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

Nature vs Science and Autophagy.pro

Conclusion: The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.


Until the day that I launched Autophagy.pro, I had only one or two Facebook posts that were marked as spam. Since December 11, 2017, I have had ~5 posts marked as spam.

See for example: This comment was marked as spam at Ciência Biomédica, when I responded to  Synthetic protein packages its own genetic material and evolves

Packaging is energy-dependent and biophysically constrained. Nothing evolves. The concept is foolish. See: A universal trend of amino acid gain and loss in protein evolution 
Excerpt: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
 
Laboratory co-oximeters determine the %HbO2 (%SaO2 ) by measuring the amount a specific frequency of light is absorbed as it passes through a known volume of blood. In contrast, pulse oximetry (SpO2) measures the change in light absorbed at systole and diastole. This allows the pulse oximeter to distinguish between the constant amount of light absorbed by the tissue, bone, venous blood, etc. from the arterial blood (the blood in the volume change due to the pulse).
 
The amount of light absorbed by the tissue, bone, venous blood etc., varies in the context of hydrogen-atom transfer in DNA base pairs in solution. Blood gas analysis in the medical laboratory links differences in hydrogen (H2) — as in H2O from quantized energy-dependent changes in the potential of hydrogen (pH) to all biophysically constrained biodiversity.
 

Measuring pH links what is known about nutritional epigenetics from the innate immune system to healthy longevity via everything known about autophagy. The measurements can be compared in the context of  what is known about virus-driven energy theft, which links stress from the replication of viruses 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.

For example in a mammal, see: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin (June 14, 2013)

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

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My comment to the Science site (submitted 6/14/13 published 6/20/13):

In my model species-specific epistasis is nutrient-dependent and pheromone-controlled. An additional example of this showed up earlier this week in the context of the epigenetically-effected microRNA/messenger RNA balance: “miR-124 controls male reproductive success in Drosophila”

miR-14 acts in neurosecretory cells in the adult brain to control metabolism and miR-124 acts in the context of brain-directed neuroendocrine control of sexual differentiation and male pheromone production, which is controlled in mammals by gonadotropin-releasing hormone (GnRH) neurosecretory cells of the hypothalamus.

We can anticipate extension to mammals of the Drosophila model from the abstract of a forthcoming Science article: “MiR-200b and miR-429 Function in Mouse Ovulation and Are Essential for Female Fertility.” Given our earlier work in the context of molecular epigenetics and the concept of alternative splicings and sexual differentiation in Drosophila and C. elegans, I suspect we will see evidence for nutrient-dependent adaptive evolution of GnRH pulse frequency-controlled LH secretion and pheromone-controlled female fertility in mice.

If I’m correct, this evidence will link glucose and pheromones to feedback loops that control reproduction in invertebrates and vertebrates. (See Nutrient–dependent / pheromone–controlled adaptive evolution: a model). Model organisms exemplify these feedback loops in microbes, nematodes, insects, and other mammals. The mouse to human example that Kamberov et al., and Grossman et al., detailed is the most telling.

A single amino acid substitution appears to result in what seem to be nutrient-dependent changes in the thermodynamics of intracellular signaling, intranuclear interactions, stochastic gene expression, and selection for phenotype via organism-level thermoregulation in a human population that arose in what is now central China during the past ~30K years.

Using a model that integrates what is known about the common molecular mechanisms may help establish whether adaptive mutations lead to thermodynamic effects on organism-level thermoregulation and epistasis, or whether epigenetic effects of nutrients and their metabolism to species-specific pheromones that control reproduction via changes in the microRNA/messenger RNA balance are the driving force behind adaptive evolution in species from microbes to man.

See: Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys
Reported as:  Estrogen discovery could shed new light on fertility problems December 12, 2017

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

The feedback loop is food energy-dependent and pheromone-controlled.
See: Feedback loops link odor and pheromone signaling with reproduction
Energy-dependent autophagy is the link from feedback loops to ecological adaptation. Science Magazine now has the opportunity to challenge the pseudoscientific nonsense of published works from the Nature Publishing Group. There is no need to consider mutations and evolution outside the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.
See also: Combating Evolution to Fight Disease

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

The retraction of Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication attests to the amount of pseudoscientific nonsense published by the “Nature Publications Group” during the past few decades.
See: Retraction Watch

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

How many others who published via the Nature Publishing Group were blinded by their belief in pseudoscientific nonsense that failed to link the food energy-dependent creation of enzymes and the creation of RNA from blood gas analyses to patient outcomes?
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 dependent.

Who did not know that? How did non-enzymatic RNA replication become a non-energy-dependent consideration for anyone associated with the Nature Publishing Group?
See for comparison: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40

Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB–mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis.

The global conformational change that allosterically realigns active-site residues (i.e., amino acids), accelerating catalysis, is an energy-dependent change.
Reported as:  Scientists unlock structure of mTOR, a key cancer cell signaling protein

1) Like many proteins, mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules.

The creation of the enzymatic activity of mTOR is quantized energy-dependent and it links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency via autophagy. The retractions of Jack Szostak’s nonsense about the magical creation of enzymes after the energy of life emerged and organisms subsequently evolved in the context of differences in H2 to all biodiversity on Earth, can be placed into the context works by serious scientists.

