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

Ecological adaptation: A new definition of heredity (3)

Excerpt:
Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

OMCD: OncoMir Cancer Database

Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.

The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer.  Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements.

Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

My “Disqus” comment (and nearly 2000 others): Gene expression is energy-dependent, RNA-mediated, and biophysically constrained.
See: FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.

MicroRNA-mediated gene silencing is a fundamental mechanism in the regulation of gene expression.

MicroRNAs do not create themselves.
See also:  Energy as information and constrained endogenous RNA interference
8 of my 9 most recent comments to Disqus have been removed.
See for comparison: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Reported as: In nature, an imperfect immune system drives the evolution of deadly pathogens

…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.

…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.

By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology.  That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies
A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype

…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.

See also: Microhomology-assisted scarless genome editing in human iPSCs

Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.

Reported as: Gene Editing Is Now Precise Enough to Modify a Single Letter of DNA

To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.

See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR

Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.

Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (5)

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)


The list of those scheduled to present has changed. Michael Rosbash has been added. John E. Walker is not scheduled, which suggests that everyone else already knows that the creation of the sun’s anti-entropic virucidal energy is the link from the creation of ATP to the creation of RNA and all biophysically constrained viral latency via feedback loops and the physiology of reproduction.
Rosbash, as all serious scientists know,  started with energy-dependent changes in cycles of RNA biosynthesis. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990). Pseudoscientists failed to link the energy from feedback to biophysically constrained viral latency.
But see: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM).

Other serious scientists have consistently linked photophosphorylation from oxidative phosphorylation to all biodiversity via the physiology of pheromone-controlled reproduction in species from soil bacteria to humans
Speakers (new copy-protected list)
Speakers (old list)
See also: Viral Resistance Project
The differences in innate immunity and ecological adaptation are obviously nutrient energy-dependent and transgenerationally inherited in the context of the epigenetically-effected physiology of pheromone-controlled reproduction and the affects of hormones on behavior. For instance, pheromones biophysically constrain viral latency via the fixation of amino acid substitutions.
See for comparison: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
There are several neo-Darwinian theorists who are scheduled to present, which means they may be ready to accept the ridicule from serious scientists.
See for example: A universal trend of amino acid gain and loss in protein evolution

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

See also: Why I got rid of my friends
Some of my former friends kept dumping their garbage about evolution on others in the same way that I. King Jordan and Eugene Koonin did it with their comment about the evolution of the amino acid composition of proteins. See for comparison: All About that Base (Meghan Trainor Parody) 12/10/14 and Energy as information and constrained endogenous RNA interference 2/15/17
Help others who are Combating Evolution to Fight Disease

5th-6th Sept 2018 Dublin, Ireland

Light-activated carbon fixation did not evolve (4)

Summary: Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
See: Light-activated carbon fixation did not evolve (3),(2),(1) and RNA mediated molecular epigenetics and virus driven entropy and The origin of information (2)
For comparison, see: Genome editor CRISPR’s latest trick? Offering a sharper snapshot of activity inside the cell

…this tool can record exposure to light, antibiotics, and viral infection or document internal molecular events.

The “tool” links the anti-entropic virucidal energy of sunlight to the creation of enzymes, which link the metabolism of food energy to the physiology of reproduction in the context of autophagy and viral latency.

The facts about autophagy and biophysically constrained viral latency have been placed into the context of phage-activated continuous evolution (PACE) by people who do not want others to learn the facts about how autophagy protects all organized genome from the virus-driven degradation of messenger RNA.
See: Evolution in Action – Literally

The idea is that you use bacteriophage as your vehicle for evolving proteins, because of their extremely short generation time. These infect E. coli bacteria, and the two of them are modified in this system so that you can use selection pressure to get to a protein with specific binding properties. It’s been used to look at protease inhibitor resistance and DNA-binding specificity, and now it’s put to work for a protein-protein interaction.

All protein-protein interactions are energy-dependent, RNA-mediated and biophysically constrained in the context of the physiology of reproduction and transgenerational epigenetic inheritance.
See for contrast: Church Speaks George Church [2.14.18]

  1. Maybe it would help if the very top scientists believed in neo-Darwinism or something.
  2. We found the enzymes that occur in nature, which was not obvious, and both companies have patents on making those alkanes.

Top scientists who believe in neo-Darwinism are more likely to believe Church’s claim that the anti-entropic energy of sunlight was not the obvious link to the creation of enzymes and all biophysically constrained life on Earth. The creation of enzymes was required to biophysically constrain viral latency.

