Energy-dependent biodiversity

A general alkyl-alkyl cross-coupling enabled by redox-active esters and alkylzinc reagents
Abstract excerpt:

…the same activating principles used for decades to make simple C–N (amide) bonds from carboxylic acids with loss of water can be used to make C–C bonds…


The ready availability of numerous carboxylic acids (which are easily converted to esters) contributes to the reaction’s versatility.

My comment: Light energy-induced chemical reaction versatility links what is known about biophotonics to the physiology of energy-dependent pheromone-controlled reproduction in soil microbes to human infant brain development. For example, microRNAs (also found in breast milk) and RNA-mediated amino acid substitutions differentiate all cell types in all individuals of all living genera.
This claim appeared in the context of an editorial comment: “Carbon links without helpful neighbors”

The ready availability of numerous carboxylic acids (which are easily converted to esters) contributes to the reaction’s versatility.

My comment: The reaction’s versatility is biophysically constrained in the context of chemotaxis and phototaxis, which link sensory input from metabolic networks to genetic networks in all living genera via carboxylic acids and light-induced changes in protein folding biochemistry. The reaction’s versatility can be discussed in the context of the claims that Dobzhansky (1973) made in “Nothing in Biology Makes Any Sense Except in the Light of Evolution.”
Dobzhansky presciently linked the anti-entropic virucidal energy of sunlight in my model from ultraviolet (UV) light to RNA-mediated DNA repair when he wrote: “I am a creationist and an evolutionist.” If he was not still dead, he still could not support his claims about the light of evolution with experimental evidence of biologically-based cause and effect.
He would probably admit that he was wrong about evolution and accept the fact that he was right about the light and everything currently known about energy-dependent RNA-mediated cell type differentiation that occurs via amino acid substitutions.
For a historical approach to what Dobzhansky (1973) got right, see the claim in Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

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 they call point mutations are nutrient energy-dependent amino acid substitutions. Their mutations, which are really amino acid substitutions, were not put into the context of the physiology of reproduction. The physiology of pheromone-controlled reproduction enables population-wide fixation of amino acid substitutions. But that fact was not considered. Fixation of amino acid substitution limits the transgenerational epigenetic inheritance of mutations.  The fact that mutations consistently link virus-driven energy theft to all pathology was not considered.
Population-wide fixation of amino acid substitutions links the energy-dependent physiology of reproduction to healthy longevity and all biodiversity.
For examples, see: Dobzhansky (1973):
Excerpt 1 (with my emphasis)

The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

My comment: For examples of claims made by people who prefer to use terms such as “minimal mutational differences,” see anything written by neo-Darwinian theorists.
Excerpt 2)

…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.

My comment: For examples that link energy-dependent amino acid substitutions to all biodiversity see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See also: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

My comment: I presented a model of energy-dependent cell type differentiation for comparison to ‘modern evolutionary theory’ and included examples that linked terms such as ‘amino acid’ to biologically-based cause and effect. Andrew Jones failed to provide “…any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.” I suspect that Jones knows nothing about biophysically constrained protein folding chemistry because he wrote an undergraduate thesis on abiogenesis.
See for comparison to that nonsense: Giraffe genome sequence reveals clues to its unique morphology and physiology

Giraffe FGFRL1 contains seven amino acid substitutions that are unique at fixed sites in other mammals and/or are predicted by Polphen2 analysis to alter function (upper panel).

Reported as: How did the giraffe get its long neck? Clues now revealed by new genome sequencing

“These adaptations include unique amino-acid-sequence substitutions that are predicted to alter protein function, protein-sequence divergence, and positive natural selection,” Cavener said.

Also reported as: What researchers are learning as they sequence, map, and decode species’ genomes By Catherine Offord | May 17, 2016

…the team found that the giraffe’s long neck is likely a result of mutations in two sets of protein-coding genes—one controlling gene expression patterns during limb development, the other controlling the expression of growth factors.
The researchers also linked a number of genes in giraffes to the evolution of a more powerful cardiovascular system to cope with the strain of a longer neck.

My comment: Note the difference between the two reports about the same study results. In one report, what Dobzhansky knew about amino acid substitutions and biodiversity was placed into the context of adaptations and protein function, protein-sequence divergence, and positive natural selection.
In the second report, mutations in genes were linked to growth factors and genes were also linked to the evolution of the longer neck.
The disparity between the reports exemplifies the difference between what serious scientists have learned from genome sequencing, and what pseudoscientists still attribute to mutations and evolution. The amino acid substitutions are nutrient-dependent and fixation in organized genomes is enabled by the physiology of reproduction. Mutations are not fixed population-wide except when energy-dependent RNA-mediated DNA repair fails to protect organized genomes from virus-driven pathology. Everything from that point on is linked to extinction by virus-driven energy theft.
See for example, from last year: What researchers are learning as they sequence, map, and decode species’ genomes By Jenny Rood | April 16, 2015

Pathogenicity is measured by the ability of the strain to produce disease in chickens, so it is not known how the new strain will impact wild birds.

See also: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. Author’s comment: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
Summary: Pathogenicity may be determined by a single energy-dependent amino acid substitution in the virus.
I intended to link the physiology of reproduction in soil bacteria from changes in the speed of light on contact with water to temperature changes and change in pH, which are linked to energy-dependent plant growth. Plant growth links carboxylic acids/phenols to the cancer treatment drug taxol. Taxol was initially made from the bark of a yew tree.
If I linked phenols from plant growth to the bull sperm microRNAome and from microRNAs in human breast milk to brain development, biophysicists and biochemists could link physics and chemistry to the conserved molecular mechanisms of cell type differentiation,  or to cancer. But, neo-Darwinian theorists would attribute healthy longevity and cancer to mutations in the context of population genetics.
I have abandoned all hopes of convincing any theorist that healthy longevity and cancer cannot both be linked from mutations to energy-dependent biodiversity.

Add a Comment

Your email address will not be published. Required fields are marked *