2)  …mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules. From that 2013 study, which took more than five years to complete, the team learned some key things about the protein, such as what the ATP-binding site looks like…

The study that took more than 5 years to complete was published as: mTOR kinase structure, mechanism and regulation

The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.

They had experimental evidence of energy-dependent changes in active-site residues (i.e., amino acids). They subsequently failed to link anything known to serious scientists about the energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction. They seemingly ignored all claims about RNA-mediated amino acid substitutions in the context of autophagy, which links base pair changes from changes in the microRNA/messenger RNA balance to RNA editing.
How could the Nature Publishing Group not know what all serious scientists know?
See for example: All Nobel Laureates in Physiology or Medicine

The Nobel Prize in Physiology or Medicine 2017

Jeffrey C. Hall, Michael Rosbash and Michael W. Young

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The molecular mechanisms are energy-dependent.
Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels  (1990) Hardin, Hall and Michael Rosbash
Who, besides Jack Szostak, does not know that the creation of energy must be linked to RNA-mediated cell type differentiation via messenger RNA levels?

The Nobel Prize in Physiology or Medicine 2009

Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”

Where did the enzyme telomerase come from?
Face the facts, Jack (Szostak) and others. Cell type differentiation is food energy-dependent and biophysically constrained at every level of examination. Biophysical constraints on viral latency are required for ecological adaptation. The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It’s all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.
See:  Structural diversity of supercoiled DNA

For God and Country

Faith in evolution: Paleontology as a molecular science

Keeping the faith

For the last 20 years, Mary Schweitzer, a paleontologist at North Carolina State University in Raleigh, has amassed a wealth of evidence that she’s isolated protein fragments from dinosaurs as much as 80 million years old. That bucks the conventional wisdom among paleontologists who argue that proteins, which are made of chains of amino acids, can’t survive more than 1 million years or so. So far, no group other than Schweitzer and her collaborators has managed to replicate the findings. She contends that’s because others don’t follow her methods. If Schweitzer is right and outside researchers eventually do confirm her findings, it could transform dinosaur paleontology into a molecular science. That, in turn, could help researchers answer long-standing questions, such as whether dinosaurs were warm- or cold-blooded, and work out the dinosaur family tree.

The evidence does not show that the protein fragments are from dinosaurs as much as 80 million years old. No experimental evidence of biophysically constrained biologically-based cause and effect suggests that is possible. But she is keeping her faith in evolution despite the fact the nothing but mathematical models support that pseudoscientific nonsense.
See for comparison: Paths of the Trinity: Being-in-Relationship as Theology, an Answer to Zen Buddhism
In the comments, Jay Kimooyoung wrote:

As people get more informed of the range of interpretive tools that have been avalialbe across different times and different cultures, with their commonality and distinctions, both apparent and real, hopefully they will interact with the world more freely, and then collectively enter into a more ‘enlightend’ stage in the next chapter of our history.

The 2017 Nobel Laureates in Chemistry shared their prize for linking energy-dependent changes from electrons to ecosystems in all living genera via the cryo-EM technology that enables observation at the level of changes in atoms and hydrogen-atom transfer in DNA base pairs in solution. Virus-driven theft of quantized energy occurs at that level of examination, which is how the degradation of messenger RNA is linked to all pathology. If you are not willing to “inform yourself” or to believe serious scientists, do not wait for anyone to “…enter into a more ‘enlightend’ stage in the next chapter of our history.”
Energy is information. The virus driven energy theft that links the degradation of messenger RNA to all pathology is proof that the number of biologically uninformed science idiots who claim to be scientists is greater than the number of serious scientists. The number of self-serving theologians is of secondary concern.
Jay Kimooyoung

New discoveries are made through numerous attempted experiements. Such attempts require huge investment of energy and accumulated information. In the development of science, they are as much the integral part as pigeonhalling confirmed data. Attempted memes are the background soil for the progress in science.

And more so is with the situation of theology. What ultimately validates is not correspondence according to objectified criteria. It is the extent of sincere dedication that serves to carry the weight of life. In that sense, every theology contains element of self-service. Concern could be a matter of degree rather.

To my horror, “Answers in Genesis” just published Celebrate Your Inner Virus — a reversal of their long-standing theological perspective that links the “Curse” from the virus-driven degradation of messenger RNA to all pathology.

It is important that we understand the design present in viruses because God made them

See for comparison: Did God Make Pathogenic Viruses?

Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.

