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.

 

Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics (5)

Researchers criticize the Mukherjee piece on epigenetics: Part 2

Excerpt:

…the organisms that have taught us the most about development – flies (Drosophila) and worms (C. elegans)—do not have the enzymes required for DNA methylation.

My comment:

James V. Kohl

Posted May 9, 2016 at 7:36 pm | Permalink

Please see Structural diversity of supercoiled DNA
Serious scientists have linked the epigenetic landscape to the physical landscape of supercoiled DNA via everything known about the innate immune system and energy-dependent changes in hydrogen-atom transfer in DNA base pairs that link angstroms to ecosystems via metabolic networks and genetic networks.
This report is a problem for pseudoscientists: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Weekend evolution of the bacterial flagellum is not consistent with any theoretical approach. Siddhartha Mukherjee refuses to let neo-Darwinism die without more obfuscation of facts.
See also: The New Yorker screws up big time with science: researchers criticize the Mukherjee piece on epigenetics
Excerpt:

…epigenetic processes analogous to those performed by the Yamanaka factors are performed by bacteria that entirely lack histones and DNA methylation.

My comment: That attests to the need to consider energy-dependent hydrogen-atom transfer in DNA base pairs in solution. Even without the histones and DNA methylation, the physiology of reproduction in bacteria is nutrient energy-dependent and controlled by pheromones. It’s time for everyone to start over in the context of rabbinical debate. Start with: “You fool…” Link Schrodinger’s claims about the anti-entropic energy of sunlight to Dobzhansky’s claims about amino acid substitutions that differentiate all cell types in all individuals of all living genera, and leave the biologically uninformed science idiots with their ridiculous theories. Serious scientists have done that during the past two decades or more.
See also: Dreadful science journalism at Vox: all interpretations of science are equal, but some are cuter than others
Excerpt:

The truth is that Mukherjee didn’t even mention transcription factors (or micro-RNAs that turn gene regulation down or off).

My comment: What have other theorists told us about microRNAs for comparison? Why are his claims being discussed outside the claims of other theorists?
See also: Functional Implications of Human-Specific Changes in Great Ape microRNAs
Conclusion

…miR-299-3p and miR-541-3p are conserved miRNAs with neuronal functions and thus evolutionary changes in these miRNAs may have had an impact in gene regulatory networks ultimately related to the evolution of the nervous system. Conversely, miR-503-3p and miR-508-3p regulate a low number of genes, have a restrictive pattern of expression and, although they seem to be involved in development, their functional role is still very vague. We show that specific nucleotide substitutions in the mature region and/or changes in the length of existing miRNAs may affect miRNA expression and hypothesize that both could be mechanisms by which miRNAs acquire new regulatory functions. Our study addresses for the first time the role that human-specific substitutions in miRNAs could have had in our recent evolutionary history and enlarges our understanding of how the non-coding genome may have contributed to shape human-specific traits.

Reported on 5/9/16 as:  Specific changes to non-coding RNA may be part of what makes us human

MicroRNAs are post-transcriptional gene regulators known to be involved in almost every biological function. They are highly conserved among species and, while some differences exist, the effect of the variations is often unclear. The authors of the present study analysed over 1500 microRNAs to identify variations between humans and other great ape species, including orangutans, gorillas, bonobos and chimpanzees, and the possible effect of these variations on function.

The authors found that changes in the sequence and length of four microRNAs may be specific to humans. Two were highly expressed in brain tissue and may exert effects on genes with neural functions, while two exhibit restricted expression patterns that the authors posited implied a role in development. The authors also found that “age” might matter; in an evolutionary sense, “younger” microRNAs had less sequence conservation, expression and disease association, and were more isolated than “older” microRNAs.

My comment: Nutrient energy-dependent changes in microRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution from the innate immune system to cell type differentiation via the physiology of reproduction in all living genera. Focus on RNA-mediated events outside the context of DNA methylation in bacteria enables a connection across all species. The physiology of reproduction links chemical ecology from variation in the epigenetic landscape to adaptation, which is manifested in supercoiled DNA. The supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
When you read about the criticisms of anyone’s work who has attempted to address what is known to serious scientists about epigenetically effected top-down causation in the context of healthy longevity compared to virus-driven pathology, keep in mind that evolutionary theorists have ignored the role that energy plays in cell type differentiation, which explains their need for a scapegoat. Revisit the claim that “…Mukherjee didn’t even mention transcription factors (or micro-RNAs that turn gene regulation down or off).” When was the first time you saw an evolutionary theorist mention energy-dependent microRNA-mediated gene expression?
For example, see: Mutation-Driven Evolution

MicroRNAs (miRNAs) and other small RNAs encoded by the noncoding regions of DNA are known to control the level of protein production by degrading mRNAs. Changes in these small RNAs may then alter the expression of phenotypic characters.  (p. 136)

Conclusion:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

For comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.

