5th-6th Sept 2018 Dublin, Ireland

Nutrient-dependent pheromone-controlled feedback loops

Summary: The link from positive selection to one food energy-dependent base pair change and fixation of the mouse-model-to-human-specific EDAR V370A allele in populations on different continents attests to sympatric speciation at every level of examination that refutes the pseudoscientific nonsense of neo-Darwinian mutation-driven evolution.

Reported on 5/3/18 as: SWAT team of immune cells found in mother’s milk 

1)

“There is a feedback loop,” says Yu. It’s known that some immune cells like leucocytes, another white blood cell that fights infection, increase in the milk in response to an infection in the baby.

2)

…the largest immune cell population in breast milk is macrophages, which ILCs are known to direct. Macrophages, which literally means ‘big eaters,” are the largest of the white blood cells and much-better studied than ILCs. They are known for their ability to envelop unwanted items like bacteria, viruses…

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk 4/23/18

The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers’ milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids.

Reported as: Gene linked to breastfeeding may have boosted survival of earliest Americans (4/23/18)

…they carried a genetic mutation—revealed in ancient teeth—that boosted the development of milk ducts in women’s breasts, which may have helped nursing mothers pass more nutrients to their infants.

The obvious link from infant nutrition to healthy longevity was reported in the context of a ridiculous gene-centric theory of species survival. Gene-centric theories are all that pseudoscientists have left. They use them to hold back the scientific progress made by serious scientists like those who reported this:
Feedback loops link odor and pheromone signaling with reproduction (2005)

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

Who created your virus-driven death gene? (2)

Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity

These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity.

The difference between an energy-dependent RNA-mediated amino acid substitution and a mutation has been largely ignored as pseudoscientists linked accidents to evolution.
See for example: Can watery asteroids explain why life is ‘left-handed’? (2009)

Sandwalk readers will know that I [Larry Moran] prefer an evolutionary explanation.

My summary of his evolutionary explanation:
The simplest amino acid is glycine where the R group is just a hydrogen atom. Glycine is not a chiral compound and there’s no such thing as L-glycine or D-glycine. All other natural amino acids are chiral. Larry Moran claims that glycine might have formed spontaneously. If so, the exclusive presence of L-amino acids instead of D-amino acids is just an accident. But it is an accident that somehow started with the spontaneous formation of glycine. The spontaneous formation of anything would be considered to be a miracle by those who  do not believe in evolutionary explanations.
Anyone who does not recognize the fact that people like Larry Moran think in terms of the accidental creation of the only achiral amino acid, which stabilizes the organized genomes of all vertebrates, should not read further.
It is a waste of time to examine facts after you decide to believe in more pseudoscientific nonsense than any serious scientist has ever considered. If you have not learned the difference between a mutation and an energy-dependent amino acid substitution, are you a well-trained medical practitioner?
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

Difference in mass resulting from the change of a single amino acid 

The mass of normal alpha chain is 15126.3 Da and that of the normal beta chain 15867.5, the changes induced by single point mutations are given above (only those allowed by the genetic code are given). As an example the change from Asp to His will increase the normal mass by 22 units and the reverse change will decrease the mass by the same amount.

The example links an increase in the stability and/or a decrease in the stability of the organized genome to a mutation and also to an amino acid substitution. The stability of all organized genomes is food energy-dependent and biophysically constrained via differences in hydrogen atom transfer in DNA base pairs in solution. The differences are measured in the context of blood gas analyses, and you should already know that the potential of hydrogen (pH) will determine the patient outcome — before you order the test.

If you do not understand this, find someone from the medical laboratory me to discuss it with. You may feel like a fool, but you will be less likely to kill someone via your ignorance.

See Fig. 2 Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively.

The differences in the network of hydrogen bonds between high- and low-altitude Hb variants should be placed into the context of why medical laboratory scientists must be trained to calibrate blood gas analyzers based on the barometric pressure at the location of the lab. For comparison to a somewhat less technical approach to the link from the circulatory system to nutrient energy-dependent microRNAs and pheromone-controlled biodiversity, see: Primo Vascular/Meridian System 2016

Thornton Streeter claimed that this a small contribution to understanding energy medicine. It links everything known about the creation of energy-dependent hemoglobin variants to all food energy-dependent biodiversity via the pheromone-controlled physiology of reproduction and the vascular/meridian system of humans.

See also: Ugur Murat Ozdemiroglu Admin of WORLD CONGRESS OF OBSTETRICS & GYNECOLOGY FORUM reported Yesterday at 3:36am on 12/11/17

By far the most important disease resulting from a mutation to an abnormally functioning hemoglobin is sickle cell disease, in which a single base change in the DNA results in a substitution of valine for glutamic acid at the sixth position in the beta globin chain.

Like all other quantized energy-as-information/food energy-dependent ecological adaptations, this hemoglobin variant is frequently reported to be a mutation. The link from one base pair change to the pheromone controlled physiology of reproduction and fixation of an amino acid substitution in the organized genomes of human populations protects them from extinction. The extinctions are caused by the virus-driven degradation of messenger RNA that most people indirectly link from malarial parasites to hemoglobin variants such as Hemoglobin S. Most people do not link viruses to all pathology, despite the historical record.

See: Biology, molecular and organismic (1964)

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.

See also: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

Link opens pdf:  Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

Ten years after McEwen et al., (1963) linked the creation of ATP to the creation of RNA via an endogenous substrate in all cell types of all living genera, Dobzhansky placed everything known about the creation of all biodiversity on Earth into the context of: Nothing in Biology Makes Any Sense Except in the Light of Evolution (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.

A single base pair change and one amino acid substitution differentiates the cell types of gorillas compared to chimpanzees and modern humans. That fact has finally forced pseudoscientists to begin to examine the role that viruses play in all pathology.

See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

The virus-driven degradation of messenger RNA in bacteria is linked to the creation of archaea and the virus-driven degradation of messenger RNA in humans is linked to the creation of non-human primates by the conserved molecular mechanisms that were reported in MicroRNAs: Milk’s epigenetic regulators

Our perception of milk has changed from a “simple food” to a highly sophisticated maternal-neonatal nutrient and communication system orchestrating early programming of the infant. Milk miRNAs delivered by exosomes and milk fat globules derived from mammary gland epithelial cells play a key role in this process. Exosomes resist the harsh intestinal environment, are taken up by intestinal cells via endocytosis, and reach the systemic circulation of the milk recipient. The most abundant miRNA found in exosomes and milk fat globules of human and cow’s milk, miRNA-148a, attenuates the expression of DNA methyltransferase 1, which is critically involved in epigenetic regulation. Another important miRNA of milk, miRNA-125b, targets p53, the guardian of the genome, and its diverse transcriptional network. The deficiency of exosomal miRNAs in infant formula and the persistent uptake of milk miRNAs after the nursing period via consumption of cow’s milk are two epigenetic aberrations that may induce adverse long-term effects on human health.

