A common hypothesis in evolutionary circles is evolution by gene duplication. It posits that duplicated genes are free to evolve new functions without affecting the primary gene. This idea has been dealt a serious blow by a paper published in Complexity on Dec. 22, http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract.
Joseph Esfandiar and Hannon Bozorgmehr first dealt a falsifying blow to natural selection as a creative force for genetic information:
“Research into the evolution of genes has shown that the peptides they code for are of a finicky and precarious nature, both marginally stable and prone to aggregation. Protein folding happens to be a highly complex and synergistic process, involving a number of epistatic relationships among many residues. This phenomenon, compounded with the issue of interactions between protein molecules, can significantly complicate adaptive evolution such that in the majority of cases the overall effects on reproductive fitness are very slight. Many arguably “beneficial” mutations have been observed to incur some sort of cost and so can be classified as a form of antagonistic pleiotropy.
“Indeed, the place and extent of natural selection as a force for change in molecular biology have been questioned in recent years. Detecting the incidence of any beneficial substitutions in genes has so far relied on statistical inferences as empirical evidence is less readily available. In many instances, nonsynonymous changes and shifts in allelic diversity may be induced by factors that can serve to imitate selective effects—biased gene conversion, mutational and recombinational hotspots, hitchhiking, or even neutral drift being among them. Moreover, several well-known factors such as the linkage and the multilocus nature of important phenotypes tend to restrain the power of Darwinian evolution, and so represent natural limits to biological change. Selection, being an essentially negative filter, tends to act against variation including mutations previously believed to be innocuous.”
That’s right out of the starting gate in this paper. What about gene duplication? Isn’t evolution free to “tinker” with the copy (paralog) without affecting the function of the original? The idea that natural selection is more permissive with duplicated genes was analyzed by Esfandiar and Bozorgmehr, as well as the best examples presented by evolutionary biologists. For a duplicate to be preserved at all, rather than eliminated by negative selection (also called purifying selection), it must provide some benefit:
“Were selection to be completely relaxed and any manner of changes permitted, this would only serve to guarantee complete degeneration. It would invariably lead to the introduction of null and nonsense mutations, scrambling the open reading frame (ORF), and degrading the cisregulatory elements involved in transcription—leading to the gene’s pseudogenization. Thus, a measure of purifying/stabilizing selection seems necessary for duplicate preservation, and any evolutionary divergence would proceed under a relaxed regime rather than none at all.”
Their primary purpose was to see if novel genetic information can arise by gene duplication. They first defined evolution in functional terms (contra Shannon information): genetic information is “The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome.” The paper then described how to test for novel genetic information, described the way evolutionists believe it arises in duplicated genes, and looked at the best examples cited in the literature.
When citing one case, they stated a principle Darwinians need to keep in mind: “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.” Finally, the authors spent a paragraph on “de novo recruitment without duplication,” the emergence of new genetic information out of the blue. “This represents a return to the idea of the hopeful monster at the molecular level,” they said of recent attempts to revive Goldschmidt’s long-discredited hypothesis. After looking at the examples, they said, “de novo recruitment of noncoding DNA would seem extremely improbable and implausible.”
In conclusion, they noted that accidental gene duplication clearly adds to the size of some genomes. “However, in all of the examples given above, known evolutionary mechanisms were markedly constrained in their ability to innovate and to create any novel information, they said. “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.” They allowed that subfunctionalization (division of function between copies) might act in some cases, but that, too, provides no new functional information. Of cases of co-option cited by Darwinists, they found that “a proclivity toward functional stability and the conservation of information, as opposed to any adventurous innovation, predominates.”
In short, neo-Darwinism fails by both natural selection and tinkering with duplicate genes.
“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. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.”
Their ending paragraph is like a good-news-bad-news joke on neo-Darwinism. Good news: “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.” Bad news: “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.” So what comes next? They didn’t offer a replacement evolutionary theory, but warned that any new contender must think holistically about the cell. “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.”