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: Regulation of the unfolded protein response by noncoding RNA
See: Endoplasmic reticulum stress signaling: the microRNA connection
See also: ER homeostasis and autophagy

The endoplasmic reticulum (ER) is a key site for lipid biosynthesis and folding of nascent transmembrane and secretory proteins. These processes are maintained by careful homeostatic control of the environment within the ER lumen. Signalling sensors within the ER detect perturbations within the lumen (ER stress) and employ downstream signalling cascades that engage effector mechanisms to restore homeostasis. The most studied signalling mechanism that the ER employs is the unfolded protein response (UPR), which is known to increase a number of effector mechanisms, including autophagy.

Place the unfolded protein response (UPR) into the context of how virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology. Link femotosecond blasts of ultraviolet light to the creation of enzymes and energy-dependent RNA-mediated DNA repair to complete the picture of creation vs neo-Darwinism.
See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
If you are a top scientist who believes in neo-Darwinism, retire as soon as possible to avoid the ridicule that will be linked to the lack of funding for your so-called research.
See also: miRs-103/107 regulate autophagy in the epidermis

We found that antagomir-107 treatment in epidermis: (i) depleted endogenous miR-107; (ii) increased GFP-LC3 puncta in epidermal basal layers of GFP-LC3 transgenic mice, indicative of an accumulation of autophagosomes; (iii) inhibited LC3 turnover and increased p62, suggesting an inhibition of autophagy flux; and (iv) increased phosphorylated dynamin (p-dynamin, an inactive form), a key enzyme in end-stage autophagy. Conversely, miR-107 mimic treatment in mouse epidermis: decreased GFP-LC3 puncta in basal layer as well as p62 protein levels; and diminished p-dynamin, indicative of activation of this enzyme.

See also: CCPG1: A new breed of autophagy cargo receptor: 3:00pm GMT / 10:00am EST / 7:00am PST on Thursday 1st March
The anti-entropic energy-dependent creation of receptors is enzyme-dependent and RNA-mediated in the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
The overwhelming complexity prevents most attempts to link quantum physics from quantum chemistry to the molecular mechanisms of epigenetically-effected cancer prevention and treatment. Despite that fact, prevention and effective treatments will continue to link the speed of light on contact with water from hydrogen-atom transfer in DNA base pairs in solution via the creation of microRNAs linked to biophysically constrained viral latency.
Do you remember what Barry J. Marshall did to link H. pylori to prevention of gastric cancer?
See: Neutrons identify critical details in bacterial enzyme implicated in gastric cancer

Ronning’s team focused on H. pylori’s use of a unique biosynthetic pathway to synthesize vitamin K2, which aids in the electron transfer processes, or chemical reactions, of all organisms.

Ronning’s team linked Barry J. Marshall’s energy-dependent changes (e,g., hydrogen-atom transfer in DNA base pairs in solution) from electrons to ecosystems and healthy longevity in all living genera via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I asked the evolutionary theorist, John Hewitt (a so-called science journalist): “Are you still planning to do that by starting with the magical creation of selenocysteine?”
I’ve heard nothing from him, since then.
See also: Is Maternal Food Security a Predictor of Food and Drink Intake Among Toddlers in Oregon? (2012)

CDC Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

The 35-year-old author works as a team lead for the CDC’s Division of Population Health.

Authorities say he called in sick on February 12, 2018 and has not been heard from since.

In 2014 he was the first author of: Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states

This work adds to a growing body of research suggesting that ACEs may contribute to health problems later in life and suggesting a need for program and policy solutions.

The link from the anti-entropic virucidal energy of sunlight to healthy longevity and the link from stress-induced biophysical constraint-breaking mutations reaffirms that suggestion.
Cunningham’s brother, Anterio Cunningham, does not want to assume the worst, yet he is worried something horrible has happened for him to leave his family and prized job with no notice.
The CDC did not immediately respond to ABC News’ request for comment.

Anyone with information is urged to call 911 or the Atlanta Police Homicide/Adult Missing Persons Unit at 404-546-4235.

The need for program and policy solutions at the CDC could bring the current practice of medicine to an end. The end requires all practitioners to acknowledge the facts about disease control. The facts link the creation of sunlight from fixation of light in cyanobacteria to the physiology of reproduction in humans and to all biodiversity via biophysically constrained viral latency.
See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

 I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

Dozhansky supposedly assumed that:

Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

But he may also have been joking. He wrote:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
Anyone who places Dobzhansky’s claims from 1964 and the claims of McEwen et al. (1964) into the context of Frohlich’s assertions in 1968 would close the door on evolutionists in three steps.
Dobzhansky compared theorists to bird watchers and butterfly collectors.
McEwen et al., (1964) linked the creation of ATP to the creation of RNA.
Frohlich (1968) linked the creation of RNA to all biophysically constrained biodiversity.
The cell biology game “Cytosis” can be used to teach people like George Church about cell biology. Alternatively, Church could ask a serious scientist what was known about the energy-dependent creation of naturally occurring enzymes.
For comparison, retracted works by Jack Szostak’s group are the only works that might make that fact not obvious (e.g., to other theorists). Serious scientists know that all enzymes naturally occur in the context of their energy-dependent microRNA-mediated creation. If George Church shared Dobzhanky’s creationist beliefs, he might have avoided the shame that comes from his claim that it was not obvious where all naturally occurring enzymes come from.
See: Retraction Watch Also reported as: Oops! Scientific retraction a major blow to evolution theory

Szostak’s study reopens what is perhaps the largest hole in evolutionary theory, as scientists remain unable to explain how the building blocks of life were “spontaneously” created.