Only the best medical practitioners and researchers have grasped the fact that Carl Woese was wrong when he reported there were three domains of life. There is only one domain of life and the virus-driven degradation of messenger RNA is linked to all pathology in all living genera.

November 22, 2017 Sci-Hub, often referred to as the “Pirate Bay of Science,” lost three of its domain names this week.

Sci-hub.io, sci-hub.cc, and sci-hub.ac now have the infamous “serverhold” status which suggests that the responsible registries intervened. The status, which has been used previously when domain names are flagged for copyright issues, strips domains of their DNS entries.

November 23, 2017 RNA quality  Items: 1 to 20 of 604

Unless you can find access to Sci-Hub, you might find it difficult to access information on RNA quality.

See: The determinants of alternative RNA splicing in human cells

Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.

See also Neuropathological and transcriptomic characteristics of the aged brain

…we compared gene measures of RNA quality (RIN) and of dementia status (before and after accounting for RIN).

See also: Study finds infection and schizophrenia symptom link November 22, 2017

…activation of the maternal immune system in rats was sufficient to produce impaired timing, which is likely critical to other schizophrenia symptoms and impairments.Impaired ability to judge time accurately is a primary symptom in patients and this is also thought to be related to other symptoms, such as hallucinations, and cognitive impairment.

All Brain Perception is Rhythmic and Cyclical Says Newest Neuroscience

“We have suspected for some time that the senses are not constant but are processed via cyclical, or rhythmic functions; these findings lend new weight to that theory.”

It’s not a theory. Experimental evidence of biophysically constrained top-down causation links the energy-dependent RNA-mediated constraints on viral latency to healthy longevity via everything known to serious scientists since the time that the energy-dependent creation of ATP was linked to the energy-dependent creation of RNA.
See: Olfaction Warps Visual Time Perception
For comparison: This is a ridiculous theory.
Evolution of Epigenetic Mechanisms in Animals and Their Role in Speciation

DNA methylation is involved in gene regulation, silencing of transposons, imprinting, polyphenism, and consolidation of speciation. It may even act as a driver of evolution via stochastic developmental and environmentally induced epigenotype diversification, transgenerational inheritance of epigenetic patterns with phenotypic effects, and differential selection and genetic fixation of these phenotypes.

All ridiculous theories can be compared in the context of: To forget or to remember? Memory depends on subtle brain signals, scientists find

“The idea is, constantly as we learn information, there is a slow process that whittles away memories, and it continues whittling them away unless another part of the brain signals the memory is important and overrides it,” Davis said.

It may be that the process of acquiring and forgetting memories ebbs and flows in a state of balance, he said. Important memories like the taste of mom’s pumpkin pie might be forever retained, but trivialities like what you wore 10 years ago can fade into oblivion without consequence.

“If you have too much memory that is old and unnecessary, why keep them around? Why shouldn’t you have a system for removing those for optimal function of the brain?” Davis asked. “We’re getting all this information, all this learning during the day, and the brain may be saying, ‘No, no, bring me back to my basal, my happy state.'”

Many questions remain to be solved, Davis noted. “We need to figure out what is downstream—walk down the pathway to find the complete signaling system for forgetting,” he said. “We are very early in this research.”

Researchers who think “WE” are very early in this research are biologically uninformed science idiots. The COMT Val158Met amino acid substitution links food odor and pheromones to the biophysically constrained creation of one enzyme, which has been linked to differences in the dopaminergic reward system during the transition from adolescence to adulthood.
See:Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
I’m not sure why anyone would not already know how to link food odors and pheromones to enzymes and metabolism in humans in the context of the Human Microbiome Initiative and Precision Medicine Initiative.  But I understand why losers tend to claim that winners are still very early in this research.
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
See for comparison: Book Review by Mark Sergeant

The Scent of Eros is certainly an engaging text that informs the reader about the majority of key studies performed on human olfaction. Where it is let down is a lack of supporting evidence for some of the ideas considered, and a lack of critical consideration for some of the evidence that is presented. A reader unfamiliar with olfaction research could come away from this text unaware of several key debates within the field…

The Scent of Eros: Mysteries of Odor in Human Sexuality
By James Vaughn Kohl and Robert T. Francoeur
On page 298, we linked levels of DHEA to schizophrenia and to the odor of schizophrenics via the metabolism of DHEA to androsterone and etiocholanolone, which are indicators of nutrient stress and/or social stress. All stress-linked illnesses have since been linked from the virus-driven degradation of messenger RNA to pathology in species from microbes to humans.

See also: Epigenetic modifications poster
See also: Epigenetics round-up of 2014

Changes in histone acetylation may aid memory reconsolidation in post-traumatic stress disorder

See also: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone
The fact that the virus-driven degradation of messenger RNA has been linked to all pathology in all living genera has been established by serious scientists.
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Clearly, another question must be asked:
The first question: Who created your virus-driven death gene?

The next question: Who wants the virus-driven death gene to continue to be activated?

For example: The antagonism of the biologically uninformed science idiot who is the moderator of the Human Ethology Yahoo group increases each time scientific progress is made towards prevention of neurodegenerative diseases or suicide prevention. Instead of linking the virus-driven degradation of messenger RNA to suicide and Alzheimer’s, he posts information like this.

Choice of a suicide method: Trends and characteristics

Efforts towards suicide prevention in our veterans and others are replaced with information on their choice of a suicide method.

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Long-term adaptation replaces evolution (3)

Summary: Koonin thinks that serious scientists who have linked the creation of energy to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans must prove that everything the serious scientists know did not occur randomly after the sun’s anti-entropic virucidal energy emerged from nothing.
Other pseudoscientists have taken a step towards refuting Koonin’s moronic claim with publication of:
A mammalian blood odor component serves as an approach-avoidance cue across phylum border – from flies to humans

Feedback loops link odor and pheromone signaling with reproduction

The odor of E2D is sufficient to elicit approach response in blood-seeking animals. (A) Chemical structure of trans-4,5-epoxy-(E)-2-decenal (E2D). (B) Schematic drawing of the Y maze olfactory assay used for the fly behavioral experiment. (C) Mean percentage of flies choosing between E2D in a background of host odor and host odor only (left) and between E2D and cattle blood both in a host background. (D) A wolf displaying biting on the scented log, one of the eleven behaviors present in the ethogram. (E) Mean total number of interactions during a session with the four odor stimuli for the wolf pack. Error bars indicate standard error of the mean (SEM). *p < 0.05, ***p < 0.001.

