Epigenetically effected affects on adaptations

Vol. 342 no. 6164 pp. 1367-1372
DOI: 10.1126/science.1243490

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

Excerpt: “Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.”

The Hidden Codes That Shape Protein Evolution 

Perspective excerpt: “…a transcription factor “binding code” may influence codon choice and, consequently, protein evolution. This “binding” code joins other “regulatory” codes that govern chromatin organization (3), enhancers (5, 6), mRNA structure (7), mRNA splicing (3), microRNA target sites (6, 8), translational efficiency (9), and cotranslational folding (10), all of which have been proposed to constrain codon choice, and thus protein evolution…”

My comment: Submitted on Fri, 12/13/2013 – 14:46 and published to the Science Magazine site on Tue, 12/17/2013 – 13:33

Is the intrinsic flexibility attributed to exploitation by natural selection epigenetically effected by nutrient uptake? If so, natural selection for nutrients via seemingly futile cycles of themodynamically constrained protein biosynthesis and degradation might enable transcription factor binding that is limited by non-random nutrient-dependent changes in base pairs. The changes in based pairs would be accompanied by alternative splicings and amino acid substitutions in cells that stochastically express genes, which are most beneficial to species-specific cell types in different tissues.

The metabolism of nutrients to species-specific pheromones that control the physiology of reproduction could then epigenetically control transcription and gene expression from the top down via reproduction. We might then expect to see seemingly futile cycles of thermodynamically controlled nutrient-dependent protein biosynthesis and degradation result in conservation of genes associated with increased fitness in one ecological niche that might not be conserved in an organism that was competing for survival in the same ecological niche.

Clearly, the organism that was most capable of nutrient acquisition, which enabled the thermodynamics of its intercellular signaling to result in better organism-level thermoregulation, would establish its social niche among equally successful conspecifics that adapted to their ecological niche and proliferated more rapidly.

Symbiotic relationships might then result from cooperation among heterospecifics in situations where the failure to cooperate with other organisms and live from a different nutrient source would mean death to a unicellular organism or to a multicellular vertebrate. However, organisms that managed to somehow acquire more than an appropriate share of nutrients would be subjected to conserved molecular mechanisms for species diversification that suddenly were no longer adaptive.

Nutrient stress linked to thermal stress via abundance, but not by starvation or social stress, would then be the most likely cause of mutations that are not eliminated by the finely-tuned molecular mechanisms of adaptation to the epigenetic landscape that occur via its incorporation into the physical landscape of DNA in the organized genomes of species from microbes to man.

I welcome comments from anyone who thinks this theory might benefit progress, since I cannot properly evaluate my own model.

About James V. Kohl 1308 Articles
James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones. Recently, Kohl integrated scientific evidence that pinpoints the evolved neurophysiological mechanism that links olfactory/pheromonal input to genes in hormone-secreting cells of tissue in a specific area of the brain that is primarily involved in the sensory integration of olfactory and visual input, and in the development of human sexual preferences. His award-winning 2007 article/book chapter on multisensory integration: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences followed an award winning 2001 publication: Human pheromones: integrating neuroendocrinology and ethology, which was coauthored by disinguished researchers from Vienna. Rarely do researchers win awards in multiple disciplines, but Kohl’s 2001 award was for neuroscience, and his 2007 “Reiss Theory” award was for social science. Kohl has worked as a medical laboratory scientist since 1974, and he has devoted more than twenty-five years to researching the relationship between the sense of smell and the development of human sexual preferences. Unlike many researchers who work with non-human subjects, medical laboratory scientists use the latest technology from many scientific disciplines to perform a variety of specialized diagnostic medical testing on people. James V. Kohl is certified with: * American Society for Clinical Pathology * American Medical Technologists James V. Kohl is a member of: * Society for Neuroscience * Society for Behavioral Neuroendocrinology * Association for Chemoreception Sciences * Society for the Scientific Study of Sexuality * International Society for Human Ethology * American Society for Clinical Laboratory Science * Mensa, the international high IQ society