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

The eternal significance of microRNAs (5)

Excerpt: Researchers in South Korea, for example, have reminded the God-less Communist dictator of North Korea that one microRNA-mediated amino acid substitution in the influenza B virus could decimate the human populations that he thinks he rules.
Conclusion: Conserved energy biophysically constrains viral latency.

Ridiculously ignorant objections to my publication in what others claim is a predatory journal can be compared to my objection to publication of this article in PNAS.

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk
1) They linked environmental selection to the frequency of the EDAR V370A variant in the mouse model via positive selection for modulation of thermoregulatory sweating.
2) They linked environmental selection to similarities in human populations in North Asia, East Asia, and the New World. But they virtually ignored the mouse model of food energy-dependent pheromone-controlled biophysically constrained ecological adaptation.
I linked the same food energy-dependent pheromone-controlled base pair change and microRNA-mediated fixation of the same amino acid substitution to all biodiversity in all living genera via feedback loops. See: Feedback loops link odor and pheromone signaling with reproduction

Others see what passes peer-review published in journals that support the expense of efforts made by pseudoscientists and other theorists, but they claim that the OMICS journals are predatory. I claim that pseudoscientists and other theorists do not know the difference between predation and sympatric speciation because they place predation into the context of evolved biodiversity.

For comparison see: Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization, according to new research from investigators in Sweden and Germany.

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

Reported as:

“The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes. A clear-cut result like that was not what he had necessarily expected.

Neo-Darwinian theorists and other biologically uniformed pseudoscientists have failed to use any common sense in attempts to link what organisms eat from the physiology of reproduction to biophysically constrained biodiversity.  For comparison, serious scientists have forced the denuclearization of North Korea by reminding others to start with what is known about how food energy-dependent autophagy protects all life on Earth from the virus-driven degradation of messenger RNA.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…as a reviewer, it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 …appropriate assays depend in part on the question being asked and the system being used.

Researchers in South Korea, for example, have reminded the God-less Communist dictator of North Korea that one microRNA-mediated amino acid substitution in the influenza B virus could decimate the human populations that he thinks he rules.

See: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

A protein model is built into an electron density map, amino acid by amino acid. The result is a snapshot of the protein or protein complex at work. Image courtesy of Dr Sebastian Guettler.

The "walking fish" walks straight from quantum physics to quantum souls (2)

Summary: Cell fate conversion is food energy-dependent and pheromone-controlled in the context of the physiology of reproduction and autophagy, which links biophysically constrained viral latency to the differences in C. elegans and P. pacificus, a predatory nematode with teeth.

Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans 1/01/2018

Summary

This protocol describes how to study cellular processes during cell fate conversion in Caenorhabditis elegans in vivo. Using transgenic animals,allowing heat-shock promoter-driven overexpression of the neuron fate-inducing transcription factorCHE-1 and RNAi-mediated depletion of the chromatin-regulating factor LIN-53germ cell to neuron reprogramming can be observed in vivo.

Cell fate conversion is food energy-dependent and pheromone-controlled in the context of the physiology of reproduction and autophagy, which links biophysically constrained viral latency to the differences in C. elegans and P. pacificus, a predatory nematode with teeth.
System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
Food energy arises only in the context of the creation of  The Immensity of the milky way…(video)

The facts that link sunlight on contact with water in this video from pheromone-controlled biophysically constrained viral latency to all biodiversity on Earth via the physiology of reproduction have been largely ignored since the time this article was published [in Russian] in 1994. [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] https://www.ncbi.nlm.nih.gov/pubmed/7995515

Non-human primates are the best example of how subatomic particles protect humans from all pathology in the context of food energy-dependent RNA-mediated cell type differentiation that links microRNAs to fixation of amino acid substitutions that differentiate all cell types in all individuals of all living genera.
See: Five reasons we’re excited by how structural biology is advancing cancer research Posted on 15 June, 2017

A protein model is built into an electron density map, amino acid by amino acid. The result is a snapshot of the protein or protein complex at work. Image courtesy of Dr Sebastian Guettler.

