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.

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)

 
 
 

https://media.springernature.com/lw900/springer-static/image/art%3A10.1038%2Fs41467-017-02632-8/MediaObjects/41467_2017_2632_Fig6_HTML.jpg

The MicroRNAome Strikes Back: A Sokalian hoax (4)

In this Sokalian hoax series, all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera via the physiology of reproduction and autophagy, the innate phage defense mechanism.
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

I reiterate the most obvious facts by mentioning again:

 Virus-mediated archaeal hecatomb in the deep seafloor

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

See also: The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

The John Templeton Foundation typically seems to be involved in funding research reported that obfuscates facts that link science to Biblical Genesis. The claims about understanding energy-dependent biomolecular recognition in biophysical systems, which must biophysically constrain viral latency, invite more criticism of the Templeton-funded biologically uninformed theorists.

Does the “Extended Synthesis” Replace or Not Replace Neo-Darwinism? — What Has Templeton Funded?

Many terms in science have a different meaning from the public usage, because they depend on particular definitions of the phenomena to which they apply.

See for comparison: Do Human Pheromones Exist? January 23, 2018

The people interviewed are not Nobel Laureates. For comparison, LInda Buck, co-author of Feedback loops link odor and pheromone signaling with reproduction is a 2004 Nobel Laureate.
I suspect that all serious scientists have since learned that pheromones biophysically constrain food energy-dependent viral latency in species from insects to mammals via the conserved molecular mechanisms of microRNA-mediated cause and effect. Serious scientists tend to be more likely than theorists or other pseudoscientists to recognize patterns.
For instance: Insect pheromone in elephants

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

That claim links what insects eat to the pheromone-controlled physiology of reproduction of s via the food energy-dependent creation of microRNAs in species from microbes to mammals.

See: Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, Signaling, and role of MicroRNA (with my emphasis)

Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

insects, arachnids, and crustaceans are arthropods. No experimental evidence of biologically-based cause and effect suggest that complex mechanisms evolved in any species. For contrast, the link from microRNAs to juvenile hormone crosses species via the molecular mechanisms that link the food energy-dependent creation of microRNAs from what is known about gonadotropin releasing hormone (GnRH) pulsatility to luteinizing horrmone secretion via the food energy-dependent GnRH-directed physiology of pheromone-controlled feedback loops in all mammals.

That fact has been placed into the context of ecological variation and biophysically constrained ecological adaptations.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes 

…lack of genome information hinders the understanding of the adaptation

See for comparison: Differential expression of microRNAs in luteinising hormone-treated mouse TM3 Leydig cells

Results showed that miRNAs might be involved in the regulation of LH to Leydig cells.

One way to understand the adaptations revealed in the context of mussel genomes involves ignoring all claims about how complex mechanisms “evolved to regulate” anything. The overwhelming systems complexity of biophysically constraints demand that all ecological adaptations be examined from the intelligent perspective of serious scientists.

The well-detailed understanding of how the light energy-dependent creation of microRNAs is linked to all nutrient-dependent pheromone-controlled ecological adaptations. But the facts were again placed back into the context of complex mechanisms that automagically evolved in  Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

…pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4.

The established biodiversity is obviously pH-dependent and oxidative phosphorylation was linked to the stability of organized genomes in 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Other serious scientists moved forward in the context of the energy-dependent hydrophobicity of supercoiled DNA.
See: 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.

Outside the context of the epigenetic effect of anti-entropic virucidal energy from sunlight on supercoiled DNA, or perhaps in the context of minimal exposure to ultraviolet light, the metagenomic diversity of bacteria in caves with sulfur water springs led  Bautista et. al., (2018) to conclude:

…20,901 reads of bacterial 16S rRNA gene sequences spanning V1–V3 hypervariable regions corresponded to seven phyla: Proteobacteria, Firmicutes, Chloroflexi, Chlorobi, Bacteroidetes, Actinobacteria and Acidobacteria. Proteobacteria phylum dominance could be due to the increased presence of organic matter, not only of bat guano but also that caused by man and animals, directly or through infiltrations. For the UJAT5 sample, we generated 6,691 reads, which, due to the
physicochemical characteristics (Table 1) and relative frequency obtained (Figure 4), could confirm the presence of acidophilic Proteobacteria in VL caves. All the bacterial communities identified are characteristic of caves, while Acidobacteria, Proteobacteria, and Actinobacteria are typical of volcanic surface terrain.

Simply put, they seem to assume that the increased presence of organic matter is the food energy that supports the pheromone-controlled physiology of reproduction in the different species. But they do not link the creation of sunlight to differences in the food the organisms eat.
By skipping the link from the creation of sunlight — as did Nonomura (2018) in his Sokalian hoax, evolutionists have tried to convince others who are biologically uninformed that the eyes of blind cave fish exemplify evolution in the process of the fish becoming blind.
See: Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
See (pun intended) Blind Cavefish Can Produce Sighted Offspring  (2008)

It’s a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.

