Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Virus-driven cystinosis

A friend asked about nephropathic cystinosis, which is a disease caused by the virus-driven theft of quantized energy. All serious scientists have linked viruses from the degradation of messenger RNA to mutations and all pathology.

Nephropathic cystinosis (NC) is the most frequent cause of Fanconi syndrome (FS) in young children. It will be linked from the virus-driven degradation of messenger RNA to azoospermia and/or progressive neuromuscular degeneration via the conserved molecular mechanisms of RNA-mediated cell type differentiation compared to mechanisms that link viruses to mitochondrial degeneration.

See: Impact of atypical mitochondrial cyclic-AMP level in nephropathic cystinosis

Treatment with the non-hydrolysable cAMP analog 8-Br-cAMP restored mitochondrial potential and corrected mitochondria morphology. Treatment with cysteamine, which reduces the intra-lysosomal cystine, was able to restore mitochondrial cAMP levels, as well as most other abnormal mitochondrial findings.

The link to treatment of the atypical mitochondrial cyclic-AMP level has not yet been detailed because biologically uninformed science idiots have linked mutations to evolution. But see: Combating Evolution to Fight Disease  and the preprint: Reappraising the human mitochondrial DNA recombination dogma 

The facts about human mitochondrial DNA recombination, which link quantized energy and supercoiled DNA to viral latency, played a significant role in North Korea’s denuclearization. But that fact may not be accepted until the article on human mitochondrial DNA recombination is published in a peer-reviewed journal.

It will then take several more years for medical practitioners to learn how to effectively treat all diseases with food energy-dependent changes in the microRNA/messenger RNA balance.

See for details: Energy as information and constrained endogenous RNA interference

Until all pseudoscientists accept the facts, there will be many others who try to profit from misinformation or from partial information about virus-driven pathology. Most people will not read my reviews and journal articles like this:  MicroRNA Regulation of RNA Virus Replication and Pathogenesis

Instead, most are willing to accept the claims of others who have “blown the whistle” on vaccines more than two decades after I first published this review of RNA-mediated cell type differentiation in a peer-reviewed journal. From Fertilization to Adult Sexual Behavior

See:  Doctor Blows Whistle on Flu Shot: ‘It’s Designed to Spread Cancer’

Treague confirmed that this year’s flu strain, that has left thousands of citizens dead, was caused by the vaccines itself, saying: “I believe that the low effective rate of the vaccine this year is due to the mutations that the virus made in the processing of the vaccine itself.

Claims that viruses make mutations are the claims of fools who do not know that the virus-driven degradation of messenger RNA has been linked from mutations to all pathology in more than 72,000 published works.

See: microRNA

Watering Young Plant - Vintage Effect

Environmental selection is natural selection (5)

Summary: Atheistic Chinese Communists realize that vaccinations cannot protect them. Their attempts to develop a universal vaccine have failed. Bill Gates promotes vaccinations, which led us to the brink of the next pandemic.

Vaccines prevent ecological adaptations in some cell types. Does Bill Gates, a non-scientist, think that people from God-fearing non-communist countries can do better than the atheistic Communists?

Bill Gates calls on U.S. to lead fight against a pandemic that could kill 33 million

Gates and his wife, Melinda, have repeatedly warned that a pandemic is the greatest immediate threat to humanity. Experts say the risk is high, because new pathogens are constantly emerging and the world is so interconnected.

New pathogens do not emerge. Read Quantico. The viruses that cause all pathology ecologically adapt by stealing the quantized energy that all differentiated cell types need to survive.

Bill Gates thinks a coming disease could kill 30 million people within 6 months — and says we should prepare for it as we do for war

If you were to tell the world’s governments that weapons that could kill 30 million people were under construction right now, there’d be a sense of urgency about preparing for the threat, Gates said.

The one time the military tried a sort of simulated war game against a smallpox pandemic, the final score was “smallpox one, humanity zero,” Gates said.

See also: Nov 17, 2016 Obama Advisers Urge Action Against CRISPR Bioterror Threat

…a strategy was developed in 2009, but it’s carried out by several government agencies in an uncoördinated approach…

Bill Gates has been promoting vaccinations as a strategy. The vaccinations led us to the brink of the pandemic. Vaccines prevent ecological adaptations in some cell types. The atheistic Chinese Communists now realize that vaccinations cannot protect them. Their attempts to develop a universal vaccine have failed, miserably. Does Bill Gates, a non-scientist, think that people from non-communist countries can do better than the atheistic Communists?
Perhaps he doesn’t know how South Korea forced the denuclearization of North Korea, which will probably lead to proclamations of world peace.
See: Engineered virus has artificial amino acid allowing it to serve as a vaccine (2016)

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus.

Their “new approach” failed. The uncoordinated strategy against the CRISPR bioterror threat has failed to address the established scientific facts. All ecological adaptations are quantized energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans. That fact is presented in the context of the Holy Bible, which explains why scientific creationists from South Korea were able to force denuclearization on atheistic communists.
Now Gates accuses the US Government (the Trump Administration?) of failing to protect US citizens.
On April 26, 2018, I discussed factual representations of biologically-based cause and effect that probably led to the death of Timothy J. Cunningham. I told a friend that Cunningham’s publication record clearly reveals his ability to link viruses to the failed differentiation of all cell types in all living genera.
See his publications on

1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
and
4) “Health and Safety Issues for Travelers”