Conclusion:

Taken together, our results strongly suggest that E2D is a blood signature substance that serves as an approach-avoidance cue across phylum borders; it elicits approach responses in blood-feeding invertebrates as well as in mammalian predators, while eliciting avoidance behavior in mammalian prey species. These results demonstrate the existence of a cross-species food- and alarm cue that affects behavior in both human and non-human animals alike.

Reported as: A universal food and alarm cue found in mammalian blood

The omnipresent adaptation to E2D indicates that the selection pressure for this chemical cue is preserved through evolution. This can shed light on human evolution, our formation as a species. “Our finding in humans fits in with the paleontological data showing that early primates were small-bodied insectivores. There is no question that humans are opportunistic predators, but we probably evolved from a prey species and some aspects of this trait lingers on,” says principal investigator Johan Lundström, associate professor at the Karolinska Institutet in Sweden.

Ecological variations are linked to ecological adaptations via what is known to serious scientists about quantum physics, which recently were placed into the context of observations that link electrons to ecosystems in all living genera via the 2017 Nobel Prize-winning cryo-EM technology. With the help of many others and also via my monographs and my presentations during the past 25 years this fact has become perfectly clear. The human ability to detect DNA differences in tissue type via the sense of smell is the link to biophysically constrained viral latency and all biodiversity.
There is no question that the passive-aggressive behavior of researchers like Johan Lundström is displayed as their failure to cite any of my published works.
See also: Smelling DNA with Joseph Orkin
Our ability to smell DNA arises only after the quantized energy-dependent creation of G protein-coupled receptors.
See also, from 1985: THE QUANTAL NATURE OF CONTROLLING STIMULUS-RESPONSE RELATIONS AS MEASURED IN TESTS OF STIMULUS GENERALIZATION

…the quantal interpretation, proposes that a stimulus-response relation functions as a unit that may or may not occur. From the latter viewpoint, the continuity typically obtained during generalization tests is deemed to be artifactual and to result from averaging across multiple controlling stimulus-response relations.

The “omnipresent adaptation to E2D” links multiple controlling stimulus-response relations from the energy-dependent de novo creation of G protein-coupled receptors to the foraging behavior of bacteria and to the physiology of pheromone-controlled human reproduction. Without the ability to sense differences in the fixation of amino acid substitutions in organized genomes DNA, biologically uninformed science idiots have no way to explain omnipresent pathology. Simply put, they have failed to link our choices to all pathology.
Clearly, serious scientists have linked the physiology of pheromone-controlled human reproduction from food energy to the ability to reproduce in all living genera. That is how the omnipresent pathology links the virus-driven degradation of messenger RNA from bacteria to the creation of archaea and L-forms. The L-forms are the last representation of what happens to all life forms that cannot find enough food energy to biophysically constrain viral latency.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

For comparison, see: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

Eugene Koonin knows that: “The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…”
That fact forces him to fight against the claims of adaptationists who have refuted his pseudoscientific nonsense about mutations and evolution.
See: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution
Koonin thinks that serious scientists who have linked the creation of energy to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans must prove that everything the serious scientists know did not occur randomly after the sun’s anti-entropic virucidal energy emerged from nothing.

See for comparison:
“Light Unshackled” will be shown in its entirety during a special screening at 527 Forge Mill Road in Morganton, GA on Tuesday, October 24, at 6 p.m.
 
The game “Cytosis” is also already being distributed. Everyone over age 10 can learn to link the creation of anti-entropic virucidal light to all biophysically constrained biodiversity via what is known about the molecular mechanisms that link the physiology of pheromone-controlled reproduction to RNA-mediated viral latency.
 

No one I know expects you to understand the overwhelming complexity of the links from quantum physics to chemistry and molecular epigenetics to quantum souls. Many people I know expect you to be able to understand the claims about “Light Unshackled.”

2/4: Lighting a Flame – Light Unshackled – English

Episode 3 has been released, and Episode 4 will be released on October 27.
See: Light Unshackled Film

See also: Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy

In this study, across 60 melanoma cell lines, we find bimodal expression patterns of MHC-II, while MHC-I expression was ubiquitous. A unique subset of melanomas are capable of expressing MHC-II under basal or IFNγ-stimulated conditions. Using pathway analysis, we show that MHC-II(+) cell lines demonstrate signatures of ‘PD-1 signalling’, ‘allograft rejection’ and ‘T-cell receptor signalling’, among others.

UV light induced changes in the microRNA/messenger RNA balance have been linked to healthy longevity via the food energy-dependent RNA-mediated fixation of pheromone-controlled amino acid substitutions in organized genomes. Differences in the amino acid substitutions have been found in the organized genomes of all species.

The virus-driven theft of quantized energy such as UV light has been linked from the degradation of messenger RNA to all pathology.

See also: Medical Breakthroughs: Cancer

During clinical trials, the medication was famously used to treat former President Jimmy Carter, who two years ago announced he had cancer in his brain and liver and said his fate was “in the hands of God, whom I worship.” Four months later, his cancer was gone.

Was it God who caused the cancer, or did God cause its demise? From my perspective on light energy as information and energy-dependent RNA-mediated DNA repair, it is clear that  melanoma-specific MHC-II expression represents a link from the virus-driven degradation of messenger RNA to a predicatable response from the innate immune system. That response has been made somewhat more predictable in the context of the phenotype that predicts the response to anti-PD-1/PD-L1 therapy.

See also:  New Dancing Couple: PD-L1 and MicroRNA

MicroRNAs are regulatory molecules (~20 nt in length) with the ability to regulate the expression of genes. The recently described PD-1 and PD-L1 molecules have great importance for potential use in immunotherapy of many cancers. These molecules are associated with immune checkpoints and provide an opportunity for the treatment of advanced NSCLC patients with synthetic monoclonal antibodies. PD-L1 expression is strictly associated with microRNA function in lung cancer cells. The group of microRNAs related to PD-L1 includes, among others, miR-200, miR-197 or miRNA-34. Expression of these molecules may be useful in lung cancer diagnosis, qualification to anti-PD-1 or anti-PD-L1 antibody therapy and could be a potential therapeutic target. However, studies on PD-L1-related microRNAs are necessary to develop advanced targeted molecular therapies.

Studies of studies on PD-L1-related microRNAs and other microRNAs link the changes in electrons to ecosystems in all living genera. Focus on prevention and effective treatments of all pathology has been delayed by the focus on the CRISPR/Cas 9 gene editing technology. That focus is much more closely linked to the pseudoscientific nonsense touted by neo-Darwinian theorists who failed to link the virus-driven degradation of messenger RNA to all pathology.