This means that even though the fish are blind, they basically have functional visual systems that have been deactivated by a few key mutations, said Jeffery, who was unaffiliated with the study.

See also: The fish evolved from surface-dwelling ancestors during the past million years. (2003)
Everything biologically uninformed theorists report must be linked toi evolution and back by mutations. They refuse to differentiate between mutations and food energy-dependent ecological adaptations because they cannot accept the fact that all biophysically constrained biodiversity is food energy-dependent and constrained by energy-dependent viral latency.
For comparison, what serious scientists see happening in the blind cave fish is the regression of food energy-dependent visual acuity in organisms that can find food without  the energy-dependent creation of G protein-coupled photoreceptors. Only the energy-dependent creation of chemoreceptors is required to link pH-taxis to survival of the microbes and the blind cave fish via what is known about oxidative phosphorylation in other species that display receptor-mediated behaviors.
What science journalists see happen is causing them to back away from their pseudoscintific claims from the past. See for example:

Hydration as a design element in biomaterials  Philip Ball January 24, 2018

John Hewitt January 24, 2018 N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications 
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

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.

Darwinian adaptation: a clear evolutionary trail?

Summary: The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that.
 

Origins of photosynthesis in plants dated to 1.25 billion years ago

The world’s oldest algae fossils are a billion years old, according to a new analysis by earth scientists. Based on this finding, the researchers also estimate that the basis for photosynthesis in today’s plants was set in place 1.25 billion years ago.

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 for comparison:  Energy as information and constrained endogenous RNA interference (video)
For contrast, Philip Ball separates the origin of photosynthesis in plants from the origin of bioluminescence in bacteria in the ocean.
See: Water is an active matrix of life for cell and molecular biology

1) Water is a complex fluid in its own right (4, 5), and Darwinian adaptation to a complex milieu might be expected to generate much the same kind of enmeshing and interplay of the biological and environmental at the molecular scale that we find at higher levels of life’s organizational hierarchy.

Higher levels of organization are no different than other levels of organization. Organization is organization. But Philip Ball is a deceptive journalist. Neo-Darwinian evolution becomes Darwinian adaptation, which links the sun’s anti-entropic virucidal energy from feedback loops and the physiology of pheromone-controlled reproduction to microRNA-mediated autophagy and biophysically constrained viral latency in species from microbes to human. That causes the biologically uniformed journalist to claim:

2) All of this touches on the astrobiological question mentioned at the outset: should we, like Henderson (88) in 1913, regard water as uniquely “biophilic” and “fit” to act as life’s matrix?

There is no astrobiological question.  See the comments section on Understanding and accounting for relational context is critical for social neuroscience
George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
I wrote:  Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).
Philip Ball has since changed the clear evolutionary trail that links the sense of smell to ecological adaptation. Ecological variation links the creation of enzymes that metabolize food and drugs to his claim about  Darwinian adaptation.
See also for a recent representation of his word-play: Quantum common sense

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

There are stark difference in his claims about a Universe that is always looking that can be compared via claims about the creation of a universe in which viral latency is biophysically constrained by feedback loops. The feedback loops link food odors and pheromones from the physiology of reproduction in all living genera to all biodiversity via autophagy and the microRNA-mediated creation of supercoiled DNA.
In the spirit of the Christmas season and an attempt to stop the pseudoscientific nonsense touted by biologically uniformed theorists and journalists like Philip Ball, see: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2 (video excerpt <2 minutes long)
Remember, Santa Claus (or someone like him) is coming soon. Philip Ball may not be prepared for that. He has been a very bad boy. At the same time that President Trump, who tries his best to be good, has been accused of censorship and compared to Hitler.  I do not think that President Trump would try to change neo-Darwinian evolution to Darwinian adaptation without mentioning how the speed of light on contact with water changes everything.
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … 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.
All the theories can be linked via facts to creationist science that has been supported with experimental evidence of biophysically constrained viral latency as presciently foretold by
1) Schrodinger,
2) Feynman,
3) Dobzhansky
4) McEwen,
and by
5) Eshel Ben-Jacob, who wrote: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment 
Note his use of the term adaptability. It may have led Philip Ball to change Darwinian evolution to Darwinian adaptation.
See also: Learning from Bacteria about Natural Information Processing

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

See also: QuEBS 2018: Workshop on Quantum Effects in Biological Systems  has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that. If Philip Ball just realized that, he knows he has a long-standing problem with misrepresentations of  top-down causation. In any case, it is important to know that he has forced all theorists and journalists to acknowledge the likelihood that Santa Claus is not just a figment of a child-like imagination, and that the creation of sunlight must be linked from its contact with water to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency in all living genera.
 

