DS Wilson’s view of biophysically constrained life (3)

By: James V. Kohl | Published on: February 26, 2019

A Different Kind of Theory of Everything (2/19/19)

1) In 1964, during a lecture at Cornell University, the physicist Richard Feynman articulated a profound mystery about the physical world.

2) It seems inconceivable that this intricate web of perfect mathematical descriptions is random or happenstance. This mystery must have an explanation.

3) Some researchers are attempting to wean physics off of space-time in order to pave the way toward this deeper theory.

In 1964, McEwen et al., reported that “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” in the context of Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
In 1964, Dobzhansky reported that “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.” in the context of Biology, molecular and organismic, albeit after starting with what most thought was a joke.

“The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!”

In 1973, Dobzhansky reported that differences in the fixation of amino acid substitutions in the different peptides of different cell types in different individuals of different species, linked one amino acid substitutions to differences between chimpanzees and modern humans compared to gorillas.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, 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.

In the same published work, Dobzhansky reported on the established link from the creation of Cytochrome C, which is an enzyme that plays an important role in the metabolism of aerobic cells, to differences in the fixation of amino acid substitutions in diverse organisms, from man to molds. A comparison of amino acid sequences in cytochrome C was linked to differences in mammals and birds by 17 amino acids; differences in classes of vertebrates by 7 to 38 sequences;  differences in vertebrates and insects by 23 to 41 sequences; and differences in animals via 56 to 72 amino acids linked to yeasts and molds.
See for comparison: Genetic dissection of assortative mating behavior, which was subsequently published in PLOS Biology.

Ecologically relevant mating cues (sometimes known as “magic traits” [2,6]) are now predicted to be widespread in nature [6,7], and the last few years have seen considerable progress in our understanding of their genetic basis.

That claim about ecologically important “magic traits”  was reported on 2/7/19 as:

Butterflies are genetically wired to choose a mate that looks just like them.

Who thinks that the link from “magic traits” to biodiversity via visual input makes sense in the context of Dobzhansky’s claims? Who thinks the links from”magic traits” to biodiversity can be placed into the context of claims made by any other serious scientist? Serious scientists understand what is known about the food energy-dependent pheromone-controlled fixation of amino acid substitutions in different species, as detailed above. They also understand why Feynman placed the thoughts of theorists and their ridiculous beliefs about the magic of evolution into the context of his comments on human idiocy.

Indeed, Wolchover’s claim about the need to  wean physics off of space-time in order to pave the way toward this deeper theory reflects on the fact that Olfaction Warps Visual Time Perception and the fact that Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signalling, which was reported on 2/20/19 as:  The smelling of food controls cellular recycling and affects life expectancy

‘The impact of odours at the cellular level is a poorly investigated field’, says Thorsten Hoppe.

I dare say that Thorsten Hoppe,  exemplifies Feynman’s claim about human idiocy, and that Natalie Wolchover now appears to be reporting on it without naming names. The claim about the need for a new deeper theory attests to the fact that theorists still don’t understand anything about the creation of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.
Structural diversity of supercoiled DNA (2015)

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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.

Alternatively, theorists may still claim that everything known about supercoiled DNA arises in the context of “magic traits.”

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