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.

 

Light-induced-conformer-intercoversion-of-hydrogen-bond

Light-activated feedback loops vs self-organization of ecosystems

John Lieff has been trying to update his ridiculous misrepresentations of biologically-based cause and effect to match the accurate representations we made in a section on molecular epigenetics in our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior

Nothing can stop him, but this will provide the next source for material that he must borrow as if he learned about it somewhere else.

Apoptosis analysis guide | Free ebook download

Virus-driven energy theft causes apoptosis, which releases cell contents for recycling in the context of autophagy, which helps to ensure food energy-dependent pheromone-controlled RNA-mediated DNA repair in species from microbes to humans.

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

Journal article abstract excerpt (figure: Epigenetic regulation of cranial NC cell identity.)

A Polycomb-dependent poised chromatin organization underlies the positional plasticity of cranial premigratory NC cell progenitors. This chromatin prepattern is maintained through migration. In response to local cues encountered by the NC cells during or after their migration, the regulatory elements (E) and promoters (P) of differentially expressed genes switch from a poised to an active chromatin state, establishing transcriptional identities specific to subpopulations of NC cells.

The use of the term “chromatin prepattern” must be linked from endogenous RNA interference to all all biodiversity via transgenerational epigenetic inheritance. Watch closely as all pseudoscientists, atheists and other biologically uninformed theorists finally realize there is no such thing as mutation-driven evolution except in the context of virus-driven energy theft, apoptosis, and the evolution of pathology. Virus-driven energy theft causes degradation of messenger RNA in the absence of nutrient energy-dependent pheromone-controlled RNA-mediated amino acid substitutions and DNA repair.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability.

Reported as: The role of tiny RNA in genetic diversity March 28, 2017

All species, from zebrafish to humans, possess a genetically diverse collection of traits that allow them to adapt to changing environments. Yet scientists do not fully understand how organisms reach a state of optimal diversity—just enough variability to respond to environmental risks but not too much to function properly.

Natural selection for energy-dependent codon optimality is the link to optimal diversity. Conserved molecular mechanisms of nutrient-dependent pheromone-controlled biodiversity have been linked from quorum sensing in bacteria to all cell type differentiation in all individuals of all species.
See: Feedback loops link odor and pheromone signaling with reproduction

These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

Escherichia coli and the peppered moth typically are typically used by biologically uninformed theorists as examples of mutation-driven evolution.
See: The Man Who Bottled Evolution
See the refutation: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

…this system enables us to understand the adaptive process in detail at the genetic and phenotypic level [over the weekend]. We identified a tractable model for gene network evolution and observed, in real time, the rewiring of gene networks to enable the incorporation of a modified component (NtrC′) creating a novel regulatory function by a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.

They failed to differentiate between the term mutation and what occurs in the context of energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance via fixation of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

See for comparison: Helicoverpa armigera images

Identification and Evaluation of Suitable Reference Genes for Normalization of MicroRNA Expression in Helicoverpa armigera (Lepidoptera: Noctuidae) Using Quantitative Real-Time PCR

…10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions….  miR-9 and U6 snRNA for developmental stages, miR-100 and U6 snRNA for larval tissues, miR-100 and miR-305 for adult tissues, miR-9 and miR-279 for parasitic treatment, miR-998 and U6 snRNA for nuclear polyhedrosis virus infection, miR-9 and U6 snRNA for insecticide treatment, miR-92a, miR-100, and miR-279 for temperature treatment, miR-92a, miR-305, and miR-998 for starvation treatment, miR-9 and miR-279 for light treatment, miR-305 and miR-998 for hormone treatment, and there was not one reference gene suitable for all samples.

Nutrient-dependent pheromone-controlled reproduction in this moth species links the works of Karlson and Luscher (1959) Pheromones: a new term for a class of biologically active substances to the Bruce McEwen’s works on stress via Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) and Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Taken together, these works are linked to energy-dependent Normalization of MicroRNA Expression. The anti-entropic virucidal energy of sunlight is the obvious link from the de novo creation of microRNAs to the ATP-dependent biosynthesis of messenger RNA and healthy longevity.  Virus-driven energy theft clearly links the degradation of messenger RNA, which would otherwise link the creation of microRNAs from sunlight to the nutrient energy-dependent pheromone-controlled biosynthesis of ATP and all cell type differentiation in all living genera.