For God and Country

Energy-dependent structure and function: Until death (5)

Summary: If a player starts with evolution instead of the creation of energy that links ATP to the creation of RNA, the player is a loser.
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
Secular: Ancient Viruses Are Buried in Your DNA (2017) by Carl Zimmer

…early embryos may have come to depend on the tricks viruses use to manipulate them. “We’re exploiting a property that has evolved for the virus’s benefit,” Dr. Katzourakis said.

Science fiction novelist: The Darwin Code by Greg Bear

In 1996, I proposed to my publishers a novel about the coming changes in biology and evolutionary theory. The novel would describe an evolutionary event happening in real-time–the formation of a new sub-species of human being. What I needed, I thought, was some analog to what happens in bacteria. And so I would have to invent ancient viruses lying dormant in our genome, suddenly reactivated to ferry genes and genetic instructions between humans.

To my surprise, I quickly discovered I did not have to invent anything. Human endogenous retroviruses are real, and many of them have been in our DNA for tens of millions of years. Even more interesting, some have a close relationship to the virus that causes AIDS, HIV.

Serious Young Earth Creationist: Did God Make Pathogenic Viruses? (1999)

…viruses are not living, and in order to reproduce and to make ATP, they require all of the complex cellular machinery present in bacterial cells.

Serious scientist: Where do viruses come from? (2004)

“Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.’ — Holmes, B., Who Rules the Waves? New Scientist 152(2054):8–9, supp, 1996

Serious Young Earth Creationist/Scientist: Viral Genome Junk Is Bunk

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

Secular/Young Earth Creationist: Celebrate Your Inner Virus (2017)

It is important that we understand the design present in viruses because God made them. All creatures of our God demonstrate his handiwork, and viruses are no different.

Infographic: Evolving Virulence

…under natural conditions, a newly emergent, highly lethal pathogen that kills very rapidly is expected to evolve lower virulence. At the same time, however, the host species is evolving resistance to the infection…

Natural selection for energy-dependent codon optimality biophysically constrains viral latency in the context of the physiology of pheromone-controlled reproduction. See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
My comment to The Scientist:

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (2013)

“The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.”

One nutrient energy-dependent change in a base pair is linked to fixation of the amino acid substitution in the virus and one nutrient energy-dependent change in a base pair is linked from the physiology of pheromone-controlled physiology of reproduction to fixation of amino acid substitutions in the organized genomes of hosts. Fixation is a function of the innate immune system, which  biophysically constrains viral latency.

Simply put, it’s “All about that base” See also: Structural diversity of supercoiled DNA

Nutrient stress and social stress act on the same molecular mechanisms that link the virus-driven degradation of messenger RNA to mutations and all pathology. That fact can now be examined in the context of everything know about how the cryo-EM technology links energy-dependent changes in electrons to ecosystems via the physiology of reproduction. Alternatively, everything known to serious scientists about ecological variation and energy-dependent ecological adaptations can be place back into the context of ridiculous theories about evolution.

See for example, these claims about a model for how the brain controls foraging.
Brain modelling: Does the brain control foraging?

The brain might instead act as a mediator between controlling factors in the environment and behavioural output. Perhaps, like evolution, it functions as a tinkerer, equipped with a range of signalling or other mechanisms that allow adaptation (see F. Jacob Science 196, 1161–1166; 1977).

Claims that the brain evolved have been replaced by claims that the brain is an energy-dependent ecological adaptation. Claims about its ability to function as a tinkerer have been replaced with facts that link electrons to ecosystems via the 2017 Nobel Prize-winning technology called cryo-EM. Developers of the technology won the Prize in Chemistry.
Cryo-EM can now be viewed in this context of biophyiscally constrained protein folding chemistry and claims from 2005.
See: Feedback loops link odor and pheromone signaling with reproduction
The claims about feedback loops can be placed into the context of what anyone who is 10 years-old can learn about cell biology and virus-driven energy theft by playing the game “Cytosis.”
If a player starts with evolution instead of the creation of energy that links ATP to the creation of RNA, the player is a loser.

Alternative splicing of pre-mRNA

Methylation and the Innate Immune System

Free Webinar Training:

Methylation and the Innate Immune System

Please send your questions, comments and feedback to: support@qahomestudy.com

I sent these two questions in advance:

1) Does what organisms eat link food energy to RNA-directed DNA methylation and all healthy longevity via fixation of amino acid substitutions and transgenerational epigenetic inheritance in the context of the physiology of pheromone-controlled reproduction in species from microbes to humans?

2) Does the virus-driven theft of quantized energy link the loss of information from impaired methylation to all pathology?

——————————

See why I asked: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: Olfaction Warps Visual Time Perception



Alternative splicing of pre-mRNA

Energy-dependent epigenetic translation to mRNA stability (5)

Energy-dependent epigenetic translation to mRNA stability (4)
From Fertilization to Adult Sexual Behavior

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….

See also: The Supraspliceosome – A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus
Abstract conclusion:

…changes in these regulatory processing activities are associated with human disease and cancer. These findings emphasize the supraspliceosome as a multi-task master regulator of pre-mRNA processing in the cell nucleus.

Excerpt:

…the initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

Energy-dependent regulation of the supraspliceosome and RNA-mediated amino acid substitutions is charge-regulated and the change in the charge must be linked to fixation of the amino acid substitution in the organized genomes of all living genera before energy can be linked to biologically-based cause and effect via what is known to all serious scientists about how the physiology of reproduction must be linked to biodiversity.
The changes in the supraspiceosome must then be linked from chromosomal rearrangements to morphological and behavioral diversity.
See also: New study helps solve a great mystery in the organization of our DNA, which is a report on this peer-reviewed published work: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.

My summary: The rules integrate what is known about energy-dependent adenosine to inosine RNA editing. See: Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides
Prebiotic synthesis starts with the sun’s anti-entropic virucidal energy.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
RNA biosynthesis is energy-dependent and an endogenous substrate appears to be the link from sunlight to protometabolism. By starting from protometabolism, it is easy to link the energy from the innate immune system to polycombic ecological adaptations in all living genera via the physiology of reproduction.
See also: Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms

little is known about the mechanistic underpinnings of how differently composed Polycomb complexes instruct and maintain cell fate. Here we find that Mel18, also known as Pcgf2 and one of six Pcgf paralogs, uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. Mechanistically, Mel18 functions as a classical Polycomb protein during early cardiac mesoderm differentiation by repressing pluripotency, lineage specification, late cardiac differentiation, and negative regulators of the BMP pathway. However, Mel18 also positively regulates expression of key mesoderm transcription factors, revealing an unexpected function of Mel18 in gene activation during cardiac differentiation. Taken together, our findings reveal that Mel18 is required to specify PRC1 function in both a context- and stage-specific manner.