What Bill Gates Fears Most may be the revelations of facts about vaccines. Gates seems to be still promoting the live (or dead) virus-containing vaccines that have failed to protect anyone since the time they were supposed to start protecting us all.
Is he aware that An error made in 1925 led to a crisis in modern science?
The error replaced the creation of energy with models of statistical significance as if the answer to the question “What is Life?” was akin to computers that automagically emerged with the energy to run themselves.
See also: Arrowsmith (1925). If Bill Gates had studied US history, he might have learned that the 1925 Scopes Trial in Dayton, Tennessee predicted that teaching neo-Darwinian evolution would cause the next pandemic.
Instead see: Gates Foundation launches $12M Grand Challenge for universal flu vaccine, as Bill Gates urges world to prepare for war on pandemics
When Europeans “invaded” the Americas, indigenous human populations were decimated by the virus-driven degradation of their messenger RNA. Few American Indians had the amino acid substitution that protected them from the virus-driven pathology manifested in the deep sea. The virus-driven pathology has been linked to all physical and mental diseases/disorders on Earth via the 1918 Spanish influenza pandemic.
For comparison, everything known to all serious scientists about quantized energy-dependent RNA-mediated cell type differentiation has been linked to biophysically constrained viral latency.
See: Virus-mediated archaeal hecatomb in the deep seafloor and Cytosis.
See for comparison: Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk
The V370A adaptation came from populations in what is now Central China, but dietary changes eliminated the need for the adaptation in the Americas, where indigenous populations had adapted to other viruses. When Europeans introduced the viruses to indigenous populations on other continents, the 6,000 year history of ecological adaptations in species from mice to humans became clear.
See: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
The EDAR variant is V370A, which is also known as The ectodysplasin receptor variant (EDARV370A) and as rs3827760, which is also known as 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. The fact that one food energy-dependent variant in one SNP was linked from the creation of a receptor to biophysically constrained RNA-mediated cell type differentiation in species from mice to humans proved that environmental selection links quantized energy-dependent changes in the microRNA/messenger RNA balance from the creation of sunlight to viral latency in all living genera.
See for comparison: Here Are Michelle Wolf’s Boldest Moments At The White House Correspondents’ Dinner
See also the bold moves made by scientific creationists in South Korea, who forced the denuclearization of North Korea (in the same week as the “dinner”) with prior publication of two articles that link viruses to the decimation of populations of atheistic Communists.
Whether or not the US, and/or if South Korea invades, they could decimate the populations of atheists without firing more than one shot to deliver a payload of virus-modified yeasts. The lives of well-nourished troops could be saved for the take-over/occupation.
See:
1) A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses 4/13/18

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses.

2) Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events 4/18/18

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed.

See also: South Korea: Kim Seeks U.S. Guarantee Against Invasion

If the only thing atheistic Communists want is to not be invaded, they probably know that vaccines and nuclear weapons cannot protect them from the decimation that could be caused by a single amino acid substitution in a virus.

Why tempt our Creator to show them the error of their ways, when atheistic Communists do not believe in Him? Ask also, “Who killed Timothy J. Cunningham?” — and/or anyone else who is killed or goes missing during the transition to Global Peace.
See also:  [evol-psych] Sorry but Yahoo! groups have blocked all my news items — Robert Karl Stonjek 4/30/18
Wait for this to happen with the Human Ethology Yahoo group, where you can still find the atheistic pseudoscientific nonsense touted by the moderator, Jay R. Feierman.
See for example:
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.
See also: 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.
See for comparison: Tracking niche variation over millennial timescales in sympatric killer whale lineages

  1. Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
  2. The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

Many evolutionary theorists and Big Bang cosmologists are among the hate-mongers who would rather combat Christianity than make any efforts towards Combating Evolution to Fight Disease.

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

MicroRNA-mediated denuclearization (4)

Summary: Christ’s lab showed that in vivo formation of I-motif structures is pH dependent and helped to put the “fear of God” into atheistic communists.

I-motif DNA structures are formed in the nuclei of human cells (4/23/18)

Reported as: In human cells, scientists find DNA that looks like a twisted knot instead of a double helix (4/23/18)

Also reported as: New Twisted ‘Knot’ Human DNA Structure Discovered—and It Looks Nothing Like the Double Helix (4/23/18)

Christ’s lab showed that in vivo formation of I-motif structures is pH dependent. Clearly, the potential of hydrogen (pH) and pH-dependent cell cycles link the quantized energy of virucidal sunlight to protection from the degradation of messenger RNA that links mutations to all pathology.
In that context, denuclearization has been forced on North Korea and other communist countries by scientific creationists in South Korea. The creationists have indirectly revealed that they could decimate human populations in China via the creation of a virus with one base pair change linked to one amino acid substitution.
See also: 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.

Until recently, the pseudoscientific nonsense about vaccines that could protect human populations from the forthcoming viral apocalypse was tightly linked from communism to atheism. For comparison, Christ’s lab appears to have put the fear of God into its proper context; the 1918 Spanish flu.
Previously reported as: Structural diversity of supercoiled DNA (2015) and parodied in:

See also: The Pharmacology of Regenerative Medicine (2013)
See also: Energy as information and constrained endogenous RNA interference (2017)

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.

5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Conclusion:

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.
 

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Polymaths and paradigm shifts: from Asimov to Bear (3)

Polymaths and paradigm shifts: from Asimov to Bear (2)

Teilhardism And The New Religion: A Thorough Analysis of the Teachings of Pierre Teilhard de Chardin”, p.18, TAN Books

The evolutionist thesis has become more stringently unthinkable than ever before. — Dr. Wolfgang Smith (2015).

A Chat with Information Scientist Pedro Marijuán (2017)

I’ve based my informational scheme of the cell on this thinking of “distinction on the adjacent” — where molecular recognition is the essential phenomenon over which biological complexity has been developed.

Biological complexity develops in the context of the olfactory code. Molecular recognition of food odors and pheromones biophysically constrains viral latency.

See: Fundamental principles of the olfactory code  Volume 164, February 2018, Pages 94-101 open access

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response.

Alternative splicing of microRNAs (aka pre-mRNAs) are required for a behavior response.

The splicing code  Volume 164, February 2018, Pages 39-48

…the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Algorithms define nothing. The availability of quantized energy as information must be linked to biophysically constrained viral latency and all biologically based cause and effect.

What is code biology?  Volume 164, February 2018, Pages 1-10

The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes.

New codes do not automagically occur. The new codes are energy-dependent and RNA-mediated in the context of the fixation of amino acid substitutions that differentiate the cell types of all living genera.

On universal coding events in protein biogenesis  Volume 164, February 2018, Pages 16-25

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases…

The energy-dependent creation of the tRNA synthetases links hydrogen-atom transfer in DNA base pairs in solution to all energy-dependent biodiversity.

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow  Volume 164, February 2018, Pages 26-38

An important issue related to code biology concerns the cell’s informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows.

Quantized energy is the information that flows through every cell type in all prokaryotes.

Causation, constructors and codes  Volume 164, February 2018, Pages 121-127

A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The diverse range of processes starts with the creation of energy-dependent enzyme action. The anti-entropic virucidal energy of sunlight was first linked to the creation of all biodiversity on Earth in 1944: What is Life?

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

If you think you can link anything except sunlight to all biodiversity on Earth, see: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
If you know that serious scientists do not link viruses to the evolution of anything except pathology, see:
Schrödinger at 75 – The Future of Biology – September 2018
The future of biology will not be left in the hands of biologically uninformed theorists.

Alternative splicing of pre-mRNA

Diet-driven RNA interference and cancer prevention (3)

Excerpt: They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2.  Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

The fact that a peer-reviewed work published in 2018 links autoregulatory feedback loops to automagically altered gene expression and apoptosis via alternative splicings of pre-mRNAs suggests it is time for all serious scientists to retire. The magic of pseudoscientists has prevailed for more than 2 decades.

See for comparison: In clinical trial, cream reduces squamous cell carcinoma risk

Results of a new randomized, double-blinded, controlled clinical trial in veterans showed a 75 percent reduction in the risk of needing surgery to treat a squamous cell carcinoma for a year after applying a skin cream for up to four weeks.

How Fluorouracil Works: (with my emphasis)

The ability of chemotherapy to kill cancer cells depends on its ability to halt cell division. Usually, the drugs work by damaging the RNA or DNA that tells the cell how to copy itself in division. If the cells are unable to divide, they die. The faster the cells are dividing, the more likely it is that chemotherapy will kill the cells, causing the tumor to shrink. They also induce cell suicide (self-death or apoptosis).

Chemotherapy drugs that affect cells only when they are dividing are called cell-cycle specific. Chemotherapy drugs that affect cells when they are at rest are called cell-cycle non-specific. The scheduling of chemotherapy is set based on the type of cells, rate at which they divide, and the time at which a given drug is likely to be effective. This is why chemotherapy is typically given in cycles.

Chemotherapy is most effective at killing cells that are rapidly dividing. Unfortunately, chemotherapy does not know the difference between the cancerous cells and the normal cells. The “normal” cells will grow back and be healthy but in the meantime, side effects occur. The “normal” cells most commonly affected by chemotherapy are the blood cells, the cells in the mouth, stomach and bowel, and the hair follicles; resulting in low blood counts, mouth sores, nausea, diarrhea, and/or hair loss. Different drugs may affect different parts of the body.

Fluoruracil belongs to the category of chemotherapy called antimetabolites. Antimetabolites are very similar to normal substances within the cell. When the cells incorporate these substances into the cellular metabolism, they are unable to divide. Antimetabolites are cell-cycle specific. They attack cells at very specific phases in the cycle. Antimetabolites are classified according to the substances with which they interfere. Fluoruracil is classified as a pyrimidine analog because it interferes with DNA and RNA synthesis by mimicking the building blocks necessary for synthesis.

The term antimetabolites is confusing. Metabolism is enzyme-dependent. Cell type differentiation is energy-dependent and the creation of microRNA links ATP to the creation of enzymes that metabolize food to the species-specific pheromones.
Pheromones biophysically constrain viral latency. That is how they prevent all pathology in the context of metabolism. Enzyme-dependent cycles of metabolism are the key to healthy longevity. Simply put, pheromones prevent the transgenerational epigenetic inheritance of nearly all viruses that have not been biophysically constrained by food energy-dependent metabolism.

Hardin, Hall and Rosbash (1990) put that fact into the perspective of Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. The feedback loops are food energy-dependent and biophysically constrained by naturally occurring RNA interference (i.e., natural selection for energy-dependent codon optimality). The feedback links the metabolism of food to pheromone-controlled biophysically constrained viral latency.
 

Rosbash shared the 2017 Nobel Prize in Chemistry, which attests to the fact that all serious scientists probably know how to prevent or to effectively treat cancer as a disorder of cyclic changes in the chemistry of energy-dependent RNA mediated cell type differentiation. Prevention should include limiting exposure to nutrient stress and/or social stress because stress alters microRNA-mediated alternative splicings that link food energy to the biophyiscally constrained chemistry of protein folding.

See: Microrna-mediated regulation of splicing factors SRSF1, SRSF2 and hnRNP A1 in context of their alternatively spliced 3’UTRs

The microRNAs targeting SRSF1 and SRSF2 are involved in a regulatory feedback loop. microRNAs miR-183-5p and miR-200c-3p that target SRSF2, affect the expression of genes involved in apoptotic regulation.

They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2.  Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

The fact that a peer-reviewed work published in 2018 links autoregulatory feedback loops to automagically altered gene expression and apoptosis via alternative splicings of pre-mRNAs suggests it is time for all serious scientists to retire. The magic of pseudoscientists has prevailed for more than 2 decades.

See for comparison:

From Fertilization to Adult Sexual Behavior (1996)

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 [model organisms.]

See also:
Feedback loops link odor and pheromone signaling with reproduction (2005)
The feedback loops are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Sarcasm alert: The treatment of automagically dysregulated apoptosis should probably begin with a change in diet.

Changes in diet have been linked from the energy-dependent creation of enzymes that specifically link an energy-dependent base pair change to microRNA-mediated DNA repair via fixation of an RNA-mediated amino acid substitution. The substitutions are linked to energy-dependent cell type differentiation and healthy longevity without the magic.

Just add food energy or the virus-driven theft of quantized energy to eliminate the term autoregulatory and you could prevent or effectively treat all virus-driven pathology. 

Energy-dependent RNA interference links the enzyme-dependent metabolism of food and drugs to cell type differentiation via feedback loops that link pheromones to biophysically constrained viral latency.

Do not claim to have a logical philosophy if you cannot link the creation of the sun’s anti-entropic virucidal energy to every aspect of the biophysically constrained pheromone-controlled physiology of reproduction in species from microbes to human by starting with the obvious need to control viral replication in the ocean and linking the control to healthy longevity in modern human populations via fixation of RNA-mediated amino acid substitutions in all differentiated cell types.