For God and Country

Trump challenges the CDC to remember 9/11

Synopsis: If you do not understand the experimentally established facts… use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condescending,  you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA (2015)
Federal Officials and Scientists Respond to Purported CDC Word Ban

…it seems that The Scientist has been highjacked by people that believes that science is fighting Republicans and promoting liberal ideas, right or wrong. For those that were not even born then, most of the advances in medicine and biology occurred during the war of cancer that President Richard Nixon initiated and supported. –dmarciani

Since then, the evolved use of meaningless words, such as evolved, and the use of meaningless phrases by the Center for Disease Control (CDC) has left the citizens of the United States of America (USA) comparatively unprotected from the forthcoming world-wide viral apocalypse. The last one (in 1918) killed ~50 million people.
See: Bill Gates warns that a new kind of terrorism could be coming, and the ‘potential damage is very, very huge’
The biologically uninformed masses know nothing about how viruses kill, or how fast they kill.  Most people know little or nothing about viruses in vaccines, which may be slow killers. That explains why, on the eve of the 100th anniversary of the year of the 1918 viral terror, the Trump administration is being criticized by non-scientists and pseudoscientists. Researchers who are biologically uniformed science idiots have helped to bankrupt the economy of the USA by submitting proposals for research that include meaningless words and phrases. The biologically uninformed masses (who are not idiots) have not learned the difference between pseudoscience and science, because they have been taught to believe in mutation-driven evolution. The difference between a scientific truth about ecological varaiation and ecological adaptation for comparison to pseudoscientific nonsense can be placed into the context of words, such as: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender”
With one exception, none of these words or phrases has anything to do with the purpose of the CDC, which is largely to protect the USA from virus-driven pathology. For comparison, the difference between food energy-dependent amino acid substitutions and mutations, which are caused by the virus-driven theft of quantized energy-as-information, clearly shows why USA Patriots for Donald Trump want to change what’s happening at the CDC.
See also: Trump administration forbids CDC officials from using 7 words and phrases

The claims of Trump-haters cut to the heart of the disrespect some people show for the President of the USA — and also the disrespect they show for the serious scientists who support him. As a medical laboratory scientist, I can point out the difference that one letter in one word makes to help other USA Patriots for Donald Trump understand what is known about how to protect us all from the next viral apocaplyse.
 
 
WORD→WORE→GORE→GONE→GENE. Implicit in this analogy is the idea that epistasis constrains evolution—for example, the original parent sequence does not tolerate three of the four eventual changes, as GORD, WERD and WOND are not words.
 
Serious scientists know that proteins do not evolve and that viruses do not automagically mutate! Similarly, the serious scientists known that new words, such as GORD, WERD and WOND are not created outside the context of biophysically constrained viral latency. Simply put, new words are not created, and new genes are not created from changes in base pairs outside the context of biophysically constrained viral latency at the level of energy-dependent base editing of food energy-dependent ACTG-linked changes in amino acid substitutions.
 
 
Trump knows that the CDC has virtually ignored the facts about food energy-dependent amino acid substitutions via the use of these meaningless words: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender.”

In the language of serious scientists, these words cannot be linked to what happens when the virus-driven theft of quantized energy causes a change in one base pair that leads to one amino acid substitution in a virus. Simply put, the change in the virus is linked to constraint breaking mutations. And the change in a virus causes all pathology in all cells of all hosts. Eventually, all human hosts die from the virus-driven degradation of messenger RNA.

Trump knows that. He also knows that viruses cause suicide and glioblastoma in veterans who have served overseas. (SARCASM ALERT: That does not mean he is required to tell John McCain.)  But, the facts have been discussed in the context of articles published in the American Legion Magazine.

It is a wonder that everyone does not know about the virus-driven activation of the death gene, since the death gene was discovered about 20 years ago by researchers at Abcam. Since then the discovery has been linked to this report:  Redox-sensitive alteration of replisome architecture safeguards genome integrity.

See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene.

Whose going to explain how John McCain gets cured — if he is not sacrificed for the sake of the CDC?

If you are easily bored by details but want to learn about what science advisors are telling President Trump, see: Epigenetic modifications poster (Just kidding. If you are bored by the details you won’t look at the details in the poster.) Instead, you are more likely to compare the President of the United States to Hitler, when Trump knows enough about epigenetics to try and help all serious scientists to protect us from the next viral apocalypse, and to protect us from the practice of corporate medicine, which is an assault on our freedom.

Epistasis biophysically constrains viral latency. The constraints are food energy-dependent and pheromone-controlled. All serious scientists have known that since this article was published in 1994. [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

Two of Eugene Daev’s subsequent works cited my award-winning publications, yet I have been unfriended on Facebook by many who will continue to not face the facts known to Trump and to all serious scientists in the world.

See for example: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014)

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also:  Effect of two pyrazine-containing chemosignals on cells of bone marrow and testes in male house mice (Mus musculus L.)

The induction of genetic instability leading to a higher genetic heterogeneity in cells of vital tissues and organs may differentially change
the fitness of animals and their progeny. Such olfactory effects can affect rates of microevolutionary transformations [5]. With regard to the conservatism and the significant role of the chemical communication in a wide range of mammals, including Homo sapiens [25], we believe extremely promising the study of genetic mechanisms underlying regulation of reproduction and immunity by volatiles that work through the olfactory system.

25 is Kohl, J.V., The Mind’s Eyes, J. Psychol. Human Sexual., 2007, vol. 18, pp. 313–369. (Concurrently published as this award-winning book chapter from the Handbook of the Evolution of Human Sexuality: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences.)
My former FB friends and others have the freedom to claim that I am a crank, because veterans suffered and died to protect your freedom.
See for contrast:  One crank dies, another rises to take his place
I have the freedom to continue to defend the country from the claims of biologically uniformed science idiots (i.e., PZ Myers) and anyone who compares Trump to Hitler.

BANNED: CDC Gets List Of ‘Forbidden Words’ From The Trump Administration

Activists immediately accused the Administration of censorship, even hysterically comparing the Administration’s move to Orwell’s “1984” and Adolf Hitler’s efforts to control information in Nazi Germany.

Despite the CDC’s own director, Dr. Brenda Fitzgerald, insisting the ban did not extend beyond the scope of a handful of budget documents, it was immediately clear to Democrats that the Trump Administration was moving to throttle all scientific research.

Find out who might benefit from a move to throttle all scientific research.
See: Alphagenomix.com and download this sample report. On page 19, the interpretation of results is placed into the context of the food energy-dependent creation of enzymes that are altered by drug therapies. The Trump administration was virtually forced to alter the funding process at CDC by the fact that Jack Szostak’s works with others led to retractions. They thought enzymes could create themselves. Two retractions in 10 years led to the embarrassment of all biologically uninformed theorists.
See “Retraction watch”

  1. A Nobel Laureate has retracted a 2016 paper in Nature Chemistry that explored the origins of life on earth, after discovering the main conclusions were not correct.
  2. In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

The problem with ridiculous complacency-based beliefs has plagued serious scientists for decades. It was recently placed into the context of claims made by the former President of the USA.

Obama warns of complacency, notes rise of Hitler

Despite the democracy of the Weimar Republic, Adolph Hitler rose to power, he continued.

“Sixty million people died. … So, you’ve got to pay attention. And vote.”

While some could see the remark as a veiled jab at President Trump, Obama did not mention Trump by name during the event, according to the newspaper.

Now, the claims others are making link Obama’s claims to complaints about the fact that Trump took actions against the misinformation coming from the CDC. The complaints are predictably linked to Hitler’s censorship via: Godwin’s Law 

(or Godwin’s rule of Hitler analogies)[1][2] is an Internet adage that asserts that “As an online discussion grows longer, the probability of a comparison involving Hitler approaches 1”;[2][3] that is, if an online discussion (regardless of topic or scope) goes on long enough, sooner or later someone will compare someone or something to Adolf Hitler or his deeds.

The former President of the USA was caught in a thinly veiled attack on President Trump, and that attack was based on Obama’s ignorance — or based on his motives. What motives? Godwin’s Law existe only the context of pseudoscientific nonsense. That nonsense includes nothing known to the serious scientists who are physicists, chemists, biologists, or polymaths ( e.g., some medical laboratory scientists).
See for comparison: Caught in the act: Papillomaviruses promote non-melanoma skin cancer November 30, 2017

…papillomaviruses associated with UV light promote the development of non-melanoma skin cancer. The investigators provide an explanation why the viruses can be detected in benign human cancer precursors but not in advanced carcinoma.

Everyone is infected with skin-typical (“cutaneous”) human papillomaviruses (HPV) at some point in their lives, usually in early childhood already. In healthy people, the immune system can fight off the viruses, but this often changes in older age.

Those claims about biophysically constrained viral latency were used as the basis for development and use of the HPV vaccine at a time when all serious scientists knew this: “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.” Did I mention that before more than 60 times? See: Search Results for “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site”
The anti-entropic effect of virucidal sunlight links RNA-mediated amino acid substitutions to healthy longevity. That fact was presciently detailed in “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.) (pp. 73 and 74)

The fact that virucidal light links the food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction to epistasis was placed into the context of this 2016 video representation:
What is life when it is not protected from virus driven entropy (6:37) Published on 30 Mar 2016

Abstract:

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

If you do not understand the experimentally established facts from this presentation, please use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condesending,  you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA.
All structural diversity is energy-dependent and the pheromone-controlled physiology of reproduction links feedback loops from biophysically constrained viral latency to healthy longevity in all living genera.

