Seemingly futile cycles are not thermodynamically futile

By: James V. Kohl | Published on: September 20, 2014

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Scientists discover an on/off switch for aging cells

The switch controls the growth of telomeres, the timekeepers of cells

September 19, 2014

Excerpt: Understanding how this “off” switch can be manipulated–thereby slowing down the telomere shortening process–could lead to treatments for diseases of aging (for example, regenerating vital organs later in life).”
My comment: Seemingly futile thermodynamic cycles of protein biosynthesis and degradation appear to be confusing. I’m somewhat certain that the folks at Salk realize that cycles of biophysically-constrained nutrient-dependent RNA-mediated protein folding limit how the switches are epigenetically-effected by olfactory/pheromonal input. I’m unsure that what they know is being conveyed to others.
This news report says nothing about how the conserved molecular mechanisms of nutrient-dependent, RNA-mediated, pheromone-controlled cell type differentiation via amino acid substitutions differentiates cell types in species from microbes to man during their life-cycle transitions.See for example:

The journal article is behind a paywall. I have requested it from the corresponding author and may be able to link “Regulated assembly and disassembly of the yeast telomerase quaternary complex” to the thermodynamics of protein structure and function from what they say about “The balance between the assembly and disassembly pathways, which dictate the levels of the active holoenzyme in the cell…” and homeostasis. Obviously, homeostasis is manifested in organism-level thermoregulation.
Hopefully, I can match what is known about biophysical constraints on light-induced amino acid substitutions to nutrient-induced amino acid substitutions in plants and animals via Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins. The rest of the story can then be compared to the ‘Just-So’ stories of evolutionary theorists who left physics and chemistry out of their ridiculous theories based on population genetics.
An open access article places the thermodynamic cycles of protein biosynthesis and degradation into the context of my model. Thermodynamics with continuous information flow.
See: “FIG. 2. Bipartite examples” They use the terms from biology to link the sun’s biological energy to the de novo creation of light-induced amino acid substitutions and enzymes. They link nutrient-dependent RNA-directed DNA methylation from the enzymes to receptor-mediated cell type behavior.
Excerpt: “Measurement and feedback is performed through a nonautonomous process that simultaneously flips the bits, while switching the energy landscape. By biasing uphill potential flips with a nonequilibrium force (not shown), the particle can be driven preferentially uphill in order to extract work.”
My comment: The “nonequilibrium force (not shown)” is probably the anti-entropic “force” of the sun, which altered the equilibrium of cell from the time of their energy-dependent creation. The “flips”probably are base pair flips, which are linked from differences in hydrogen bond energies to cell type differentiation via amino acid substitutions in my model of nutrient-dependent ecological adaptations.
Excerpt: “Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).”
Again See: “FIG. 2. Bipartite examples”
Excerpt: “…the enzyme, through a sequence of reactions (purple dotted), speeds up the removal of bound methyl groups M (purple). This feedback loop shifts the enzyme’s stability, so as to maintain it in the same adapted distribution…
My comment: The adapted distribution is nutrient energy-dependent RNA-directed via DNA methylation. Ecological adaptations occur via amino acid substitutions that stabilize RNA-mediated protein folding during thermodynamic cycles of protein biosynthesis and degradation that are RNA-mediated and perturbed by mutations. These facts link physics from chemistry to the conserved molecular epigenetics of RNA-mediated cell type differentiation in all genera.
Obviously, more physicists should be taught to understand the accurate representations made of biologically-based cause and effect in “Life as physics and chemistry: A system view of biology.” However, most of them seem unwilling to abandon the pseudoscientific nonsense of their ridiculous theories and would rather prevent scientific progress than admit that they didn’t realize that the link to life from the sun’s biological energy was a more important consideration than mutations, natural selection, and evolutionary theory could ever become — even if serious scientists were not Combating Evolution to Fight Disease.