RNA-mediated events and "The Theory of Everything"

By: James V. Kohl | Published on: November 26, 2014

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The Large Scale Structure of Space-Time

Co-author George F.R. Ellis won the 2004 Templeton Prize
People like him are likely to recognize the top-down link from light-induced de novo creation of nucleic acids and nutrient-dependendent RNA-mediated amino acid substitutions to epigenetically-effected neuronal structure and function. In my model, light-induced amino acid substitutions are linked to the nutrient-dependent amino acid substitutions that differentiate all cell types of all individuals of all organisms. Neuronal cell type differentiation is linked to behavior. See for example: Affective Neuronal Selection: The Nature of the Primordial Emotion Systems. See also, the comments by George F.R. Ellis on Understanding and accounting for relational context is critical for social neuroscience.
I wrote: “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.”
Professor Ellis responded: “This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here:
Moving forward with the help of other experts and the expertise of Professor Ellis, which extends across disciplines to biophysics, see the recently published book: Life on the Edge: The Coming of Age of Quantum Biology, which was reviewed as Nature, the physicist: How quantum theory is helping to explain the mysteries of life science
Apparently, the 2014 book, which I have not read, incorporates the works of others like Ellis and Hawking. The book review links quantum physics, quantum smell, and quantum biology. The extension to quantum consciousness by Stuart Hameroff is clearer via what is known about nutrient-dependent amino acid substitutions that differentiate all cell types of all individuals of all organisms.
It is obvious that increasing organismal complexity arises in the context of the laws of physics and The Large Scale Structure of Space Time (portrayed in The Theory of Everything). Earlier today I learned that George F.R, Ellis is portrayed in the movie. I am anxious to see it, but will wait until it is showing in the area (It is currently showing in Forsyth, Georgia, which is nearly 2 hours away.)
Clearly, any theory of everything must now include epigenetic links from amino acid substitutions in plants and animals to amino acid substitutions that determine the structure and function of neurons. Cell type structure and function arise only in the context of nutrient-dependent amino acid substitutions and the pheromone-controlled physiology of reproduction. This can be viewed in the context of examples of RNA-mediated events, which are linked from amino acid substitutions to cell type differentiation via DNA in organized genomes. See: Comparison of the transcriptional landscapes between human and mouse tissues.
Alternatively, everything currently known about quantum level links from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man can be viewed in the context of evolutionary theory. Evolutionary biologists and evolutionary psychologists attribute all comparative similarities and differences in cell types to random mutations as if their theories made sense in the context of pattern recognition that we can expect to see revealed in “The Theory of Everything.”
How much will be revealed?
Differences in theories can be compared in the context of Mutation-Driven Evolution “In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199) However, that conclusion reveals nothing about biologically-based cause and effect. It attests only to the pseudoscientific nonsense of population genetics. See also: Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era. “…we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation…” What if biophysical constraints on the chemistry of protein folding, which are known to people like Professor Ellis eliminate theories about mutations and evolution.
For comparison 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: Top-down causation: an integrating theme within and across the sciences
Excerpt: “What is crucially needed is predictions of new tests that will confirm the hypothesis that top-down causation is real, and not just an epiphenomenon.”
My comment: Top-down cause can be considered in the context of nutritional epigenetics, which links food odors and the metabolism of nutrients to the species-specific pheromones that control the physiology of reproduction in species from microbes to man. Tests now available link amino acid substitutions to physiology and to behavior via genetic networks and metabolic networks. For example, based on results from 10,000 patients, an amino acid substitution associated with homocysteine levels has been linked from metabolism to heart disease risk, and a different amino acid substitution has been linked from metabolism to decision making and to neuropsychiatric disorders such as schizophrenia and attention deficit hyperactivity disorder.
Pre-emptive pharmacogenomics testing appears to confirm that biologically-based cause and effect link top-down causation from food odors to their epigenetic effects on RNA-mediated amino acid substitutions. For example, the de novo creation of olfactory receptor genes and the nutrient-dependent pheromone-controlled physiology of reproduction link metabolic networks to the physical landscape of DNA in organized genomes of species from microbes to man via conserved molecular mechanisms. Whether or not pre-emptive pharmacogenomics can be integrated into a “Theory of Everything” remains to be seen, but a model that links atoms to ecosystems may be important to consider since ideas about mutations and evolution clearly have not been substantiated by experimental evidence from physics, chemistry, or molecular biology.