Skip the politics; embrace the facts

By: James V. Kohl | Published on: November 2, 2015

It’s Not Brain Surgery, Ben Carson


…“Heal Inspire Revive,” invokes an image of him pounding on the chest of a pulseless America. Whether or not he actually knows how to handle a crash cart of that size, many voters don’t seem to doubt that he can. And he doesn’t doubt it either.

My comment: I do not expect anyone who understands what is currently known about how physics and chemistry are linked to the biophysically constrained conserved molecular mechanisms of nutrient-dependent RNA mediated protein folding to have doubts about how to restore America’s pulse. President Obama, who is not a brain surgeon, led the way in his 2015 State of the Union address when he focused, albeit briefly, on the need to link nutritional epigenetics to precision medicine via what is known about the stability of organized genomes, which is perturbed by viruses. The viruses are linked to all pathology. For example, Richard Dawkins can be compared to a virus.

Richard Dawkins: ‘Terrible Indictment’ of Ben Carson That He’s ‘Ignorant’ on Evolution


…evolution is a fact, not a belief, and “you can’t not believe in it unless you’re ignorant.”

My comment: Dawkins ignores the claim that the bacterial flagellum re-evolved over-the-weekend in the study reported here: Evolutionary Rewiring

“Their experiments show how a biological function—in this case, flagellar motility in Pseudomonas fluorescens—can re-evolve after the deletion of a seemingly critical gene. The bacteria regained motility not by reacquiring the lost gene . . . but instead by mutations in other genes that put their products to new uses.”

My comment: That claim about the “re-evolved” function after gene deletion can be placed into the context of claims of how metabolic networks are linked to genetic networks by evolutionary theorists outside the context of the nutrient-dependent pheromone-controlled physiology of reproduction. Typically, they report evolved functions outside the context of DNA repair and the physiology of reproduction.
For example, see:

Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage


1) …89% of spontaneous base-pair mutations in aerobically grown E. coli have been attributed to ROS (Sakai et al., 2006).
2) Bacteria often react to stresses by increasing their mutation rate to help them adapt and indeed exposure of aerobically grown E. coli to sublethal levels of bactericidal antibiotics increases the mutation rate (Kohanski et al., 2010a).
3) … the underlying molecular mechanism is thought to involve incorporation of oxidized nucleotides into nascent DNA coupled with a temporary suppression of mismatch repair so that they are not removed (Gutierrez et al., 2013).
4) …the evolution of a system that increases ROS-dependent mutagenesis under the stress of low levels of antibiotics would have been beneficial.
5) … the ROS-dependent component of killing by clinically used concentrations of antibiotics that is due to DNA damage could be a deleterious consequence of a strategy that is normally beneficial for adaptation under less stressful conditions (Dwyer et al., 2015).

My comment: The challenge to all evolutionary theorists is the requirement to place excerpts 1-5 into the context of evolved or re-evolved functional structures without linking evolution or re-evolution via DNA repair and the physiology of reproduction.
RNA-mediated events during thermodynamic cycles of protein biosynthesis and degradation appear to be required to link to gene duplication and nutrient-dependent amino acid substitutions that repair DNA to the stability of organized genomes. The organization of genomes is perturbed by viruses that link mutations to genomic entropy.
How could “89% of spontaneous base-pair mutations in aerobically grown E. coli” be “beneficial for adaptation under less stressful conditions”?
The ability or inability to answer that question may attest to the differences between Dawkins and Carson. They appear to be the differences common to biologically uninformed science idiots, like Dawkins, compared to serious scientists and medical practitioners like Carson.
The biologically uninformed science idiots continue to tout ridiculous theories about mutations and evolution, and wonder why intelligent people don’t accept theories. Serious scientists explain how what is known about nutritional epigenetics links the physiology of reproduction to RNA-mediated cell type differentiation in all individuals of all living genera.
For example, amino acid substitutions and supercoiled DNA are required to protect organized genomes from virus-driven genomic entropy in species from microbes to man.
Claims that species evolved can be placed into the context of the “re-evolved” flagellum, which took 4 days, or in the context of this report: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.

…approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years.

My comment: That experimental evidence was reported as Past 5,000 years prolific for changes to human genome

1) Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years…
2) 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.
3) … the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago.
4) …[this] suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

My comment: In the context of everything known to intelligent people like Ben Carson about how nutrient-dependent RNA-mediated events link metabolic networks to genetic networks via biophysically constrained protein folding chemistry and the physiology of reproduction in species from microbes to humans, no experimental evidence suggests that the bacterial flagellum evolved or that it re-evolved in 4 days.
Similarly, no experimental evidence suggests that humans evolved or that increased rates of deleterious mutations will link natural selection to the evolution of a new human species via diseases linked from virus-driven pathology to the entropy of genomes in all living genera via perturbed protein folding. Dawkin’s claims that Carson is ignorant of evolution require someone to explain how the bacterial flagellum re-evolved in 4 days, or how humans and chimpanzees evolved from gorillas via a single nutrient-dependent RNA-mediated amino acid substitution.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).

See also: Combating Evolution to Fight Disease

…chaperones such as heat shock protein 90 (Hsp90), proteins that massage subideal (mutant) proteins into functional conformations but abandon their regular client proteins during heat and other stresses that destabilize proteins. This causes a stress-inducible release of phenotypic diversity, which may drive evolution (with phenotypes ultimately stabilized by subsequent genetic changes). Both of these molecular mechanisms of protein-based inheritance are major departures from the modern synthesis views of solely mutation-directed variation, solely genetic inheritance, and independence of the generation of variation from environmental conditions.

My comment: The phenotypes that ultimately are stabilized by subsequent genetic changes link metabolic networks to genetic networks and nutrient-dependent RNA-mediated DNA repair, not via mutations to evolution. Thus, Dawkins should clearly be recognized as would be any other pathology that Carson must try to remove from the brains of intelligent people who got confused by neo-Darwinian nonsense.

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