Excerpt: “They found that E. coli O157 is unable to attach itself to host tissue in high concentrations of D-Serine. Other strains, such as those that cause meningitis, thrive in the presence of the amino-acid.”
My comment: Three steps are required to link the amino acid substitution in E. coli to RNA-mediated stability of the DNA in the organized genome of a nutrient-dependent strain.
1) nutrient-dependent potentiation makes a trait possible;
2) receptor-mediated actualization makes the trait manifest via nutrient uptake and metabolism;
3) pheromone-controlled refinement fixes the amino acid substitution, which makes it effective.
Effectiveness of the amino acid substitution in manifested when RNA-directed DNA methylation links thermodynamic cycles of protein biosynthesis and degradation from metabolic networks to genetic networks that stabilize protein folding in the DNA of organized genomes.
In the words of Blount, Barrick, Davidson, & Lenski, the three-step process “…is probably typical…” of how many new functions arise. Evolutionary theorists typically replace that 3-step process and claim that Lenski’s experiments proved beneficial mutations cause evolution. See, for example: The Man Who Bottled Evolution See for comparison Combating Evolution to Fight Disease
In the context of combating evolution, it is important to note that Dobzhansky (1973) was aware that a single amino acid substitution differentiated the blood cell types of humans, gorillas, and chimpanzees. “…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.”
This research report links microbes (E. coli) to man (humans) via the conserved molecular mechanisms we first detailed in our 1996 Hormones and Behavior review “From Fertilization to Adult Sexual Behavior”
Everything learned about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation attests to the fact that nothing about RNA-directed DNA-methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species has changed during the past 18 years. That suggests it has never changed. That means conserved molecular mechanisms link ecological variation to ecological adaptations without this pseudoscientific nonsense: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199) “Mutation-driven evolution”
See also: Natura non facit saltus (Latin for “nature does not make jumps”)
This was an essential element of Charles Darwin’s treatment of natural selection. Erwin Schrödinger’s objections to de Vries quantum jumps, which led to the definition of mutations, supported Darwin’s claims that “conditions of life” must come before any consideration for natural selection. Erwin Schrödinger’s support for Darwinian natural selection without the definition of mutation was dismissed along with Darwin’s “conditions of life,” which theorists seem to think somehow followed from whatever was naturally selected. The “cart before the horse” bastardization of Darwin’s theory by population geneticists is still more popular among evolutionary theorists today. They were taught to believe that natural section occurred and that it established the “conditions of life” and evolution of biodiversity by eliminating mutations despite no experimental evidence of biologically-based cause and effect to support their ridiculous claims.
“In the biological context, the principle [that nature does not make jumps] was used by Charles Darwin and others to defend the evolutionary postulate that all species develop from earlier species through gradual and minute changes rather than through the sudden emergence of new forms. Modern evolutionary biology has terminology suggesting both continuous change, such as genetic drift, and discontinuous variation, such as mutation. However, as the basic structure of DNA is discrete, nature is now widely understood to make jumps at the biological level, if only on a very small scale.”
Excerpt: “This locus codes for a D-serine deaminase (DsdA), a D-serine inner membrane transporter (DsdX) and an essential LysR-type regulator of the system (DsdC).
My comment: The biologically uninformed may continue to portray the three step process above as if the amino acid substitution could be called a mutation. However, this research on E. coli refutes the concept of jumps that have been reported as mutations since the invention of neo-Darwinism.
Nutrient-dependent energy is obviously the only way to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. The sun’s biological energy is linked from light-induced amino acid substitutions in plants and animals to nutrient-dependent pheromone-controlled fixation of amino acid substitutions in organisms from microbes to man.
Although amino acid substitutions clearly link jumps in energy, which are exemplified in the ecological speciation via amino acid substitutions in viruses, yeasts, nematodes, invertebrates, and vertebrates, the example of a single amino acid substitution that differentiates cell types in E. coli is a welcome addition.