Let there be anti-entropic light (2)

Physics
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Without knowing anything about the biophysically constrained chemistry of protein folding that links light-induced amino acid substitutions to the stability of DNA is the organized genomes from plants via bioluminescent bacteria in squid, the pattern of nutrient-dependent biologically-based cause and effect is still clear. See, for example:

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans Conserved non-coding elements (CNEs) and gene regulatory networks (GRNs) are consistently linked across species.

Excerpt: “…alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes.”

My comment: The links between CNEs and GRNs are also consistently misrepresented in the context of evolution. The links do not evolve. Mutations do not link what is currently known about ecological variation and ecological adaptations. Adaptations are nutrient-dependent and directed by RNA via DNA methylation and RNA-mediated amino acid substitutions. The amino acid substitutions have not been linked to co-evolution as has typically been implied by theorists.

See instead: A universal trend of amino acid gain and loss in protein evolution

Excerpt: We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

My comment: I claim that nutrient-dependent metabolism is a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms. Light-induced RNA-mediated amino acid substitutions link entropic elasticity to anti-entropic RNA-mediated epigenesis and epistasis. Epistasis links the emergence of metabolism to the sun’s biological energy via what is currently known about physics, chemistry, and molecular biology. The physics, chemistry, and molecular biology are required to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all genera.

There is no pattern of co-evolution for comparison to the pattern of nutrient-dependent metabolism and epistasis. Claims that a pattern of nutrient-dependent metabolism and epistasis emerged appear to be based on the untestable pseudoscientific nonsense of population geneticists and theoretical physicists.

In the world of biologically-based cause and effect we have seen that nutrient-dependent mismatch repair is required to maintain the stability of DNA in organized genomes. See: Residues in the N-Terminal Domain of MutL Required for Mismatch Repair in Bacillus subtilis

Excerpt: “We also found that three missense mutations [mutL(E30A), mutL(N34H), and mutL(R176G)] conferred a dominant negative phenotype, supporting the notion that the corresponding mutation in human MLH1 would have a pathogenic role leading to genome instability in HNPCC patients.”

My comment: Mutations perturb protein folding and lead to phyiopathology. Nutrient uptake links feeding patterns to biodiversity. For example, see: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes. This experimental evidence  was reported as “The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans“, Ralf Sommer concludes.

In the context of the “…excellent coordinated evolutionary selection of amino acids…” Kochman (2012) and DNA repair,  I am reminded of another pattern. This pattern was mentioned in the context of vertebrate biodiversity.

Kochman (2012) also concluded: “The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful.”

My comment: Ecological variation has been linked to nutrient-dependent ecological adaptations via the physiology of reproduction in species from plants and from animals (microbes to humans) via conserved molecular mechanisms that link physics to the chemistry of protein folding via amino acid substitutions. In no model and no model organism does rapid diversification fit the pattern of entropic elasticity linked to anti-entropic epigenesis and epistasis via amino acid substitutions; the sun’s biological energy; and RNA-directed DNA methylation.

Ralf Sommer’s group reports Rapid diversification associated with a macroevolutionary pulse of developmental plasticity in nematodes. Others have reported that Differential DNA mismatch repair underlies mutation rate variation across the human genome. Serious scientists also are Predicting phenotypic variation in yeast from individual genome sequences, which links nutrient-dependent pheromone-controlled cell type differentiation at the advent of sexual differentiation of RNA-mediated cell types in yeasts to mammals in our 1996 review.

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.”

My comment: It would be difficult to imagine a more complete picture of RNA-mediated cell type differentiation that the one linked from nutrient-dependent pheromone-controlled biodiversity in bacteria to Drosophila melanogaster and Caenorhabditis elegans. The fact that conserved molecular mechanisms link the biophysically constrained chemistry of protein folding to nutrient-dependent ecological adaptations in all animal species suggests that the nutrient-dependent physiology of reproduction in all animal species is controlled by pheromones.

See: Signaling Crosstalk: Integrating Nutrient Availability and Sex and Feedback loops link odor and pheromone signaling with reproduction. Obviously, the signaling crosstalk links nutrient availability to the pheromone-controlled physiology of reproduction in species from microbes to man. But see: Researchers identify a human DNA element that spurs neurogenesis and brain growth when placed in mice.

DNA elements may appear to link brain growth, but cell type differentiation is clearly nutrient-dependent and pheromone-controlled, which forces claims made about the role of human DNA to fit a model of amino acid substitutions that links quantrum physics, quantum smell, and quantum biology via the chemistry of nutrient-dependent RNA-mediated protein folding to cell type differentiation in all cells of all tissues of all organs in all organ systems of animals with a brain.

