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.

 

diseases-disorders

Atoms to ecosystems: Evolutionary theory vs the coelacanth

Biodiversity: Life ­– a status report

“Species are disappearing quickly — but researchers are struggling to assess how bad the problem is.”

I want to eliminate some of the researcher’s struggles, but a moderator at Nature has blocked all my comments for several months, perhaps permanently. I think my past comments on articles, like this one, explain why other comments are blocked. In the past, I commented each time I saw a misrepresentation of biologically-based cause and effect. The misrepresentations are often found in their news features, which draw from publications in “Nature” and other well-respected sources of peer-reviewed information. Unfortunately, sometimes even peer-reviewed publications support ridiculous theories about the evolution of biodiversity. I suspect that “Nature” does not want critical comments on their representations of how biodiversity arose. For example, in the report published on December 10, 2014, Richard Monastersky wrote: “Of all the species that have populated Earth at some time over the past 3.5 billion years, more than 95% have vanished…”

He starts by setting up an argument for the evolution of biodiversity across 3.5 billion years. That argument has not been supported by experimental evidence of biologically-based cause and effect. Instead, evidence of at least one extant species attests to errors made by assuming that evolution occurred anytime during the past 65 million years. For example, Until 1938, the coelacanth was thought to have gone extinct with the dinosaurs 65 million years ago. This fact attests to the uncertainty about the past that is already incorporated into the Modern Synthesis, the evolutionary theory taught today.

Note, however, subtle changes to the Modern Synthesis are consistently being made to prevent the ridicule of theorists. They used to insist that mutations could somehow lead to increasing organismal complexity. But the nonsense about mutations is gradually disappearing and most of the nonsense about natural selection in the context of mutations has already disappeared. See for example: “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.” — Carl Zimmer (2013) However, the uncertainty from the past about how evolution might somehow have occurred have led to more uncertainty about the future.

Biodiversity: Life ­– a status report Excerpt 1) ““There is a huge uncertainty in projecting future extinction rates,” says Henrique Pereira, an ecologist…””

My comment: Errors made in representations of past extinction rates are exemplified by the coelacanth. They lead to uncertainty in projecting future extinction rates and the errors attest to problems associated with the pseudoscientific nonsense of population genetics. Without experimental evidence that links the epigenetic landscape to the physical landscape of DNA via what is known about physics and chemistry, pseudoscientists must guess about what already is understood by ecologists. They know that ecological variation leads to bio-physically constrained ecological adaptations.

For example, in my model of chemical ecology,  the conserved molecular mechanisms of bio-physically constrained nutrient-dependent amino acid substitutions are linked to cell type differentiation by the metabolism of nutrients to species-specific pheromones. The pheromones control fixation of the amino acid substitutions in the organized genomes of species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction links morphological and behavioral diversity across all species. An organism’s response to changes in the chemical ecology of its epigenetic landscape is enabled by the de novo creation of receptors. These creation of these receptors allows experience to dictate the organism’s response via the organisms innate ability to create the receptors that enable nutrient uptake. Unless you are an evolutionary theorist, you are more likely to attribute individual survival and species survival to nutrient uptake and the physiology of reproduction than to mutations.

If you are not an evolutionary theorist, you may already know that receptor-mediated behaviors are linked to biodiversity in species from insects to mammals. The behaviors appear to arise in the context of the nutrient-dependent chemistry of protein folding. Nutrient-dependent RNA-directed DNA methylation and RNA-mediated events link amino acid substitutions to the stability of protein folding in the DNA of organized genomes via alternative splicings of RNA linked to the de novo creation of olfactory receptor genes. But, I digress. What does “Nature” tell us about all this?

Richard Monastersky writes: “One approach is to develop comprehensive computer models that can forecast how human activities will alter ecosystems. These general ecosystem models, or GEMs, are in their infancy…”

My comment: Are general ecosystems in their infancy because pseudoscientists have assumed that extant species evolved across 3.5 billion years and that natural selection occurred in the context of extinctions? If so, it may be long past time to recognize the obvious role of ecological variation and nutrient-dependent ecological adaptation. For example, any species that cannot quickly adapt to ecological changes is already extinct. The coelacanth is not. WHY?