See also: Metabolic Labeling and Profiling of Transfer RNAs Using Macroarrays

Transfer RNAs (tRNA) are abundant short non-coding RNA species that are typically 76 to 90 nucleotides in length. tRNAs are directly responsible for protein synthesis by translating codons in mRNA into amino acid sequences.

See also: Molecular mechanism of promoter opening by RNA polymerase III

RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs.

Nothing happens without the energy-dependent creation of the enzymes and the biophysically constrained viral latency that links the creation of G protein-coupled receptors to the functional structure of supercoiled DNA. The claims about molecular mechanisms of promoter opening appear to be deliberate attempts to obfuscate cause and effect.
Activation of G protein-coupled estrogen receptor signaling inhibits melanoma and improves response to immune checkpoint blockade

Female sex and history of prior pregnancies are associated with favorable melanoma outcomes. Here, we show that much of the melanoma protective effect likely results from estrogen signaling through the G protein-coupled estrogen receptor (GPER) on melanocytes. Selective GPER activation in primary melanocytes and melanoma cells induced long-term changes that maintained a more differentiated cell state as defined by increased expression of well-established melanocyte differentiation antigens, increased pigment production, decreased proliferative capacity, and decreased expression of the oncodriver and stem cell marker c-Myc. GPER signaling also rendered melanoma cells more vulnerable to immunotherapy. Systemically delivered GPER agonist was well tolerated, and cooperated with immune checkpoint blockade in melanoma-bearing mice to dramatically extend survival, with up to half of mice clearing their tumor. Complete responses were associated with immune memory that protected against tumor rechallenge. GPER may be a useful, pharmacologically accessible target for melanoma.

Sex-specific cell type differentiation links yeasts to primates via the nutrient-dependent pheromone-controlled physiology of reproduction that links the food energy-dependent structure and function of enzymes and G protein-coupled receptors to the biophysically constrained Structure and dynamics of GPCR signaling complexes, which are required to biophysically constrain viral latency in the context of effect of androgens and estrogens on difference in the cell type of males and females.
Any focus on G protein-coupled estrogen receptors compared to G protein-coupled androgen receptors  should be viewed with suspicion in the context of what has been known to all serious scientists about hormones and behavior since our Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior (1996)
Simply put, the alternative splicings of pre-mRNAs, which are now called microRNAs, biophysically constrain energy-dependent viral latency and prevents the transgenerational epigenetic inheritance of nearly all virus-driven pathology until excess nutrient stress or social stress takes its toll on the innate immune system.
Eventually, our food energy-dependent RNA-mediated DNA repair fails, and the accumulation of viral microRNAs predicts the failure of cell type differentiation in the tissues that are required to sustain our physical health and mental health.

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Autophagy is the antiphage defense strategy (2)

2/15/17 Energy as information and constrained endogenous RNA interference (video)
The 6.46 minute-long technical presentation (above) from the Precision Medicine Virtual Conference is difficult to understand.Thus, 10 months later, Nik Willmore asked:

12/24/17 What are your insights into CRISPR and mTOR, for a young audience? I’m not mocking you…yet, Humpty Dumpty. What is the basis of your unifying principle? Vibration? Bohmian morphogenetic fields? Modified Darwin? God? –Nik Willmore 

12/25/17 Replying to

God created the anti-entropic virucidal energy of sunlight and all energy-dependent biodiversity via the physiology of pheromone-controlled reproduction. I co-authored a book about that for a young audience in 1995/2002, and a 6-part series for today.

1/1/18 Replying to

Do you understand any aspect of how to model biophysically constrained biologically-based energy-dependent top-town causation and bottom-up effects on cell type differentiation via the physiology of reproduction and autophagy? The “walking fish” walks straight from quantum physics to quantum souls (2)

1/9/18 Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

My paraphrased summary:

RNA interference (RNAi) is our indispensable antiphage defense mechanism. Viruses escape the defense system by the theft of quantized energy, which encodes RNAi suppressors that prevent elimination of viral RNAs. The suppressors ensure energy-dependent virus accumulation.

1/12/18 Human cytomegalovirus-encoded miR-UL112 contributes to HCMV-mediated vascular diseases by inducing vascular endothelial cell dysfunction

The significantly altered pathways mainly include the mitogen-activated protein kinase signaling pathway, cell adhesion molecules, chemokine signaling pathway, cytokine-cytokine receptor interaction, circadian rhythm-mammal, mineral absorption, protein processing in the endoplasmic reticulum, proximal tubule bicarbonate reclamation, vasopressin-regulated water reabsorption, and arachidonic acid metabolism. In conclusion, hcmv-miR-UL112 could serve as a potential biomarker, and the miRNA-mediated regulation of signaling pathways might play significant roles in the physiological effects of hcmv-associated diseases.

1/12/18 H5N1 influenza virus-specific miRNA-like small RNA increases cytokine production and mouse mortality via targeting poly(rC)-binding protein 2

We conclude that miR-HA-3p is the first identified influenza virus-encoded microRNA-like functional RNA fragment and a novel virulence factor contributing to H5N1-induced ‘cytokine storm’ and mortality.

Virus-encoded microRNA-like functional RNA fragments are not novel virulence factors. They link the virus-driven degradation of messenger RNA to all pathology in all living genera via the theft of quanitzed energy, which typically links the fixation of RNA-mediated amino acid substitutions to healthy longevity.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs
All serious scientists know what goes wrong in the context of host microRNA-mediated regulation of viruses. They also know how it goes wrong. See Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

The serious scientists do not claim that viruses evolve. Scientists who make claims about evolution  typically do not know how to link the creation of sunlight from ecological variation to food energy-dependent pheromone-controlled ecological adaptation via the physiology of biophysically constrained reproduction and biophysically constrained viral latency. Indeed, most pseudoscientists do not know the difference between a mutation and an RNA-mediated amino acid substitution.
See for comparison: Mechanisms of Recombination conference Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Description

Genetic recombination provides an important mechanism for the repair of chromosome breaks caused by DNA damage or replication fork demise. Defects in the recombination process have been linked to cancer predisposition, in particular breast cancers caused by mutations in BRCA1, BRCA2 and PALB2, and also acute leukemias associated with the rare genetic disease Fanconi anemia. Understanding precisely how recombination occurs is of interest to workers in the fields of meiosis, DNA repair, replication, chromosome architecture and interactions, and chromatin biology.

