Asking the right questions (1)

By: James V. Kohl | Published on: October 7, 2016

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My comment: Communication among different microbial cell types and all other cell types is biophysically constrained by the nutrient energy-dependent pheromone-controlled physiology of reproduction. Autophagy is the link from nutrient-energy-dependent viral latency to healthy longevity in all individuals and species on Earth. That fact was established in the context of details about what was known about RNA-mediated cell type differentiation, which were published in this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior
Excerpt:

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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.

My comment: Since 1996, all neo-Darwinian theorists and most “Big Bang” cosmologists have hated the fact that they could no longer claim that sex determination and differences in behavior automagically emerged in the context of everything else that emerged from nothing and then mutated so that natural selection could determine the survival of all species.
What’s worst is that we also mentioned this possibility:

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 (Runge and Zakian, 1996; Wu and Haber, 1995).

Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine for helping to reestablish facts that were established by the Nobel Laureates, Richard Axel and Linda Buck, who won the same prize in 2004. What has happened during the past two decades since we published our 1996 review attests to the fact that theorists may continue to ignore all experimental evidence of biologically-based cause and effect until they die from the virus-driven energy theft that has killed all other dead things on Earth.
For example, these researchers are living with the denial of this fact: Feedback loops link odor and pheromone signaling with reproduction

Many researchers have simply failed to ask the right questions about how biophysically constrained nutrient energy-dependent viral latency is maintained across life history transitions in all living genera.
See for example: Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect
Conclusion:

Despite the obvious differences between humans and other animals, understanding social learning and culture in animals holds a key to understanding the evolutionary roots of the peculiarities of social learning and culture in humans. It is clear from our study and others on cultural diffusion in animals that once experimenters create the conditions under which such diffusion is beneficial (often via allowing access to desirable nutrition via man-made devices that must be operated in specific ways), they can be instantly observed in many animals. Early tool-using hominids are likely to have created the conditions for themselves that favored the further evolutionary fine-tuning of social learning processes that results in high-fidelity transmission and cumulative culture [21,64]. Our findings add to the accumulating evidence suggesting that the capacity of culture may be within most animals with a relatively basic toolkit of learning processes as described here, in turn shedding light on the evolutionary precursors of the more sophisticated forms of culture in humans.

In reponse to that nonsense, I wrote on the PLOS Blog site: The honeybee model organism links energy-dependent changes from angstroms to ecosystems in the context of autophagy, which prevents virus-driven energy theft by linking the innate immune system from RNA-mediated amino acid substitutions to supercoiled DNA.
Structural Dynamics and Mechanochemical Coupling in DNA Gyrase
Abstract conclusion:

Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.

Co-author Angelica Parente asked: Do you have a source on this? I study bacterial supercoiling in the context of topoisomerase II structural biology. I’m assuming in honeybees it’s affecting chromatin dynamics? My lab would be really interested in learning more about this.
My comment: The Journal of Molecular Biology topic is “Mechanisms and Functional Diversity of Macromolecular Remodeling by ATP-Dependent Motors.” The authors have linked energy-dependent changes from angstroms to ecosystems via the conserved molecular mechanism of autophagy. The mechanisms link the innate immune system of bacteria to their nutrient-dependent pheromone-controlled physiology of reproduction, which biophysically constrains virus-driven energy theft and all pathology in all living genera.
See: Asking the right questions (2)