diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

IMG_2329-e1413855233208-958x718

From deep time into real time: What evolutionary processes?

Rapid evolution of a native species following invasion by a congener

Abstract excerpt: “…the lizard Anolis carolinensis moved to higher perches following invasion by Anolis sagrei and, in response, adaptively evolved larger toepads after only 20 generations.”
My comment: This indicates that the behavior evolved before the species, in response, evolved larger toepads.
Reported as: Florida lizards evolve rapidly, within 15 years and 20 generations
Karl Grammer’s comment: “Proofs for evolutionary processes…

What evolutionary processes?

RNA-directed DNA methylation links the epigenetic landscape to the ecological adaptations manifested in the morphology of the toepads. The changes require epigenetically-effected nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types. The morphological changes manifested in the cell types linked to larger toepads exemplify cell type differentiation that must be controlled by the physiology of reproduction and properly timed reproductive sexual behavior.
Everything currently known about biophysical constraints; the chemistry of protein folding; and the conserved molecular epigenetics of molecular biology attests to the fact that 1) moving to higher perches and 2) larger toepads requires a series of simultaneous nutrient-dependent pheromone-controlled ecological adaptations.
News Article excerpt: “To put this shift in perspective, if human height were evolving as fast as these lizards’ toes, the height of an average American man would increase from about 5 foot 9 inches today to about 6 foot 4 inches within 20 generations — an increase that would make the average U.S. male the height of an NBA shooting guard,” said Stuart.”
My comment: Sex differences in height and other morphological and behavioral traits assure us that the epigenetically-effected changes in the lizards cannot be put into any perspective outside the context of nutrient-dependent pheromone-controlled sex differences in cell type differentiation. All differences in cell types link ecological variation to ecological adaptations via the pheromone-controlled physiology of reproduction in species from microbes to man.
By reporting their findings outside the context of biologically-based cause and effect that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, the authors suggest that evolution somehow occurred. What they have actually shown is another example of nutrient-dependent pheromone-controlled ecological adaptations, which are manifested in the morphological and behavioral phenotypes of all species.
Journal article excerpt: “Brown and Wilson called evolutionary divergence between closely related, sympatric species “character displacement” (1), and our data constitute a clear example of this. Resource competition has been the interaction suggested most often as the source of divergent selection during character displacement [sometimes specifically called “ecological character displacement” (13)].”
Character displacement is a vague term used eight years before Dobzhansky (1964) claimed “…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!” Others have recently claimed “Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].”
Use of vague terms like character displacement, indirect genetic effects, cooperating genetic events, and genome dynamics events instead of ecological character displacement (i.e., ecological speciation) continue to contribute to the confusion manifested in yet another report of biologically-based cause and effect that is meaningfully interpreted as if the findings support a ridiculous theory of evolution. However, that theory must now be divorced from claims that evolution occurs over eons of time via mutations and natural selection, because no evolutionary events have been described that link one species to the evolution of another.
This statement makes that fact clear: “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…” That statement changes evolutionary events to the virtually unusable term genome dynamics events. It follows from the fact reported in A universal trend of amino acid gain and loss in protein evolution: “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.” (So, why not use the term ecological speciation, since that is what obviously occurs via RNA-mediated genome dynamics events? Must researcher compete to invent new terms and claim that they are the first to detail the obvious?)
If it is not yet obvious to everyone that nutrient-dependent metabolism emerged as the link to ecological adaptations and ecological speciation “…before the last universal common ancestor of all extant organisms,” it might be clearer after reading Arrival of the Fittest: Solving Evolution’s Greatest Puzzle. Unfortunately, Wagner insists on using the terms commonly used by population geneticists. He focuses on “innovability” in that context. I’m not sure who invented that term for ecological speciation. However, for a quick claim that requires less thought about use of vague terms, see: “Genetic and metabolic networks drive all biological processes. You can think of them as bridges between the organism and the individual molecules – proteins and genes – that form all living cells.” — from the Genetic and Metabolic Networks page of Professor Andreas Wagner’s Wagner Lab Research site. You can also think of ecological speciation as the process that is driven by all biological processes that involve genetic and metabolic networks. (Hint: all biological processes clearly involve genetic and metabolic networks.)
The research reported here answers the question about “What evolutionary processes?” in the context of genetic and metabolic networks that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. See also, Dobzhansky (1973) “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” It was clear to Dobzhansky that the amino acid substitutions differentiated the cell types of these primates, although he could not have known what epigenetic effects led to the RNA-mediated amino acid substitutions and differentiation of the cell types.
What is the answer to questions about evolutionary processes in the context of these amino acid substitutions? See: From Fertilization to Adult Sexual Behavior (1996): “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…” To avoid further confusion about biologically-based cause and effect, which continues to be placed into the context of evolutionary theory, 41 years after Dobzhansky (1973) and 18 years after our Hormones and Behavior review, see Nutrient-dependent/pheromone-controlled adaptive evolution: a model. (2013).
Examples of amino acid substitutions, which differentiate the cell types of all individuals of all species from microbes to man, are included in the review. The examples answer the question “What evolutionary processes?” by placing biologically-based cause and effect into the context of Darwin’s ‘conditions of life’ and ecological speciation instead of the context of neo-Darwinism, which bastardized his theory by making it appear that mutations could lead from natural selection to the evolution of biodiversity over eons of time. That exemplifies pseudoscientific nonsense!
Ecological adaptations are nutrient-dependent and pheromone-controlled by the physiology of reproduction, which enables amino acid substitutions and chromosomal rearrangements to move what some people may still claim are evolutionary processes from deep time into real time via ecological speciation.
That forward movement into the scientific reality of real time has been mentioned in three recent reviews of biologically-based cause and effect that move Dobzhansky’s claims from 1964 and 1973 into the real time of today’s accurately reported research. See for example: Combating Evolution to Fight Disease and RNA and dynamic nuclear organization and Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans. See also Dobzhansky (1972) “Reproductive isolation evidently can arise with little or no morphological differentiation.”
Many serious scientists have realized that organisms like the lizards starve to death when competition for nutrients displaces them, unless they quickly adapt and establish a new ecological niche, which is obviously what all extant species have done via their nutrient-dependent RNA-mediated pheromone-controlled reproduction. The species that didn’t adapt are extinct, because too many individuals starved to death before their cell types could reproduce.