Download provisional conference program
Excerpts:

Douglas Bishop (University of Chicago, US)
A primary function of the ATPase activity of E. coli RecA is to prevent accumulation of a toxic form of the protein bound to undamaged chromosomal sites

Maria Jasin (Memorial Sloan Kettering Cancer Center, US)
Protecting the genome by homologous recombination

The energy-dependent microRNA-mediated creation of enyzmes protects all organized genomes from the virus-driven degradation of messenger RNA that links the theft of quantized energy from mutations to all pathology.  Pseudoscientists who do not start with the creation of energy, have bastardized Darwin’s claims. His claims were based on placing “conditions of life” before natural selection. Conditions of life are energy-dependent and biophysically constrained by the mechanisms of pheromone-controlled recombination, which have been linked to autophagy by all serious scientists since 1925.
See also my RNA-mediated Facebook page and/or my RNA-mediated Facebook group and other tweets @jvkohl
The number of my tweet impressions since December 21, 2017 has climbed to more than 68,000 as the number of published works that mention “microRNA” has climbed to nearly 69,000. See for comparison: The tipping point (revisited): 68,000 publications, which was published to my other blog site on December 21, 2017.
See also: What Darwinists Fail to Consider (discussion attempt)
See also, this discussion attempt about the “spark of life.”
See also: Noncoding RNA Helps Cells Recover from DNA Damage

“The most logical, simple explanation is that the [noncoding RNA] counteracts the protein encoding form…”

My comment to the Scientist:

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

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…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

See also: Search Results for “autophagy”

GPX4-Cys bypasses the requirement of selenoproteins for cell viability

Quantized energy-dependent viral trophism

…mutations cause activation of your death gene.
Conclusion: You may be able to stop the ongoing activation of your death gene by a change in diet.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
——————————————–
Daniel L.Hurdiss (@DanielHurdiss) announced publication of this refutation of neo-Darwinian pseudoscientific nonsense in his twitter feed before the start of the new year with no indication that it refutes all theories of emergence and evolution.
Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

…receptors are important determinants of viral tropism…

The quantized energy-dependent creation of the receptors biophysical constrains viral latency via feedback loops that link the de novo creation of enzymes from microRNA-mediated metabolism to the species-specific pheromones that biophysically constrain autophagy.
That fact has become clearer since the 1994 publication of  Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus musculus L.)
The exquisite clarity led to this:

Previously, , Ariane Briegel @BriegelAriane blocked me from following her tweets (one of which led me to the tweet by Daniel Hurdiss).
In 2014, (with others) she published Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling [Two of the authors are not based in the United States and Ariane Briegel now has her own lab in Leiden — in the Dutch province of South Holland.]

Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm.

Phototaxis must first be linked to energy-dependent pH-taxis and chemotaxis, which is why I commented on her publication of The dark side of the new popularity of cryo-electron microscopy.  It appeared to be yet another attempt to keep people in the dark about what is already known to serious scientists about light-activated endogenous substrates and cell type differentiation.
[Researchers based outside the United States are probably less likely to support the Trump administration’s efforts to drain the academic swamp.] See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
My invited review of nutritional epigenetics was returned without review and Briegel has since decided it is a good idea for reviewers to be fair. I will add that blocking specific people from seeing your tweets is not an effective strategy. Simply put, it is not fair. If it was, the President of the United States of America would probably have used a tweet blocking strategy by now.
Instead, he was falsely accused of censorship when the director of the CDC suggested that certain key words, such as “transgender” should not be used in funding attempts. What about Briegel’s censorship?
I suspect that President Trump will keep tweeting away in his attempts to drain the academic swamp. In any case, that’s what I will keep doing. Watch what happens to those who hide their claims each time a serious scientist asks them to explain why they failed to link their results from quantum physics to quantum souls — in the context of words that might otherwise be used in future funding attempts. For example, words like food and energy could be used in funding attempts that would clearly show that food energy biophysically constrains viral latency.
See for example: Selenium Utilization by GPX4 Is Required to Prevent Hydroperoxide-Induced Ferroptosis

… a variety of dietary compounds such as… selenium… [target] a sequence of cellular and molecular pathways.

In the context of dietary microRNAs and exosomes, a change in the diet is an attractive option for the prevention/treatment of pathology.
That fact was placed into the context of Cytosis, a successful non-government funded 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!

The cell biology game links the creation of the sun’s anti-entropic virucidal energy from quantum physics to quantum souls via the creation of ATP, and the light-induced creation of messenger RNA.
The first time that experimental evidence of that fact was published may have been in 1964. See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
See also: Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959), which was published in “Science Magazine.” McEwen and his co-author, Irving B. Fritz claimed:

…it is relevant to ask by what means serum fatty acids are transported from blood vessels through the interstitial space to the active sites for fatty-acid oxidation in muscle cells.

See also: Pheromones: a new term for a class of biologically active substances (1959) Was published in “Nature.”
It made it equally relevant to ask how fatty-acid oxidation in muscle cells was biophysically constrained in the context of the food energy-dependent pheromone-controlled physiology of reproduction.
It should be obvious that the dumbing down of “Science” has not effectively eliminated the intelligent approach that the Trump administration must take to Make America Great Again, by draining the academic swamp. However, for an example of what he is fighting against, see:
pH-Taxis of Biohybrid Microsystems (published in one of the Nature Publishing Group’s journals)

The motion analysis of microrobots also sheds light on the propulsion dynamics of the flagellated bacteria as bioactuators. It is expected that similar driving mechanisms are shared among pH-taxis, chemotaxis, and thermotaxis. By identifying the mechanism that drives the tactic behavior of bacteria-propelled microsystems, this study opens up an avenue towards improving the control of biohybrid microsystems.

