Creating new genes (and controlling diversity)

By: James V. Kohl | Published on: November 3, 2012

Evolution of new genes captured October 22, 2012
Excerpt: “The most common way to increase gene expression is by duplicating the gene, perhaps multiple times. Natural selection then works on all copies of the gene. Under selection, the copies accumulate mutations and recombine. Some copies develop an enhanced side function. Other copies retain their original function.”
My comment (on the excerpt above): It is a misrepresentation to infer that natural selection works via accumulated mutations. My comments below are on the published work, instead of the misrepresentation.
Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence Subscription required to read full text from Science 19 October 2012: Vol. 338 no. 6105 pp. 384-387
DOI: 10.1126/science.1226521 
by Joakim Näsvall, Lei Sun, John R. Roth, and Dan I. Andersson.
Excerpt: “Amplification to higher copy numbers occurs at 10−2 per cell per division (3), several orders of magnitude more frequent than point mutations. Thus, whenever a limiting gene product restricts cell growth, initial escape from this restriction may initially occur by duplication events and higher amplification, rather than rare point mutations…”
My comment: In the authors’ own words, “…the accumulation of a point mutation is the rate-limiting step in the IAD process.”  And “…the innovation-amplification-divergence (IAD) model allows the evolution of new genes to be completed under continuous selection that favors maintenance of the functional duplicate copies and divergence of the extra copy from the parental allele.”
Mutations do not continuously occur, so continuous selection (above) is obviously not selection for mutations. Natural selection is for nutrient chemical-dependent maintenance of existing genes and their duplicates. Duplication, but not mutation, allows duplicates to gain important new functions. In this series of experiments, the new function is the enhanced ability to metabolize  nutrient chemicals.
That new function is not limited to unicellular organisms. Nutrient chemicals epigenetically effect intracellular signaling and stochastic gene expression in all species. Non-random, nutrient-dependent stochastic gene expression enables the enhanced ability of cells and organisms to metabolize nutrient chemicals that enhance growth and survival of the species.
The ability of cells and organisms to do this involves common molecular mechanisms in species from microbes to man. The epigenetic effects of nutrient chemicals on gene duplication and species diversity and the ability to metabolize nutrient chemicals is controlled by the metabolism of the nutrient chemicals to pheromones that epigenetically control reproduction in all species, as exemplified by the honeybee model organism in my model of adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction.

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