The stability of organized genomes (3)

By: James V. Kohl | Published on: August 5, 2015

See also:

The stability of organized genomes;

The stability of organized genomes (2)

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt from 6/14/13 

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.

Global relationships in fluctuation and response in adaptive evolution

Preprint pdf opens here

It should be noted that the essence of cellular dynamics is reproduction in which the abundance of each cellular component is roughly doubled, and this constraint imposed by cellular reproduction imposes a restriction on the time development in phenotype. Such a restriction can be represented by a high-dimensional cellular state space, in which each axis represents the abundance of each cellular component.

My comment: Simply put, this means ecological variation must lead to nutrient-dependent RNA-mediated gene duplication that is biophysically constrained by the physiology of reproduction. That simple fact is repeated at least twice — in different contexts — within this manuscript.
Excerpt 2)

…the abundances of cellular components generally exhibit fluctuations even without genomic alternations, which originate from the stochastic nature of intracellular chemical reactions.

My comment:  Nutrient-dependent intracellular chemical reactions is another way to bury this fact in rhetoric: FACT: The chemistry of nutrient-dependent RNA-mediated protein folding is biophysically constrained.
Excerpt 3)

The suggested proportionality between the response of cellular states to environmental change and genetic change, as well as between the response and fluctuations of component abundances, if confirmed, implies the proportionality among two-by-two quantities, namely, fluctuations and responses induced by environmental (noise) and genetic changes (mutation).

My comment: They imply that the effects of the epigenetic landscape (the environment) link environmental (noise) to the physical landscape of DNA via mutations. In reality, the epigenetic landscape is linked to the physical landscape of DNA via nutrient-dependent RNA-mediated gene duplication and fixation of RNA-mediated amino acid substitutions that differentiate cell types in the context of the physiology of reproduction in all genera.
Excerpt 4)

Therefore, the relationship between the responses and fluctuations, analogous to thermodynamics, is represented by the landscape of the growth rate as a function of phenotype (expression level) and the environment.

Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)
Published abstract: Chemical ecology drives adaptive evolution via 1) ecological niche construction, 2) social niche construction, 3) neurogenic niche construction, and 4) socio-cognitive niche construction (Kohl, 2012). Nutrients are metabolized to pheromones that condition effects on hormones that affect behavior in the same way that food odors condition behavior associated with food preferences. For example: glucose (Roland and Moenter, 2011) and pheromones alter the secretion of gonadotropin releasing hormone (GnRH) and luteinizing hormone (LH). Across species comparisons of epigenetic effects on genetically predisposed nutrient-dependent and hormone-driven invertebrate and vertebrate social and sexual behavior indicate that human pheromones alter the development of the brain and behavior via the same molecular mechanisms (Krubitzer & Seelke, 2012), which are conserved across all species.
5.5 minute video representation

Invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

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