See also:
Workshop on Quantum Effects in Biological Systems has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
The CDC has failed to link light-harvesting in biological systems from excitons to protection of organized genomes from the virus-driven degradation of messenger RNA in species from bacteria to humans.
That is why Trump is again being compared to Hitler. The biologically uninformed masses failed to perceive the CDC’s censorship. The CDC censorship of works published by serious scientists who have linked physics, chemistry and biology to healthy longevity via the anti-entropic energy-dependent creation of RNA and enzymes has nearly bankrupted the USA due to the costs of health care.
Who will admit that they were fooled by the use of words? Most people think they are more intelligent than that. But most intelligent people can be fooled by pseudoscientists if the pseudoscientists claim to have reached a consensus. But, what other countries base their healthcare policies on the consensus about theories of neo-Darwinists and “Big Bang” cosmologists? What other agencies can be compared to the CDC and our NIH?
See also: Science’s credibility crisis: why it will get worse before it can get better 

Several other instances of bad science have gained attention in the media. The problems in “priming research”, relevant to marketing and advertising, prompted Nobel Prize winner Daniel Kahneman to issue a publicised statement of concern about the wave of failed replication.

And a study on “power poses”, which claimed that body posture influences a person’s hormones level and “feelings of power” went first viral on TED when it was published – then again when its replication failed.

We are observing two new phenomena. On the one hand doubt is shed on the quality of entire scientific fields or sub-fields. On the other this doubt is played out in the open, in the media and blogosphere.

I dedicate this effort from the blogosphere to an attempt to reduce the tensions among those who have offered their overwhelming support for the efforts of the American Legion and the American Legion Riders who ride for God and Country.
See also The American Legion Magazine. The December 2017 issue contains another article about the stress-linked reactivation of viruses. This time its about the virus that causes shingles. When the issue is available online, see “Reactivation” by Beth W. Orenstein, and link biophysically constrained viral latency to healthy longevity via the food you eat and the pheromone-controlled physiology of reproduction.  Ask yourself “What would President Trump do?” And remember, your donations to the American Legion don not support corporate medical practices. They are used to help those who served their country and lived to continue protecting your freedom. Remember them, and everyone who has ever died trying to protect others.
 
–by Wade Youmans (Read 9/09/17 before the 9/11 Memorial Ride of the American Legion Riders–pictured above)
Remembrance
It is a moral obligation, yea indeed, a most solemn moral and spiritual duty.
To remember.
To remember is to hold fast to that which is truly important, that which is precious in the wisdom of the heart and mind.
By remembering and reflecting, upon things, objects, individual persons, anything material and physical, Which is no more, that which is no more in the mortal sense is yet sustained and can endure.
Far better to remember and reflect, even if that is painful for the heart and mind.
To forget, to blissfully disregard and discard, is a disservice to that which is gone, and ’tis a disservice to one’s own heart and mind.
For remembrance is a needful, essential endeavor for the vitality of the heart and mind, for the whole of the human spirit.

See also: ‘Whatever it took to save lives’ 

Black chicken wire over the bus windows. The odor, the heat, the tropical humidity.

“All the wounded are in the emergency room. They’re sending these sick guys to my unit. They were dehydrated. They were dirty. There was vomit. Wounds weren’t visible, but their suffering was acute and there wouldn’t be any Purple Hearts passed out for their near-death experience.

Nature’s magic helps veterans in transition

Nature’s magic” was placed into the context of the evolution of differences in H2. See: https://phys.org/news/2017-11-chemists-reveal-mechanism-dihydrogen-production.html

 
Excerpt: “This work is a critical step toward a mechanistic understanding of the nitrogenase enzyme. There is still work to be done to understand the mechanism of the other H2 evolution process that leads to N2 binding, activation, and reduction to NH3.”
 
Please help serious scientists stop those who are still touting the magic of evolution by learning how autophagy helps to protect all organized genomes from the virus-driven degradation of messenger RNA.
 

Autophagy is the link from the sun’s anti-entropic virucidal energy to the creation of enzymes and the physiology of pheromone-controlled reproduction, which has been linked to all biophysically constrained biodiversity.  For example, food energy links error-free DNA repair to all healthy longevity and the virus-driven theft of quantized energy links mutations to all pathology.

Keep in mind that as a member of the American Legion Riders, I ride for God and Country, not for Nature’s magic. Also, with 40 years experience as a medical laboratory scientist, I learned enough about the potential of hydrogen (pH) to realize that the potential did not “evolve.”

See also: https://aeon.co/essays/science-and-metaphysics-must-work-together-to-answer-lifes-deepest-questions
Metaphysics of metamorphosis

The swarming, ever-changing character of the living world challenges our deepest assumptions about the nature of reality

Excerpt: …‘physiologists in general never trouble themselves about such things because they suppose themselves to be above “metaphysics” when in fact they are only a very little above it – being up to the neck in it’.
Those who have failed to link the metaphysics of energy to biophysically constrained viral latency, have failed to link the virus-driven theft of quantized energy to the death gene by what is known to serious scientists.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166303/
When a member of the American Legion suffers and prematurely dies from the same virus-caused pathology that has not yet claimed the life of John McCain, ask yourself what is known about the life and death of all veterans who served overseas. Stop letting politics kill more veterans.
Support the Trump administrations efforts to make America great, again. They can do it without your support, but that probably will not end well for you. This is not about Trump’s behavior or about the behavior of anyone else.

