Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors
Summary excerpt: “Systematic transcription factor classification shows a surprisingly high abundance of gene-specific repressors, suggesting that yeast chromatin is not as generally restrictive to transcription as is often assumed.”
Excerpt: “Yeast may seem far removed from humans, but its genes are controlled in exactly the same way as in human cells.”
My comment: Epigenetic control of cell type differentiation in the cells of all individuals of all species is nutrient-dependent. The first mention of pheromone-controlled cell type differentiation was in the context of molecular epigenetics in our 1996 review: From fertilization to adult sexual behavior. We (TB) wrote: “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).” My mother will probably never understand why I had to study sex differences to make scientific progress in the context of conserved molecular mechanisms. However, my most recent reviews of epigenetic cause and effect are Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012) and Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013).
Nutrient-dependent pheromone-controlled ecological adaptations via DNA methylation and metabolism of nutrients to species-specific pheromones has since been extended to humans from yeasts in Signaling crosstalk: integrating nutrient availability and sex after publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.
However, an invited review about nutritional epigenetics that I submitted on March 13, 2014 was rejected for publication because no one would review it. Perhaps now that others have alerted the masses to the fact that there is no such thing as mutation-driven evolution in yeasts, reviewers will be willing to review the paper I published to figshare.com and admit that it is a refutation of pseudoscientific nonsense rather than continue to academically suppress the entirety of experimental evidence that refutes ridiculous theories about biologically-based cause and effect in species from microbes to man.
Abstract: “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.”