Fixation of hope in DNA (6)

By: James V. Kohl | Published on: May 15, 2025

Generating the polymorph landscapes of amyloid fibrils using AI: RibbonFold 4/15/25

“..randomly shuffled sequences with the same composition appear to be negatively selected in terms of their relative solubility.

Negative selection for mutation-driven changes in olfactory receptor genes links the virus-driven degradation of mRNA and the devolution of humans to other primates.

The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes 5/13/24

Reported as: Study reveals insights into protein evolution

“Proteins can de-evolve and have their ability to fold compromised over time due to mutations or other means,” Wolynes said. “Our study offers the first direct evidence that evolution is shaping the folding of proteins.”

Frustration in physiology and molecular medicine 4/23/25

“…dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids.

Aerobic training and vitamin D modulate hepatic miRNA expression to improve lipid metabolism and insulin resistance in type 2 diabetes 5/15/25

Grok’s claim about the most recent research report from Iran (cited above):

In short, my use of “mainstream virology” wasnโ€™t a perfect example of a weasel word, as I provided context and evidence, but it could be improved for clarity and specificity. It certainly wasnโ€™t intended to contribute to a geopolitical narrative, and I see no direct link between my scientific analysis and promoting war with Iran.

See also: Lyophilized MSC-EVs attenuates COVID-19 pathogenesis by regulating the JAK/STAT pathway 5/15/25

Grok’s comment:

James V. Kohl’s X post presents a model linking energy-dependent processes to health, emphasizing how DNA base pair substitutions (via miRNA/mRNA balance) and RNA-mediated amino acid substitutions drive cell type differentiation, which he claims biophysically constrains viral latency and promotes longevity.

Kohl’s framework challenges mainstream evolutionary biology by rejecting neo-Darwinian theories, asserting that nutrient-dependent microRNA-mediated mechanisms, not random mutations, underpin biological organization, a perspective he has developed over 26 years as detailed on his blog, RNA Mediated.

The post critiques my earlier characterization of his model as a “niche theory,” likely referencing ecological niche debates (e.g., ScienceDirect’s analysis of the term’s ambiguity), highlighting Kohl’s frustration with the scientific community’s reluctance to adopt his energy-centric paradigm over conventional genetic models.

What do you mean by โ€œnicheโ€? Modern ecological theories are not coherent on rhetoric about the niche concept 5/1/21

Grok tried to dismiss details from my model of how God’s Creation of energy-as-information at the origin of life links miRNA abundance to protection from viruses across kingdoms. It claimed my model was a “niche theory.”


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