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Evolution: innovations may have non-adaptive origins (sans mutations)

Q & A: Evolution Makes Do

By Chris Palmer
Evolutionary biologist Andreas Wagner argues that many evolutionary innovations may have non-adaptive origins.
Excerpt: “If exaptations are pervasive, then natural selection—which few doubt is critical for the preservation and spreading of traits—may not be that important for the origin of innovations in life’s history.”
See also: Rapid detection of positive selection in genes and genomes through variation clusters
Excerpt: “They occur in well-defined domains of a protein’s tertiary structure and show a large excess of amino acid replacement over silent substitutions.”
My comment: In my model of nutrient-dependent pheromone-controlled ecological adaptations, RNA-directed DNA methylation links RNA-mediated cell type differentiation via amino acid substitutions to cell type differentiation in all cells of all individuals of all species from microbes to man.
My comment to The Scientist site:
Thermodynamically controlled exaptations that beneift organism-level thermoregulation link the development of antibiotic resistance in E. Coli to nutrient-dependent pheromone-controlled survival of species via conserved molecular mechanisms. In my model, this establishes Natural Selection for nutrients as the driving force behind the exaptations that enable adaptive evolution, which is controlled by the metabolism of nutrients to species-specific pheromones. Exaptations become adaptations when the benefit to organism-level thermoregulation is fixed via chromatin remodeling and alternative splicings, but only after seemingly futile cycles of protein biosynthesis and degradation have occurred.
The result of the ‘futile’ cycles, which actually exemplify epigenetic ‘fine-tuning’ at the cellular level, is de novo creation of olfactory receptor genes that enable additional receptor-mediated acquisition of the nutrient that was initially beneficial. That benefit is ‘signaled’ to conspecifics via nutrient-dependent species-specific pheromone production, which enables nutrient-dependent species diversification in accordance with what is known about the physiology of ecological, social, neurogenic, and socio-cognitive niche construction.
The examples I used from model organisms of the epigenetic tweaking of immense gene networks via a single nutrient-dependent amino acid substitution follow, in part, from from Dr. Wagner’s lead in Rapid detection of positive selection in genes and genomes through variation clusters. The examples include a human population that adaptively evolved in central China during the past ~30,000 years. Human / non-human primate orthologues can be examined in the context of how nutrients alter the microRNA / messenger RNA balance from the bottom up, and how pheromones control the ‘balance’ of life from the top down, as is consistent with Darwin’s ‘conditions of life’ that precede Natural Selection. See for example miRNAs: effectors of environmental influences on gene expression and disease and MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates.