APS 2018

From photons to the proton motive force (2)

If you know someone who has linked differences in the energy of photons from the proton motive force to the physiology of reproduction and all biophysically constrained biodiversity, ask if they will attend Schrödinger at 75-The Future of Biology
For contrast, touting genetic evolution is not the future of biology.
See: Abstract: K06.00013 : A Path Integral Method for Analytically Tractable Inference of Evolutionary Dynamics

Understanding the forces that shape genetic evolution is a subject of fundamental importance in biology and one with numerous practical applications. Modern experimental techniques give insight into these questions, but inferring evolutionary parameters from sequence data, such as how an organism’s genotype affects its fitness, remains challenging. Here we present a method to infer selection from genetic time-series data using a path integral approach based in statistical physics. Through extensive numerical tests we find that our method exceeds the current state of the art in the successful classification of mutations as beneficial or deleterious in a variety of scenarios, while also yielding orders of magnitude improvements in run time. Our approach can also be extended to jointly infer other evolutionary parameters such as the effective population size and mutation rates.

Serious scientists do not infer evolutionary parameters using sequence data. They link natural selection for energy-dependent codon optimality to biophysically constrained viral latency. Virus-driven energy theft is linked from mutations to all pathology. There is no such thing as a beneficial mutation.
See also: Abstract: K06.00001 : Coarse-grained models coupling cell cycle and gene expression*

During a cell cycle, cells grow and divide. Recent single-cell experiments show that gene expression levels depend on the cell cycle. Particularly important is the proportion of the number of mRNA and protein to the cell volume. It is not clear how cells maintain a constant mRNA and protein concentration as the cells grow. Here we propose a coarse-grained gene expression model incorporating ribosomes and RNA polymerases, which captures the exponential growth of mRNA and protein number. We show that the homeostasis of mRNA and protein concentrations during the cell cycle can be achieved in a robust manner independent of cell shape. Furthermore, we show that the fluctuations in ribosome and polymerase numbers do not propagate to protein concentrations while the fluctuation in cell density does. Furthermore, our model reconciles the discrepancy between the experimentally observed negligible correlations between mRNA and protein levels, and the predicted positive correlations from previous models

Energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated cell cycles to gene expression in more than 70,000 published works. See: microRNA
See also: Applications of ligation-mediated PCR

A nick in a strand is any place where there’s a missing covalent bond between a sugar and the next adjacent phosphate. Nicks can arise from DNA damage, during normal DNA replication, or from the action of nuclease enzymes. Since a nick breaks the continuity of the backbone of one strand, it must be repaired by re-forming the missing covalent bond in order to make the DNA molecule intact again. This job of sealing nicks (specifically, nicks that occur between a sugar 3′ -OH group and the adjacent phosphate attached to the preceding sugar’s 5′ -OH group) is the function of DNA ligase. 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.

Simply put: It’s all about that base and energy-dependent RNA-mediated DNA repair.
If you are still trying to put what is known about DNA repair and cell type differentiation back into the context of neo-Darwinian evolution, you are not a winner.
See: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

See also: The spread of true and false news online
Reported as: Researchers call for large-scale scientific investigation into fake news

Additionally, the article’s authors point out that false information affects not only the political sphere but also areas not previously regarded as political, such as public health topics like nutrition and vaccinations, as well as the stock market.

Do you know someone who has consistently touted the use of vaccinations compared to nutrition? Are they paid to do that or are they biologically uninformed?

5th-6th Sept 2018 Dublin, Ireland

From photons to the proton motive force (1)

Conclusion: If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.
Fly’s Blood-Brain Barrier Has Circadian Rhythms

“the anatomic characteristics of insect and vertebrate BBB structures are quite distinct.”

The molecular mechanisms are conserved.
My comment to The Scientist:

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

The levels of complexity have since been placed into the context of how energy-dependent changes in the microRNA/messenger RNA balance link atoms to ecosystems in all living genera via feedback loops.

For instance, see: Feedback loops link odor and pheromone signaling with reproduction

When theorists fail to start with energy-dependent changes they are forced to use de Vries 1902 definition of mutation in attempts to link the virus-driven theft of quantized energy to evolution. Two forthcoming conferences will place that pseudoscientific nonsense into its proper perspective.

Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses

Schrödinger at 75 – The Future of Biology – September 2018

See also:  Here Comes Single-Cell Optogenetics

.. two-photon excitation with computer-generated holography (a way to precisely sculpt light in 3D) allow light to be focused tightly enough  to hit one cell.

OLYMPUS experiment sheds light on structure of protons

…most of the time, only one of the photons has high energy….

Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

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

Researchers who have not linked differences in the energy of photons to the proton motive force are not likely to be among those who are presenting in September: Schrödinger at 75 – The Future of Biology
See for comparison: Subatomic

Subatomic is a deck building game where players are competing to build a number of available Elements, which score them points. Each player starts with the same small deck of cards that consist of Proton, Neutron, and Electron Cards. They use these cards to build upon their current Atom (by playing these cards face-up as Subatomic Particles) in an attempt to construct one of the available Element Cards. Or players may use their hand of cards to purchase more powerful cards for later use (by playing them in combinations of face-down as energy and face-up as Subatomic Particles!) Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.