Jack W. Szostak—a professor of chemistry and chemical biology at Harvard University,  shared the 2009 Nobel Prize in Physiology or Medicine. It seems likely that he influenced the works by George Church — also at Harvard, and the claims Church made about the “not obvious” creation of naturally created enzymes.
See for comparison: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: Researchers may have solved origin-of-life conundrum

…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.

The difference between George Church’s neo-Darwinian approach, and the approach that serious scientists have taken, may be as simple as the difference between a creationist and an evolutionary theorist.
 
For comparison, see: What is life when it is not protected from virus driven entropy Published on 30 Mar 2016

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

Witzhany2018

The tipping point (revisited): 70,000 publications

Excerpt:

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”

The tipping point?: 50,000publications (May 16, 2016)
See also: The tipping point (revisited): 69,000 publications (January 20, 2018)
Nearly 1000 more published works have been added to the 69,000 on microRNAs that had already been published by last month.
All experimental evidence has been placed into the context of 12,000 more published works on microRNAs, since the time of this presentation (February 15, 2017):

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.

See: Transposons: a blessing curse (open access) with my emphasis
Conclusion:

The circumstances of transposon bursts, preferences of insertion sites, and the life cycle of many elements are not fully understood. Like in classical mutagenesis with chemical or physical treatments, unwanted side effects are likely and cannot be excluded, and new TE-related phenotypes must be thoroughly tested for genetic and epigenetic stability. However, detrimental and beneficial events can teach us both principles, and well-established advantageous interactions between TEs and genes might serve as templates for more precise and targeted genome editing and breeding.

Pseudoscientists continue to put what is known into the context of their ridiculous theories about evolution:
See for comparison (from the same issue): Despacito: the slow evolutionary changes in plant microRNAs (paywalled) with my emphasis

…this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.

No experimental evidence of biophysically constrained biologically-based cause and effect suggest that microRNAs emerged or that plant genomes evolved. All experimental evidence consistently has shown that the anti-entropic virucidal energy of sunlight creates microRNAs in the context of photophosphorylation.
See: Energy limitation of cyanophage development: implications for marine carbon cycling
Photophosphorylation is obviously:

…a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).

Simply put, photophosphorylation links the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via oxidative phosphorylation and the physiology of reproduction in all living genera. That fact has been suspected or established in the context of all works published by serious scientists since the publication of What is Life? (1944)

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 also: Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage
For extension of the research from cyanobacteria to humans see:
Quantification of microRNA expression with next-generation sequencing 2013 (coauthored by George M. Church)
Differential expression of microRNAs in the normal skin of the Han and Uyghur populations in Xinjiang Province (2018)
Any additional claims about the emergence of microRNAs and the evolution of genomes can be placed into the context of what will be presented at the forthcoming conference on “Genetic Novelty/Genomic Variations by RNA Networks and Viruses,” or the cell biology board game “Cytosis” for ages 10+.

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”
See for instance: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent. Experiments are described which show that the required ATP is produced by reactions associated with glycolysis, the citric acid cycle, and a type of oxidative phosphorylation.

An evolutionary theory killer

Conceptual critique: Innateness vs the death gene (2)

Excerpt: Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See also: Conceptual critique: Innateness vs the death gene (1)
Re: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

See for comparison: Subatomic

…is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic…

See also: Cytosis: A Cell Biology Board Game

Players start out with a number of workers and on their turn, they will place one of their workers on any available location within that cell. Some of the locations provide players with resources (e.g., mRNA, ATP); some with actions (e.g., convert resources, collect cards). Resources are used to build enzymes, hormones, and/or receptors, which score Health Points.

Science Concepts: cell biology, nucleus, free ribosomes, smooth ER, rough ER, golgi apparatus, plasma membrane, mitochondria, enzymes, hormones, receptors, cell detoxification, antibodies and viruses
Alternatively, theorists may continue to ignore the Science Concepts: in the context of  The Hidden Intelligence of Hormones — How They Drive Desire, Shape Relationships, Influence Our Choices, and Make Us Wiser (Feb 13, 2018) for comparison to From Fertilization to Adult Sexual Behavior (1996)

Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See for comparison: Conditional expression of women’s desires and men’s mate guarding across the ovulatory cycle (2006)In 2006, it became clear to most serious scientists that Martie Haselton knew nothing about biophysically constrained RNA-mediated viral latency. Now, she places everything known back into the context of neo-Darwinian pseudoscientific nonsense and eons of evolution. Fortunately,  you can read and discuss her book in the context of what other pseudoscientists have been doing for the past two decades. Simply copy and paste from Wikipedia in attempts to promote ridiculous theories.