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
See also: One amino acid substitution differentiates humans and chimpanzees from gorillas.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

Humans And Chimps Differ At Level Of Gene Splicing (2007)
Comic relief for the biologically informed. Jon Stewart interviews Greg Bear
Comic relief for seniors.
For serious scientists: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins

Using X-ray crystallography, we show that cryptophyte PBPs adopt one of two quaternary structures, open or closed. The key feature of the closed form is the juxtaposition of two central chromophores resulting in excitonic coupling. The switch between forms is ascribed to the insertion of a single amino acid in the open-form proteins. Thus, PBP quaternary structure controls excitonic coupling and the mechanism of light harvesting. Comparing organisms with these two distinct proteins will reveal the role of quantum coherence in photosynthesis.

The fact that a single amino acid substitution links energy-dependent changes in base pairs from electrons to ecosystems via the physiology of reproduction in all living genera continues to be ignored by pseudoscientists and all theorists.
For comparison see: 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.

 
rp_levels-of-organization.jpg

Effects on invertebrate GnRH and affects on primate behavior

Introduction: Energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution have again been linked to hormone-organized and hormone-activated behaviors by the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. The practical application of those details has been reported in the context of this article, published in the New England Journal of Medicine.

Effects of Testosterone Treatment in Older Men

Daily Diagnosis is emailed each weekday to members of the American Society for Clinical Pathology (ASCP).
Information about the Effects of Testosterone Treatment in Older Men was reported in “ASCP Daily Diagnosis” as:
Testosterone Replacement Gel May Provide Some Benefits To Older Men With Low Testosterone, Study Suggests.

Excerpts:

The AP (2/17, Tanner):  … finding mostly modest improvement in the sex lives, walking strength and mood of a select group of older men.

NBC News (2/17, Fox, Derenowski, Costello)  …points out that that findings “are expected later from four other related studies, which tested the hormone’s effects on mental function, bone density, heart function and anemia.”

See also the reports from the New York Times (2/18, A17, Kolata, Subscription Publication), Forbes (2/17, Weintraub), Medscape (2/17, Tucker), HealthDay (2/17, Thompson), STAT (2/17, Swetlitz), the Pittsburgh Post-Gazette (2/17, Templeton), Reuters (2/17, Emery), the Wall Street Journal (2/17, Beck, Subscription Publication), The Oregonian (2/17, Terry), and the NPR (2/17, Streeter) “Shots” blog.

This is “Big Science” that is not placed into any other context whatsoever. See also, from the New England Journal of Medicine:

On Smell.

The sense of smell links energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to testosterone levels during life history transitions in men.
Excerpt:

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732).  — Lewis Thomas (as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality).

My comment: Gonadotropin-releasing hormone (GnRH) is the link from the sense of smell to testosterone during life history transitions.
See also: From Fertilization to Adult Sexual Behavior (1996)
Excerpt:

For instance, Jakacki, Kelch, Sauder, Lloyd, Hopwood, and Marshall (1982) have shown that prepubertal children secrete luteinizing hormone (LH) and presumably gonadotropin-releasing hormone (GnRH) in a pulsatile manner, well before physical evidence of sexual maturation is apparent. Since the neuroendocrine mechanisms for the control both of gonadal and, in part, of adrenal steroidogenesis are active, if the Gd–H–B model is influenced by social-environmental sensory stimuli before puberty occurs, such stimuli also would be capable of influencing long-term behavior.

Cited in: Testosterone in utero and at birth dictates how stressful experience will affect learning in adulthood
Excerpt:

…the absence of testosterone shortly after birth organizes the ability to acquire trace memories in adulthood and dictates its modulation by stressful experience in females. These effects are generally consistent with those of sexual behaviors, which become masculinized by exposure to testosterone in utero and feminized by its absence shortly after birth (3, 9, 33, 34). Our data suggest that sexually dimorphic effects of emotional experience on cognitive behaviors in adulthood are similarly organized by a relatively brief exposure to testosterone during development.