For example see: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

To our knowledge, this is the first time that these two 3’UTR SNPs have been associated with sun-sensitivity traits. We state the potential implication of these SNPs in human pigmentation and sensitivity to sunlight, possibly as a result of changes in the level of gene expression through the disruption of putative miRNA-binding sites.

See also:: Race-dependent association of sulfidogenic bacteria with colorectal cancer

reported as: Study links sulfide-producing bacteria and colon cancer in African-Americans

“These bacteria are using nutrients associated with an animal-based diet,” Gaskins said.

For information on the biophysically constrained energy-dependent origins of race-dependent associations see:

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry…

Like all chemistry, this can be placed into the context of how quantum physics must be linked from quantum chemistry to quantum biology via food as energy.

The link from food enery to the nutrient-dependent pheromone-controlled physiology of reproduction and racial differences in colon cancer was predicted based on difference in diet and links from the National Microbiome Initiative to the Precision Medicine Initiative.

See for comparison: Sonny Williams

Re: … much ado about nothing — Jay R. Feierman.

SONNY [NEW]: As we’ve discussed many times, I reject your criteria for judging the merits of a scientific observation.  Arguing that something is “much ado about nothing,” if “the results can’t be predicted by common sense or by simple observation and deductive reasoning,” is exceptionally poor reasoning.  Frankly, I’m bewildered that someone like you would cling to it.  I’ll repeat:  any judgment that includes an evaluation based on “common sense” is DOA.  It’s useless.  Whose “common sense” do you intend to use?

More importantly, the authors DID establish a pre-observation “prediction.”

They predicted that young children will show the same variation in temperament as adults, and which is associated with the various BDNFval/66met polymorphisms.  They wrote, “To the best of our knowledge, there are no studies investigating the role of BDNFval66met with regard to individual differences in temperament during infancy, a period in which genetically-based behavioral traits are hypothesized to be more easily observed (Posner & Rothbart, 2009; Rothbart et al., 2000). Hence, the purpose of the current study was to explore the association between the BDNFval66met polymorphism and individual differences in temperament in a sample of healthy 4-month-old full-term infants.”

Moreover, the authors did a far better job than you did in discussing limitations.

They wrote as follows: “The current study had some limitations. First of all, due to sample size findings cannot be generalized and future studies with larger samples are needed in order to differentiate the impact of met-homozygous and heterozygous profiles of BDNFval66met genotype. Second, infants’ temperament was measured through a parent-reported measure. A more direct account of the effects of BDNF met allele on observed temperament and regulatory behavior is warranted to be investigated in future research. Finally, single polymorphism studies are at risk of underrepresenting the role of environmental conditions, including maternal caregiving behavior. As the quality of early caregiving has been found to regulate BDNF transcriptional functioning (Unternaehrer et al., 2015), we suggest that upcoming studies should target gene x environment interactions using genetic and epigenetic approaches.

To the best of our knowledge, this study is unique in providing evidence of an association between the BDNFval66met polymorphism and infants’ temperament at 4 months of life. The present study adds to previous genetic association research on temperament in infants looking at other polymorphisms (Auerbach et al., 2001; Ivorra et al., 2011), preliminarily suggesting a further genetic factor involved in temperament. Future research is warranted to investigate the BDNF-temperament association in greater populations of infants at low- and high-risk (e.g., preterm infants) and assuming a gene-x-gene and gene-x-environment approach (Papageorgiou & Ronald, 2013).”

Sonny Williams and Jay R. Feierman are antagonists who ignore the facts that link our predictions to all energy-dependent biophysically constrained biodiversity from our 1996 Hormones and Behavior. Our predictions were based on Bruce McEwen’s advice to start with the activation of genes. That is why we included a section on molecular epigenetics.