Rapid Evolution in Real Time

RNA-directed DNA methylation links the epigenetic landscape to the ecological adaptations manifested in the morphology of the toepads. The changes require epigenetically-effected nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types. The morphological changes manifested in the cell types linked to larger toepads exemplify cell type differentiation that must be controlled by the physiology of reproduction and properly timed nutrient-dependent reproductive sexual behavior, which probably occurs near the location of the higher perches.
Re: rapid evolution and character displacement (i.e., ecological speciation)

Everything currently known about biophysical constraints; the chemistry of protein folding; and the conserved molecular epigenetics of molecular biology attests to the fact that 1) moving to higher perches and 2) the ecological adaptation of larger toepads requires a series of simultaneous nutrient-dependent pheromone-controlled  RNA-mediated events that obviously have occurred.
The similarities to what also occurs in hummingbirds that ecologically adapt to higher elevations is clear. However, like all similarities manifested in morphological and behavioral phenotypes, which arise in the context of nutrient-dependent pheromone-controlled ecological adaptations, these lizards attest to the fact that the differences are due to RNA-mediated events, not to evolutionary events.
Creative use of the term “character displacement” can be compared to what Dobzhansky, a self-proclaimed creationist, wrote about amino acid substitutions in 1973. “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”
If he was not still dead, Theodosius Dobzhansky (January 24, 1900 – December 18, 1975), who was also a self-proclaimed evolutionist, would probably dismiss the observations of others who claim that ‘character displacement’ is proof of evolution, as he did in (1964) when he wrote:  “…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!” Observations that higher perches are linked to morphological phenotypes in these lizards are characterized by the observations of others who have virtually ignored the need for behavioral phenotypes to concurrently change to enable ecological speciation.
Moving forward
We can expect to see researchers report soon that a single nutrient-dependent RNA-mediated change leads from ecological variation to the morphological and behavioral phenotypes of these lizards, since that is how ecological adaptations occur in all species. However, we can also expect to see a few more attempts to place ecological adaptations into the context of evolutionary theories, since the theory has become more popular than biological facts.
Few people realize that Darwin’s theory placed ‘conditions of life’ before natural selection. Only after population geneticists bastardized his theory did it become popular enough to include in the context of:
1) “character displacement”
2) “indirect genetic effects”
and
3) “genome dynamics events.”
See also from the original news report: Florida Lizards Evolve Rapidly, Within 15 Years and 20 Generations
Excerpt: “This latest study is one of only a few well-documented examples of what evolutionary biologists call “character displacement,” in which similar species competing with each other evolve differences to take advantage of different ecological niches. A classic example comes from the finches studied by Charles Darwin. Two species of finch in the Galápagos Islands diverged in beak shape as they adapted to different food sources.”
My comment: Darwin did not study finches. Anyone who studies birds today has probably realized that nutrient-dependent pheromone-controlled RNA-mediated events link amino acid substitutions to chromosomal rearrangements that clearly differentiate the morphological and behavioral phenotypes of white-throated sparrows via the pattern of nutrient-dependent biologically-based cause and effect that Dobzhansky began to notice in 1964.
He wrote: “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.” What we continue to see reported as science is  ignorance associated with claims that “character displacement” is an evolutionary process, when it is evidence of nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man, which occur via conserved molecular mechanisms.
What then, is the link from amino acid substitutions to behavioral phenotypes?  Apparently, in human adolescents and adults it is a functional single nucleotide polymorphism (SNP) / a G-to-A base-pair substitution that leads from the amino acid methionine (Met) to a valine (Val) substitution. For example: Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).
The difference that the amino acid substitution makes is associated with metabolism (e.g., lower enzymatic activity) due to the difference a single base pair change makes in the context of thermodynamic cycles of protein biosynthesis and degradation. The substitution makes the nutrient-dependent pheromone-controlled organized genome less thermodynamically stable, which explains the difference in exploratory behavior.