The context- and stage-specific links from polycombic ecological adaptation are nutrient energy-dependent and the regulation of polycombic ecological adaptations is biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See: Polycombic ecological adaptation as a science, not a theory
See also: Polycombic ecological adaptation as a science, not a theory (2)
See also: Search Results for “Polycombic ecological adaptation
For contrast, see: Is inference the best way to explain the origin of consciousness?

This conversation is connected to: Consciousness is not a thing, but a process of inference

My comments:

  1. Excerpt: “On this view, a loss of consciousness occurs whenever our models lose their ‘thickness’ and become as ‘thin’ as a virus’s.”

Consciousness is energy dependent and biophysically constrained by the ability of organisms to find food and reproduce. Consciousness is manifested as increasing organismal complexity in the context of links from quantum consciousness to quantum souls.

The fact that it took only one journalist to expose all the others who have not asked the right questions about consciousness so that the questions could be answered in the context of what is known to all serious scientists about virus-driven energy theft and all pathology is revealed here, and in the first interview from the week before.

Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl

2. I just placed the essay on “Consciousness” into the context of “snake centric” evolution after scanning two published works by the author [Friston, Karl J.]

1) Top-Down Control of Visual Responses to Fear by the Amygdala http://www.jneurosci.org/content/33/44/17435.abstract

2) Bayesian inferences about the self (and others): A review http://www.sciencedirect.com/science/article/pii/S1053810014000105

See also: “Isbell calls these findings “the first neuroscientific support” for her snake-centric evolutionary theory.” excerpted from http://news.sciencemag.org/evolution/2013/10/did-snakes-help-build-primate-brain

For comparison see:

“Science is the belief in the ignorance of experts” — Richard Feynman

Feynman supported the efforts of those who laugh at ‘experts,’ especially when the experts are not among the serious scientists who were forced to link ecological variation to energy-dependent ecological adaptation in the context of what is now known about how to link food energy-dependent changes from angstroms to ecosystems in all living genera via feedback loops and the pheromone-controlled physiology of reproduction.

In “The Pleasure of Finding Things Out,” (see pages 124 and 125 for a summary) Richard Feynman presciently predicted that the ability to see interactions at the level of atomic energy would link quantized energy from sunlight to photosynthesis and pattern recognition by biologists, who would then link quantum physics from chemistry to the growth and movement of all organisms on Earth.
See also:

This comment was posted to my FB group on April 17, 2017
 

1) The findings reveal similarities and differences with a recently published report on the IP3R using a completely different method called cryo-electron microscopy.

2) The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions.

By identifying the amino acid sequence, they inadvertently linked natural selection for energy-dependent codon optimality to all biodiversity via the biophysically constrained physiology of reproduction in the context of hydrogen-atom transfer in DNA base pairs in solution.

See also Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function as cited in:The Origin of Information: How to Solve It

Search Results for “hydrogen-atom transfer in DNA base pairs”

See also: Energy-dependent epigenetic translation to mRNA stability (5)
 

terrarium-eco-system

Critical values expose virus-driven energy theft (2)

Why Don’t The Amish Get Cancer?

…the Amish commitment to simple, productive lives and clean, local food is benefiting their health in ways that the rest of America can only dream about.

They exemplify what it means to be an ecologically adapted human population.

See also: Past 5,000 years prolific for changes to human genome

The facts support the beliefs of young earth creationists. That invites ridicule and denigration of my published works. But the experimental evidence of biologically-based cause and effect shows that 86.4% of the putatively deleterious protein-coding SNVs arose in the last 5,000 to 10,000 years.

Ridiculous ideas about mutations, natural selection and evolution have never been supported, and “selection” has not purged the mutations from the population. Instead, we have the Amish as well as Seventh Day Adventists (with their networks of hospitals and medical professionals) as examples of how ecological variation must be linked to ecological adaptation via epigenetic effects on the genetic code.
 
The fact that you “must have a code that you can live by” extends to everyone else and across all living genera. It is the genetic code, but no experimental evidence suggests that it automagically created itself or that we evolved after that.

See for comparison:

For comparison see: Critical values expose virus-driven energy theft

Autophagy cannot be discussed outside the context of how sunlight is linked from chirality to the de novo creation of G protein-coupled receptors and to all energy-dependent biodiversity, or from virus-driven energy theft to all pathology.

Measurement of pH in cord blood and measurement of bilirubin in neonates link the anti-entropic virucidal epigenetic effect of ultraviolet (UV) light to the treatment of infants who are in distress. Respiratory distress is linked from pH to the treatment and bilirubin is linked to the treatment with virucidal UV light.

 Autophagy in the liver: functions in health and disease

Regulation of autophagy by amino acids.

Amino acid sensing and integration
Amino acid signalling is integrated by the RAG–Ragulator–v-ATPase complex on lysosomes to activate mTORC1 (REF. 98) (FIG. 4). Although consensus has not yet been reached, it is believed that the RAG heterodimer, composed of a RAS-related GTP-binding protein (RAG) A or RAGB monomer and a RAGC or RAGD monomer, contributes to mTORC1 activation98. mTORC1 is particularly sensitive to decreases in the levels of leucine, arginine and glutamine 88,99,100
Metabolic recycling of amino acids
The final stage of hepatic autophagy contributes to the amino acid supply through the breakdown of proteins. Hepatic autophagy is critical for maintaining systemic blood glucose levels during fasting by providing amino acids for the generation of glucose via hepatic gluconeogenesis
As autophagy has important roles in both quality control of organelles and the supply of amino acids and fatty acids to cancer cells, this degradation system is thought to support cancer survival and proliferation199. Selective autophagy enables the liver to efficiently and precisely control the quality and quantity of cytoplasmic organelles, including mitochondria, peroxisomes and lipid droplets, as well as the proper functioning of NRF2. Thus, selective autophagy is one strategy hepatocytes can utilize to adjust their cellular metabolic capacity. Conversely, inactivation of selective autophagy, which results in elevated oxidativestress and accumulation of SQSTM1-positive aggregates and lipid peroxides, is connected to chronic hepatitis virus infection, alcoholic steatohepatitis, NAFLD and HCC.
Metabolic adaptation through liver autophagy during fasting therefore proceeds via utilization of glycogen and fatty acids in the early phase and amino acids in the later phase.
See for comparison: Life is physics and chemistry and communication

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

See also: The Strange Inevitability of Evolution

These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself. That is a view long championed by Schuster’s sometime collaborator, Nobel laureate chemist Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that’s right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability.

See also: Is it Time to Upgrade Your Health Routine? Diet. Exercise. Cellular Health.