My life’s works have served to refute all the pseudoscientific nonsense touted by neo-Darwinists and “Big Bang” cosmologists. “Answers in Genesis” now appears to be supporting them.
See for comparison: https://www.youtube.com/watch?v=HaKf2VuOyl0&feature=youtu.be Video interview about the death of Robin Williams Quantum Souls Published on 10 May 2017
https://www.youtube.com/watch?v=OIkbH9dcAkw&feature=youtu.be Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
https://www.youtube.com/watch?v=iTvT0p9Q5TY Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
https://www.youtube.com/watch?v=wfPy5QDJp7w&feature=youtu.be How to Treat Cancer as a Disorder of Energy Transfer
https://www.youtube.com/watch?v=s7_fQ2fS5UY&feature=youtu.be Charles Darwin Taught Conditions of Life, Not Mutations
https://www.youtube.com/watch?v=HCQI7fMi8ts Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
https://www.youtube.com/watch?v=ObHVOdi99Rw Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

All the co-authors are from South Korea and so is Jay Kimooyoung.
I ride for God and country with the American Legion Riders. See for comparison: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

Re: The viral hecatomb
In his 2010 publication “The Great Pheromone Myth“, Richard L. Doty challenged all accurate representations of the top-down energy-dependent creation of RNA and biophysically constrained pheromone-controlled biodiversity.
On 5/16/17, he published: Olfactory dysfunction in neurodegenerative diseases: is there a common pathological substrate?

…antibodies or other evidence of viral infection have been found to be higher in the autopsied brains of people with neurodegenerative diseases with the most smell loss (figure 2), relative to the brains of healthy controls. Whether a close relationship exists between smell dysfunction and antibodies or other indicators of viral involvement is unknown.

The close relationship that exists between smell dysfunction indicators of viral involvement has been exquisitely detailed in my life’s history of published works and presentations. All of them link what is now known about the virus-driven degradation of messenger RNA from mutations to all pathology in species from microbes to humans.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Currently, only a limited number of miRNA and miRNA-like RNAs have been found in bacteria and viruses, a number that is sure to increase rapidly in the future. The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

See also: Deep-Sea Viruses Destroy Archaea
See also: High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents

…inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.

Summary: The virus-driven theft of quantized energy prevents the efficient transfer of energy that is required to link the physiology of pheromone-controlled reproduction to all biodiversity on Earth. Instead, the virus-driven degradation of messenger RNA has been linked to all pathology.
Remember, anytime a pseudoscientist like Richard L. Doty claims that mammalian pheromones and/or human pheromones do not exist, that pseudoscientist is trying to cover up a history of ignorance. The history of ignorance has caused the unnecessary suffering and premature death of millions of people during the past two decades. Pseudoscientists have placed their faith in evolution and in the nonsense touted by people like Doty, who never learned to link the metabolism of food energy to pheromones or linked species-specific pheromones from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See for comparison: “Cytosis

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also: Subatomic

Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

Lethal virus kills 5 billion people?

Until death: Virus-driven failure of multisensory integration (2)

Summary: The virus-driven degradation of messenger RNA is clearly linked to frontotemporal dementia (FTD) by altered language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.

The social and economic burden of frontotemporal degeneration

Reported as: Study reveals staggering economic burden of dementia in younger people

Frontotemporal degeneration (FTD) accounts for 20 to 50 percent of dementia cases in people under the age of 65. FTD ravages an individual’s quality of life by dramatically altering their language, personality, behavior, cognition and motor function.

FTD alters language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.
See for instance: Tumour necrosis factor-α (TNF-α) and miRNA expression in frontal and temporal neocortex in Alzheimer’s disease and the effect of TNF-α on miRNA expression in vitro
See also: miR-106b inhibits tau phosphorylation at Tyr18 by targeting Fyn in a model of Alzheimer’s disease
The facts that link the virus-driven degradation of messenger RNA to all pathology have also been placed into the context of this report: Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
I mentioned before that this was reported in the news as: Problems with senses may predict older adults’ overall health, ability to function

Researchers have mainly focused on what happens after people lose one or two of their senses. However, we know that losing more than two senses occurs frequently for older adults. Until now, no studies have examined how losing multiple senses affects older adults.

I also mentioned that the virus-driven loss of G protein-coupled receptors has been linked to the loss of multiple senses in all organisms at all ages.
See: Olfaction Warps Visual Time Perception
For comparison, pseudoscientists reported Brain wiring affects how people perform specific tasks

“Individuals organize themselves into densely interconnected communities, like the dormitories and sports teams, though individuals within these groups also have connections with people outside of those groups. Brains are the same way: Brain regions are organized into communities with lots of connections between regions in the community and fewer connections to regions outside of the community. But people’s brains are different. Some people have brains that are better described as having rigid community structure—or higher modularity—while other people have brains without such rigid community structure—or lower modularity.”

The individuals of all species must find food to reproduce. That’s how the individuals become part of a species. Their pheromone-controlled physiology of reproduction has been linked to all biodiversity in all genera. The claim “Individuals organize themselves…” is foolish. Claims about higher or lower modularity could be linked to the pseudoscientific nonsense touted in reports like this: The fusiform face area and occipital face area show sensitivity to spatial relations in faces
See also: The Blur of Pleasure: Appetitively Appealing Stimuli Decrease Subjective Temporal Perceptual Acuity
Reported as:  Appetizing imagery puts visual perception on fast forward

“Our research shows that emotionally-charged stimuli, specifically positive and negative images, may influence the speed, or the temporal resolution, of visual perception…”

See for comparison: Supercool Protein Imaging Gets the Nobel Prize

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

See for comparison: How childhood trauma affects the brain

The researchers’ conclusion is that experiencing abuse in early life “may lastingly disrupt” the connectivity between the areas of the brain that are key in cognitive and emotional processes.

