5th-6th Sept 2018 Dublin, Ireland

Polymaths and paradigm shifts: from Asimov to Bear (4)

Saying Goodbye to the RNA World Theory

RNA has a limited ability for catalysis compared to peptides, and would have struggled to maintain its catalytic activity under the changing temperature conditions of early Earth. Carter and Wills also argued that if an RNA world existed, it would have been unlikely for it to incorporate peptides later on.

See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

The energy-dependent creation of ATP synthase has since been linked to this claim from McEwen et al., (1964):

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

By starting with the energy-dependent de novo creation of enzymes, others have linked Schrödinger’s claims from “What is Life” (1944)  to all biophysically constrained biodiversity.
Say Hello again to Schrödinger at 75 – The Future of Biology
Let Timothy J. Cunningham, who disappeared from the CDC last month, reintroduce you. See his publications on:
1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
4) “Health and Safety Issues for Travelers”
Serious scientists know that all racial/ethnic disparities are food energy-dependent, RNA-mediated, and pheromone-controlled  in the context of enymes, metabolism, and amino acid substitutions. Fixation of the RNA-mediated amino acid substitutions differentiates all cell types in all living genera — including sex differences in cell types.
See for examples our section on molecular epigenetics from this 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…

See for comparison, this nonsense: Caenorhabditis elegans glia modulate neuronal activity and behavior

Introduction: a brief on evolution of neuroglia

“Nothing in biology makes sense except in the light of evolution”. — Theodosius Dobzhansky (1900–1975)

Evolution of the nervous system proceeded through an increase in number and complexity of the nervous elements and through their specialization into electrically excitable neurons connected through defined synaptic contacts and electrically non-excitable neuroglia forming networks through intercellular gap junctions. Intercellular chemical neurotransmission is, however, characteristic for both forms of the neural cells that express appropriate receptors and are capable of secreting neurotransmitters. The evolution of the nervous system was not a straight journey from less complex and accomplished networks to the more refined ones; at the turning point between invertebrates and vertebrates, a fundamental metamorphosis occurred that changed the overall structure of the central nervous system (CNS).

The difference in the energy of two photons has since been linked from the proton motive force to the creation of enzymes and metabolism of food. The pheromone-controlled physiology of reproduction in species from bacteria to humans has linked DNA methylation from the creation and fixation of RNA-mediated amino acid substitutions to viral latency and all biodiversity. Timothy J. Cunningham placed that fact into the context of his history of published works.
For comparison, see: On the Difference between Physics and Biology: Logical Branching and Biomolecules (2018) and The Large Scale Structure of Space-Time(1975) George FR Ellis was a coauthor of both published works.
He, and others like him, failed to link Physics and Chemistry from molecular epigenetics to what is known about energy-dependent RNA-mediated biophysically constrained cell type differentiation to all biodiversity on Earth. Framing what is known to all serious scientists about cell type differentiation in the context of what Ellis might think is a logical representation of biomolecules attests to his lack of logic across the time-space continuum of his life.
See for comparison: Olfaction Warps Visual Time Perception (2017).
See also Odor-induced mood state modulates language comprehension by affecting processing strategies (2016)
The 2016 citation to The impact of natural odors on affective states in humans can now be linked to the accurate representations of top-down biophysical constraints on food energy-dependent pheromone-controlled feedback loops. The feedback loops are required to biophysically constrain viral latency.
See: What is life when it is not protected from virus driven entropy (video)

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See for comparison: Gay, Straight, and the Reason Why: The Science of Sexual Orientation (2011)

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (pp. 210- 211)

See also: Gay, Straight, and the Reason Why: The Science of Sexual Orientation, 2nd edition (2016)
From the second edition of LeVay’s book:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect… (p. 115)

LeVay cites Kohl et al., (2001) Human pheromones: integrating neuroendocrinology and ethology.
He has never mentioned the fact that the effects of virus-driven entropy on cell type differentiation were linked human sexual orientation in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) and in the book chapter he cited in the first edition of Gay, Straight, and the Reason Why: The Science of Sexual Orientation.
See for comparison: Always follow your nose: the functional significance of social chemosignals in human reproduction and survival (2015) This article is part of a Special Issue “Chemosignals and Reproduction”
John Cacioppo, a Founder of Social Neuroscience, Dies

The University of Chicago psychology professor made fundamental contributions to understanding the neural mechanisms of social experiences.

My comment to The Scientist:

See also: Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism (2012)

I hope John Cacioppo is remembered for this refutation of neo-Darwinian pseudoscientific nonsense:

Although peptide chemistry has been with us since amino acids first formed, the social role of oxytocin did not exist prior to the evolutionary sculpting of the vertebrate brain.

He may have been one of the first social scientists to recognize the fatal flaw that others continue to include in their works. All other serious scientists, like him, start with the energy-dependent creation of enzymes and amino acids. Only pseudoscientists still start with the evolution of the vertebrate brain.

I remember when he and his wife turned towards me and smiled — after I asked the speaker from Argentina about the role of oxytocin in a rodent model. No studies were being done for the obvious reason that few people knew where oxytocin came from.

I invited the speaker to lunch and we laughed a lot about the works that tried to link oxytocin to differences in behavior without linking the differences to altered  RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse

RIP John Cacioppo

See also: Multilevel integrative analyses of human behavior: social neuroscience and the complementing nature of social and biological approaches (2000)
Nothing published during that 12-year period and nothing published before or since then suggests the the neuroarchitecture of intelligent creatures somehow evolved.
For comparison, see: Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior (2012) Presented at the Society for Social Neuroscience Annual Meeting 2012
See also: Neuroglia in C. elegans (2018)

The nematode C. elegans is one of the most important model organisms for understanding neurobiology. Its completely mapped neural connectome of 302 neurons and fully characterized and stereotyped development have made it a prototype for understanding nervous system structure, development, and function. Fifty-six out of C. elegans‘ total of 959 somatic cells are classified as neuroglia. Although research on worm glia has lagged behind studies focused on neurons, there has been a steep upswing in interest during the past decade. Information arising from the recent burst of research on worm glia supports the idea that C. elegans will continue to be an important animal model for understanding glial cell biology. Since the developmental lineage of all cells was mapped, each glial cell in C. elegans is known by a specific name and has research associated with it. We list and describe the glia of the hermaphrodite form of C. elegans and summarize research findings relating to each glial cell. We hope this lecture provides an informative overview of worm glia to accompany the excellent and freely available online resources available to the worm research community.

The worm research community seems to be largely unaware of this fact: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
The have failed to link food odors from the pheromone-controlled physiology of reproduction to ecological adaptatation manifested in morphological and in behavioral diversity.

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