Healthy cells “communicate” to carry out processes in our body

Cells are called the building blocks of life because that’s precisely what they are: the smallest unit of life, with between 30 and 50 trillion of them making up the average human body. Within each tiny cell are components called organelles, including familiar names like the mitochondria and the nucleus, that work together, or communicate, to carry out all of the processes in our body. They convert food to energy, help our muscles contract when we walk, and secrete serotonin that gives us the sense of well-being.

Communication is essential to proper cell function

Cells function properly with consistent communication between organelles like the mitochondria and nucleus, which are dependent on each other. Healthy communication leads to optimal performance in hundreds of functions. One of the most important communication-dependent processes is mitochondrial function, since the mitochondria turn nutrition into energy. Proper communication is the key to having sufficient energy to carry out all of the cells’ functions.

Basis is a proprietary formulation of two compounds — nicotinamide riboside (a unique form of vitamin B3) and pterostilbene (a powerful antioxidant) — in capsule form. It’s designed to support healthy levels of NAD+, which is essential to fundamental cellular function in over 500 areas, including creating energy and maintaining the integrity of our DNA.

Why Don’t The Amish Get Cancer? (revisited)

They are ecologically adapted. That’s why. Most people are not ecologically adapted. That’s why they suffer and die from virus-driven energy theft, which causes all pathology.

fruit-dove

Critical values expose virus-driven energy theft

Critical Values: is ASCP’s quarterly magazine with news and features covering trends of interest to pathologists and laboratory professionals alike.

See for example: Attentive Clinical Laboratory Scientist Discovers First Human Case of Borrelia turicatae

Critical Values spoke with technologist Dolli Lane, MLT(ASCP)CMCsCM, and the chief of the hematology section, Chris Boyd, MLT(ASCP)CM, about their findings. Their story demonstrates how attention to detail saves lives.

Every serious scientist I know is on the verge of linking the creation of the sun’s anti-entropic virucidal energy from hydrogen-atom transfer in DNA base pairs in solution to autophagy and supercoiled DNA via the physiology of reproduction in all living genera.

See for example: Cephalopod Olfaction

Several behavioral and functional studies have been conducted on nautiluses and decapods, demonstrating the role of olfactory organs in mate choice, predation improvement, defense strategy, and spatial orientation. Recent functional and morphological studies of octopods have revealed new perspectives about the role played by olfaction in the complex behavioral patterns shown by these fascinating animals.

Many of the serious scientists could explain what biologically uninformed theorists routinely ignore.  For example, every pseudoscientist and atheist is still touting the religious dogma associated with neo-Darwinian theories. Their theories failed to include a link from Darwin’s energy-dependent “conditions of life” to all biophysically constrained biodiversity. That link is the nutrient energy-dependent physiology of pH-dependent pheromone-controlled reproduction.

Most of the military-trained medical laboratory scientists I know were trained to troubleshoot procedures and instruments to avoid the errors that theorists from the evolution industry or big bang cosmology industry have continued to make. For example, the most important critical value linked to health or pathology is pH.
 

The scientific term “pH” is an abbreviation that stands for “potential of hydrogen,” which is a measure of the acidity or alkalinity of a solution.The term, which first came into use in 1909, is Germanic in origin and is derived from the word “potenz,” meaning power, plus “H,” which is the symbol for hydrogen on the periodic table.

The energy levels in a hydrogen atom can be obtained by solving Schrödinger’s equation in three dimensions. Because most people cannot do that, it may be more important for them to know that energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution must be linked to “conditions of life.”

When too much of the potential energy is used by a living organism or a virus, the organism dies. Theorists typically do not know that, or perhaps they simply don’t care where the energy came from.  Darwin claimed it must be linked from his “conditions of life” to all biodiversity via the physiology of energy-dependent reproduction.

That explains why theorists cannot trouble-shoot their ridiculous theories. If they were required to perform a blood gas analysis in a hospital medical laboratory, they probably would not understand that human life exists only in the biophysically constrained pH that ranges from ≤7.25 or ≥ 7.6. Theorists could not link calibrations and controls that are required to report accurate results to patient outcomes. Theorists are told that the outcomes are due to mutations and evolution.

See instead:Stat Profile Prime CCS Blood Gas Analyzer from Nova Biomedical

Measuring pH links nutritional epigenetics from the innate immune system to healthy longevity via everything known about virus-driven energy theft, which links nutrient stress and social stress to the replication of viruses, which link mutations to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

See also: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water

The energy-dependent interaction between water and ions is omnipresent in biological processes related to enzymes, ion channels and protein folding.

See for comparison: 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 [energy] dependent. Experiments are described which show that the required ATP is produced by reactions associated with glycolysis, the citric acid cycle, and a type of oxidative phosphorylation. These pathways can be selectively inhibited by iodoacetate, fluoroacetate, and antymycin A, and RNA synthesis is blocked in the presence of these inhibitors. However, CO, which inhibits mitochondrial oxidative phosphorylation but does not block nuclear ATP synthesis, does not affect RNA synthesis in isolated nuclei or in whole cells. The use of CO as a selective inhibitor of mitochondrial ATP synthesis has made it possible to suppress cytoplasmic protein synthesis while allowing nuclear protein synthesis to continue.

See for comparison: A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome

Serine/threonine phosphorylation also has important effects on RTK signaling. We consistently found numerous PSP hits in our screens, although most of their functions remain unknown.

Reported as: First complete interactome map of human receptor tyrosine kinases and phosphatases

The researchers were surprised to find that some PTPs defy convention and act to promote RTK signalling suggesting that their roles are more complex than previously thought. For example, a phosphatase called PTPRA activates the EGFR, which is mutated in many cancers, revealing a new way in which cancer might spread. They also found two new phosphatases, PTPRB and PTPRH, which work as expected by grinding EGFR signalling to a halt, with potential anti-tumour properties.

Phosphorylation has long been suspected or known to be the energy-dependent molecular mechanism that enables the fixation of RNA-mediated amino acid substitutions. Ffixation of amino acid substitutions in supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. That fact is placed back into the context of evolution of the  protein phosphatases from genes in this example of gene-centric theory.

… protein phosphatases evolved from distinct genes and employ different enzymatic mechanisms (Li et al., 2013). They are traditionally divided into two classes, protein Ser/Thr phosphatases (PSPs) and protein tyrosine phosphatases (PTPs). PSPs include the PPP, PPM, and FCP/SCP families (Li et al., 2013). The cysteine-based PTP superfamily includes about 100 members (Alonso et al., 2004; Tonks, 2006) grouped into classical PTPs and dual specificity phosphatases (DUSPs). Classical PTPs play critical roles in tyrosine kinase signaling (Neel and Tonks, 1997), whereas DUSPs can dephosphorylate Tyr and Ser/Thr residues. Some DUSPs function as lipid or glycogen phosphatases. The EYA family comprises a small set with an aspartate-based catalyticdomain (Alonso et al., 2004; Jemc and Rebay, 2007).