See for comparison: Evolution: Genetic Novelty/Genomic Variations by RNA-Networks and Viruses 2018 >

Preliminary List of Confirmed Speakers (41)
Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >

Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >

Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >

Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA
Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria

Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

For comparison to Martie Haselton’s February 13, 2018 publication of her pseudoscientific nonsense about hormonal women, see: Energy as information and constrained endogenous RNA interference from my February 15, 2017 virtual conference presentation on Precision Medicine.

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

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.

How to biophysically constrain the flu virus (1)

Excerpt: John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
What the flu does to your body, and why it makes you feel awful

…when you have an influenza infection, you can rest assured that it is because your body is fighting hard. It’s combating the spread of the virus in your lungs and killing infected cells.

Why suffer needlessly or die prematurely. See: 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! (2 to 5 Players, Ages 10 & up, Plays in 50 to 75 mins)

Download the “Science Behind the Game” to learn how food energy-dependent alternative splicings of pre-mRNA protect all cell types, or see Alternative splicing and the evolution of phenotypic novelty.
Link the alternative splicings to species-specific behaviors via the physiology of reproduction in From Fertilization to Adult Sexual Behavior and anything else I have published or presented during the past two decades.
All behavior is energy-dependent. The energy comes from sunlight. Quantized energy as information from sunlight is linked to healthy longevity via its anti-entropic virucidal effect.
For example: Special UV light safely kills airborne flu virus, finds study

Scientists have known for decades that broad-spectrum UVC light, which has a wavelength of between 200 to 400 nanometers, or nm), is highly effective at killing bacteria and viruses by destroying the molecular bonds that hold their DNA together.

For comparison to vaccinations:
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

A key advantage of the UVC based approach, which is in clear contrast to vaccination approaches, is that UVC light is likely to be effective against all airborne microbes. For example, while there will almost certainly be variations in UVC inactivation efficiency as different influenza strains appear, they are unlikely to be large7,10. Likewise, as multi-drug-resistant variants of bacteria emerge, their UVC inactivation efficiencies are also unlikely to change greatly9.

In the context of vaccinations:
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.

Clearly, vaccinations may not protect you and prevention via use of UV light is desirable.
When you learn how UV light protects you at the level of particle physics, you will understand the horrors of neo-Darwinian theory and big bang cosmology .
See Subatomic
The link from quantum physics to quantum chemistry was reported last month. Modern diversification of the amino acid repertoire driven by oxygen.
Schrödinger at 75, The Future of Biology is scheduled for September 2018
John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
People who have played “Cytosis” can predict what will happen at the Schrödinger at 75 conference. They will jump ahead of most academics if they play “Subatomic” and link particle physics to all biophysically constrained biodiversity.
The fun factor is important to most people. They don’t care about supercoiled DNA or the virus-driven degradation of messenger RNA. But other scientists are having fun watching the creator of the genious games teach facts to theorists. We are especially pleased about his help in teaching the facts about energy-dependent cell biology to anyone who wants to have fun, prevent or survive the flu, or to become a serious scientist.
Alternatively, play the Mutation-driven evolution game (available only as an outdated 2013 textbook).
But remember:  Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
Simply put, you could be dead by the time pseudoscientists start to tell the truth. For example, this is the truth:

There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Lander just admitted that their assumptions may have made many serious scientists wrong about every aspect of energy-dependent life on Earth.
See also: Real Heroes Have the Guts to Admit They’re Wrong

…one reason we can’t admit we have the facts wrong is that it’s too painful to our self-conception as smart, right-thinking people—or to our political tribal identity.

In the past year alone, mathematicians have pulled papers when they’ve learned their proofs don’t hold and economists have retracted work after finding they’d misclassified their data. The Harvard stem-cell biologist Douglas Melton had a hit 2013 paper that got cited hundreds of times—but when colleagues couldn’t replicate the finding, he yanked it.