Receptor mediated epigenetic effects on hormones are the link to affects on behavior via energy-dependent RNA-mediated cell type differentiation in the context of the creation of enzymes and the physiology of pheromone-controlled reproduction. See anything ever published by Bruce McEwen for examples of how a single amino acid substitution predicts differences in behavioral development.
 
Keep in mind that “Bump stock” is not a person. It’s an invention that can be examined in the context of cryo-EM to explain why someone would use reports on the “bump stock” technology to obfuscate the facts about the cryo-EM technology. The facts about cryo-EM and supercoiled DNA can be used to eradicate all virus-driven pathology.
 
For example, the ability to examine virus-driven changes in the transfer of energy in DNA base pairs can be linked to what is known about food energy-dependent RNA-mediated amino acid substitutions in organized genomes. The substitutions typically stabilize the organized genomes of people like Stephen Paddock.
 

See also: Irreversibility and the Arrow of Time in a Quenched Quantum System

Reported as: Physicists confirm thermodynamic irreversibility in a quantum system

“Our experiment shows the irreversible nature of quantum dynamics, but does not pinpoint, experimentally, what causes it at the microscopic level, what determines the onset of the arrow of time,” coauthor Mauro Paternostro at Queen’s University in Belfast, UK, told Phys.org. “Addressing it would clarify the ultimate reason for its emergence.”

For comparison, see: Charles Darwin’s 150-year-old theory of how life on earth emerged gets thumbs-up from scientists

Their ridiculous theories can be placed into the context of Lewis Carrol’s attribution of this thought process to “Humpty Dumpty.”

 

“Emergence” and “evolution” are meaningless terms outside the context of ridiculous theories and pseudoscientific nonsense touted by researchers who are biologically uninformed science idiots. They seem to think that they can put the pieces of biophysically constrained life on Earth back into their theories as if “Humpty Dumpty” exemplified a creature with an evolved shell.

Cryo-EM has helped to pinpoint why the nature of quantum dynamics is irreversible. At the microscopic level of hydrogen-atom transfer in DNA base pairs in solution, the creation of energy as information has been linked to healthy longevity in all living genera. Virus-driven energy theft has been linked from the degradation of messenger RNA to all pathology.

See also: Neuropathology of suicide: recent findings and future directions

“…the unravelling of the unique epigenetic processes that occur in the brain has opened promising avenues in suicide research.”

Reported without citation in the context of: How childhood trauma affects the brain

What led my former FB friends to claim that my life’s works and efforts toward suicide prevention were “bullspit” or that “nobody cared?” The Nobel Prize in Chemistry just validated my model in the context of what is known about cryo-EM.
 

What led researchers who are biologically uninformed science idiots to criticize my model? Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Who will be the first to apologize for the role they played in the suicide death of Stephen Paddock and the unnecessary suffering and death of his victims?

Moving forward, what role will “apologetics” play in consoling the victims of virus-driven energy theft and all pathology?

See: Celebrate Your Inner Virus 

…we seek to highlight the strengths of what makes a virus on this Virus Appreciation Day.

Answers in Genesis is an apologetics ministry, dedicated to helping Christians defend their faith and proclaim the gospel of Jesus Christ.

Virus appreciation is interesting in the context of claims this group made since 1999.

See: Did God Make Pathogenic Viruses? (1999)

Without viruses, the genetic revolution we are now experiencing would be impossible. They also serve numerous beneficial functions that we are just beginning to research and understand.

Viral Genome Junk Is Bunk (2015)

…mammalian viruses may not have existed at all before the Curse, but after mankind’s sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins.

I agree, but the Genesis account of origins puts the Curse before the creation of viruses, which have been linked from the virus-driven degradation of messenger RNA to mutations and all pathology during the past 5-10,000 years.

See: 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. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Stress has different effects on different people.

See for comparison: Epigenetic Regulation of the Kappa Opioid Receptor by Child Abuse

…this receptor may be epigenetically regulated by stressful experiences, in particular as a function of early social life.

See also: Cell stress response sheds light on treating inflammation-related cancer, aging

A Traumatic Experience Can Reshape Your Microbiome

The stress-linked reshaping of  your microbiome has repeatedly been linked from the virus-driven failure of multisensory integration to suicide.

Alternative splicing of pre-mRNA

Thanks again for asking about DNA methylation

Re: RNA-directed DNA methylation (1996) See: From Fertilization to Adult Sexual Behavior

Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes.

See also: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (2014)
See also:  Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity (2017) reported as: Humans and sponges share gene regulation
See also: Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability
Reported 10/2/17 as: Unexpected findings uncover new understanding of gene expression

What is it about the whole body of the enzyme itself that functions in development and its mutations that can result in cancer?