See also: Feedback loops link odor and pheromone signaling with reproduction (2005)
Excerpt:

Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.  (p 683)

My comment: Additional findings that support claims about how nutrient energy-dependent hydrogen-atom transfer in DNA base pairs in solution are linked from RNA-mediated events to the pheromone-controlled physiology of nematodes and ecological adaptation during life history transitions in humans are included in the reports linked here:
Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
The Gonadotropin Releasing Hormone (GnRH)-Like Molecule in Prosobranch Patella caerulea: Potential Biomarker of Endocrine-Disrupting Compounds in Marine Environments
Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
Summary: The benefits of testosterone therapy for those who are deficient have been placed into a model of biologically-based cause and effect of hormones linked to behavior. The hormones that affect behavior link physics and chemistry to every aspect of metabolic networks and genetic networks that has ever been linked to the physiology of reproduction in all living genera.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

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

See for comparison: Mutation-Driven Evolution
Conclusion:

… genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements, (p. 199).

My comment: The likelihood that anyone  who touts links from constraint-breaking mutations to biodiversity will “… fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding…” can be compared to facts that link “…the future of biological science, centuries ahead…” to what is currently understood about the links from food odors and pheromones to the physiology of reproduction in all vertebrates and invertebrates. The food odors and pheromones link metabolic networks to genetic networks via RNA-mediated events linked to supercoiled DNA that protects all organized genomes from virus-driven entropy. The organized genomes are exemplified in the morphological phenotypes and the behavioral phenotypes of all living genera.
See for example: The Genetics of Society
Excerpt:

For the first time, scientists are investigating the molecules that underlie eusocial behavior at a depth that was previously unimaginable. New, affordable sequencing technologies enable scientists to examine how genes across the entire genome are regulated to generate different caste phenotypes, the roles of DNA methylation and microRNAs in this differential expression, and what proteins are synthesized as a result.

My comment: The molecules that underlie all behavior have already been linked from hydrogen-atom transfer in DNA base pairs in solution via the role that microRNAs play in RNA-directed DNA methylation, which links alternative splicings of pre-mRNA (the microRNAs) to cell type differentiation in all genera via RNA-mediated amino acid substitutions, DNA methylation, the creation of adhesion proteins and the nutrient-dependent pheromone-controlled creation and stability of supercoiled DNA.
See also:  Organizational and activational effects of hormones on insect behavior
Excerpt:

Effects of hormones on brain and behavior occur through three mechanisms: (1) behaviors both organized and activated by hormones, (2) behaviors only organized by hormones, and (3) behaviors only activated by hormones (reviewed in Arnold and Breedlove, 1985; Diamond et al., 1996).”

My comment: Although Gene Robinson cited our 1996 Hormones and Behavior review in the article he co-authored with Elekonich, neither of them has since acknowledged the basis for any of their subsequent claims. Gene Robinson has proceeded to tout the pseudoscientific nonsense of neo-Darwinism at a time when others are trying to eliminate it from any further consideration whatsoever.
See: Molecular evolutionary analyses of insect societies
Excerpt:

Our bee molecular evolution study revealed that genes involved in carbohydrate metabolism are evolving more rapidly in eusocial relative to noneusocial bee lineages and are evolving most rapidly in highly eusocial lineages (21).

My comment: Molecules do not evolve. Hydrogen-atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance to the de novo creation of olfactory receptor genes in all vertebrates and invertebrates. Eusocial lineages do not evolve. Organisms and species adapt via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans via the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 review. That fact shows why the vision Sir Paul Nurse has for the Crick Institute will be skewed by the facts about RNA-mediated cell type differentiation.

See: Vision for the Crick Institute

…you can’t force people to work together, and just putting them in the same room doesn’t mean that is going to happen.

My comment: Gene Robinson, and many others, have pitted themselves against those who have been Combating Evolution to Fight Disease and those who have linked angstroms to ecosystems in all living genera via the Structural diversity of supercoiled DNA.
The vision for the Crick Institute requires cooperation among those who link RNA-mediated epigenetic regulation of gene expression; RNA-mediated gene silencing, RNA-mediated toxicity, RNA-mediated epigenetic heredity, via nutrient-dependent RNA-directed DNA methylation to life history transitions in levels of testosterone and behavior via RNA-mediated amino acid substitutions.
For example, see:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
In the context of Combating Evolution to Fight Disease, especially age-related diseases that link epigenetic effects on hormones to the affects of hormones on behavior via COMT Val158Met or BDNF Val66Met, if you cannot accept the fact that energy-dependent base pair changes link RNA-mediated amino acid substitutions to all biodiversity, you should not consider trying to explain top-down causation to a serious scientist.