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

Lethal virus kills 5 billion people?

Predicting who wins the 2017 Nobel Prizes (2)

Summary: Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Three Americans win Nobel medicine prize for body rhythm work [But they failed to link Americanism to Creationism]
I predicted that Wen Zhou would win for linking the energy-dependent creation of G protein-coupled receptors to all biodiversity via olfaction and the space-time continuum in the context of RNA-mediated cell type differentiation via the physiology of pheromone-controlled reproduction. See: Olfaction Warps Visual Time Perception. 
She returned to China after training in the United States of America, but is a good example of someone who appears to practice Americanism, which is an ideology that appears to be integrated into her research. I do not know what people in China refer to in the context of this ideology.

In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”[3]

After Ben Feringa (Chemistry/chirality) and Yoshinora Ohsumi (Physiology or Medicine/autophagy) won last year, I thought that all gene-centric nonsense would be eliminated. It became perfectly clear that energy-dependent changes in chirality must be linked to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA.
Instead, see:

Excerpt 1) The awardees’ work stems back to 1984, when Rosbash and Hall, who was then also at Brandeis, along with Young isolated the “period gene” in fruit flies. Hall and Rosbash found that a protein encoded by the gene accumulated during the night and degraded during daytime. A decade later, Young discovered another “clock gene.”

Excerpt 2) “The paradigm-shifting discoveries by the laureates established key mechanisms for the biological clock,” the Nobel Assembly said in its prize statement.

See for comparison: The Nobel Prize in Physiology or Medicine 1973 Karl von Frisch, Konrad Lorenz and Nikolaas Tinbergen

for their discoveries concerning organization and elicitation of individual and social behaviour patterns.

The organization and elicitation of individual social patterns of behavior is energy-dependent and it links what organisms eat to the metabolism that links the energy to the physiology of pheromone-controlled reproduction in species from microbes to humans.
Since 1973,  and especially during the past 13 years, there has not been a gene-centric theory that has successful been linked to a paradigm shift. For example, all paradigm-shifting Nobel Prizes in Physiology or Medicine during the past 13 years have linked the energy-dependent creation of ATP and the creation of messenger RNA to protection from the virus-driven energy theft that serious scientists have linked from the degradation of messenger RNA to all pathology.
See for examples:
2016: Yoshinori Ohsumi of Japan for his work on autophagy—a process whereby cells “eat themselves”—which when disrupted can cause Parkinson’s and diabetes.
2015: William Campbell (US citizen born in Ireland) and Satoshi Omura (Japan), Tu Youyou (China) for unlocking treatments for malaria and roundworm.
2014: John O’Keefe (Britain, US), Edvard I. Moser and May-Britt Moser (Norway) for discovering how the brain navigates with an “inner GPS”.
2013: Thomas C. Suedhof (US citizen born in Germany), James E. Rothman and Randy W. Schekman (US) for work on how the cell organises its transport system.
2012: Shinya Yamanaka (Japan) and John B. Gurdon (Britain) for discoveries showing how adult cells can be transformed back into stem cells.
2011: Bruce Beutler (US), Jules Hoffmann (French citizen born in Luxembourg) and Ralph Steinman (Canada) for work on the body’s immune system.
2010: Robert G. Edwards (Britain) for the development of in-vitro fertilisation.
2009: Elizabeth Blackburn (Australia-US), Carol Greider and Jack Szostak (US) for discovering how chromosomes are protected by telomeres, a key factor in the ageing process.
2008: Harald zur Hausen (Germany), Francoise Barre-Sinoussi and Luc Montagnier (France) for work on the viruses causing cervical cancer and AIDS.
2007 Mario R. Capecchi, Sir Martin J. Evans and Oliver Smithies for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.
2006 Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference – gene silencing by double-stranded RNA.
2005 Barry J. Marshall and J. Robin Warren for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease.
2004 Richard Axel (US) and Linda Buck (US) for their discoveries of “odorant receptors and the organization of the olfactory system.
Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Addendum 1)
This morning I spoke with a 10-year veteran who had served in Iraq. He was not happy with the treatment for PTSD that he was receiving from the VA because he and his wife know he is getting worse (e.g., hyper-vigilance and more nightmares).

He has a 20% disability and my antagonists are causing it to get worse with their claims that my life’s works are “bullspit” and/or that “nobody cares.”
How can anyone convince a veteran that people care at a time when most will not take the time to watch a short video like this one?  Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
See for comparison:3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.
Adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.The claim that populations are adaptively configured are nothing more than pseudoscientific nonsense.

If you let our veterans, as individuals, continue to think they are less than human because a mutation or something else causes their failure to adapt to the challenges of life after returning from military service overseas, how will you convince yourself that you are not contributing to the death rate by suicide?

Addendum 2) Las Vegas Shooting: Live Updates (with video)

Other lawmakers woke up to the news and offered thoughts and prayers. Governor Brian Sandoval of Nevada called the shooting a “heinous act of violence.”