An antagonist from Canada complained about Trump’s so-called censorship of the CDC and said his “tactics” didn’t work in Canada. I claim that similar tactics are always effective. The truth hurts but it only hurts those who believed they could keep touting pseudoscientific nonsense. Not only did Canadians get rid of the “transgender” nonsense, they helped to nearly stop James Cantor from promoting pedophilia as another form of sexual orientation.
 

See: Infamous Reparative Therapy Clinic For Transgender Youth Set To Close
Two years ago, I wrote:

The misrepresentations of the issues are out of control.

Excerpt: GIC’s “developmental model” was backwards. It blamed symptoms like depression and anxiety on the gender non-conforming behavior itself, rather than on the stigma attached to it or the conflict of not being able to fulfill one’s gender identity. This philosophy allowed the clinic to claim it was treating these negative mental health outcomes without affirming the trans behavior.”

My comment: They never had a developmental model. At best they had a philosophy based on ridiculous theories that never included anything known to serious scientists about the biological basis of cell type differentiation. These clinicians, like most sex researchers, never learned anything about links from nutrient-dependent RNA-mediated events to behavior.

For example, RNA-directed DNA methylation and RNA-mediated amino acid substitutions link sexual orientation in yeasts to sex differences in the morphological and the behavioral phenotypes of humans via conserved molecular mechanisms. We detailed that fact in the context of our 1996 Hormones and Behavior review.

Despite the extension of our molecular epigenetics section and the model of hormone-organized and hormone-activated developmental differences across species from insects to other primates, psychologists and many psychiatrists continued to link their philosophies and theories to damaging practices.

Like the practice of medicine, outcomes are more predictable if they are based on what is known about RNA-mediated cell type differences. Fixation of nutrient-dependent RNA-mediated amino acid substitutions in some patient populations compared to others allows clinicians to predict whether a medication will do more harm than good in the context of what is known about pharmacogenomics and precision medicine. Fixation of RNA-amino acid substitutions in individuals of different species is also linked to their nutrient-dependent pheromone-controlled physiology of reproductive sexual behavior in species from microbes to man.

That fact has been known to serious scientists for several decades. It is the reason that other careers will be ruined until people like Ken Zucker accept the our model of RNA-mediated cell type differentiation instead of continuing to ignore details of the biologically-based development of personal preferences published in From Fertilization to Adult Sexual Behavior (1996).

 

 

 
 
 
 

 

 

Cases of Cytosis

Narcissistic egomaniacal and deadly denial of autophagy

Summary: Viral latency is food energy-dependent and pheromone-controlled in the context of autophagy, which protects organisms from the virus-driven degradation of messenger RNA.

Workshop on Quantum Effects in Biological Systemshas established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Pseudoscientists refuse to speak the “must-talk language” of biological light-harvesting systems. When was the last time you heard a theorist mention excitons?

Light-harvesting systems link the creation of the sun’s anti-entropic virucidal energy (Schrodinger’s negentropy, 1944 ) from the creation of food energy to the physiology of pheromone-controlled reproduction in all living genera via autophagy, which protects all organized genomes from virus-driven entropy.

See: Structural diversity of supercoiled DNA

…DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

They linked energy-dependent changes in base pairs from supercoiled DNA to all biodiversity via cryo-ET, which helped to support their atomistic insight.

See for comparison: Structural Dynamics and Mechanochemical Coupling in DNA Gyrase

Gyrase… harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex.

Simply put, gyrase introduces the pathology of virus-driven negative supercoiling. Discussion with one of the co-authors, namely A.C. Parente, led me to make this claim in frustration:

No one who places “Plant Energy Biology” into the context of “Evolutionary Biology” will understand my model of the Mechanisms and Functional Diversity of Macromolecular Remodeling by ATP-Dependent Motors [autophagy]. It starts with the creation of energy and explains how virus-driven energy theft is linked to all pathology via conserved molecular mechanisms in species from microbes to humans. The mechanisms link energy-dependent changes in angstroms to ecosystems via what is known about autophagy. The energy is not destroyed. Viruses use it to replicate.

Parente, and other like her, have tried to present their findings in the context of evolution, which is why their experimental evidence makes no sense to serious scientists. Nothing except natural selection for energy-dependent codon optimality can link the energy-dependent physiology of pheromone-controlled reproduction from feedback loops to autophagy, which biophysically constrains viral latency.  Simply put, viral latency is food energy-dependent and pheromone-controlled.

Serious scientists have detailed that fact since 1994. See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: Combinatorial effects of odorants on mouse behavior

In summary, our findings indicate that the innate effect of an odorant on behavior can be context-dependent and subject to modification by other odorants. It is conceivable that signals derived from a single receptor can elicit innate behavioral attraction or aversion and involve hard-wired neural circuits. However, our studies indicate that these behavioral responses can be modulated by sensory inputs from other receptors via the interactions of signals derived from the different receptors within the brain. In short, innate behavioral output can be influenced by interactions within the brain among signals derived from different receptors in the nose.