The identified mechanism was place into the context of the weekend resurrection of the bacterial flagellum (in Science Magazine, 2015). The mechanism is food energy-dependent and controlled by the physiology of reproduction in species from microbes to humans via food energy-dependent fixation of RNA-mediated amino acid substitutions, which were reported to be mutations.The mutations cause activation of your death gene.
Conclusion: You may be able to stop the ongoing activation of your death gene by a change in diet.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
See also: Autophagy.pro

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

The α1 and β1 subunits of HH-H (light blue) and LL-L (light red) are superimposed, and van der Waals radii are shown for α-chain residues that are in atomic contact with β-chain residues of the opposing α2β2 dimer.

The overwhelming ignorance of sex researchers

Summary: J. Michael Bailey, and others like him, pretend to not know how non-coding variants are epigenetically linked from differences in hydrogen bonds to all energy-dependent biophysically constrained morphological and behavioral phenotypes.

Genome-Wide Association Study of Male Sexual Orientation [Energy-dependent changes in biophysically constrained viral latency]

We identified several [energy-dependent changes in] SNPs with p < 10−5, including regions of multiple supporting SNPs on chromosomes 13 (minimum p = 7.5 × 10−7) and 14 (p = 4.7 × 10−7). The genes nearest to these peaks have functions plausibly relevant to [biophysically constrained viral latency and] the development of  sexual orientation.

Reported as: Gene variants identified that may influence sexual orientation in men and boys

The findings by the team do not settle the argument of whether homosexuality in people is biology-based, but instead offers more evidence that suggests it is likely the case. Prior studies that looked at family histories have also offered some evidence of biology playing a role while other studies have found some differences in chromosomes. In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

I was not surprised to see J. Michael Bailey listed as a co-author. He is a biologically uninformed pseudoscientist and a passive/aggressive antagonist.

It’s been more than 4 years since food energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution were linked to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in all living genera.

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Sex researchers like J. Michael Bailey, are still among the majority of those who have paid no attention to the extant literature since the time we published this 1996 review in Hormones and Behavior (with a section on molecular epigenetics.)

From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

All serious scientists know that everyone else must also start with differences in the quantized energy of hydrogen to get from epigenetic modifications to differences in morphological and behavioral phenotypes. Serious scientists also know that social science is pseudoscience and that pseudoscientific nonsense is the cause of all preventable unnecessary suffering and premature death.

See for instance:

1) Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
2) Mutation-Driven Evolution
and my refutation of neo-Darwinian pseudoscientific nonsense. All three were published on June 14, 2013.
3) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Please join the other serious scientists who have been quietly ridiculing people like J. Michael Bailey for more than 20 years.

QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Light harvesting is the source of energy-dependent changes in hydrogen that link physics, chemistry, and molecular epigenetics to accurate representations of RNA-mediated cell type differentiation. All aspects of energy-dependent RNA-mediated cell type differentiation have been virtually ignored by J. Michael Bailey, who is the proud owner of the Sexnet listserver. It has been a consistent source of misinformation for all participants during the past two decades.
See for comparison my comments on: Evolution of a Vertebrate Social Decision-Making Network
1)

Re: Cause and effect. How could it not be the adaptive evolution from yeasts of the ligand-receptor binding exemplified across species by the conservaton of gonadotropin releasing hormone (GnRH) and diversification of its receptor? Model organisms like the threespine stickleback make clear the involvement of ecological niche construction. The honeybee invertebrate model organism makes clear the involvement of the nutrient dependent ecological niche in construction of the pheromone-dependent social niche. Invertebrate and vertebrate models collectively attest to the common molecular biology of adaptively evolved social decision-making networks. In mammals, the hypothalamic neurogenenic niche (probably located in the MPOA) responds to nutrients to enable fertility and responds to pheromones to enable sexual reproduction that has adaptively evolved from its origins in brewer’s yeast. Never before has there been such a clear reprentation of cause and effect across species from microbes to man, where nutrient chemicals calibrate the intracellular signaling and their metabolism to pheromones standardizes and controls the stochastic gene expression required for reproduction. Gene expression enables adaptive evolution of the brain and ensures that our ability to acquire nutrient chemicals is the first priority for reproduction via appropriate social behaviors, as it is in every species. For example, microbes eat the DNA of heterospecifics but not conspecifics, which indicate more social sense than what some people today are capable of recognizing in the design of biology (the evolved gene, cell, tissue, organ, organ system pathway that directly links sensory input to the mammalian neuroendocrine system and the hormones responsible for our behavior, which activates the same ‘organized’ pathway).

2)
Re: The Intersection of Neurotoxicology and Endocrine Disruption. NeuroToxicology, Bernard Weiss

Abstract excerpts: …hormones help steer the process of brain development.

…sex differences in behavior are primarily the outcomes of differences in how the brain is sexually differentiated during early development by gonadal hormones (the Organizational Hypothesis).

… environmental chemicals are capable of altering these underlying events and processes. Among those chemicals, the group labeled as endocrine disrupting chemicals (EDCs) offers the clearest evidence of such selectivity… —————– I have terminally argued to conclusion that the clearest evidence of chemicals that alter the underlying events and processes of brain development and its sexual differentiation are the nutrient chemicals and pheromones responsible for the adaptive evolution of species from microbes to man.

Focus on endocrine disruption establishes what happens when toxic chemicals alter the same events and processes of brain development and its sexual differentiation via epigenetic effects on gonadotropin releasing hormone (GnRH) pulsatility, luteinizing hormone, olfactory bulb neurogenesis, hippocampal neurogenesis, learning, and memory in vertebrates.

For contrast, I’ve modeled the epigenetic effects of food odors and pheromones on homeostasis and species diversification, and for many years, my friend Teresa Binstock and co-author (e.g., with Milton Diamond)stressed the importance of endocrine disruption (specifically due to bisphenol A and phthalates) on J. Michael Bailey’s “Sexnet”. Now that the basic principles of biology and levels of biological organization, which link sensory input from the environment directly to behavior via intracellular signaling and stochastic gene expression, have been clarified by work with model organisms, I look forward to learning if there are any reasons to avoid the incorporation of current information on endocrine disruption into existing studies of the homeostatic development of human sexual behavior.