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.

Ecological adaptation: a new definition of heredity (4)

Experimentally Induced Metamorphosis in Axolotl (Ambystoma mexicanum) Under Constant Diet Restructures Microbiota Accompanied by Reduced Limb Regenerative Capacity (2018)

Our results show that distinct bacterial communities inhabit individual organs of Axolotl and undergo substantial restructuring through metamorphosis.

The restructuring during metamorphosis is biophysically constrained by feedback loops that link olfaction from food odors and pheromones to the creation of enzymes in bacteria and the secretion of the vertebrate decapeptide hormone GnRH (gonadotropin releasing hormone).
See: Gonadotropin-releasing hormone agonist binding in tiger salamander nasal cavity (1993)
The authors presciently linked food odors and pheromones from epigenetic effects on feedback loops to gonadotropin-releasing hormone (GnRH) and microRNA-mediated morphological and behavioral diversity, and also to differences in the behavior of monogamous and polygamous prairie voles.
See: The prairie vole vomeronasal organ is a target for gonadotropin-releasing hormone (2001)
For comparison, Larry Young claimed that the evolution of viruses caused the differences in prairie vole behavior. He linked the virus-driven differences from three other hormones to the evolution of heterosexual love. See: Virus Evolution Amazing Documentary Full HD National Geographic Documentary 2015
Others, who are like Larry Young, have failed to link anything known to serious scientists from sensory input to energy-dependent changes in the creation of enzymes, receptors and hormones. The anti-entropic energy-dependent creation of enzymes by bacteria links the creation of receptors and hormones in vertebrates to protection of organized genomes from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
See for comparison: 2013 Isaac Asimov Memorial Debate: The Existence of Nothing

Isaac Asimov, “…perhaps, the last polymath of our civilization.”

Originally a zoology major, Asimov switched to chemistry and earned a Doctor of Philosophy degree in biochemistry in 1948. In 1977, he contracted HIV from a blood transfusion. He was president of the American Humanist Association, which suggests that his atheism led to his death via his ignorance.
For example, in 1964, Dobzhansky wrote:

“The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.”

If Isaac Asimov was the last polymath of our civilization, we are doomed. Clearly his ridiculous beliefs have led to the teaching of pseudoscientific nonsense about evolution despite the claims of Schrödinger (1944) and those who will link the anti-entopic virucidal energy of sunlight from the physiology of reproduction to biophysically constrained viral latency and all biodiversity during Schrödinger at 75 – The Future of Biology – September 2018
See for comparison: How One Child’s Sickle Cell Mutation Helped Protect the World From Malaria
Once again, so-called science journalist Carl Zimmer shows that he does not know the difference between a mutation and an RNA-mediated amino acid substitution.
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Single nucleotide substitutions or indels can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

Hemoglobin variants alter the oxygen carrying capacity of red blood cells. They are clear indicators of how ecological variation must be linked to ecological adaptation via food energy-dependent changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
There are more than 1700 human variants. Anyone who claims that the variants are mutations should be required to link them from the transgenerational epigenetic inheritance of morphological and behavioral phenotypes in all living genera to ecologically adapted human populations.
The alternative is sexist and racist. Much more is needed than a new definition of heredity. All intelligent people must dismiss the neo-Darwinian pseudoscientific nonsense about mutation-driven evolution. Then, we can start over with accurate representations of top-down causation and biophysically constrained viral latency.
But first see: EPA’s Scott Pruitt Doesn’t Buy Evolution

Andrew Rosenberg, director of the Center for Science and Democracy at the Union of Concerned Scientists, counters that Pruitt should not act as “the nation’s pastor.”

Andrew Rosenberg should become familiar with the extant literature or play the cell biology game “Cytosis” for ages 10+. There is no excuse for his level of ignorance.
Cytosis is a board game that details what takes place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses! In the context of everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation, a new tool is now available to help theorists link cause and effect via a mathematical model.
See: VarQ: a tool for the structural analysis of Human Protein Variants. The mathematical model has replaced neo-Darwinian theories with facts about how the energy-dependent structure of functional supercoiled DNA biophysically constrains viral latency.
See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy (2013)
and Role of bacterial efflux pumps in biofilm formation
Only a few people I know would link antibiotic resistance from Escherichia coli to Acinetobacter baumannii via the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens. Until they are willing to do it in a public forum, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.
Pseudoscientists and most other theorists are still focused on mutation-driven evolution. Isaac Asimov’s “humanist” influence has prevailed across more than one generation of students who learned how to link nothing to everything from people like Neil deGrasse Tyson, Lawrence Krauss, and Carl Zimmer.