See also my refutation of neo-Darwinian pseudoscientific nonsense: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

See for comparison, on 7/25/13, psychiatrist Jay R. Feierman wrote:

“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.”

In my opinion, Jay R. Feierman goes far beyond the claims of other narcissistic egomaniacs, like Parente, who think they can use evolution as an explanation for all biophysically constrained biodiversity. Other egomaniacs also attempt to beat serious scientists into submission with ridiculous claims that the serious scientists do not understand Darwinian biological evolution. But see the 2009 and 2017 retractions of Jack Szostak’s claims about the evolution of amino acids. Please use the retractions to help stop the pseudoscientific nonsense touted by biologically uninformed theorists.

I am a medical laboratory scientist who knows that Darwin started with his food energy-dependent “conditions of life.” He presciently linked natural selection for energy-dependent codon optimality from the “conditions of life” to the physiology of pheromone-controlled reproduction and all biodiversity in every species he examined. He could have done no better if he knew anything about genetics and focused on one model organism of fixed amino acid substitutions, but that fact has changed.

See for example: Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect

My comment: RNA-mediated associative mechanisms Posted by jvkohl on 14 Dec 2016 at 16:36 GMT

Two more articles have been reported that link the energy-dependent RNA-mediated supercoiling of DNA to all healthy longevity. The two articles also link virus-driven energy theft to negative supercoiling in bacteria and all pathology in species from archaea to humans via the transgenerational epigenetic inheritance of Zika virus-damaged DNA.

See: DNA Supercoiling Combats Environmental Challenges

See also: Honeybee memories: another piece of the Alzheimer’s puzzle?

The honeybee model organism links nutrient energy-dependent supercoiling to the pheromone-controlled physiology of reproduction in species from microbes to humans via the conserved molecular mechanisms that link autophagy to chromosomal rearrangements and all biodiversity. See the works of Nobel Laureates Thomas Hunt Morgan, Erwin Schrodinger, Linda Buck, Yoshinori Ohsumi, and Ben Feringa to help establish the facts about cell type differentiation in your future publications.

Competing interests declared: I own these domains: Pheromones.com, RNA-mediated.com and Autophagypro.com They are among others that I own and they collectively link what is currently known about energy-dependent cell type differentiation to all biodiversity via conserved molecular mechanisms.

With the launch of Autophagy.pro, I am considering the sale of the domain Autophagypro.com to someone with commercial interests.  Let the bidding begin, based on the claims of others with commercial interests who have failed to link pheromones to the prevention of pathology.
See for example: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
See also: Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys
reported as:  Estrogen discovery could shed new light on fertility problems

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

“It’s a feedback loop…

See also: Feedback loops link odor and pheromone signaling with reproduction
See also: Olfaction Warps Visual Time Perception

…we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone
Re: The deadly denial of theorists who failed to examine the stress-linked activation of the death gene to glioblastoma.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
and A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases 
Also, please note: I purchased the domain name: Subatomic.pro because the microRNA regulation of metabolic diseases links electrons to ecosystems in all living genera by protecting individuals and species from the degradation of their messenger RNA, which links mutations to all pathology.

See also: Combating Evolution to Fight Disease

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.

Exposing the 2nd Law to more ridicule (1)

Summary: Experiment demonstrates quantum mechanical effects from biological system

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him – if ever again he reasserted the facts.

After 1944, Richard P. Feynman took a stand against the human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

New Genes and Functional Innovation in Mammals 21 July 2017

We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

Reported as: Genes identified that distinguish mammals from other animals  4 December 2017

They have also identified antimicrobial peptides, which participate in the body’s defence against pathogens.

The energy-dependent creation of “…antimicrobial peptides, which participate in the body’s defence against pathogens” already was linked from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency, which protects all organized genomes from the degradation of messenger RNA. False assumptions about entropy for comparison to experimental evidence of the de novo creation of genes have been placed into the context of the “arrow of time.”

Scientists Experimentally Demonstrate the “Reversal of the Arrow of Time” 
4 December 2017

Through a remarkable experiment, an international team of scientists has found that it is possible to reverse the arrow of time without violating the second law of thermodynamics.

Pseudoscientists need no longer consider anything that cannot be linked to this experimental evidence of top-down energy-dependent causation and biophysically constrained viral latency/genomic entropy. Thank God, nothing but experimental evidence of the anti-entropic virucidal energy of sunlight has ever been considered by those who have linked feedback loops from odors and pheromones to all biodiversity on Earth.
See: 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.

Quantum effects in biological light-harvesting systems have been linked from the de novo creation of sunlight to answers about all biophysically constrained biodiversity via Schrodinger’s 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.) (pp. 73 and 74)

See for comparison: 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.