If nutrient stress associated with “invasion of a congener” in lizards had not led to increased exploratory behavior and an amino acid substitution that stabilized the organized genome of the lizards with higher perches, there would be no biologically-based explanation of how one species climbed higher up the trees and established its pheromone-controlled ecological, social, and neurogenic niche without thought. Instead, the lizards that perched higher might appear to have automagically corrected a nutrient-dependent problem in their organism-level thermoregulation. The behavior that led them to climb higher up the tree led to a nutrient-dependent pheromone-controlled epigenetic correction in organism-level cell type differentiation via changes in metabolism that lead from RNA-directed DNA methylation to beneficial amino acid substitutions. Unfortunately, that is more difficult to explain via comparison to simply stating that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” And people already believe in constraint-breaking mutations.
Telling the truth
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults was reported as Genes exhibit different behaviours in different stages of development, which links RNA-mediated events in our review From Fertilization to Adult Sexual Behavior to Organizational and activational effects of hormones on insect behavior and Honey bees as a model for understanding mechanisms of life history transitions.
The honeybee model organism links nutrient-dependent pheromone-controlled cell type differentiation via RNA-mediated events and what is currently known about Epigenomics and the concept of degeneracy in biological systems. “The reiterations of living systems are developmentally constructed and come into being through internal interactions within organisms, interactions between organisms, and interactions between organisms and their surroundings. Novelty and variation arise from these interactions. The functional redistribution of biological activity onto a group of interacting organisms and their environment effectively offloads a degree of genetic control onto epigenetic processes.’ The problem for evolutionary theorists who tout “character displacement” or anything else has become the fact that “The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, and diseases of the X chromosome (Honeybee Genome Sequencing Consortium, 2006). Included among these different aspects of eusocial species survival are learning and memory, as well as conditioned responses to sensory stimuli (Maleszka, 2008; Menzel, 1983).” — Kohl (2012)
Links from nutrient-dependent pheromone-controlled morphological and behavioral phenotypes in the honeybee now extend across species via the conserved molecular mechanisms of RNA-mediated events that link amino acid substitutions to cell type differentiation and ecological speciation. Thus, it is clear that the popularity of evolutionary theory has prevented scientific progress that could have been made if all researchers were taught enough about biologically-based cause and effect to become serious scientists. Instead, many of them were taught to explain their findings as if organisms like lizards evolved into different species of lizards and dinosaurs evolved into different species of birds.
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Addendum: Val158Met polymorphism in COMT gene could be a candidate for low penetrance breast cancer susceptibility in Shanghai population, especially among premenopausal women and early-onset breast cancer patients.
The Val158Met amino acid substitution also shows up in the neurodegenerative disorder, Alzheimer’s disease.
A GOOGLE search for Val158Met might also surprise others who had no idea of how important a single amino acid substitution can be in the context of morphological and behavioral phenotypes because they were taught that species evolve via mutations and natural selection.
Fortunately, companies like Alpha Genomix are leading the way in attempts to link metabolism and pharmacogenetics to the RNA-mediated events that differentiate the cell types of all individuals of all species via amino acid substitutions, which are manifested as differences in genotypes and phenotypes as differences in morphological and behavioral phenotypes, not merely difference in the genes that evolutionary theorists still claim link mutations to the evolution of increasing organismal complexity.
Catechol-O-Methyltransferase (COMT) is an enzyme responsible for the metabolism of catecholamines and Catechol-estrogens in both the central nervous system and other organs. Dopamine is cleared mainly by COMT in the frontal cortex and a reduced activity of this enzyme results in higher synaptic levels of dopamine, which affects prefrontal cortex cognitive response to certain drugs. A single nucleotide polymorphism of the COMT gene produces an amino acid change from Valine to Methioinine (Val158Met) and reduces enzyme activity by 3 to 4 folds. The COMT assay tests for Mutations associated with decreased activity of COMT.
Several complex associations between COMT the Val158Met Variant as a risk factor for numerous diseases have been found but they all seem to have a limited predictive value. However, the response to some psychotropic medications seems to be dependent to some extent upon COMT status. In general, the wild-type genotype predicts a good response to methylphenidate and amphetamines in the treatment of attention deficit hyperactivity disorder.