Foundamentals of theory

By: James V. Kohl | Published on: October 8, 2015

There are foundations of epigenetics and fundamentals of molecular mechanisms. They have been detailed in this atoms to ecosystems model of RNA-mediated cell type differentiation. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.

I have never seen anyone mention the “foundamentals” of epigenetics. It appears the word has been invented. Similarly, the word “mutation” was invented in 1904 by de Vries.

Inventing words and defining them to fit ridiculous theories about neo-Darwinian evolution is required to continue convincing theorists that they are something more than biologically uninformed science idiots.

See for comparison:

Absence of canonical marks of active chromatin in developmentally regulated genes


…strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA…

Reported as:

Shaking up the foundamentals of epigenetics


The results of this study contrast sharply with the generally accepted view of the key roles that these epigenetic marks play in regulating gene expression.

My comment: If true, this should have been reported before the top three 2015 Nobel Prizes for science were awarded to researchers who linked physics, chemistry, and conserved molecular mechanisms of epigenetically effected RNA-mediated cell type differentiation in species from microbes to man via DNA repair in the context of the physiology of reproduction. See: DNA Repair Pioneers Win Nobel
Pretending there is any contrast to the accurate representations of what experimental evidence has clearly detailed in the context of an atoms to ecosystems model is like returning to the 20th century definition of “mutation” and trying to link it to evolution while all serious scientists are linking nutrient-dependent RNA-mediated amino acid substitutions from ecological variation to ecological adaptation via DNA repair.
See also: A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient.

Reported as: 

Nutrient availability can cause whole-genome recoding


“When queuine is abundant, organisms naturally recode its codons to favor the use of ones that are more efficiently translated by Q-modification,” Drummond said. “In this way, a single nutrient causes a snowballing effect that leads to wide-spread changes in how proteins are encoded

The “snowballing effect” was manifested as “re-evolution” of the bacterial flagellum over-the-weekend. See: Evolutionary Rewiring
The epigenetic effect of nutrient stress can also be placed into the context of the anti-entropic epigenetic effects that link heat shock proteins to nutrient-dependent ecological adaptations or compared to virus-driven genomic entropy during thermodynamic cycles of protein biosynthesis and degradation.
In the model organisms that reportedly are Shaking up the foundamentals of epigenetics, ecological variation is linked to ecological adaptation via the anti-entropic effects of food and the pheromone-controlled physiology of reproduction that link the biodiversity of all species from atoms to ecosystems as shown in the collective works of this year’s Nobel Laureates in Physics, Chemistryand Physiology and/or Medicine.
See also: Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress

Proteins synthesized in response to heat shock, such as the chaperone Hsp104, show an increase in both pre- and post-shock ratios, indicating new synthesis; increased signal in both channels reflects incorporation of imported post-shock amino acids and residual or recycled pre-shock amino acids (Figure 6B).

My comment: The synthesis of proteins links nutrient-dependent thermodynamioc cycles of protein biosynthesis and degradation to RNA-mediated cell type differentiation in the context of feedback loops.  See: Feedback loops link odor and pheromone signaling with reproduction
See also: Mechanisms of stress in the brain
Abstract excerpt:

…continually changing pattern of gene expression mediated by epigenetic mechanisms involving histone modifications and CpG methylation and hydroxymethylation as well as … the activity of retrotransposons … may alter genomic stability.

The continually changing patterns of epigenetically effected gene expression linked to genomic stability are perturbed by viruses, which steal the nutrient energy that is required for proper RNA-mediated protein folding chemistry that is mediated by amino acid substitutions.
Journal article excerpt:

Glucocorticoids are not the sole mediators of these effects, in which excitatory amino acids and many other cellular mediators also play important parts (Box 1). These mediators span influences from extracellular adhesion molecules to cytoskeletal elements and at least one nuclear pore complex protein.

My comment: The role of RNA-mediated events that link amino acid substitutions to cell type differentiation in all cells of all tissues of all organs and all organ systems attests to the amount of pseudoscientific nonsense touted by evolutionary theorists who still can’t seem to stop making claims that are unsupported by any experimental evidence of biologically-based cause and effect.

See also: Archaeal ancestors of eukaryotes: not so elusive any more

The challenge lies in the investigation of the biology of these organisms. Although we can never know what precisely happened more than a billion years ago, to me, demonstration of the archaeal–bacterial endosymbiosis in the laboratory would mean the completion of the bridge. This is an extremely tall order but then again, who would have predicted 25 years ago that complete genome sequencing of microbes that do not grow in culture would become a near routine exercise?

My comment: Who would have predicted that Koonin would continue making unsupported claims about the origin of endosymbiosis after he admitted “The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
Why hasn’t he searched for information about RNA-mediated epigenetic regulation of gene expression or RNA-mediated gene silencing. What is know about cell type differentiation in species from microbes to man should be considered in the context of how viruses perturb protein folding before any more unsubstantiated claims are made by Koonin or anyone else.

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