Thanks again for asking. It is the fact that RNA-directed DNA methylation is energy-dependent and the fact that virus-driven energy theft causes the degradation of messenger RNA, which serious scientists have linked to all pathology.
Everything known to serious scientists about energy-dependent increasing organismal complexity has been portrayed by pseudoscientists in the context of mutation-driven evolution.
The pseudoscientists are not going to stop until serious scientists force them to start helping those who are “Combating Evolution to Fight Disease.”
See for comparison: Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity

…there is evidence that some of the selected genes may contribute to the formation of different cell types. One route might be through the modification of stem cell activity in response to a greater functional diversity of the proteins that modulate epigenetic status to either maintain or promote differentiation [35,36].

Beneath the surface of what you see reported about organismal complexity in the mainstream media, you can see: Eligo Bioscience Secures $20 Million Series A from Khosla Ventures and Seventure to Bring Precision Medicine to the Microbiome

A growing body of research shows that the microbiome, made up of the ten trillion bacteria residing within and on the human body, sits “at the interface of health and disease.”

The company’s approach uses the innate immune system of bacteria (CRISPR) to edit the genetic material of antibiotic-resistant bacteria.  The microRNAome links the virus-driven degradation of messenger RNA in bacteria from the energy-dependent pheromone-controlled physiology of reproduction to all pathology biodiversity via changes in the healthy microbiome. The concept of endogenous RNA interference is rapidly replacing the nonsense about virus-driven gene editing, which has not yet earned a Nobel Prize for pseudoscientific representations of cause and effect.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

This is what one of my former Facebook friends called “bullspit.” It is about “bull sperm.” It is not what other former Facebook friends say “nobody cares” about. It is the link from energy-dependent changes in soil bacteria to all biophysically constrained life on Earth. It is also what other researchers who are biologically uninformed science idiots tell you is the link from virus-caused mutations to evolution.
See for comparison: Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See for comparison: Nobel Prize in Medicine Awarded to Circadian Rhythm Researchers
I do not expect anyone who has not already linked what is known about quantum physics to quantum souls to understand why this year’s Nobel Laureates in Physiology or Medicine have abandoned all experimental evidence of biophysically constrained top-down causation to continue touting their ridiculous gene-centric theories.
Do you? But, I understand why they do not want to admit to the facts.

Military-related trauma tied to eating disorder symptoms

…when they controlled for other trauma types, military-related trauma was the only trauma type that was uniquely associated with eating disorder symptoms. Examination of different types of military-related trauma indicated that the association was not driven by exposure to combat.

Predictably, it was an exposure-driven association with the stress-linked failure to adapt to virus-driven changes in gut microbiome and behavior that lead veterans who have served overseas to commit suicide.

See also: Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms

Reported as: The dust storm microbiome

The researchers found that during a dust storm the concentration of bacteria and the number of bacterial species present in the atmosphere rise sharply, so people walking outdoors in these storms are exposed to many more bacteria than usual.

Greg Bear put this into the perspective of Homeland Security in his techno thriller “Quantico.” At times, all that serious scientists can do is laugh about the pseudoscientific nonsense touted by theorists. Bear checked the facts from “Darwin’s Children” with me before he sent the manuscript for publication. And then came this interview with Jon Stewart.

See for comparison the simple-minded misrepresentations of human ethologists in Human Ethology Bulletin » 2017 »
HEB 32(3)
For example: “Y/Our Vocal Sounds – Towards an Ethological Classification of Human Vocalizing Behavior and Sounds
by Jay R. Feierman 

This article is a first attempt at an ethological classification of human vocalizing behaviors and the sounds they make. Lastly, how human ethologists could study these two different types of human vocalizing behaviors, using the sounds they make as proxies, will be discussed.

Summarized in part in Ourselves Explained link opens pdf

A Review of the book

THE SECRET OF OUR SUCCESS. HOW CULTURE IS DRIVING HUMAN EVOLUTION, DOMESTICATING OUR SPECIES, AND MAKING US SMARTER By Joseph Henrich. 2016

The key to this book’s 18-word title can be summed up in five: Cumulative culture drives
human evolution.

The failure of this book to explain any aspect of biophysically constrained biologically-based cause and effect can be summed up in seven words. No species evolved from any other species.
Energy-dependent RNA-directed DNA methylation links ecological variation from biophysically constrained viral latency to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
 
 

Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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.

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

 …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’.

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

Cytosis

Energy and neural plasticity

Summary: Food energy is required because proteins do not create themselves and virus-driven energy theft causes the degradation of messenger RNA in all living genera.

See for comparison: Neural plasticity wanes with age, but increasing the protein Arc—abundant earlier in life—in the visual cortex of mice can fend off this decline.

The restoration of neural plasticity requires the food energy-dependent pheromone-controlled de novo creation of genes. For example, see: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Desperate attempts to invent new theories that link trophic coherence to evolution should not be be confused with the facts that have been detailed in works published by serious scientists. See the pseudoscientiific nonsense in this published work: Looplessness in networks is linked to trophic coherence
For comparison: Feedback loops link odor and pheromone signaling with reproduction
There is no desperation manifested in the works of serious scientists who understand the facts about natural selection for energy-dependent codon optimality and de novo gene creation. The energy-dependent creation of new genes links feedback loops to the restoration of juvenile plasticity via the creation of G protein-coupled receptors.
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis

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.