They discount the fact that any claims that have been placed into the context of neo-Darwinian theories have been invalidated first by Schrödinger in “What is Life? (1944) and since then by all serious scientists who have linked  the sun’s anti-entropic virucidal energy from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See also: Windowed Granger causal inference strategy improves discovery of gene regulatory networks

Significance

Discovery of gene regulatory networks (GRNs) is crucial for gaining insights into biological processes involved in development or disease. Although time-resolved, high-throughput data are increasingly available, many algorithms do not account for temporal delays underlying regulatory systems—such as protein synthesis and posttranslational modifications—leading to inaccurate network inference. To overcome this challenge, we introduce Sliding Window Inference for Network Generation (SWING), which uniquely accounts for temporal information. We validate SWING in both in silico and in vitro experimental systems, highlighting improved performance in identifying time-delayed edges and illuminating network structure. SWING performance is robust to user-defined parameters, enabling identification of regulatory mechanisms from time-series gene expression data.

Reported as: New machine learning algorithm uncovers time-delayed interactions in cells

SWING puts together a more complete picture of the cause-and-effect interactions happening among genes by incorporating time delays and sliding windows. Rather than only looking at the individual perturbations and responses, SWING uses time-resolved, high-throughput data to integrate the time it takes for those responses to occur.

Researchers will continue to scramble in attempts to put their findings into the context of what has already been presented in: Olfaction Warps Visual Time Perception
and in:

 

 

An evolutionary theory killer

Subatomic: From thermophiles to humans (3)

Summary: RNA-mediated cell type differentiation in species from insects to primates can be linked from claims about the lower percentage of food energy-dependent DNA methylation in Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae) to the conclusion from “Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility.”
See also: Starfish reveal the origins of brain messenger molecules (February 9, 2016)

One of the neuropeptides found is similar to kisspeptin, a chemical that triggers the onset of puberty in humans.

The link from kisspeptin to GnRH helped to establish the link from food odors and pheromones to the RNA-mediated physiology of reproduction in all invertebrates and vertebrates.
Placing facts about neuropeptides into the context of human brain evolution thus seems to exemplify incredible ignorance of physics, chemistry, and molecular epigenetics.
See for comparison: The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution
Conclusion:

The increasing number and diversity of these small and long ncRNAS in relation to the complexity and adaptability of living beings, explains that they have been paramount in complex biological processes and are not an evolutionary paradox.

The fact that miRNAs can be mobilized by the fluids of plants and animals, allows them to act at different distances to where they were transcribed, much like hormones or pheromones do. In addition, they can respond to environmental stimuli, favoring the adaptation of organisms through the modification of epigenetic marks and also a transgenerational inheredity and the evolution of species as part of a Neo-Lamarckian model.

There has never been a neo-Lamarkian model for the evolution of species. Lamarck put his observations into the context of Darwin’s “conditions of life.” If the conditions of life are met, ecological variation can be linked to food energy-dependent ecological adaptations. Only the bastardization of Darwin’s claims put natural selection for mutations first — when biologically uninformed theorist invented neo-Darwinian pseudoscientific nonsense.
SARCASM ALERT: Please do not tell anyone about this 2013 refutation of neo-Dawinism. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

Conclusion:

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

See for comparison. Others are  making the same claims:
Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells

…identification of vitamin C-dependent microRNA regulation is important for understanding the basic mechanisms underlying BMSC differentiation and tissue engineering.

All cell type differentiation in all tissues of all species with tissues is energy-dependent and RNA-mediated. That fact is consistently thrown into the political ring of nonsense touted by theorists who attack the President of the United States.
See: Trump: Tell us about your flu shot

Why are so few Americans getting the flu vaccine? And why isn’t the CDC doing more to change that?

The CDC can do nothing. Intelligent people know that the flu virus adapts each season. The CDC will abandon their claims about mutations, which were linked to evolution. More people will be angry when they learn that only a single amino acid substitution can cause an adaption.
Trump-hating liberals may be forced to repurpose their anger and use it to rid the academic swamp of their idiot minions — the so-called science journalists who refused to join the serious scientists who are Combating Evolution to Fight Disease
Most of the anger will be directed toward biologically uninformed science journalists who have failed to present the facts about all virus-driven pathology. For example see: The Quest to End the Flu (2013)

New pandemics don’t come out of the blue. They evolve from viruses that infect animals—typically birds.

Pandemics “evolve” from viruses? What kind of so-called science journalist makes a claim like that?
Is Most of Our DNA Garbage? (March 5, 2015)

…junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

The triumph is not slow and slovenly. One base pair change and fixation of one amino acid substitution is all that is required to start the process of ecological adaptation.
See for comparison: It’s time to put America’s health first

While the CDC neglected its mission here, Obama committed billions to build labs and train health personnel in Africa during the Ebola scare. Billions for a disease that killed only one person in the United States — and even he got infected elsewhere.

The so-called science journalists who also are Trump-haters have contributed to more unnecessary suffering and premature death than most people can begin to imagine. They spread their ignorance and hatred across the country and across the world. It is the pathology of their ignorance that must be removed if ever we are to put America’s health first. The first thing we must do, is rid ourselves of the unethical so-called science journalists.
 