All heinous acts of violence are caused by the virus-driven degradation of messenger RNA, not by the natural selection for mutations as claimed in Mutation-Driven Evolution

(2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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

Alternative splicing of pre-mRNA

Epigenetics and autophagy vs mutations and evolution (6)

Bird embryos uncover homology and evolution of the dinosaur ankle


The early formation of the limb skeleton is often assumed to be well known from ‘classic’ published lines of work using traditional techniques and model species. However, it is worth revising this basic information. New methods and better taxon sampling can provide increased detail and substantial revision, with important evolutionary implications. In addition to the fossil record, reliable embryological data from birds are important to understand their evolution from dinosaurs17.

Reported as: The dinosaur ankle re-evolved amphibian-like development in birds

This work has revealed that the ascending process does not develop from either the heel bone or the ankle bone, but from a third element, the intermedium. In the ancient lineage of paleognath birds (such as tinamous, ostriches and kiwis) the intermedium comes closer to the anklebone, producing a dinosaur-like pattern. However, in the other major avian branch (neognaths), which includes most species of living birds, it comes closer to the heel bone; that creates the impression it is a different structure, when it is actually the same. “It puts the final nail in the anti-dinosaur coffin” says Jacques Gauthier, a vertebrate paleontologist and professor at Yale University “The dinosaurian ascending process is retained in all birds, though it has changed its association from ankle to heel bones in neognath birds.”

My comment: The report that an evolutionary process automagically changed as increasing nutrient energy-dependent pheromone-controlled morphological and behavioral phenotypes disappeared and reappeared gives much more credit to the magic of evolution than ever before.

For comparison see: This is an example of energy-dependent virucidal UV fluorescence. It was reported in the context of mutation-driven evolution and the weekend resurrection of the flagellum in Pseudomonas fluorescens. The claim that an irreducibly complex functional structure could be resurrected links the nutrient-dependent pheromone-controlled physiology of reproduction to all differences in morphological and behavioral phenotypes in all living genera. Pseudoscientists, atheists, and ever some researchers who claim to be young earth creationists seem to believe this example of energy-dependent autophagy is an example of autofluorescence.


Insect homology and diversity attributed to mutations

Ancient homology underlies adaptive mimetic diversity across butterflies

Excerpt: “Surprisingly, our results suggest that modulation of this conserved developmental gene has occurred in tandem between these two deeply divergent butterfly lineages, implying an unexpected and remarkable level of predictability in the evolutionary process.”
Reported as: A single evolutionary road may lead to Rome
Excerpt: “Copying errors and genomic viruses directly lead to the wing patterns of these beautiful butterflies,” Gallant said. “It’s these accidents that allow the evolutionary process to move forward. When I look over a field of butterflies, it makes me wonder what types of ‘mistakes’ are happening right now that may lead to important evolutionary changes years from now? What evolutionary processes will we someday be able to predict?”
My comment: Dobzhansky (1964) predicted that bird-watchers and butterfly-collectors would never become serious scientists, and his predictions are still coming true in reports like this one.
Two more generations of researchers have since been taught to believe in a ridiculous theory about mutations, natural selection. and the evolution of biodiversity, which is clearly nutrient-dependent and pheromone-controlled by RNA-mediated events in species from microbes to man. Instead, this group finds that the nutrient-dependent ecological adaptations manifested in the wing morphology of butterflies is caused by mutations that somehow predictably lead to evolution.
Would that be by natural selection — instead of by the nutrient-dependent pheromone-controlled physiology of reproduction? It could be if perturbed protein-folding linked nutrient uptake to increasing organismal complexity. But in all other species from microbes to man the epigenetic landscape is linked to the biophysically-constrained physical landscape of DNA in organized genomes via the pheromone-controlled physiology of reproduction.
Take Darwin’s pigeons, for example, because 1) the EphB2 gene is a strong candidate for the derived head crest phenotype  2) that trait evolved just once and 3) it spread throughout the species. 4) The crest also originates early in development by 5) localized molecular mechanisms and the reversal of feather bud polarity.” See: Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon
Link the EphB2 gene and nutrient-dependent amino acid substitutions and chromosomal rearrangements in white-throated sparrows to their pheromone-controlled physiology of reproduction and you have the established link to morphology and behavior of the butterflies, birds, bees, and all other species on this planet via conserved molecular mechanisms.
Try to link mutations and natural selection for anything but food to biodiversity and you must invent theories about how random changes lead to predictable outcomes via changes in one gene in vertebrates and invertebrates.
Go ahead, make my day! Watch the butterflies and make predictions about evolutionary processes. Keep touting your ridiculous theories as serious scientists recognize why Dobzhansky (1973) mentioned that  “…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.”
He seems to have predicted serious scientists would learn about nutrient-dependent amino acid substitutions that differentiate all cell types in all individuals of all species, but that evolutionary theorists would not. Did he believe the theorists would never be more than butterfly collectors and bird-watchers who didn’t learn anything about molecular biology? Did he believe that theorists could never grasp the facts about how ecological variation leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man?