wrote in his comment about the article by Richard Monastersky:  “…apart from ecological modelling, what is critically needed is more effort in taxonomy.”
After my failed attempt to comment on the article, I also attempted to reply to that comment. I wrote: Taxonomy based on the nutrient-dependent de novo creation of receptors that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all vertebrates via amino acid substitutions and GnRH seems to be a good place to start. http://www.sciencedirect.com/science/article/pii/S0016648014002986
My reply was blocked: “We are unable to post your comment because you have been blocked by Nature News. Find out more. Someday I might be inclined to find out more, but for now…
The link I provided is to GnRH receptors and peptides: Skating backward
Excerpt: “Skate and coelacanth are the only examples of animals with both type I and II GnRH receptors and all three peptide types, suggesting this was the ancestral condition in vertebrates.”
My comment: GnRH (gonadotropin releasing hormone) is the focus of my model. That fact suggests a model of chemical ecology could link taxonomy from the coelacanth to the skate via differences and similarities in the amino acid substitutions found in molecules of GnRH and GnRH receptors. Indeed, the differences in the amino acid substitutions might taxonomically link the epigenetic landscape to the physical landscape of DNA in organized genomes of species from microbes to man via an extant species, the coelacanth,  that researchers thought was extinct, unless they can explain why it is not.
I suspect the species ecologically adapted via the same conserved molecular mechanisms that link receptor-mediated behavior from nutrient uptake to the pheromone-controlled physiology of reproduction via feedback loops. There is a model for that!
There is no model for the evolution of biodiversity as it is portrayed in the context of neo-Darwinism. The Modern Synthesis assumed that mutations and natural selection of something led to the evolution of diversity or that evolution “just happened.” Theorists must now attempt to extract mutations from their theories, since serious scientists know that mutations perturb protein folding and amino acid substitutions stabilize it.
Still, extracting mutations from their theories leaves pseudoscientists likely to be the butt of jokes. Without mutations in their theory, how can they continue to claim that any species evolved. Clearly, in the context of feedback loops that link nutrient-dependent pheromone-controlled reproduction to RNA-medicated amino acid substitutions and biodiversity show that all species, including the coelacaths, must have adapted to ecological variation, which is why the adaptations are manifested in different morphological and behavioral phenotypes.
Indeed, a recent report attests to this fact. “Although the Type I receptors had previously been known only from mammals, we found full length sequences of this receptor type in the genomes of a coelacanth (Latimeria chalumnae) and a chimaera (the elephant shark Callorhinchus milii), as well as partial sequence orthologs in the genome of the little skate (Leucoraja erinacea)(see Additional file 1: Table S1 and below). Like the Type I receptor in mammals, those in coelacanths and chimaera lack the cytoplasmic tail, terminating at the same amino acid.”
That fact cannot simply be placed into the context of mutations and evolved biodiversity. Continuing to claim that evolution has occurred during millions to billions of years can be placed into the context of experimental evidence and biologically-based cause and effect that is irrefutable.
Attempts to refute the experimental evidence with arguments based on what was learned from population geneticists – in their day — would already have been dismissed if they had paid attention to one of their own. Dobzhansky (1973) wrote: “… 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.”
After the discovery of the coelacanth, a so-called “living fossil, theorists should have begun to pay more attention to claims about mutations. After 1973, theorists should have begun to ask questions about why nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions appear to be essential to the genomic stability of species from microbes to man.
Instead, this claim was made again, today: “The issue of human ‘pheromones’ is a controversial topic…. However, it is fair to say that, on balance, social odors play a much more subtle and much less critical role in human reproduction when compared to other mammals.” See: Introduction to the special issue on Chemosignals and Reproduction by Aras Petrulis. In Press, Accepted Manuscript, Available online 11 December 2014
Summary: Cell type differentiation occurs via conserved molecular mechanisms in species from microbes to man. It is nutrient-dependent and pheromone-controlled. The claim that social odors, which are commonly called pheromones in species from microbes to man, “…play a more subtle and much less critical role in human reproduction…” than they play in any other species is akin to claiming that food odors are less important to human reproduction.
Anyone who does not yet understand the difference between epigenetic effects of olfactory/pheromonal input on hormones and the affects of hormones on behavior should not make claims about biologically-based cause and effect. It has become too obvious that biologically-based cause and effect extends across all species. That includes those that are extinct and those that were thought to be extinct, like the coelacanth, and any that may become extinct due to the ignorance of theorists who continue to tout their pseudoscientific nonsense about the issue of human pheromones. It not a controversial topic among serious scientists. Only theorists claim that social odors play a less critical role in human reproduction than they play in the physiology of reproduction in other species. Only theorists are human pheromone-deniers.