Energy-dependent epigenetic translation to mRNA stability (6)

By: James V. Kohl | Published on: May 22, 2017

See: Energy-dependent epigenetic translation to mRNA stability (5)
Five energy-dependent amino acid substitutions are linked to differences in RNA content and biodiversity in 4 mammalian species.

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

In my model, the metabolism of food to pheromones controls species specific and tissue specific variation in food energy-dependent mitochondrial transfer RNA (mt-tRNA) and the transgenerational epigenetic inheritance of morphological and behavioral phenotypes. In all models of biologically based cause and effect, the “RNA world” must be linked by metabolism to the pheromone-controlled fixation of RNA-mediated amino acid substitutions in supercoiled DNA. That is how the RNA world is linked from chromosomal rearrangements to energy-dependent RNA-mediated chromosomal inheritance and to protection from virus-driven energy theft, which links mutations to all pathology in species from microbes to humans.
See:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model (published 2013 Jun 14)
My model of “ecological adaptation” was placed into the context of “adaptive evolution” because many theorists do not seem to understand why serious scientists do not believe in “Big Bang” cosmology or neo-Darwinian pseudoscientific nonsense about Mutation-Driven Evolution (also published 2013 Jun 14)
Anyone who tries to tell a theorist that no experimental evidence of biologically-based cause and effect supports their theories about mutation-driven evolution is not likely to see their work get past peer-review. And, when the threat to their ridiculous theories becomes known, theorists are more likely to accept criticisms of a model — even in the absence of a comparable model.
During the past 4 years, there has been no scientific support for neo-Darwinian theories and overwhelming support for the model of food energy-dependent amino acid substitutions and Darwin’s claims about “conditions of life.”
See for instance: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization (published 2017 May 20)

…initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

See also: Human mitochondrial ribosomes can switch their structural RNA composition

Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.

The switches are food energy-dependent and they obviously link ecological variation to ecological adaptation via the Laws of Physics and basic principles of chemistry. In my model, for example, light-induced changes in hydrogen-atom transfer in DNA base pairs in solution cause initiator-transfer RNAs in the nucleus to become charged with an amino acid. Light energy-as-information subsequently appears to biophysically constrain all conditions of life in all living genera by protecting organized genomes from virus-driven energy theft and genomic entropy.
The link from quantum physics via electron resonance to quantum souls is clearer than it has ever been.
See: Electron resonance pervades the brain

Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.

See also: What is life when it is not protected from virus driven entropy
Energy as information and constrained endogenous RNA interference
An endogenous substrate was linked from the biosynthesis of RNA to endogenous RNA interference in this full text .pdf from 1963: PARTICIPATION. OF GLYCOLYSIS. AND THE CITRIC ACID CYCLE. IN NUCLEAR ADENOSINE TRIPHOSPHATE SYNTHESIS

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

I do not know any pseudoscientist who has linked the energy-dependent creation of nucleic acid precursors to the energy-dependent creation of new genes, or to the activation of genes via the endogenous substrate. Indeed, the fact that there is an endogeneous substrate has been ignored, unless it has been replaced by an alternative fact which was somehow linked to all biodiversity via the physiology of reproduction.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

See for comparison: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Darwin explained how species evolve. Church wants to turbocharge that process by putting new genes into organisms rather than waiting around for them to evolve those genes on their own.

Darwin did not explain how species evolve. Darwin presciently linked natural selection for food energy-dependent codon optimality to RNA-mediated amino acid substitutions and the physiology of reproduction, which biophysically constrains the hecatombic evolution of all pathology. Nothing known to serious scientists suggests that new genes “evolve.”

In between tRNA and CRISPR, Church coauthored hundreds of scientific papers, from “Predicting regulons and their cis-regulatory motifs by comparative genomics” to “Characterization of Cas9-guide RNA orthologs.”