This is a potent obfuscation of the facts known to all serious scientists who have linked ecological variation to energy-dependent ecological adaptation via what is known about biophysically constrained protein folding chemistry.

PPPs are typically multi-subunit proteins, composed of a catalytic subunit and scaffold/regulatory subunits that serve to determine their substrate specificities.

The regulatory subunits are energy-dependent RNA-mediated amino acid substitutions. Theorists know that refutes their neo-Darwinian nonsense so they pretend not to know that substrate specificities are energy-dependent and that the energy is linked to species-specific differences in morphological and behavioral phenotypes by what organisms eat.

Here’s another misrepresentation of that fact.

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

The human brain is a complex and highly evolved structure. Mouse models do not fully recapitulate cell-type diversity or lineage trajectories of the human brain (Florio et al., 2015; Konopka et al., 2012; Pollen et al., 2015; Reilly et al., 2015; Silbereis et al., 2016; Thomsen et al., 2016). Furthermore, human neurodevelopmental diseases such as autism spectrum disorders and schizophrenia are incompletely modeled in mouse.

The only way to keep fooling people into believing that the human brain evolved, is to keep teaching them to ignore what is known about energy-dependent autophagy.

See for example: Autophagy fan club

Sena Latagan We would prefer not to censor our members, but we do ask that members be respectful and try to remain on topic.
Sena Latagan James, for the purposes of this group’s discussions autophagy is defined as an intracellular bulk degradative process whereby intracellular contents are engulfed in a double membrane structure that then fuses with lysosomes. We ask our members to restrict their discussions to issues related to this definition of autophagy.
James Kohl Thanks. In other words, you are claiming that autophagy is energy-dependent. Please tell me which post was not about autophagy and advise the group of your determination on the validity of any complaints. My publication history spans 20 years, and I hate to see complaints from those who are biologically uniformed force me to leave because of a definition.
Olfaction is the link from autophagy to supercoiled DNA and pseudoscientists have failed to recognize that fact since the time that de Vries defined the term mutation.
See what’s next, and try to stop the dissemination of accurate information if you like. Cephalopod Olfacton
Censors can only do so much damage, and the time has come when serious scientists are doing damage repair, whether or not anyone in this group likes it. Similarly, chirality links the sun’s biological energy from the speed of light to autophagy and RNA-mediated DNA repair. If you would rather others not know that fact, change the name of the group to something that does not infer it is a group for discussion of autophagy.
Perhaps, “Definition Fan Club” would be more appropriate.

Sena Latagan Member James Kohl has been removed for posting unrelated topics. We the admins would like to remind everyone to please stay on topic in respect to the other members who are here to discuss autophagy as it is currently defined in the literature. Thank you.

Autophagy cannot be discussed outside the context of how sunlight is linked from chirality to the de novo creation of G protein-coupled receptors and to all energy-dependent biodiversity, or from virus-driven energy theft to all pathology. Definitions, such as de Vries 1902 definition of mutation are used only by the biologically uninformed who chose to stay uninformed. They will never know what it takes to know something about biologically-based cause and effect.

See: Critical values expose virus-driven energy theft (2)

Alternative splicing of pre-mRNA

Energy-dependent chirality

See also: Achiral glycine
Summary: Virus-driven energy theft alters the interactions between physics and chemistry that maintain biophysically constrained biodiversity. That’s how viruses are linked from mutations to all pathology. Nutrient energy-dependent changes in the context of the pheromone-controlled physiology of reproduction biophysically constrain biodiversity via the fixation of amino acid substitutions in supercoiled DNA, which protects organized genomes from virus-driven pathology.
Chirality (chemistry)

Two enantiomers of a generic amino acid that is chiral
The chirality of amino acids is energy-dependent and biophysically constrained by the physiology of reproduction in all living genera. For example, the substitution of achiral glycine in position 6 of the decapeptide gonadotropin releasing hormone (GnRH) stabilizes the organized genomes of all vertebrates by helping to protect them from virus-driven energy theft.

(S)-Alanine (left) and (R)-alanine (right) in zwitterionic form at neutral pH

See also:The acid-base behavior of amino acids

There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge.

Energy as information is placed into the context of the sun’s anti-entropic virucidal link from hydrogen-atom transfer in DNA base pairs in solutions. For example, as water in the ocean can be linked to all biodiversity via the physiology of reproduction and fixation of RNA-mediated amino acid substitutions in the supercoiled DNA of all living genera.

Any nutrient energy-dependent change in pH can be linked from hydrogen-atom transfer in DNA base pairs in solution to healthy longevity. All virus-driven energy theft can be linked from changes in pH and hydrogen-atom transfer in DNA base pairs in solution to pathology.
The difference between healthy longevity and pathology is viral latency. Unless the virus-driven energy theft is biophysically constrained by the anti-entropic virucidal force of the sun’s energy, life on Earth is not possible.
See also: A single ion impacts a million water molecules
That fact helps to explain what is intuitively obvious to all serious scientists. They understand how the energy-dependent difference between bacteria and archaea links the degeneration of messenger RNA from bacteria to the degenerate mophological and behavioral phenotypes of archaea.
See: Virus-mediated archaeal hecatomb in the deep seafloor
For comparison, see: From Fertilization to Adult Sexual Behavior

… 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 (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

All differentiation in all cell types of all living genera exemplifies nutrient energy-dependent pheromone-controlled RNA-mediated polycombic ecological adaptation. That fact can be compared to the fact that virus-driven energy theft exemplifies the hecatombic evolution of all pathology. Both facts can be placed into the context of everything known about energy-dependent alternative splicings and amino acid substitutions in supercoiled DNA.
For comparison, see this representation of how “minimal mutational distance” might still be used by biologically uninformed theorists who do not know the difference between a mutation and an amino acid substitution:
Construction of Phylogenetic Trees

Determining the Mutation Distance The mutation distance between two cytochromes is defined here as the minimal number of nucleotides that would need to be altered in order for the gene for one cytochrome to code for the other. This distance is determined by a computer making a pair-wise comparison of homologous amino acids (8).

The choice is perfectly clear. You can accept the claims of theorists who use computers to make “…a pair-wise comparison of homologous amino acids,” or accept the claims of serious scientists who have linked energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which typically protects all living genera from virus-driven energy theft and all pathology.
See also: Multipurpose Plant Sensors Startle Scientists
See also: J. B. S. Haldane [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
This discussion attempt failed to convince anyone that Haldane, who was one of the theorists who helped to invent neo-Darwinism, was like all the others who knew nothing about biophysically constrained energy-dependent cell type differentiation.