 

Alternative splicing of pre-mRNA

The Origin of Information (4)

Summary: Others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See: The Origin of Information (3)
Finally, someone is asking questions that can be summarized in one question (see below). Until now, on the International Society for Human Ethology’s Yahoo group, and elsewhere, the moderator: Jay R. Feierman has prevented the dissemination of accurate information on this topic. Now others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See the discussion attempt at: 88233 Re: DNA Begins As a Quantum Wave, According to New Science

Excerpt: Much of the information in this article came from The Synchronicity Key: The Hidden Intelligence Guiding The Universe and You

Conclusion: Clearly though, our view of the universe and life itself is changing as these concepts are understood by more people each day.

The fact that DNA begins as a quantum wave linked to biophysically constrained amino acid substitutions was addressed in the context of: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Natural selection for quantized energy-dependent codon optimality and the stability of messenger RNA during transgenerational epigenetic inheritance has since been placed into the context of experimental evidence reported as Olfaction Warps Visual Time Perception.
See also the series of presentations at virtual conferences that began with: The Origin of Information: How to Solve It.
When I realized that people might not understand that the origin of information must be linked from quantum waves to RNA-mediated healthy longevity and from virus-driven energy theft to all pathology, I split the original presentation submission into two parts. The revised title was RNA mediated molecular epigenetics and virus driven entropy.
From hydrogen atom transfer in DNA base pairs to ecosystems was presented during the same virtual conference.
Several more presentations added information about top-down energy-dependent RNA-mediated biologically-based biodiversity. For example, this may be my final presentation at Labroots virtual conferences Energy as Information and Constrained Endogenous RNA Interference
The journalists from Labroots have ignored my presentations despite a series of my comments on their attempt to continue touting pseudoscientific nonsense about neo-Darwinian theories.  It seems unlikely that any science journalist will admit to their overwhelming ignorance.
See for comparison:168949 From the evolutionary psychology Yahoo group. Re: DNA Begins As a Quantum Wave, According to New Science
Jay R. Feierman admits:

This claim is above my level of expertise to refute. It comes from a peer reviewed article in The American Chemical Society’s Journal of Physical Chemistry B. See below, which is taken from https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html.
“Scientists are reporting evidence that intact, double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. And then like friends with similar interests, the bits of genetic material hangout or congregate together. The recognition — of similar sequences in DNA’s chemical subunits — occurs in a way once regarded as impossible, the researchers suggest in a study scheduled for the Jan. 31 issue of ACS’ Journal of Physical Chemistry B”.
Read more at: https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html#jCp

There are many things in physics and physical chemistry that seem incredulous to me. That includes some of the claims of quantum mechanics. What about the Penrose Hameroff Theory of Quantum Consciousness. See http://www.quantumconsciousness.org/sites/default/files/1998%20Hameroff%20Quantum%20Computation%20in%20Brain%20Microtubules%20The%20Penrose%20Hameroff%20Orch%20OR%20model%20of%20consciousness%20-%20Royal%20Society_0.pdf.

On several occasions, Feierman has threatened to ban me from the Human Ethology Yahoo Group. Then, he simply fails to post my comments when they do not support his nonsense.
I’ve added some comments to this discussion because it seems to be progressing nicely at a time after Feierman has admitted he knows virtually nothing about biophysically constrained biologically based RNA-mediated cell type differentiation.
See: Discus for discussion of

How to teach evolution when students hold creationist views


Feierman, and others like him, have been teaching neo-Darwinian theories either directly or indirectly. But Feierman’s nonsense has consistently been the most offensive to me personally. After publication of my 2013 review, I attempted to discuss the refutation of neo-Darwinian nonsense he had been touting since I first met him at a conference in 1995.
His responses to Nutrient-dependent/pheromone-controlled adaptive evolution: a model include:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
Now, he admits, albeit elsewhere, that he knows nothing about how food energy as quantized information must be linked to healthy longevity via the pheromone-controlled physiology of reproduction, or be linked from the virus-driven degradation of messenger RNA to mutations and all pathology.
See also this example of a false dichotomy: Scholars who believe nurture trumps nature also tend to doubt the scientific method

One group, made up of psychologists, economists, philosophers and political scientists believes more strongly in the genetic influences on behaviour, beliefs and culture. The other group, consisting sociologists, non-evolutionary anthropologists, women’s and gender studies scholars and all humanities scholars (except philosophy), believes in the primacy of environmental influences.

No Genetics without Epigenetics? No Biology without Systems Biology?

…there has never been a genetics without an epigenetics.

Energy-dependent changes link the epigenetic landscape to the physical landscape of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that all serious scientists have linked from mutations to all pathology in all living genera.
See: microRNA  for more than 63,000 examples of that fact.

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

Energy-dependent physical and biophysical constraints (9)

Summary: Energy determines genome compaction because activity in the nucleus is energy-dependent. Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. It’s all about the base.

Energy-dependent physical and biophysical constraints (8)

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
Excerpt 1)

The chromatin structure of DNA determines genome compaction and activity in the nucleus.

My comment: Energy determines genome compaction because activity in the nucleus is energy-dependent.
Excerpt 2)

Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.