An evolutionary theory killer

Subatomic: From thermophiles to humans

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. — Max Planck
Every great scientific truth goes through three stages. First, people say it conflicts with the Bible. Next they say it has been discovered before. Lastly they say they always believed it. — Louis Agassiz  (1807-1873)
The claims of neo-Darwininan theorists and big bang cosmologists bastardized the scientific truth that he included in his “conditions of life.” The theorists made it appear that the greatest of all scientific truths did not come from the Bible because their ridiculous theories were nowhere to be found in the context of links from the creation of energy to the physiology of reproduction and all morphological and behavioral diversity on Earth.
See for comparison:

Subatomic

Subatomic is themed around the intersection of particle physics and chemistry! At it’s core, Subatomic is a deck-building game with a light Area Majority mechanic for end game points. Players start with a hand of Up Quarks, Down Quarks and Particle/Wave Duality cards, which they use to form protons, neutrons, and electrons. Players combine these subatomic particles to either build available Elements or buy even more powerful cards for their deck.

See also: Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells (Nutrients, February 8, 2018)

We hypothesized that vitamin C mediates these biological processes partially through miRNA regulation.

MiRNA regulation is quantized energy-dependent. The energy comes from the sun. Their hypothesis appears to be based on my claims in my invited review of nutritional epigenetics, which was returned without review by the guest editors of the journal “Nutrients.”
I linked the anti-entropic virucidal energy of sunlight from the claims in Schrodinger (1944) “What is life?” via the quantized energy-dependent creation of microRNAs and vitamin C.
See  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

The likelihood that hemoglobin variants are associated with other beneficial nutrient energy-dependent changes in microbiota populations in the gut can be considered in the context of how balanced nutrition, which includes access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction (McNulty, et al., 2011).

Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional G protein-coupled genes such as olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).

Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).

Conclusion:

In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports (Grossman, et al., 2013; Kamberov, et al., 2013).

The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

See also: The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding

…our study demonstrates that NONO post-transcriptionally coordinates circadian mRNA expression of metabolic genes with the feeding/fasting cycle, thereby playing a critical role in energy homeostasis.

Reported as: Researchers discover how liver responds so quickly to food

“After mice eat, it looks as if NONO brings all these RNAs together and processes them so they can be used to make proteins,” says Panda.

Panda linked what serious scientists know about food energy-dependent RNA interference to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA and all mutations, which have been linked to all pathology.
See: Energy as information and constrained endogenous RNA interference (video 6.46 minutes)
See also: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy

Wednesday, February 7, 2018 12PM EST (available on demand with registration)

Everything I claimed about the need to link microRNAs to RNA-mediated amino acid substitution ins proteins was included in the context of this Webinar

Within the first 10 minutes, the speaker describes the ability to link specific amino acids to the structure of the protein strand, which allows for the differentiation of pathology from healthy longevity.

Within the first 17 minutes, he links energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution from microtubules to neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, Lewy Body Disease, and ALS.

He adds that others who are interested in his approach may contact him and he many help them to refine their approach.

Simply put, he does not seem to be among a group of competitors with interests that might prevent the dissemination of accurate information or to prevent rapid scientific advances linked from preventative medicine to Precision Medicine via cryo-EM technology.

Keep in mind the fact that Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973), and this claim:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

Refine your approach to include this fact: Humans And Chimps Differ At Level Of Gene Splicing (2007)

Splicing is the process by which the coding regions of genes are joined to generate genetic messages that specify the production of proteins, the key structural and functional constituents of cells. Splicing can occur in alternative ways in the same genetic message to generate more than one type of protein. The new findings reveal that the alternative splicing process differs significantly between humans and chimpanzees.

See also: Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks (2012)
Stop touting ridiculous theories before everyone who understands the fact that cryo-EM links everything known to serious scientists about the creation of the sun’s anti-entropic virucidal energy from the physiology of reproduction to healthy longevity. Only then will you begin to understand how the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.
Teach your children well. If you teach them to believe in ridiculous theories, your hell will become theirs. Alzheimer’s is a form of hell on Earth, for example.

Crosby, Stills, Nash & Young – Teach Your Children

Here Comes the Sun: A Tribute to George Harrison by Paul Simon, Crosby and Grahm Nash

 

An evolutionary theory killer

A reversible TCA cycle in a thermophile (3)

A pathway for mitotic chromosome formation

The combination of nested loops distributed around a helically twisted axis plus dense chromatin packing achieves the 10,000-fold compaction of chromatin into linearly organized chromosomes that is required for accurate chromosome segregation when cells divide.

The compaction of chromatin in the context of hydrophobicity is the topic of: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Differential recognition of proteins clearly involves this link from natural selection for energy-dependent codon optimality to the physiology of reproduction via RNA-directed DNA methylation.
See for comparison: DNA-Methylation: Master or Slave of Neural Fate Decisions?