From Fertilization to Adult Sexual Behavior

All predictions have since been linked from the anti-entropic virucidal energy of sunlight to biophysically constrained RNA-mediated biodiversity by changes in base pairs linked from amino acid substitutions to differences in morphological and behavioral phenotypes during the development of moths and humans. The epigenetic effects of sunlight were predicted in the context of the nutrient energy-dependent de novo creation of microRNAs.
Anything ever linked to the gene-centric theories of neo-Darwinists has been replaced by what is known about energy-dependent endogenous RNA interference and all biophysically constrained biologically-based biodiversity on Earth. For example, pheromones biophysically constrain the physiology of reproduction in all living genera. They protect against virus-driven entropy by linking what organisms eat to the species-specific pheromone-controlled transgenerational epigenetic inheritance of species from microbes to humans.
See also: Epigenetic regulation of face formation
See also: Explaining the accelerating expansion of the universe without dark energy

See also: A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer
Reported by Genentech as: Cancer stem cells have long been thought to influence tumor growth, but a clear link has been difficult to show. Now, in a new study in Nature, our scientists show for the first time that removing cancer stem cells in a model of colorectal cancer can indeed reduce tumor growth. See how these findings could help guide new therapies aimed at targeting cancer stem cells.
What took them so long to link virus-driven energy theft from messenger RNA degradation to the negative supercoiling of DNA via G protein-coupled receptors?
Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons 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. 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.

 

Alternative splicing of pre-mRNA

The essence of precision medicine

…Trump’s labeling of the media as the enemy of the state was unfortunate and dangerous.

It was an accurate label that has been supported by Bill Gates and the Allen Institute in the context of the forthcoming viral apocalypse.
See for comparison this enemy of the state-issued media representation:
 

“We are all proud of professor Filipp’s accomplishments,” Vice Chancellor for Research Samuel Traina said. “He exemplifies the attributes of a great UC professor.”

 This biased representation was framed in the context of: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

Filipp misrepresented everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation and supercoiled DNA when he made this claim:
 
 

The Precision Medicine Initiative and National Microbiome Initiative link food energy to biophysically constrained RNA-mediated protein folding chemistry and viral latency. Virus-driven energy theft has been linked to all pathology in all living genera via the molecular mechanisms of chromosomal inheritance.

Evidence of chromosomal inheritance led to the 1933 Nobel Prize in Physiology or Medicine, which was awarded to Thomas Hunt Morgan.

The essence of precision medicine involves an understanding of how atomic energy-dependent RNA-mediated fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction, which has been linked to chromosomal inheritance by all serious scientists since Schrodinger (1944) in What is Life?.
 
For example, Horton et al (2014) put the facts about chromosomal inheritance into the context of epigenetic effects of food and pheromones on estrogen receptors and biodiversity of behavior in a single species.
 
 

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Filipp and others like him probably do not want the details of chromosomal rearrangements to be linked from energy-dependent changes in estrogen receptor polymorphism to virus-driven energy theft and androgen receptor polymorphism in prostate cancer. 
For an example of threat to pseudoscientists posed by facts about sex differences in androgen and/or estrogen receptor polymorphism and healthy longevity compared to virus-drive pathology, see: A third of Americans don’t believe in evolution
My comment to Phys.org:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

There is no other model or model organism that so clearly integrates what is known to all serious scientists about energy-dependent endogenous RNA interference at a time when Church et al (2015) are waiting to cash in on this patent application. RNA-Guided Human Genome Engineering

Anyone who claims to be proud of professor Filipp’s accomplishments should be asked how he thinks the essence of precision medicine will link drug targets from each person’s unique genetic and epigenetic makeup to what others have claimed is a “billion dollar baby.”

Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

See also: Obituary: Robert L. Moss

 Most recently, his efforts were directed towards establishing the role of pheromonal signals in activating GnRH neurons.

The nutrient energy-dependent pheromone-controlled activation of GnRH neurons links the androgen and/or estrogen receptor context of different tissues to healthy longevity or to virus-driven pathology in all vertebrates via substitution of achiral glycine in position 6 of the GnRH decapeptide.

Other energy-dependent RNA–mediated amino acid substitutions also link morphological and behavioral phenotypes to all biodiversity via conserved molecular mechanisms in the context of the physiology of reproduction.

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.