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From genotype to phenotype: Part One

Posted on February 20, 2013 by James Kohl.

Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

Cell, Volume 152, Issue 4, 691-702, 14 February 2013

Abstract excerpt: “This interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.”

My comment:

Click on this link and then on “PaperFlick” (displayed above the diagram). Watch the video: “Human evolution: from genotype to phenotype.” You will be taken away from random mutations theory to a theory of adaptive variations. The adaptive variations quickly become adaptive mutations in the context of Natural Selection and population genetics. The conflation of mutations theory with epigenetic cause is an attempt to represent biologically based cause and effect in a human population. Unfortunately, as Shari Grossman says in the video: “Without a prior hypothesis of an adaptive trait it is difficult to know where to begin.”

This is a short story of adaptive evolution. It begins with a variant allele that somehow arose in central China approximately 30,000 years ago. Each specialist seems to have a slightly different idea about how to describe the allele. The allele is a variant; a mutation; an adaptive variant; or an adaptive mutation in the changing context of genotypic and phenotypic cause and effect. No matter what the allele is called, its effect is adaptive and it is manifested in the context of an affect on sweat, skin, hair, and teeth.

Therein lies the problem. The affect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans. Adaptive evolution is nutrient-dependent and pheromone-controlled in species from microbes to man.

One amino acid substitution cannot simultaneously cause and control adaptive evolution from the bottom up and from the top down. The only way that the nutrient-dependent substitution of alanine could result in species-specific organism-level changes in skin, glands, and hair, would be through pheromone-controlled reproduction. Pheromone-controlled reproduction is required for fixation of the nutrient-dependent substitution. That’s why, in contrast to what has been stated in theory,  one mutation or variant cannot alter the life cycle transitions of one species, let alone enable adaptive evolution via species diversification. A mutation can cause an effect but an affect on behavior must link the effect to adaptive evolution.

In what first appears to be an explanation of an adaptive mutation, this video  teaches that control of adaptive evolution from the bottom up is amino acid-dependent and that the metabolism of nutrients like amino acids and sugars to pheromones controls adaptive evolution from the top down. The epigenetic tweaking of a genetically predisposed nutrient-dependent variation enables changes in immense gene networks via interactive changes in intracellular signaling and stochastic gene expression. Those changes are required to get from the sensory environment to de novo protein synthesis. In this study, the effect is presumably on thermoregulation of intranuclear interactions and effects on microRNA-controlled Toll-like receptor-mediated immunity.

The allele does not simply arise. The ability to express a genetically predisposed variation exists in the genome of the cell. The sensory environment must cause intracellular changes that result in de novo protein synthesis required for the allele to arise. Nutrients fuel the changes in the microRNA / messenger RNA balance and provide the energy required for chromatin remodeling via alternative splicing that result in de novo protein synthesis. The requirement remains to link the allele to behavior and back to genes.

I will address that requirement in part 2.



James Kohl
Retired medical laboratory scientist

James Kohl

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