Conclusion: 

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

Coyne and others want to make an issue out of Mukherjee‘s ignorance and his failure to mention microRNAs. What are they claiming for comparison, and how does weekend evolution of the bacterial flagellum fit into the context of any theorist’s ridiculous claims? Serious scientists have reached the point where they can discuss human specific microRNAs in the context of healthy longevity or virus-driven pathology.
See also: Evolution of the human-specific microRNA miR-941 reported as: New brain gene gives us edge over apes, study suggests 11/14/12
Excerpt:

…this gene emerged fully functional out of non-coding genetic material, previously termed “junk DNA,” in a startlingly brief interval of evolutionary time.

My comment: The “emergence” of a fully functional gene from non-coding genetic material is a representation that only a neo-Darwinian theorist could make.
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment

In many experiments, bacteria are exposed to lethal constraints in order to select mutants that happen to have the appropriate trait for surviving. The selective conditions are conceived as an imitation of the environmental action in natural selection. Usually, the effect of one specifc selection factor is tested under uniform and constant conditions. The above-described approach is well developed and provides an efficient test bed for studying issues related to the selection for which they were designed. It is not suitable, however, for revealing the significant continuous role of the environment in bacterial `self-improvement’ between the rare events of selection, due to a large sudden change in a specific factor.

The evolution of gene expression and the transcriptome-phenotype relationship

Evolutionary models are only useful in the extent to which they can accurately predict the biological relationships they supposedly mirror.

Signaling Crosstalk: Integrating Nutrient Availability and Sex

 The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.

Masculinization of Gene Expression Is Associated with Exaggeration of Male Sexual Dimorphism
Reported as: The Ultimate Wingman
Excerpt:

Behavior and social environment may have an even greater effect on the male turkey’s phenotype than his genes do.

My comment to The Scientist: At the evolutionary advent of sexual reproduction in yeasts, increased nutrient uptake determines  “male” morphogenesis and the pheromone-controlled physiology of reproduction. See for example: Signaling Crosstalk: Integrating Nutrient Availability and Sex and our 1996 review for information on the molecular epigenetics of sexual orientation and sex differences in behavior.
Molecular epigenetics
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…. 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… That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”
The molecular mechanisms of sex determination via nutrient-dependent alternative splicings do not change in species from microbes to man, which means that sexual dimorphism is also nutrient-dependent and pheromone-controlled in turkeys. (See Bird odour predicts reproductive success.)

IMG_2329-e1413855233208-958x718

Genes and Race: Human History?

Roundup of Book Reviews of Nicholas Wade’s A Troublesome Inheritance

My comment: Many reviewers of Wade’s book on genes and race appear to think he has accurately represented issues of differences in cell types that evolutionary theorists associate with mutations, natural selection, and the evolution of human biodiversity. This may be cause for concern among those who are interested in accurate representations of biologically-based cause and effect.

In this century, it has become clear that ecological variation results in biodiversity, which is manifested in morphological and behavioral phenotypes that exemplify ecological adaptations in species from microbes to man. Therefore, most people might want to escape the criticisms associated with evolutionary theories based on population genetics that have received no support from experimental evidence of biologically based cause and effect. Yet, Wade sticks with mutations and natural selection as the cause of differences that somehow evolved. Reviewers claim no knowledge of biological facts that refute Wade’s outdated assertions. That’s scary, but no one says, BOO!

Indeed, he even discusses the modern human population that arose in what is now central China as if mutations and natural selection enabled the changes that occurred in hair, teeth, sweat glands, and mammary tissue — supposedly during the past ~30K years. The changes followed the climate change associated with disappearance of Neanderthals. That climate change and the associated dietary change can clearly be linked to reproductive success via a change in a single base pair linked to the substitution of a single amino acid in the organized genome of what may be the most successful human population on this planet.

If humans were frugivorous bats that ecologically adapted due to the availability of dietary ascorbic acid via the de novo creation of olfactory receptor genes, the human population would represent another population of mammals, albeit without wings, that successfully radiated to different regions of the planet via the conserved molecular mechanisms that enable adaptive radiation. If humans were mice, the amino acid substitution would be manifested in the same changes in cell types. Humans are not mice, but the same changes in cell types occur due to the same amino acid substitution. Amino acid substitutions also differentiate the cell types of other human populations.
The question arises, do serious scientists still think that mutations and natural selection enable adaptive radiation? Is there a model for that? If so, the model could be compared to what is known about the conserved molecular mechanisms of biolophysically constrained cause and effect. See for example: Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles. The article links genes to differences in morphology and behavior without resorting to claims made by neo-Darwinists.
Indeed, the focus is more on the fact that Darwin set forth when he repeatedly urged consideration of  the ‘conditions of life’ that must be met before natural selection could occur. His conditions of life require selection for food, which is manifested in changes in the microRNA/messenger RNA balance and cell type differentiation in bats and humans — if not all species, or some that might have mutated into existence. The report on the article mentions the fact that “With the recent discovery that non-coding microRNA’s in food are capable of directly altering gene expression within human physiology,[1] this new study further concretizes the notion that the age old aphorism ‘you are what you eat’ is now consistent with cutting edge molecular biology.”
Nicholas Wade’s book includes nothing known about the molecular biology of cause and effect. Reviewers seem to know about nothing but evolutionary theory.