The involvement of splicing as effector of changes in DNA methylation is an exciting new angle to pursue with more precise epigenetic engineering tools. Distinguishing essential from specific, and causal from secondary marks will be essential for neuro-epigenetics. New approaches promise to answer long outstanding questions and will likely facilitate the discovery that DNA modifications might have new unexpected roles in the brain.

Splicing is not the effector of changes in DNA methylation, energy-dependent changes in the microRNA/messenger RNA balance must be given first consideration. But, this article is part of the Research Topic: Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex

The topic is an example of human idiocy for comparison to this report on alternative splicing, which was linked to energy-dependent biophysically constrained viral latency in the context of:

 Alternative splicing and the evolution of phenotypic novelty and the cell biology game: Cytosis

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

The origins of morphological diversity cannot be evaluated outside the context of the origins of energy-dependent behavioral diversity, which requires that RNA-mediated DNA methylation be linked to differences in cell fate in all tissues of all individuals of all species on Earth. Typically, serious scientists do this by linking the creation of the sun’s anti-entropic viral latency from  subatomic particles to creation of atoms and ecosystems in the context of human brain development via mitotic chromosome formation.

See for instance: The Excitable Mitochondria and The vibrational theory of olfaction for the win by John Hewitt.
If he did not believe that “evolution did it” after the emergence of energy, he would not have placed his bets on ridiculous theories and criticized my life’s history of publications and presentations, which he claimed were BS.
See for comparison to his claims: Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity
We placed the facts about alternative splicing and increasing organismal complexity into the context of our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The sexual differentiation of all cell types in species from yeast to humans was presciently placed into the context of what was known about pre-mRNA mediated biophysically constrained viral latency in 1996. Food energy-dependent pre-mRNAs are now referred to as microRNAs (miRNAs). The creation of the miRNAs links the anti-entropic virucidal of the sun to all biodiversity via the physiology of reproduction,  and our details from 1996 have been extended across species via this recently published work:
Reproductive role of miRNA in the hypothalamic-pituitary axis

The hypothalamic-pituitary-gonadal (HPG) axis plays a critical role in regulating reproductive function. Gonadotropin-releasing hormone (GnRH), which is secreted by the hypothalamus, acts on pituitary gonadotrophs to stimulate luteinizing hormone (LH) and follicle-stimulating hormone (FSH) synthesis and secretion, ultimately affecting the animal’s fertility. MicroRNAs are small, non-coding RNAs that are widely expressed throughout the brain and can fine-tune gene expression post-transcriptionally. Recently, growing evidence has unveiled the central position of miRNAs within a key regulatory process involving GnRH secretion and subsequent activation in the pituitary. Although transcriptional regulation of reproduction has been well studied, the post-transcriptional processes are less well understood. In this review, we elaborate comprehensively on the critical role of miRNAs in the reproductive process, including both temporal and spatial aspects. A better understanding of how miRNAs impact the neuroendocrine system may improve our knowledge of reproduction and provide novel targets for therapeutic development.

For comparison, see: No Missing Link: Knowledge Predicts Acceptance of Evolution in the United States

Using a new demographically representative survey (N = 1100) that includes a detailed measure of evolution knowledge, we find that knowledge predicts level of acceptance, even after accounting for the effects of religion and politics. These results demonstrate that Americans’ views on evolution are significantly influenced by their knowledge about this theory and therefore might be amenable to change.

Reported as: Better knowledge of evolution leads to greater acceptance of the concept

…actual knowledge of the science seems to play a role, and we’ve documented that here for evolution for the first time in a representative population.”

If that claim was true, we would not see so many examples of people in other countries who have replaced the teaching of ridiculous evolutionary theories with facts that their students learn about ecological variation and ecological adaptations.
For example: Israeli Middle Schools School to Include Theory of Evolution (2014)

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

See also: Turkish schools to stop teaching evolution, official says (2017)
If you are willing to consider the facts about why many countries do not teach humans to believe in ridiculous theories, please see:
Subatomic: From thermophiles to humans (in prep)

 
 
 

An evolutionary theory killer

A reversible TCA cycle in a thermophile

Make no mistake, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
For comparison, see:

“…considering that we have just 3 such round Nos ‘100’ ‘1000’ ‘10000’, its just three out of all realistic possibilities, no? Admit its looks cool just bec. we calc in Dec system. History books claims was invented by ancient societies; but I think its evolution: We have 10 fingers!”

My reply (SARCASM ALERT):

Thanks. The correlations are intriguing. Templeton funding might help you prove that the numbers game of evolution is true in the context of Cosmopsychism. With enough correlations, facts that link physics and chemistry to viral latency can be dismissed.