My comment: Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction.
Reported as: Scientists solve longstanding biological mystery of DNA organization

Besides potentially upending the textbook model of DNA organization, the team’s results suggest that controlling access to chromatin could be a useful approach to preventing, diagnosing and treating diseases such as cancer.

“We show that chromatin does not need to form discrete higher-order structures to fit in the nucleus,” adds O’Shea. “It’s the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine-tune the functional activity and accessibility of our genomes.”

The packing density of supercoiled DNA is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. Sunlight is the source of all biophysically constrained energy on Earth.The anti-entropic virucidal effect of sunlight biophysically constrains the degradation of messenger RNA.
Virus-driven energy theft causes negative supercoiling of supercoiled DNA. Without food energy-dependent RNA-mediated DNA repair (autophagy), viruses cause the degradation of messenger RNA that links mutations to all pathology. The sun’s anti-entropic virucidal energy links changes in chirality to autophagy and the de novo creation of enzymes, hormones and receptors that are needed to protect all organized genomes from viruses.
The textbook model of DNA organization was represented in Mutation-driven evolution for comparison to “Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day more than 4 years ago.
Masatoshi Nei used an ambiguous definition of mutation and linked any energy-dependent nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc, (any change in the structure of supercoiled DNA) from natural selection to an evolutionary process initiated by mutation.
In my review, I used examples of food energy-dependent changes in base pairs to link the honeybee model of nutrient-dependent pheromone-controlled biodiversity to a history of published works that began with The Scent of Eros: Mysteries of Odor in Human Sexuality (reviewed by Mark Sergeant)
The index from The Scent of Eros: Mysteries of Odor in Human Sexuality may help others to establish all the known links from the energy-dependent de novo creation of microRNAs to the creation of G protein-coupled receptors and gonadotropin releasing hormone (GnRH) secretion, which was linked to all biodiversity. See, for example, these entries from page 217:

See also: Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also: Energy-dependent physical and biophysical constraints (10) in prep

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

Energy-dependent physical and biophysical constraints (6)

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology.

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

See first: Energy-dependent physical and biophysical constraints (5)
See next: Design of a synthetic yeast genome
They use what occurs in the context of natural selection for quantized energy-dependent changes in base pairs and link RNA-mediated amino acid substitutions from changes in enzymes and feedback loops. The feedback loops link the pheromone-controlled de novo creation of more receptors via the physiology of reproduction, which biophysically constrains viral latency in all organized genomes.
Their work was reported today, July 26, 2017 in the context of Scientists build DNA from scratch to alter life’s blueprint with my emphasis

Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to “rewrite” the yeast genome, following a detailed plan they published in March.

The research may reveal basic, hidden rules that govern the structure and functioning of genomes.

All serious scientists known that the structure and function of all organized genomes is energy-dependent and RNA-mediated. For example, in all animals the functional structure of supercoiled DNA is controlled by food odors and pheromones in the context of the physiology of energy-dependent reproduction that links food energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Alternatively, virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.

See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The question arises: Does Boeke or anyone like him know that the organized genome of yeast is rewritten only in the context of the food energy-dependent pheromone-controlled biophysical constraints on viral latency? I ask because he may be hiding something. Anyone who does not know how chirality and autophagy biophysically constrain viral latency is not likely to have written a book chapter like this, which was co-authored by J.D. Boeke in 1988.

See: Yeast Ty Elements as Retroviruses in  Viruses of Fungi and Simple Eukaryotes

The title of J.D. Boeke’s latest effort: Design of a synthetic yeast genome, would make any young earth creationist proud of his Boeke’s accomplishment. It attests to facts about “design” that atheistic hate mongers like Richard Dawkins and other pseudoscientists have linked from mutations and natural selection to evolution.

See: Mutation-Driven Evolution

See also for example: Magnus S. Magnusson’s comments on Richard Dawkins event cancelled over his ‘abusive speech against Islam’ Magunsson started removing my responses a few hours ago.

I attempted to discuss the fact that Boeke and others use base substitutions within ORFs to introduce or remove enzyme recognition sites. That is how they facilitate the energy-dependent assembly of synthetic chromosomes.

But there’s more! Boeke’s history of publications links nearly 30 years of pseudoscientific nonsense to an impressive refutation of neo-Darwinian theory. The design of the synthetic yeast genome via the energy-dependent assembly of synthetic chromosomes attests to the fact that natural selection for energy-dependent codon optimality is the link to the design of all biophysically constrained biodiversity.

See for instance: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Some people might think that pseudoscientists can recover from refutation linked to the stability of messenger RNA (mRNA), but the recovery time ended two decades ago with publication of From Fertilization to Adult Sexual Behavior

See our section on 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…

The proteins do not automagically create themselves. Energy-dependent changes in chirality must be linked from autophagy to biophysically constrained viral latency. In that context, this report is another clear refutation of mutation-driven evolution.

See: Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing

These data reveal the immense promise of in situ albumin targeting for development of translational, carrier-free RNAi-based cancer therapies.