Peter Berean who invented the term “bio-functional information” concluded:

What is your chain of logic (in your own words) that leads to your belief that energy = information?

—————————–
DEFINITION

—————————–
in·for·ma·tion
1. facts provided or learned about something or someone.
“a vital piece of information”
synonyms: details, particulars, facts, figures, statistics, data; More
2.
what is conveyed or represented by a particular arrangement or sequence of things.
“genetically transmitted information”

—————————–
en·er·gy

1.
the strength and vitality required for sustained physical or mental activity.
“changes in the levels of vitamins can affect energy and well-being”
synonyms: vitality, vigor, life, liveliness, animation, vivacity, spirit, spiritedness, verve, enthusiasm, zest, vibrancy, spark, sparkle, effervescence, ebullience, exuberance, buoyancy, sprightliness; More
2.
power derived from the utilization of physical or chemical resources, especially to provide light and heat or to work machines.
—————————–

Conclusion: Energy and Information are two completely different things. They are NOT the same thing.

Claims that energy is not information, which are based on definitions, continue to frustrate the effort of intelligent scientists who are combating evolution to fight disease.
The casualties on the side of the serious scientists can be attributed to theorists and journalists who write articles with conclusions like this.
See: The queen does not rule

Division of labour is a human innovation, drawing on our ability to learn and improve by practice, and to trade goods and services. The growing recognition that natural processes work differently from our symphonies and armies will allow us to see the natural world more clearly. Ant colonies are not factories or fortresses; instead they use simple interactions to adjust to changing conditions. Ant societies, organised by distributed algorithms rather than division of labour, have thrived for more than 130 million years.

Division of labor is nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in all living genera. For example XIST links differences in energy-dependent RNA-directed DNA methylation to chromosomal rearrangements and sex differences in species from yeasts to humans via the pheromone-controlled physiology of reproduction.
See: Chemical tags on RNA silence female X chromosome

“We found that methyl modification is a normal feature of most RNAs in the cell,” he said. “This includes messenger RNAs that encode proteins, as well as noncoding RNAs such as XIST.”

Others have shown that energy-dependent changes in the microRNA/messenger RNA balance link methylation to every aspect of healthy longevity and that they link virus-driven energy theft to all pathology via the conserved molecular mechanisms of cell type differentiation in all living genera.
See: microRNA
For one of 56,700 other examples see: MicroRNA-29 impairs the early phase of reprogramming process by targeting active DNA demethylation enzymes and Wnt signaling
See also: The real problem

…fundamental aspects of our experiences of conscious selfhood might depend on control-oriented predictive perception of our messy physiology, of our animal blood and guts. We are conscious selves because we too are beast machines – self-sustaining flesh-bags that care about their own persistence.

We are not self-sustaining. The real problem is the ignorance of theorists who have failed to tether their ridiculous theories to facts about Darwin’s “conditions of life” that have been detailed by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction
See also: Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus
See for comparison: My comment to the Science site and to the Atlantic site:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.

The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.

If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).

If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.

Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

My comment was removed from the Science site and this appeared:

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

My comment is still available from the Atlantic site
See also: Virus-driven mutation or amino acid substitution
See also: Energy-dependent chirality (2)

Alternative splicing of pre-mRNA

Sudden death indel polymorphism

An insertion/deletion polymorphism within 3’UTR of RYR2 modulates sudden unexplained death risk in Chinese populations.

…different alleles of rs10692285 could alter the local structure of RYR2 mRNA and microRNA (miRNA) binding.

See for comparison: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

The differences between the 370A knockin mouse phenotypes and those of loss- and gain-of-function models emphasize the advantage of a more accurate mouse model.

In this study an adaptive variant links the mouse model to a modern human population via changes in the microRNA/messenger RNA balance. The adaptive variant is referred to as rs3827760, but it is also known as 1540T/C, 370A or Val370Ala.
It is an energy-dependent single nucleotide polymorphism in the ectodysplasin A receptor EDAR gene on chromosome 2. Reporting it as the Val370Ala amino acid substitution links the energy-dependent change in the base pair to the biophysically constrained pheromone-controlled fixation of the amino acid substitution via the physiology of reproduction, which links autophagy to supercoiled DNA and all energy-dependent biodiversity in all living genera.
Simply put, the supercoiled DNA protects all organized genomes from virus-driven entropy. Supercoiled DNA is the “energy as information-dependent” source of all biodiversity. See for details:

What is life when it is not protected from virus driven entropy

Abstract:

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

Antagonist Peter Berean repeatedly asserts that energy is not information. He has invented the term bio-functional information in an attempt to continue linking mutations to evolution, which is what was done in: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant.
For contrast, An insertion/deletion polymorphism within 3’UTR of RYR2 modulates sudden unexplained death risk in Chinese populations links virus-driven energy theft to the pathology via loss of function associated with the insertion/deletion (indel) polymorphism. The energy-dependent polymorphism links different alleles of rs10692285 from amino acid substitutions in viruses to sudden unexplained death risk in Chinese populations. There is no mention of the fact that the amino acid substitutions that stabilize viruses would otherwise link an energy-dependent amino acid substitution from a single base pair to cell type differentiation in the sudden death-causing cells.
That fact can be viewed in the context of my model and these two reports:
1) Structural diversity of supercoiled DNA (supercoiling)
2) Structural Dynamics and Mechanochemical Coupling in DNA Gyrase (negative supercoiling)
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Reported as: Past 5,000 years prolific for changes to human genome

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report.

On average, 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. “There’s so many of [variants] that exist that some of them have to contribute to disease,” says Akey

Once again, we see that theorists must learn the difference between an energy-dependent RNA-mediated amino acid substitution and a mutation before they can grasp the levels of complexity that must be integrated into models of biophysically constrained energy-dependent biodiversity.
The problem that most theorists have with the concept of energy as information is due to the fact that they do not know the difference between an energy-dependent amino acid substitution and a mutation, which is caused by virus-driven energy theft.
See: Virus-driven mutation or amino acid substitution

Pseudoscientists invented a theory based on de Vries definition of mutation, and more theories were added in the absence of experimental evidence that could link top-down causation to cell type differentiation in all genera. Instead of energy-dependent cell type differentiation, we got this:

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

Unfortunately, some medical laboratory scientists are still not getting the message about the difference between a mutation and fixation of an amino acid substitution.

See also the attacks on my credibility and my model in this discussion attempt, which drew participation and more antagonism from the group’s administrators, John L. Leonard and Peter Berean.