplication Perform As Advertised?

In my previous post, I highlighted a recent peer-reviewed paper which challenged a key tenet of neo-Darwinian evolution -- specifically, the causal sufficiency of gene duplication and subsequent divergence to account for the origin of novel biological information. In this follow-up blog, I want to consider some of the case-studies examined in the paper and relay some of the conclusions drawn.

The paper discusses the case of Sdic (which has been discussed on this blog before), a flagellar dynein gene found exclusively in Drosophila melangoaster, which is purported to be an example of a tandem duplicated chimeric gene "caught in the act" of evolving (Ponce and Hartl 2009), formed when two adjacent genes, AnnX and Cdic, were duplicated and a deletion-mediated fusion occurred with one pair.

Bozorgmehr explains,

Sidc is found to be composed of four paralogs having itself been duplicated twice over. The 5' untranslated region (UTR) and part of the promoter sequence of the gene derives from AnnX, whereas the translated part and all 300 base pairs (bp) of the 3' UTR come from the Cdic gene. A sequence comparison of Sdic2 and Cdic reveals that 522 out of 527 residues (99%) can be aligned without difficulty. Sdic has been observed to be expressed in the testes and incorporated into the sperm tail and this is because it has acquired a testis-specific core element, homologous with those of other promoter sequences, from the 3'UTR of AnnX. It is unclear whether the element is a translational enhancer or has some other regulatory role in the AnnX gene such as, for example, the mRNA localization. Either way, the gene would seem to contribute to greater fecundity.

As it turns out, however, it is the loss of over 100 codons from the N-terminus of Cdic which is responsible for the main shift in function -- that is, the acquisition of the basic characteristic of cytoplasmic dyneins, specifically the loss of Sdic's motifs necessary for its interaction with dynactin. It thus seems that, in this case, deletion was one of the necessary factors involved in the gene fusion. The author notes that "[t]his presents a problem in terms of explaining any accretion of cistron size with reference to the most naturally applicable evolutionary process."

The paper also examines another proposed case of the evolution of novel exonic information proposed in the now-famous case of Nylon-digesting bacteria, citing Ohno (1984), a study in which it was documented that a nylon oligomer hydrolase was present in bacteria near sites involved in the production of the synthetic material. However, the author cites another, more recent, study by Negoro et al. (2005), in which it was argued that a likely source was an esterase containing a β-lactamase fold. Bozorgmehr notes that:

Two amino acid replacements in the catalytic cleft greatly increased the Ald-hydrolytic activity, in some measure already provided by a serine active site, necessary for the degradation of the oligomers. However, this does appear to have come at some cost to part of the esterolytic function and the enzyme does not have nearly the specificity constant and efficiency, with respect to its alternative functionality, of a hydrolase such as aminoacylase. Therefore, although there is an appreciable gain in operational capability, no new information was generated that specified oligomer degradation.

Bozorgmehr notes a challenge to the very concept of evolutionary novelty being acquired via frameshift mutations in that they almost inevitably incur premature stop codons, which results in protein truncation. After discussing a few more papers (interested readers are referred to the original article for further reading), he concludes that:

...although frameshifts have the potential to cause more rapid sequence divergence than can individual point mutations, it is wrong to assume that they can produce any novel information even if they do result in the emergence of novel characters within proteins. Therefore, a divergence in sequence need not result in a change in functionality or affect behavior, as the same information can be constructed using a number of different amino acid arrangements. In duplicates, and also singletons, changes may be compensatory and in response to prior degeneration rather than representating any innovation.

The paper even passingly alludes to a challenge to the theory of evolution similar to irreducible complexity: "A key problem associated with the Darwinian mechanism of evolution is that many of the putative incipient and intermediate stages in the development of a biological trait may not be useful themselves and may even be harmful." Moreover, "The hypothesized metamorphosis would have required widespread and related changes that must have been coordinated and synchronized -- and so representing something to the effect of a directional saltation. However, this is not something a blind, unsupervised process that can be achieved."

Although the paper does not mention design or teleology as a candidate hypothesis, this is the very problem which the design hypothesis overcomes -- intelligence has the unique property of being able to visualise complexity, and it possesses the foresight necessary in order to bring everything together to actualize a complex end point. But there is something else discussed in the paper which makes more sense under a design paradigm than it does under a Darwinian one:

Moreover, the antifreeze proteins that have been found in Arctic cod are completely different in sequence and organization from their Antarctic cousins -- this means that the same tryspinogen-like gene could not have been the ancestral gene in this case. Although this is passed off as evidence of 'convergent evolution', this serves only to provide another problem as to how a gene believed to be of a more recent origin could have evolved.

The paper also critiques the model of de novo recruitment of "junk" or non-coding DNA to become functional sequences, concluding that "as a mechanism for the creation of novel motifs and protein domains, de novo recruitment of non-coding DNA would seem extremely improbable and implausible."

The paper concludes that:

Gene duplication and subsequent evolutionary divergence certainly adds to the size of the genome and in large measure to its diversity and versatility. However, in all of the examples given above, known evoutionary mechanisms were markedly constrained in their ability to innovate and to create any novel information. This natural limit to biological change can be attributed mostly to the power of purifying selection, which, despite being relaxed in duplicates, is nonetheless ever-present.

Moreover,

the various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality.

The author concludes his review by offering the following advice to Darwinists:

Gradual natural selection is no doubt important in biological adaptation and for ensuring the robustness of the genome in the face of constantly changing environmental pressures. However, its potential for innovation is greatly inadequate as far as explaining the origination of the distinct exonic sequences that contribute to the complexity of the organism and diversity of life. Any alternative/revision to Neo-Darwinism has to consider the holistic nature and organization of information encoded in genes, which specify the interdependent and complex biochemical motifs that allow protein molecules to fold properly and function effectively.

Papers continue to flood in on a more and more frequent basis, challenging long-held assumptions regarding the origin and means of subsequent diversification of life. How long the Darwinian paradigm is able to withstand the onslaught before the evidential dikes are broken remains to be seen.