Comparing typical and atypical epigenetic effects that appear to extend to those that are transgenerational seems even more important now than in 1996.

Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338

See also: Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci

Our study shows that noncoding disease variants in OCRs can affect neurodevelopment, and that analysis of open chromatin regions can help prioritize functionally relevant noncoding variants identified by GWAS.

After Alan R. Sanders and others published this, the claims in Genome-Wide Association Study of Male Sexual Orientation can be viewed in the context of two decades of false claims and pleas for more funding.

Conclusion:

In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

Alternative splicing of pre-mRNA

Light-activated error free DNA repair (2)

Summary: In the diagram and diatribes that accompany claims about de novo changes in electrons and the production of nucleotides, the amount of pseudoscientific nonsense becomes perfectly clear. Pseudoscientists start with energy-dependent changes but call the changes de novo changes in electrons. That allows the pseudoscientists to dismiss any facts about how the creation of energy must be linked to the creation of enzymes. The creation of enzymes does not automagically occur and the creation of all biodiversity must occur via the enzymatic metabolism of food to pheromones and the physiology of pheromone-controlled reproduction. Use of the phrase de novo changes is a clear indicator that pseudoscientists know nothing about biophysically constrained viral latency and nothing about cell type differentiation. All changes are energy-dependent and virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.
In Light-activated error free DNA repair, I wrote:

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera.

See also: Endogenous adenosine maintains cartilage homeostasis and exogenous adenosine inhibits osteoarthritis progression

We conclude that adenosine, acting at A2AR, is an important homeostatic regulator of chondrocytes and cartilage and adenosine repletion may represent a novel approach to treating OA (Fig. 6).

The link from exogenous adenosine to the endogenous adenosine that inhibits pathology is food energy-dependent and RNA-mediated.That is why adenosine repletion will almost undoubtedly be effective. Some friends have already found that supplements of curcumin and nicotinamide/niacinamide are helpful.
Science needs reason to be trusted to link the creation of visible light to the creation of the nicotinamide-dependent enzyme known as ketoreductase, which can be transformed from a carbonyl reductase into an initiator of radical species and a chiral source of hydrogen atoms.
If hydrogen-atom transfer in DNA base pairs in solution is not linked to healthy longevity, the virus-driven degradation of messenger RNA will not be linked from mutations to all pathology.
See: Accessing non-natural reactivity by irradiating nicotinamide-dependent enzymes with light
The link from the quantized energy of the sun has been placed into this context:

We demonstrate this new reactivity through a highly enantioselective radical dehalogenation of lactones-a challenging transformation for small-molecule catalysts. Mechanistic experiments support the theory that a radical species acts as an intermediate in this reaction, with NADH and NADPH (the reduced forms of nicotinamide adenine nucleotide and nicotinamide adenine dinucleotide phosphate, respectively) serving as both a photoreductant and the source of hydrogen atoms.

The photoreductant source of hydrogen atoms links the quantized energy of sunlight from quantum physics to quantum souls via error-free RNA-mediated DNA repair in the context of the physiology of pheromone-controlled reproduction and the creation of all morphological and behavioral diversity on Earth via what is known about the stability of the gonadotropin releasing hormone (GnRH) decapeptide. The creation of achiral glycine and its position at position 6 in the GnRH decapeptide is linked from food odors and pheromones to the stability of all vertebrate genomes.
See how easily the facts about the stability of supercoiled DNA in the organized genomes of all vertebrates was placed back into the context of evolution.
A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
Explanations from classical physics cannot be used to support the theory and nothing but that facts about chemistry links sunlight to the creation of enzymes that metabolize food and link the food energy to biophysically constrained life via the physiology of pheromone-controlled reproduction, which protects organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.

We suggest that DHA is one Darwin’s “Conditions of Existence” [conditions of life] which made DHA the master of DNA

How Popper killed Particle Physics

Even in his worst moments Popper never said a theory is scientific just because it’s falsifiable. That’s Popper upside-down and clearly nonsense. Unfortunately, upside-down Popper now drives theory-development, both in cosmology and in high energy physics.
It’s not hard to come up with theories that are falsifiable but not scientific. By scientific I mean the theory has a reasonable chance of accurately describing nature.

11/20/17
Jay R. Feierman:

Science is about predicting, not post hoc explaining except under the conditions stated above. I still find Popper’s methods useful for crafting theories in the bio-behavioral sciences. I’m not ready to declare his philosophy as dead.

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.
Popper’s upside-down theory can be replaced in the context of the inside-out olfactory receptor, which links the epigenetic landscape to the physical landscape of DNA via two epigenetic traps
An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

We’ve got the evolution of complex cells inside-out

Almost everybody agrees that the complex eukaryotic cell evolved from a simple ancestor. The question is how.

All serious scientists know that the energy-dependent creation of ATP (epigenetic trap #1) must be linked from the creation of RNA (epigenetic trap #2) to all biodiversity on Earth via the physiology of pheromone-controlled reproduction in species from microbes to humans. For example, without the energy-dependent de novo creation of G protein-coupled receptors, there is no way to link any light-induced endogenous substrate to the creation of enzymes and the metabolism of food to the energy that sustains life in electron eating microbes and microbes that “eat” light.

 
“…Golden didn’t set out from school intent on pursuing a career in chronobiology. The field only barely existed when she did her graduate work in the 1980s. Her specialty was, and still is, studying bacteria that use light as a source of energy.

See also: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

The fact that bacteria eat electrons and produce uranium isotopes can now be linked from light-harvesting to all pheromone-controlled biophysically constrained biodiversity on Earth by what was known to Susan S. Golden in the 1980s.

Two Questions remain:

1) Where do the electrons come from?

2) Why doesn’t every serious scientist know how to link energy-dependent changes from electrons to ecosystems via the link from ultraviolet light to the vibrational theory of olfaction and RNA-mediated feedback loops that link food odors and pheromones to the physiology of reproduction in species from microbes to humans?

