An epigenetic trap (the prequel)

By: James V. Kohl | Published on: February 23, 2015

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See also: An epigenetic trap (the sequel)
Excerpt: “Support for the link from one epigenetic trap to cell type differentiation was included in the molecular epigenetics section of our 1996 review, which detailed how RNA-mediated chromatin remodeling occurs.”
My comment: One epigenetic trap leads to the de novo creation of olfactory receptor genes and cell type differentiation. See also: Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons. The first epigenetic trap links the sun’s biological energy to cell type differentiation.
The first epigenetic trap is set by water molecules. The trap the biological energy from the sun and convert it to spectral energy. That trap has forced theoretical physicists to revise their claims about entropy. See for example: The second laws of quantum thermodynamics reported as: “…there are additional second laws which constrain the way in which disorder can increase.” See also: A New Physics Theory of Life and Cosmology from quantum potential reported as No Big Bang? Quantum equation predicts universe has no beginning.
For comparison see: How Did the Code Of Life Pass Through Primitive Cells?
Excerpt: “We have certain templates that can replicate themselves by taking two complementary subsequences and then use a chemical reaction to bond the replication product.”
My comment: The templates do not automagically arise, and the chemical reactions link the sun’s energy to photosynthesis in plants, algae, sea slugs and other organisms. See also: Impact of regulatory variation from RNA to protein reported as: RNA measurements may yield less insight about gene expression than assumed
Excerpt: “Our observations point to a previously under-appreciated property of gene regulation, namely widespread buffering of protein levels so that a cell can sustain some amount of RNA variation without it affecting proteins,” Gilad said. “This appears to be a common phenomenon and motivates us to look for the mechanisms that can account for it.”
My comment: The mechanisms that account for buffering of protein levels are described in Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation which was reported as Researchers find new mechanism that controls immune responses.
An innate adaptor protein called MAVS is essential for interferon induction by RNA viruses. Interferon induction controls the immune system response to RNA viruses and other pathogens. Nutrient-dependent phosphorylation of innate adaptor proteins appears to be a conserved molecular mechanism that is essential to stability of DNA in organized genome of species from microbes to man.
Nutrient-dependent phosphorylation of an amino acid sequence by enzymes appears to occur in the adaptor protein MAVS and two other adaptor proteins. Phosphorylation of the amino acid substitutions in the enzymes “…ensures that type-I interferons are produced only when a proper adaptor protein is engaged in cells that are infected by pathogens.”
Summary of the first epigenetic trap: Phosphorylation links the sun’s biological energy to nutrient-dependent pheromone-controlled cell type differentiation of animals via amino acid substitutions that differentiate the cell types of plants and animals.
Evolutionary theorists are trapped by their misrepresentations of “evolved” DNA. For example, when placed into the context of evolution, one researcher claimed that “DNA might have initially evolved for the purpose of storing phosphate, and the various genetic benefits evolved later…” When placed into the context of light-induced and nutrient-dependent amino acid substitutions, the link from ecological variation to epigenetically trapped light is clear in the context of photosynthesis in plants, and in algae, and in sea slugs.
When placed into the context of the second epigenetic trap, which enables the nutrient-dependent odor-induced de novo creation of olfactory receptor genes, phosphorylation links light energy to prevention of cell type damage by viral microRNAs. Cell type damage is prevented by nutrient-dependent microRNAs.
Both types of microRNAs play roles in control of the microRNA/messenger RNA balance. Nutrient uptake fuels changes in the microRNA/messenger RNA balance during thermodynamic cycles of protein biosynthesis and degradation. Unless nutrient stress or social stress perturb the microRNA/messenger RNA balance during thermodynamic cycles of protein biosynthesis and degradation, cell type differentiation occurs when amino acid substitutions lead to genomic stability and health.
Alternatively, nutrient stress and/or social stress lead to mutations, which perturb protein folding. The mutations that perturb protein folding lead to physiopathology, such as that manifested in the autoimmune disorders associated with the adaptor proteins. When stress-induced production of viral microRNAs is not controlled, organisms are less likely to adapt because amino acid substitution – dependent DNA stability is perturbed by virus-induced mutations.
See for review: Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Excerpt: “…alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties…”
My comment: Accumulated evidence argues that alternative splicing of viral microRNAs and nutrient-dependent microRNAs links sexual differentiation of cell types to differentiation of all cell types in all cells of all individuals of all species via epigenetic traps and conserved molecular mechanisms.
1) “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.” Diamond, Binstock, & Kohl (1996).
2) “The concepts of hormone organization and activation provide a framework for thinking about the influence of hormones on development, brain, and behavior in vertebrates. There is good evidence for activational effects of hormones on the nervous system and behavior in insects, but organizational effects are almost never discussed in the insect literature. This paper explores the utility of the concepts of hormonal organization and activation of behavior in insects. We describe the two concepts as developed from studies of vertebrates, review some insect examples that appear to fit this classification scheme, and consider how explicit use of the concept of organization might benefit studies of the insect brain and behavior.” Elekonich & Robinson (2000)
3) “…currently there is no model system where the evolution, development, physiology, molecular biology, neurobiology and behavior of such a transition can all be studied in the same organism in its natural habitat. With a large literature covering its evolution, behavior and physiology (plus the recent sequencing of the honey bee genome), the honey bee is uniquely suited to integrative studies of the mechanisms of behavior. In this review we discuss the physiological and genetic mechanisms of this behavioral transition, which include large scale changes in hormonal activity, metabolism, flight ability, circadian rhythms, sensory perception and processing, neural architecture, learning ability, memory and gene expression.” Elekonich & Roberts (2005).
Viral microRNAs are linked from changes in the microRNA/messenger RNA balance to cell type differentiation in:
The pig as a large animal model for characterization of host-pathogen interactions
Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses
See also:

Viral Virtuosos

New understanding of noncoding RNAs may solve a long-standing puzzle about how viruses orchestrate lifelong infections.

The video protrays the accurate and prescient representations of science fiction author Greg Bear. I’ve addressed the accuracy of his approach to ecological adaptation in a human subspecies, and he has addressed my input and feedback in his blog posts and discussions of Darwin’s Radio and Darwin’s Children. The clarity of the fact that nutrient uptake is linked to microRNAs and genomic stability is revealed in:
Complete Genes May Pass from Food to Human Blood
Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation

Combined agonist–antagonist genome-wide functional screening identifies broadly active antiviral microRNAs
Clearly, accurate information that links the sun’s biological energy to the biophysically constrained chemistry of protein folding has not failed to reach those who are Combating Evolution to Fight Disease.
Only those with dedicated allegiance to the “Big Bang” cosmology industry and evolution industry are among the biologically uninformed combatants who refuse to examine experimental evidence of biologically-based cause and effect. Creationists are now moving forward with that experimental evidence, which predicts the eventual end to the biologically uninformed or to their elimination from intelligent discussions among serious scientists — whether or not the serious scientists also are creationists. See:

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