See also: What is life when it is not protected from virus driven entropy (video) 30 Mar 2016

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.

See for comparison: On causal roles and selected effects: our genome is mostly junk December 5, 2017

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable.

Conclusion:

That is to say, many of our uniquely human traits are probably the contingent products of drift and historical accidents—they make us us, but were not selected to have that, or necessarily any, effect. So we are back to Ohno’s conundrum. If lungfishes have junk, or at the least extraordinarily weakly or diffusely functional DNA in their genomes, why is it that we think we do not?

The concept of “junk DNA” is inconsistent with anything known to serious scientists about energy-dependent biophysically constrained viral latency.  Feedback loops link top-down causation to the pheromone-controlled physiology of reproduction via RNA-mediated fixation of amino acid substitutions in the organized genomes of all living genera.
See: Understanding and accounting for relational context is critical for social neuroscience
My comment: New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: [Top-down causation: an integrating theme within and across the sciences?] http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
See also: What Bacteria Can Tell Us About Human Evolution December 5, 2017

See for comparison: Learning from Bacteria about Natural Information Processing
The link from biological light-harvesting systems to the pheromone-controlled physiology of reproduction in species from microbes to humans exemplifies everything known to serious scientists about biophysically constrained viral latency, which links ecological variation to ecological adaptations in the context of physics, chemistry, and molecular epigenetics. The facts refute all neo-Darwinian nonsense and the nonsense touted by “Big Bang” cosmologists.
Sunlight is quantized energy as information and it is virucidal.
See also: Generation of photonic entanglement in green fluorescent proteins

…our prepared state is free from environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. Our photonic entanglement generation and characterization indicate that the SFWM process in EGFP is a promising quantum process for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials.

Reported as: Experiment demonstrates quantum mechanical effects from biological system

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology.

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him.
After 1944, Richard P. Feynman took a stand against human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

See for comparison: Microbiome-Centric Human Health: A Call for Systems Biology
Stop calling for more microbiome-centric systems biology and link what is known about energy-dependent changes in electrons to ecosystems in all living genera via pheromone-controlled biophysically constrained viral latency.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

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

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

From base editing to RNA editing

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

“Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist.

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
See for comparison: All about that base (video parody)
See also: RNA Editing Possible with CRISPR-Cas13

Introducing specific sequence changes into RNA molecules could allow researchers to answer questions about alternative splicing mechanisms, translation, and even editing, he says. “There’s a lot of scope.”

The entirety of that scope was addressed in the context of energy-dependent RNA-mediated cell type differentiation in our section on molecular epigenetics from this 1996 Hormones and Behavior review. 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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
All biophysically constrained RNA-mediated energy-dependent cell type differentiation has since been linked from the pheromone-controlled physiology of reproduction to supercoiled DNA via the fixation of amino acid substitutions and chromosomal rearrangements.
The facts about the amino acid substitutions in the context of transgenerational epigenetic inheritance link electrons to ecosystems via the cryo-EM technology that won the 2017 Nobel Prize in Chemistry.
See: Chemists know (video parody)
See also:

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

Long-term adaptation replaces evolution (2)

The food energy-dependent “doubling up” on ‘junk DNA’ is biophysically constrained by the physiology of pheromone-controlled reproduction. The metabolism of food to species-specific pheromones links the conserved molecular mechanisms of RNA-mediated cell type differentiation in all individuals of all living genera to healthy longevity via what is known about amino acid substitutions in supercoiled DNA, which link energy-dependent changes in chirality to autophagy.

See: It’s all about that base

The virus-driven degradation of messenger RNA in bacteria links top-down causation to what happens to archaea and L-forms in the context of the viral hecatomb, which links the destruction of G protein-coupled receptors to all pathology because the de novo creation of G protein-coupled receptors links the creation of the sense of smell to all biodiversity.

Our ability to detect differences in amino acid substitutions in the blood has been linked to the ability of flies to find food and to reproduce via the physiology of food-energy-dependent pheromone-controlled reproduction.

See: A mammalian blood odor component serves as an approach-avoidance cue across phylum border – from flies to humans
See also:

Adaptive evolution by spontaneous domain fusion and protein relocalization

Phenotypic heterogeneity promotes adaptive evolution

My 2013 model of energy-dependent ecological adaptations: Nutrient-dependent/pheromone-controlled adaptive evolution: a model refuted neo-Darwinian pseudoscientific nonsense. That that model is being revisited each day that another publication is added to those that link the energy-dependent de novo creation of microRNAs to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. See: microRNA

For example:Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

See also:

Overview of microRNA biology. Mohr AM et al. Semin Liver Dis. (2015)

MicroRNA Therapeutics: the Next Magic Bullet? Simonson B et al. Mini Rev Med Chem. (2015)

MicroRNAs in cancer: biomarkers, functions and therapy. Hayes J et al. Trends Mol Med. (2014)