Dominance hierarchy arising from the evolution of a complex small RNA regulatory network

Excerpt: “Although some of the underlying genetics and mechanisms of self-incompatibility are understood, the evolution and maintenance of the system have remained mysterious.”

My comment: The mysterious evolution and maintenance of this system of entropic elasticity and anti-entopic energy from the sun are typically placed into the context of theories, not models of biologically-based cause and effect.

In my model, entropic elasticity and anti-entopic energy link the epigenetic landscape to the physical landscape of DNA in the organized genomes of plants and animals via amino acid substitutions that differentiate all cell types of all individuals of all species.

In animals, the dominance hierarchy is clearly nutrient-dependent and pheromone-controlled, but it is also altered by the balance of viral microRNAs and nutrient-dependent microRNAs. In plants, light-induced changes in the microRNA/messenger RNA balance are the key to RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types.

Ecological variation is linked to ecological adaptations in plants and in animals by the biophysically constrained RNA-mediated chemistry of protein folding and conserved molecular mechanisms of epigenetically-effected morphological and behavioral phenotypes.

Plant behavior and human behavior are comparatively more constrained due to differences associated with their epigenetically-effected life history transitions, not by differences in the molecular epigenetics or physics and chemistry of life.

Conclusion: “When such data will be extended to more alleles, it will be interesting to compare the results with further theoretical expectations based on evolutionary arms race or mutualistic interactions models.”

It has since become perfectly clear that only mutualistic interactions models can be considered in the context of ecological variation and ecological adaptations.

‘DNA spellchecker’ means that our genes aren’t all equally likely to mutate

Claims based on evolutionary arms race or mutualistic interactions models can be compared in the context of epigenetically-effected transmission ratio distortion (TRD). It becomes more clear that different groups like to use different terms to describe the same thing. TRD could be compared to theories about the role constraint-breaking mutations play in the evolution of biodiversity. See for example: Mutation-Driven Evolution “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199) See for comparison: http://figshare.com/…/Nutrient_dependent…/994281

No matter how obvious it is that the molecular mechanisms of nutrient-dependent cell type differentiation are conserved across all domains and kingdoms, there is no reason for anyone else to make claims based on what’s known about physics and chemistry that put life into its proper context. Those claims make theorists angry. In any case, everyone will sooner or later realize that Life is physics and chemistry and communication.

The only reason to make prescient claims about conserved molecular mechanisms is to focus on the anti-entropic effect of the sun’s biological energy. It links amino acid substitutions and RNA-mediated cell type differentiation to what is known about nutritional epigenetics and pharmacogenomics.

Anyone who tries to link light from nutritional epigenetics to pharmacogenomics will probably bring up other facts about cell type differentiation that have caused theorists to break Mendel’s century-old “law of segregation.” It states there is an equal probability of inheriting each of two copies of every gene from both parents. Few serious scientists are willing to talk about pseudoscientists who have been breaking the “law of segregation.” However, facts about the nutrient-dependent pheromone-controlled physiology of reproduction at the advent of sexual reproduction in yeasts show that the cell type differentiation is RNA-directed. Those facts link RNA-directed DNA methylation to the nutrient-dependent pheromone-controlled reproduction of cell types in microbes. Cell type differentiation in microbes is linked from viral microRNAs to the nutrient-dependent cell type differentiation of prokaryotes by the light-induced amino acid substitutions in all plants and all animals. Differentiation occurs via alternative splicings of pre-mRNAs. See for details: From Fertilization to Adult Sexual Behavior.

In our section on molecular epigenetics, we (TB) 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 (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.”

Much more is now known about alternative splicings. See, for example: Alternative RNA Splicing in Evolution.Even when it is placed into the context of evolution, alternative splicing captures the essence of the sun’s biological energy in the context of the chemistry of protein folding.

Quantum smell’ idea gains ground.

Other researchers have suggested that quantum mechanics in biological processes aren’t limited to photosynthesis but can be extrapolated to how the brain functions, the way in which we smell

One science idiot said to another:

Patterns develop on their own.

The other responded:

Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid

This pattern is typical of communication among science idiots who known nothing about physics, chemistry, or molecular biology.

They see a pattern in the formation of molecules and attribute it to the evolution of the molecules even when light supplies the biological energy that links physics to chemistry and molecular biology.

See also: Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

My comment: They decimated ideas about mutation-driven evolution with representations of global changes that are epigeneticcally effecdt by as little as one amino acid substitution

For example in sticklebacks A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

Excerpt:

This Gly380Arg substitution leads to a constitutively active FGF receptor that is thought to confer a selective advantage to spermatogonial cells (Tiemann-Boege et al. 2002, Choi et al. 2008).

This links to the role of glycine in the coelacanths and light and DHA in the cell walls that link Crawford’s light to electricity conversion back to light in McFall-Ngai’s squid.

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