The vibrational theory of olfaction for the win by John Hewitt

On 11/21/17, John Hewitt alerted me to the fact that the information in this article might be linked from the de novo creation of olfactory receptor genes to all biodiversity on Earth via links from the physiology of pheromone-controlled reproduction in bacteria to human adult hippocampal neurogenesis. The monoallelic disease(s) known as Kallmann’s Syndrome clearly link the transgenerational epigenetic inheritance of virus-driven pathology to deficits in olfactory acuity and specificity. The olfactory deficites link interactions among all neuronal systems in the brain to healthy longevity via the substitution of the achiral amino acid glycine in position 6 of the GnRH decapeptide.

See: Long-Range GABAergic Inputs Regulate Neural Stem Cell Quiescence and Control Adult Hippocampal Neurogenesis

Taken together, these findings delineate a GABAergic network involving long-range GABAergic projection neurons and local PV interneurons that couples dynamic brain activity to the neurogenic niche in controlling NSC quiescence and hippocampal neurogenesis.

See for comparison: Guidelines for Genome-Scale Analysis of Biological Rhythms

1) Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day.

2) …we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.

This suggests they are going to try to make it appear that Schrodinger’s link from the anti-entropic virucidal effects of sunlight has only recently been discovered to be the key to the prevention of the virus-driven degradation of messenger RNA, which all serious scientists know is the link from mutations to all pathology.
SS Golden is the co-author and they propose 3 broadly applicable “golden rules” of light-activated biological rhythms. The “Golden Rules” do not link more than 66,000 published works on microRNAs to Kohl’s “Laws of Biology” in this 2014 invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The Law’s of Biology are Darwin’s “conditions of life.” Simply put, all organisms must eat and the physiology of pheromone-controlled reproduction must be linked to all morphological and behavioral biodiversity on Earth after the creation of light made life possible. Natural selection for anything that was selected after the creation of energy, should not be viewed in the context of explanations of anything else.
Nothing on Earth exists outside the context of biophysically constrained energy and viral latency. Nothing on Earth exists outside the context of energy-dependent natural selection for codon optimality in the context of fixation of RNA-mediated amino acid substitutions, the creation of enzymes and the interactions among complex systems in humans that link achiral glycine in position 6 of the GnRH decapeptide to all morphological and behavioral phenotypes.

See also: An epigenetics gold rush: new controls for gene expression

‘A-to-I editing’ can alter a protein’s coding sequence, and, in humans, is crucial for keeping the innate immune response in check.

See for comparison: Redox-sensitive alteration of replisome architecture safeguards genome integrity

DNA replication requires coordination between replication fork progression and deoxynucleotide triphosphate (dNTP)–generating metabolic pathways

The safeguards are energy-dependent and they have been linked from light-activated endogenous substrates in all cell types to changes in immune system function. That fact is ignored in the context of a “genome survellance mechanism.”

Studying this genome surveillance mechanism in cancer cells with elevated ROS levels and increased replication adaptability may provide opportunities to specifically target tumors.

Reported as: Redox sensing controls DNA replication!

Redox sensing controls DNA replication!

New DNA is generated in human cells from tiny building blocks called nucleotides produced by an enzyme called RNR (ribonucleotide reductase).

By starting with de novo changes in electrons, the diagram that accompanies the pseudoscientific nonsense of their claim makes the nonsense perfectly clear. They intend to leave out anything known to serious scientists who have linked the creation of energy to the creation of enzymes and to the creation of all biodiversity via the metabolism of food to pheromones and the physiology of pheromone-controlled reproduction.
For comparison, serious scientists have linked energy-dependent changes from atoms to ecosystems via the conserved molecular mechanisms of base editing, microRNA editing, and RNA editing as detailed in Light-activated error free DNA repair.
See for examples:
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis

…adenosine-to-inosine (A-to-I) RNA editing occurs in microRNAs (miRNAs)…

Thanks to Dr. Phil Mills for bring this to my attention in the context of more than 40 skin cancer excisions I have had during the past few years. RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

Our findings imply that the editing effect on RNA secondary structure is context dependent and underline the intricate regulatory role of ADAR1 on global RNA secondary structure.

See: Scientists demonstrate the importance of RNA editing in melanoma development

…a lack of RNA editing, a process by which information inside RNA molecules is transformed, leads to tumor growth and progression through manipulation of proteins.

See also: Study: Vitamin B3 might help against skin cancer

…people who took a specific type of vitamin B3 for a year had a 23 percent lower rate of new skin cancers compared to others…

The link from sun exposure to vitamin C production in plants and vitamin D production in human populations that might be protected from skin cancer by niacinamide, led me to become more focused on prevention. For example, a 23 percent lower rate of skin cancers translates to 10 less excision surgeries if I can achieve a better energy-dependent microRNA/messenger RNA balance.
Energy-dependent base editing has been linked to microRNA editing and linked from RNA editing to the fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera via the pheromone-controlled physiology of reproduction. Any presentation of data that fails to start with energy-dependent changes in the microRNA/messenger RNA balance implies a deliberate attempt to support the pseudoscientific nonsense of evolutionary theorists and/or big bang cosmologists.
It’s time for pseudoscientists to admit they’ve been wrong about mutation-driven evolution and move forward via consideration of experimental evidence.
See also: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
MicroRNA-mediated RNA editing links energy-dependent changes in base pairs from the creation of nucleotides to the stability of organized genome in all living genera via the physiology of pheromone-controlled reproduction in species from microbes to humans.  All serious scientists know that. However, the number of pseudoscientists is more than the serious scientists who will be presenting at this conference.
See: Mechanisms of Recombination conference
For comparison, the pseudoscientists have their own conferences. See for a possible example: Neuroimmunology and Neurological disorders
I’ve already asked the conference organizer “Who will be linking the molecular mechanisms of recombination to neuroimmunology via autophagy or help serious scientists to link the virus-driven degradation of messenger RNA to all pathology?” 
I no longer expect any answer to my questions from those who have not linked the creation of quantized energy to all biodiversity via the pheromone-controlled physiology of reproduction in species from microbes to humans.
See instead, more information on: A-to-I RNA editing