Thanks to the Ralser lab for bringing this to my attention with a claim about:
A reductive TCA cycle in a thermophile, which uses the same citrate synthase [enzyme] both for the oxidative and the reductive directionality.

“Every day it looks more likely that primoridial and modern metabolism look similar”

A link was provided to: A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

…raises the possibility of a facultatively chemolithomixotrophic origin of life.

Has anyone else considered that possibility?
I tried to look at it from the perspective of chemoorganoheterotrophic metabolism and electron-eating microbes that enzymatically (not automagically) create uranium isotopes, but I got side-tracked by the claims about mutations and evolution. I could not link those claims from the physiology of reproduction in microbes to claims that link the metabolism of food energy to pheromones that biophysically constrain viral latency in species from microbes to humans.

Now, the physiology of pheromone-controlled reproduction in electron-eating microbes that create uranium isotopes suggests the same thing that the Ralser lab suggested: SARCASM ALERT: “It’s turtles all the way down” (the infinite regress problem in cosmology).Unless, like the folks at the Ralser Lab,  you are a serious scientist.

The problem for pseudoscientists, theorists, and many so-called science journalists may be familiar to those at the Ralser lab. McEwen et al., (1964) reported “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” All serious scientists know “ATP controls the crowd.

These findings suggest an additional way for cells to use ATP to maintain proteostasis in the crowded cytoplasm and also fine-tune the material properties of nonmembrane-bound organelles and the cell interior in general.

Obviously, there are now several groups of serious scientists that can make fun of all the pseudoscientists and so-called science journalists who have failed to link physics and chemistry to biophysically constrained viral latency via energy-dependent changes in base pairs in species from thermophiles to those that create uranium isotopes. But Kudos to the first group, or one of the first, to do that:

12/10/14 All about that base and Structural diversity of supercoiled DNA 10/12/15

Sarcasm Alert: I hope that claims about the emergence of energy and mutation-driven evolution did not confuse others as much as they confused so-called science journalists such as John Hewitt, Philip C. Ball, Carl Zimmer, and many others.
When you see the facts reported by an intelligent science journalist, please tell others about the claims that link the creation of energy from the game “Subatomic” to biophysically constrained viral latency in “Cytosis.” Comparisons will be made. It will become clearer that pseudoscientists, theorists and many others have lost their games.
See for example: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding…

…proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.”

Alternatively, everyone can simply accept the fact that food energy typically restricts the virus-driven degradation of messenger RNA, and tell all the pseudoscientists and so-called science journalists where to put their pseudoscientific nonsense (e.g., where the sun don’t shine).
For example: Is the Universe a conscious mind?

Cosmopsychism might seem crazy, but it provides a robust explanatory model for how the Universe became fine-tuned for life

For comparison: A Big Bang in spliceosome structural biology and Alternative splicing and the evolution of phenotypic novelty
But remember to link the claims about the evolution of phenotypic novelty to the missing claims about behavior, and see the claims made by Bruce McEwen and Martin Picard in:
Psychological Stress and Mitochondria: A Conceptual Framework (Part 1)

Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.

Reported as: Cellular ‘powerhouses’ may explain health effects of stress
in the same context as Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Evidence from metabolomic, proteomic, and transcriptomic studies also suggest additional layers of regulation by which stressful experiences may alter mitochondrial components among rodents. Although these metabolites, protein composition, and gene expression outcomes do not reflect the functionality of mitochondria, when assessed in parallel with functional outcomes, they will help explain and refine our understanding of the mechanisms by which stress influences mitochondrial function and health. In addition, whereas functional changes should be regarded as primary indicators of MAL (21), stress-induced molecular changes within mitochondria may also reflect compensatory mechanisms or recalibrations that contribute to long-term changes in mitochondrial function and to the accumulation of MAL. [mitochondrial allostatic load (MAL)]

Review: Subatomic
See also: Self-evident: Contrary to recent opinion, there is such a thing as the self, and it is empirically amenable to scientific investigation 
It has been investigated at every level of investigation that links quantum physics from quantum chemistry to quantum souls in the context of what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry that protects supercoiled DNA from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
Conclusion (from self-evident):

The multitudinous self mediates scientific explanations of the complexity of real people with and without mental disorders. It also provides resources for enhancing the moral agency that permits people to flourish. For me, flourishing is simply the development of a person’s psychological and social skills in engagement with herself and with others, in the face of the challenges triggered by her physical, social and psychological environment. If we know the characteristics of the self, we might be able to improve the lives of those whose self-experiences are not conducive to flourishing. The self is not an idle concept, either scientifically or ethically; it organises human experience and proliferates moral possibilities. So, yes, know thyself. Every single part.

See: 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).

Make no more mistakes, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.