Another failed rescue attempt

By: James V. Kohl | Published on: January 16, 2016

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Social Darwinism, A Case of Designed Ventriloquism
Excerpt:

In Wilson’s view, Social Darwinism “is perhaps the most important example of a term that became tainted and needs to be rescued.” According to him, from the very beginning, this term “was used as a pejorative to brand laissez faire policies that Darwin did not endorse.

My comment: Darwin knew nothing about genetics. He stressed the fact that “conditions of life” must be placed before natural selection. Others ignored that fact and bastardized Darwin’s theories beyond recognition. Clearly, a long-awaited rescue attempt was required.
In “Mutation-driven evolution,” Masatoshi Nei attempts to rescue “mutation” from its use by biologically uninformed neo-Darwinian theorists.
Excerpt:

Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The rescue attempt is futile. He doesn’t seem to realize that changes in genomic structure start with nutrient energy-dependent base pair substitutions that are linked to the physiology of reproduction in all living genera.
Every aspect of RNA-mediated reproduction is biophysically constrained by the availability of energy, which is linked to all biodiversity in the context of models that link atoms to ecosystems.
Nei concludes:

“…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

All serious scientists know that constraint-breaking mutations are the source of pathology, not increasing organismal complexity. That fact makes it impossible to rescue neo-Darwinism from its definitions and assumptions.
See also: A failed theory of cancer: two more decades of pseudoscience
Excerpt:

The example of weekend evolution occurred in the context of only two nutrient-dependent amino acid substitutions and the RNA-mediated events that linked them to the physiology of reproduction. The physiology of reproduction is linked to chromosomal rearrangements, which are required for the biodiversity of morphological and behavioral phenotypes to exist in all living genera.

The DNA of Human Evolution

Excerpt:

…the same sequence is in the chicken genome and has only two differences between chimp and chicken. There have been hundreds of millions of years of evolution separating chicken and chimp, and yet we only see two changes. Whereas in six million years, a blink of the eye in evolution’s time, we see 18 changes in this stretch of the human genome.

[Editor’s note: Such acceleration in the rate of change in the genome is a hallmark of what biologists call “positive selection,” in which mutations that help an organism survive and reproduce are more likely to be passed on. The sequence of 118 letters Pollard found became known as human accelerated region 1 (HAR1).]

My comment: The editor immediately placed the two substitutions in the sequences of amino acids into the context of mutation-driven evolution. For comparison, see Dobzhansky (1973):

Excerpt:

…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)

My comment: In the example of weekend evolution of the bacterial flagellum, the gain of the functional structure was attributed to two amino acid substitutions that also were reported to be mutations.

Excerpt:

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

My comment:

What we see is a pattern of denial. There is no DNA of Human Evolution outside the context of an atoms to ecosystems model of nutrient energy-dependent top-down causation. That model is linked to the physiology of reproduction and RNA-mediated amino acid substitutions. The substitutions are linked to the stability of all organized genomes via chromosomal rearrangements. The two nutrient-dependent RNA-mediated amino acid substitutions, T97P and R442C, were fixed via the physiology of reproduction. If they had not been fixed in the organized genome of the organism that re-evolved its flagellum, its colonization of the culture mediated would have ended. The colony and all its individuals would have starved to death.

Typically, colonization ends with the shock to the organisms that occurs when the culture plates are placed into the refrigerator. A mistake led from leaving them in the incubator to the weekend evolution. The mistake attests to the mistake that neo-Darwinian teleophobes made when they refuse to recognize any aspect of cell type differentiation that cannot be attributed to mutations. They assume that mutations caused the weekend evolution.

Mutations link the theft of energy by viruses to perturbed protein folding. The energy theft links failed nutrient energy-dependent RNA-mediated DNA repair to all pathology. Only one amino acid substitution in a virus is required to exemplify the link to all pathology.

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution and the author’s comment:

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

My comment: That amino acid exemplifies the theft of energy by the virus. The theft helps to explain why two nutrient-dependent RNA-amino acid substitutions are required for DNA repair until one of them is fixed in the organized genome. One fixed nutrient-dependent RNA-mediated amino acid substitution then differentiates the cell types of different species, as Dobzhansky noted 43 years ago.

…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)

My comment: Any attempt to rescue theories that fail to explain how cell type differentiation occurs with claims that mutations are linked to the evolution of new species is a rescue attempt grounded in pseudoscientific nonsense. That nonsense is touted by those who used a definition of “mutation” as the basis of their assumptions about how long it might take for accumulated mutations to lead to the evolution of a new species.

See: [W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.

My comment: Collectively, these experts can overthrow nothing. For example, among these paradigm shift preventers are people: Dimitar Sasselov: Generation II — Let There Be Light.

Excerpt:

There is clearly the realm of atoms and small molecules to consider, which is chemistry, and there is also something that emerges under conditions we are still trying to figure out.

See for comparison:

Let there be anti-entropic light (1)

Let there be anti-entropic light (2)

Let there be anti-entropic light (3)

My comment: The de novo creation of nucleic acids and the energy-dependent de novo creation of receptors that enable the ability of nutrients to enter cells, which facilitates nutrient-dependent RNA-mediated DNA repair via fixation of amino acid substitutions in the organized genomes of all living genera is something still missing from their explanations of biologically-based cause and effect.

The expertise of the “Paradigm Shifters” can be compared to the expertise of serious scientists who have linked atoms to ecosystems.

See: Structural diversity of supercoiled DNA

Conclusion:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

My comment: The modulation of DNA metabolic processes links Dobzhansky’s light of evolution from the sun’s biological energy to RNA-mediated cell type differentiation via nutrient-dependent amino acid substitutions, which are required for cell type differentiation that is linked to all biomass, all morphological phenotypes, and all behavioral phenotypes by fixation of only one amino acid substitution.