After he characterized naturally occurring energy-dependent changes in RNA orthologs, George Church refuted neo-Darwinian evolutionary theories when he and others filed this patent application. RNA-Guided Human Genome Engineering

FIG. 3A-1 and FIG. 3A-2 depict a human codon-optimized version of the Cas9 protein and full sequence of the cas9 gene insert.

Human codon-optimized changes in proteins are energy-dependent, RNA-mediated, and the changes are biophysically constrained by the food that organisms eat and the physiology of reproduction in all living genera. That fact was placed into the context of the Structural diversity of supercoiled DNA in the context of this review: Feedback loops link odor and pheromone signaling with reproduction
The review was co-authored by 2004 Nobel Laureate, Linda Buck who helped to link the sun’s anti-entropic virucidal energy to biophysically constrained cause and effect in all species that need to eat to reproduce. Richard Feynman may have been one of many others who also did that.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.

See for comparison: George Church refutes theistic evolution

The future of genetic codes and BRAIN codes (video)

My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.

Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.

Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.

See also: Peter Godfrey Smith: “Other Minds: The Octopus, the Sea, and the Deep Origins…”

See for comparison:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull
In this case, Anna Di Cosmo’s group already linked what is known about the physiology of pheromone-controlled reproduction from the gut bacteria of the octopus to the nutrient energy-dependent pheromone-controlled physiology of reproduction of the octopus. See: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Her group also linked the conserved molecular mechanisms of chemical perception and gene expression in flies to consciousness in octopuses. See: Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare via my model, albeit without citation to: Nutrient-dependent/pheromone-controlled adaptive evolution: a model or citation to Electron spin changes during general anesthesia in Drosophila.
Without an energy-dependent change in electron spin, the findings that link virus-driven energy theft to all pathology cannot be linked from cryo-EM to the biophysically constrained changes that link angstroms to ecosystems in all living genera. None of the claims that Richard Feynman made about energy, including his claims about food energy, can be linked from quantum physics to chemistry and biologically-based cause and effect via the physiology of reproduction.
Until recently, I thought that Eugene Koonin was prepared to challenge the nonsense about evolution. No other theorists seem to be willing to address the facts about energy-dependent increasing organismal complexity.
See: Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

Virus-driven energy theft links the degradation of messenger RNA to all pathology, which is biophysically constrained by conserved molecular mechanisms that link food energy from viral latency to all energy-dependent healthy longevity.
Watch for Koonin and other theorists to use experimental evidence of biologically-based cause and effect to eliminate the pseudoscientific nonsense about evolution touted by those who still know nothing about virus-driven pathology manifested in Alzheimer’s and other neurodegenerative diseases. Alternatively, watch for Koonin and other theorists to continue playing their evolution game until everyone who is more than one decade old learns to play this game:

Cytosis: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Cytosis is a worker placement game that takes place inside a Human Cell! Players utilize the organelles within a cell to collect cellular resources such as mRNA from the Nucleus, Lipids from the Smooth E.R., ATP from the Mitochondria, etc. and score points when they use these resources to complete Hormones, Receptors or Enzymes! 2 to 5 Players, Ages 10 +, Plays in 50 to 75 mins – (Shipping Aug/Sept 2017 – US, EU, CA & AU will ship from WITHIN their country / region) 

See for comparison: How Statistics Weakened mRNA’s Predictive Power

More than 60,000 published works link food from energy-dependent changes in the microRNA/messenger RNA balance to differences in amino acid substitutions in mitochondrial transfer RNA (mt-tRNA).

The amino acid substitutions in different mammals appear to protect the mitochondria from virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.

The link from mt-tRNA to healthy longevity via species- and tissue-specific variation in the structure and function of supercoiled DNA may limit further consideration of neo-Darwinian theories because there is nothing to suggest that supercoiled DNA automagically evolved.

See for example: Figure 1

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

See also: Noncoding RNA Helps Cells Recover from DNA Damage

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

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…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.


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