Epigenetic (re)programming of behavior (2)

The reports on this research bear repeating.

Ants Can Change Their Roles, Study Finds


The researchers found that certain compounds could modify proteins called histones, which affect how tightly DNA is coiled and whether certain other proteins are able to gain access to it.

My comment: The molecular mechanisms of nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions in histones that stabilize supercoiled DNA in the organized genomes of all invertebrates and invertebrates are conserved across all living genera. If they were not, organisms could not behave appropriately in during their ever-changing ecological niche construction and social niche construction.

In another ant species, the molecular mechanisms link UV light to c in the context of foraging behavior. In bacterial the conserved molecular mechanisms link UV light from hydrogen-atom transfer in DNA base pairs to the NORAD system of cellular protection against virus-induced genomic entropy.

Dobzhansky (1973) put all this into perspective when he noted in Nothing in Biology Makes Any Sense Except in the Light of Evolution that

“…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).” 

The light of evolution is sunlight (see Schrodinger, 1944).  But people did not understand Dobzhansky’s sense of humor. Like Schrodinger, Dobzhansky linked ecological variation to ecological adaptation. The links were established at a time when serious scientists were not allowed to openly challenge the dogma of the neo-Darwinists. The serious consequences of challenging unarmed peers to a battle of wits were typically avoided. So, Dobzhansky framed his claim in the context of a joke about the difference between the definition of mutation and the facts about amino acid substitutions.

The neo-Darwinists thought he meant that the mutations, which cause all pathology were like virucidal light. In moderation, UV light enables the energy-dependent links from hydrogen-atom transfer in DNA base pairs to unperturbed RNA-mediated amino acid substitutions and protein folding chemistry during theromodynamic cycles of protein biosynthesis and degradation. Outside the context of the fine-tuned balance of these thermodynamic cycles, organisms that cannot find enough food or that eat too much, are like those that are exposed to too much sunlight.  They do not mutate and evolve. They die from starvation or social stress. That was the joke. The neo-Darwinists still don’t get it.

When Dobzhansky made the claim about the single amino acid substitution that differentiates three primate species, he knew that protein folding was nutrient-dependent and that the physiology of reproduction was controlled by pheromones in species from microbes to primates. He established the claim about the amino acid substitution in this context (with my emphasis):

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. 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.

Dobzhansky obviously did not want to offend anyone who preferred to express their findings in the context of de Vries definition of mutation and their ridiculous assumptions about how long it might take for one species to evolve into another. No matter how politely you try to tell someone whose research is reported in terms of mutations and evolution that they are unenlightened, when they realize you are telling them that they did not consider the role of nutrients in their explanation, they will hate you for exposing their ignorance.

Some things about academia never change until after the paradigm shift has come and gone.

For example, see: Origins of De Novo Genes in Human and Chimpanzee

Conclusion: Our results indicate that the expression of new loci in the genome takes place at a very high rate and is probably mediated by random mutations that generate new active promoters. These newly expressed transcripts would form the substrate for the evolution of new genes with novel functions.

For comparison, Dobzhansky (1973) wrote:

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

My comment: God’s method of Creation appears to link sunlight to biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry via amino acid substitutions that differentiate all cell types in all individuals of all living genera.

Caveat: Dobzhanzky (1973) added:

Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

My comment: Of course he knew that would placate the neo-Darwinists who believed the fossil record provided evidence of mutation-driven evolution via natural selection. The theorists have remained unenlightened, and Dobzhansky must have known that they will always remain unenlightened.

So, like all other serious scientists today, he threw insults at the unenlightened that they still do not understand. They are too unenlightened. They didn’t even get his joke about mutations in the LIGHT of ecological adaptations. Mutations prevent the adaptations, which supports one of Dobzhansky’s earlier claims:

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! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

See also: Metabolic theory predicts whole-ecosystem properties

My comment: The flow of carbon through ecosystems is nutrient-dependent and controlled by the physiology of reproduction. Evolution controls nothing.  Darwin’s “conditions of life” control everything. Neo-Darwinian evolution is based on pseudoscientific nonsense.

See for comparison:

See also:

Bipolar drug turns foraging ants into scouts

My comments to her antagonists:

Elizabeth Pennisi is one of few science journalists who have, like John Hewitt, consistently and accurately represented both sides of the evolution vs creation argument by reporting on Lenski’s experiments for comparison to what is known about the links from nutrient-dependent microRNAs to adhesion proteins and supercoiled DNA, which protects organized genomes from virus-driven entropy.
If she included everything she knows about top-down causation for comparison to ridiculous theories about mutations and evolution, only a few people could grasp the extent of her claims and she would invite attacks by the biologically uninformed masses of neo-Darwinian theorists and their minions.
Your claim about her deficiency in this article attests to your inability to link atoms to ecosystems across all genera. She has already done that via the reporting in: “Inching toward the 3D genome” and many other representations that link what is known about how “…the nucleome structure changes as cells age, differentiate, and divide….”

She didn’t mention the RNA-mediated single amino acid substitution that links the nutrient-dependent life history transitions of all invertebrates to vertebrates and the life history transitions from adolescence to adulthood in humans, either.
But, IF SHE HAD, I am sure that reporting the Val158Met substitution in the context of drug metabolism and the dopaminergic reward system, which links metabolic networks to genetic networks via histones and supercoiled DNA, would lead someone to claim that the amino acid substitution is a mutation.

Really? A trip to the library? Where did you first read about this (at the library)? I’m thinking you were on a computer some where, which means you could quickly have found more information.
The fact that she is a great science writer changes everything. It encourages those who know the scientific facts to investigate them and learn more.
Most science journalists simply report whatever pseudoscientific nonsense they see reported in other venues.
“All in the (bigger) family” was a report on a conference, which put her ahead of all science journalists who did not attend the conference that preceded publication of this article:
“The phylogenetic utility and functional constraint of microRNA flanking sequences”
The flanking sequences biophysically constrain RNA-mediated cell type differentiation in all invertebrates and vertebrates. The question arises: “Why is anyone reporting their results in terms of mutations and evolution?”
Have other journalists and researchers never attended a conference where serious scientists were presenting results based on what is known about the microRNA/messenger RNA balance and all nutrient-dependent cell type differentiation that is not perturbed by viruses?
Re: “We finally have a mechanism to understand ‘nurture’ in molecular terms,” says Gene Robinson… The ant study, he adds, highlights “how the environment gets under the skin to affect gene expression, and consequently, neural activity and behavior.”
Nurture has been understood in the context of molecular terms since we first linked the molecular mechanisms of RNA-mediated cell type differentiation in species from microbes to humans in the molecular epigenetics section of our 1996 Hormones and Behavior review: “From Fertilization to Adult Sexual Behavior.” Gene Robinson cited it in Elekonich and Robinson (2000) “Organizational and activational effects of hormones on insect behavior.”
The comment about how the environment gets under the skin appears to come from a review article by Bruce McEwen: “Brain on stress: How the social environment gets under the skin”
Bruce McEwen is one of the few researchers I know who consistently differentiates between epigenetic effects on genes and hormones for comparison to the affects of hormones on behavior. The comparisons are required to link nutrient stress and/or social stress from ‘nurture’ to ‘nature.’
The manifestation of top-down causation in the context of epigenetic effects on histone modifications links RNA-mediated foraging behavior to amino acid substitutions that stabilize the organized genomes of ecologically adapted species in the context of the physiology of reproduction. The molecular mechanisms of nutrient-dependent ecological adaptation link ecological variation from atoms to ecosystems in all living genera.


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