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 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

Energy-dependent physical and biophysical constraints (7)

See first: Energy-dependent physical and biophysical constraints (6)
Stems Cells in the Hypothalamus Slow Aging in Mice
My comment to The Scientist

Cai says microRNAs could be a potential mechanism by which hypothalamic neural stem cells have such wide-ranging effects on aging, yet he believes that neurogenesis may also be involved.

See also: Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

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

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

More than 63,000 indexed articles on PubMed link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Many of them also link the virus-driven theft of quantized energy from mutations to pathology such as John McCain’s glioblastoma. He will probably be treated with microRNAs, but that fact may not be reported because the effective treatment is a refutation of neo-Darwinian pseudoscientific nonsense about mutations, natural selection, and evolution.

Alternative splicing of pre-mRNA

Virus-driven downsizing of the human brain (4)

Excerpt:

Chad Lerner

We house our animal mouse models in pathogen free environments (aside from transponson). They still age and die with pathological features. Sorry

Chad Lerner claims to be a Postdoctoral Researcher at Buck Institute for Research on Aging

On Saturday, 4/22/17, which was the day of the “March for Science” he wrote:

You should not have featured me. It is out of context and you have no idea what you’re talking about. You just want there to be a god like the other children . Leave me out of this quackery. Remove my name. Never contact me.

See also: Heading into Today’s March, Here’s When to Doubt a Scientific “Consensus”

 Excerpt: There’s an old legal proverb:

If you have the facts on your side, argue the facts. If you have the law on your side, argue the law. If you have neither, attack the witness. When proponents of a scientific consensus lead with an attack on the witness, rather than on the arguments and evidence, be suspicious.

Chad Lerner attacked me as if I was a witness for Creationism and Americanism. Tomorrow is another day.

See Behavior related genes, dietary preferences and anthropometric traits,which is scheduled for presentation on 4/24/17

Reported as: Could genetics influence what we like to eat?

…little is known about how natural variation in these genes could affect eating behaviors in healthy people. Gene variation is a result of subtle DNA differences among individuals that make each person unique.

All serious scientists know that natural variation in genes is nutrient energy-dependent and controlled by the biophysically constrained physiology of reproduction. The also know this: Feedback loops link odor and pheromone signaling with reproduction
Natural selection for energy-dependent codon optimality links the feedback loops to all biophysically constrained biologically-based cause and effect. There is a model for that: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
This claim makes no sense: “…little is known about how natural variation in these genes could affect eating behaviors in healthy people.”

See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

rp_levels-of-organization.jpg

Energy-dependent biodiversity (2)

This will be my next post to the “Creationism” FB group, where biologically uninformed antagonists have been attacking me on all my other posts or my comments on the posts of others. See, for example:
In a series of four presentations during three online conferences: “Neuroscience” “Molecular Diagnostics” “Genetics and Genomics,” I linked Einstein’s math and physics, from Schrodinger’s claims about anti-entropic energy to Dobzhansky’s claims about amino acid substitutions and cell type differentiation in many different species…
Currently, more than 100 hate-filled responses have overwhelmed discussion attempts, and only a few supporters are willing to make themselves known. It is time to try to move forward.
Combinatorial effects of odorants on mouse behavior [open access] Conclusion:

“…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.

My comment: The senior author is 2004 Nobel Laureate, Linda Buck. Her group again makes it more difficult to argue for beneficial mutations and natural selection in evolution because she has continued to link the mouse model to humans via the energy-dependent de novo creation of olfactory receptor genes and the nutrient-dependent innate immune system.
The article links olfaction and the innate immune system to transgenerational epigenetic inheritance of morphological and behavioral phenotypes via innate responses to odors and the physiology of reproduction. All the confusion about linking the mouse model to humans via energy-dependent hydrogen-atom transfer in DNA base pairs, which are linked to supercoiled DNA and protection of organized genomes from virus-driven energy theft and genomic entropy is missing.
I suspect that is because all serious scientists know that the conserved molecular mechanisms of cell type differentiation link all invertebrates to all vertebrates. Anna Di Cosmo​’s group has shown that at several different levels of examination, and perhaps all of them can be placed into the context of this published work.
If so, I hope someone from the committee nominates Anna Di Cosmo for a Nobel Prize in Physiology and/or Medicine, which should probably be shared with Eugene Daev, since both have stayed at least a decade ahead of all other researchers who are studying RNA-mediated cell type differentiation in the context of healthy longevity compared to mutations and all pathology.
See for example:

Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
See also, my new post to the Creationism FB group. There’s been no progress towards discussion during the past 3 hours.