The increased amount of information on naturally occurring energy-dependent RNA interference (RNAi) linked to cancer treatment was reported as: Molecular hitchhiker on human protein signals tumors to self-destruct

“What fascinates and excites me most about this approach, in addition to improved tumor penetration, is lack of toxicity at a relatively high dose,” she said. “We could potentially use our siRNA delivery system to target several genes simultaneously or sequentially. Most cancers are driven by multiple abnormal genes, so targeting one often leads to activation of others as the tumor adapts.”

Tumors do not adapt. Viruses quickly adapt via energy theft and the substitutions of amino acids in their genomes. The amino acid substitutions in the tumors cause the tumors to adapt to the lack of energy-dependent microRNAs carried by albumin. That is how virus-driven energy theft is linked to the proliferation of undifferentiated cell types in all tissues of all organisms.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The energy-dependent microRNA flanking sequences do not evolve and genes do not assemble themselves.  Quantized energy as information biophysically constrains virus-driven energy theft, which would otherwise link mutations to all pathology.

Young earth creationists recently placed the virus-driven theft of quantized energy into the context of Cancer Research Confirms the Curse.

…the cancer-suppressing molecule NAD+ diminishes with age appeared in the same Science issue.3Harvard Medical School News summarized the findings. As NAD+ lessens, “DNA breaks go unrepaired and, as these breaks accumulate over time, precipitate cell damage, cell mutations, cell death and loss of organ function.”4 It seems the only way to cure cancer would be to somehow reach into and constantly correct every cell’s mutations.

Carrier-free gene silencing links femtosecond blasts of UV light from the anti-entropic virucidal effects of sunlight on contact with water to everything serious scientists know about food energy-dependent top-down causation and changes in the microRNA/messenger RNA balance, which have been linked to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

A femtosecond is the SI unit of time equal to 10−15 or 1/1,000,000,000,000,000 of a second; that is, one quadrillionth, or one millionth of one billionth, of a second.[1] For context, a femtosecond is to a second as a second is to about 31.71 million years; a ray of light travels approximately 0.3 µm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.[2]

For comparison: One picosecond is equal to 1000 femtoseconds (fs). Theoretical physicists who thought they knew something about the nature of quantum coherence based their theories on measurements of timescales up to 1.5 picoseconds (ps), but they have since learned that decoherence occurs within 60 fs. The transfer of energy in the context of photosynthesis clearly links the anti-entropic virucidal energy of UV light to RNA-mediated DNA repair in much less time than theorists realized.

See: Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

See also: OLYMPUS experiment sheds light on structure of protons

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The differences in the energy of photons and the amount of time it takes for energy-dependent RNA-mediated DNA repair link displays of ignorance by Magnus S. Magnusson and other atheistic hate-mongers that can be compared to any display by anyone who has ever been involved in linking pattern recognition to biophysically constrained life on Earth.

For comparison, that is what young earth creationists have done with the information about energy as information from Biblical Genesis.

See also: One billion suns: World’s brightest laser sparks new behavior in light

The light’s coming off at different angles, with different colors, depending on how bright it is.

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

See: The Reality of Color Is Perception

Color is one of the longstanding puzzles in philosophy, raising doubts about the truthfulness of our sensory grasp on things, and provoking concerns as to the metaphysical compatibility of scientific, perceptual, and common sense representations of the world. Most philosophers have argued that colors are either real or not real, physical or psychological. The greater challenge is to theorize the subtle way that color stands between our understanding of the physical and the psychological.

See for comparison: Olfaction Warps Visual Time Perception

The fact that olfaction warps visual time perception links the speed of light on contact with water from the visual appeal of a rainbow to the integration of all sensory input and our appreciation of how energy and mass are linked across the time-space continuum via what is known about the sense of smell in bacteria and the food energy-dependent pheromone-controlled physiology of reproduction in all living genera.

For comparison, Magnus S. Magnusson co-authored “Complex spike patterns in olfactory bulb neuronal networks”  He and his colleagues failed to link fast decoherence from the anti-entropic virucidal energy of sunlight to all biodiversity via the physiology of reproduction and RNA-mediated DNA repair.

In the world of those who have consistently linked olfaction to our visual perception of energy and mass in the context of the space-time continuum, Magnusson can be referred to as a biologically uninformed science idiot — if only because he has no expertise in any scientific discipline.

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology via the difference between “Nature” and God’s perfect “Creation.”

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

Although that fact has been repeatedly revealed in the extant scientific literature, which includes texts like the Holy Bible, atheistic hate-mongers refuse to read anything that challenges their beliefs at the same time they either claim to believe in nothing or attack the beliefs of intelligent scientists.

See for examples of what pseudoscientists are likely to believe.

This New Equation Could Unite The Two Biggest Theories in Physics

Quantum entanglement… describes the way that two particles can interact in such a way that they become inexorably linked, and essentially ‘share’ an existence.

The Universe According to Emmy Noethe

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

That claim forced others to make their ridiculous theories fit into the context of “…the idea that the Universe expanded just like a balloon shortly after the Big Bang.”

Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

…three physicists heavily criticised inflation theory – the idea that the Universe expanded just like a balloon shortly after the Big Bang. The article went as far as claiming that the model “cannot be evaluated using the scientific method” – the academic equivalent of saying it isn’t even real science.