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Ecological adaptation: A new definition of heredity (3)

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

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

OMCD: OncoMir Cancer Database

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5th-6th Sept 2018 Dublin, Ireland

Ecological adaptation: A new definition of heredity (1)

Excerpt: ” …long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans…”
She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity May 29, 2018 | 672 Pages
From the description of the book:

1) We need a new definition of what heredity is…

2) …Zimmer ultimately unpacks urgent bioethical quandaries arising from new biomedical technologies, but also long-standing presumptions about who we really are and what we can pass on to future generations.

The long-standing presumptions led to the claims made by biologically uninformed theorists who failed to link biophysically constrained viral latency to the recent origin of most protein-coding variants via the physiology of pheromone-controlled reproduction in species from microbes to humans. For comparison to the long-standing presumptions, see:
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants May 11, 2012
Evolution and functional impact of rare coding variation from deep sequencing of human exomes May 17, 2012
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Reported as: Past 5,000 years prolific for changes to human genome November 28, 2012

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Akey dismissed everything known about the epigenetic effects of food energy and the metabolism of food to pheromones, which biophysically constrains viral latency in the context of the physiology of reproduction in species from microbes to humans.
See for comparison: A third of Americans don’t believe in evolution January 1, 2014
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

When food energy-dependent pheromone-controlled autophagy (see: Autophagy.pro) fails to protect organized genomes from the virus-driven degradation of messenger RNA, organisms pass on mutations to future generations. Clear evidence of that fact was published in the context of this article: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants January, 2013.

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1, 2 and will help to facilitate the development of new approaches for disease-gene discovery3.

The facts about the age of all mutations have since been placed into the context of:
Sperm epigenetics and influence of environmental factors February, 2018

… epigenetic variation may be genetically selected [41], which is in contradiction with the opposite model in which epigenetic variation is a cause of genetic variation. While both models can cooperate, more experimental evidence, other than computationally-based, should be provided to address the mutagenicity of regions subjected to environmentally-induced epigenetic variation and the evolutionary implications.

Conclusion:

Future research efforts may be able to identify a unified epigenetic remodeling response to lifestyle stress across species. Understanding the role of environmentally-driven epigenetic changes in gametes on the phenotype of the offspring constitutes not only a fascinating biological question on its own but also represents a moral obligation for the health of future generations.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression December, 2014

MicroRNA present in mature sperm… may actually serve important regulatory roles in fertilization and early developmental processes.

To see how much experimental evidence of biophysically constrained food energy-dependent pheromone-controlled biologically-based cause and effect has been ignored during the past two decades, see: From Fertilization to Adult Sexual Behavior December 1996

…we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.” Although many, and perhaps most, important sex differences arise from gonadal and hormonal development, also important are sex differences which are neither gonadal nor hormonal. All these factors affect the internal workings of the individual and intervene in structuring how the social environment might or might not modify sexual behavior. This discourse calls attention to features that are central to the so-called nature-nurture discussion.

Our section on molecular epigenetics may have been the first to detail what is now being reported in the context of the cryo-EM technology, which links energy-dependent changes from electrons to ecosystems in all living genera via what is known about pre-mRNAs. Pre-mRNAs are now also referred to as microRNAs in more than 70,000 published works.
See: microRNA and/or pre-mRNA 
Clearly, what is known to all serious scientists about biophysically constrained viral latency and healthy longevity has forced Carl Zimmer to suggest that “We need a new definition of what heredity is…”
See also:
7/31/16 From hydrogen atom transfer in DNA base pairs to ecosystems
7/31/16 RNA-mediated physics, chemistry, and molecular epigenetics
7/30/16 What is life when it is not protected from virus driven entropy
7/29/16 RNA-mediated molecular epigenetics and virus-driven entropy
4/10/14 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
8/8/13 Nutrient-dependent / pheromone-controlled adaptive evolution
3/8/13 Nutrient-dependent / Pheromone–controlled thermodynamics and thermoregulation
2/17/13 Nutrient-dependent / Pheromone-controlled Adaptive Evolution
Watch for Philip C. Ball’s newest book: Beyond Weird  March 22, 2018

Over the past decade or so, the enigma of quantum mechanics has come into sharper focus. We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information: about what can be known and how.

See: 5/8/17 Energy as information and constrained endogenous RNA interference May 8, 2017
See also: New Giant Viruses Further Blur the Definition of Life

“The gap between cellular organisms and viruses is starting to close,” Deeg said. “Which then brings us back to: What is a virus, and what is life?”

Has anyone else linked biophotonics to the energy-dependent proton motive force via the cryo-EM technology?
See for instance: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase.
And preview, Schrödinger at 75 – The Future of Biology – September 2018
Nobel Laureates, Linda Buck, Ben Feringa, Michael Rosbash are among other Nobel Laureates who are scheduled to present.
See also: Are Humans “Smeller Underachievers?” Not So Fast…

…they will share their data and experience on the psychological influences on eating and behavior, the chemosensory properties of food and how we experience them, the role of food as medicine, and the history and evolution of flavor and flavor perception.

No experimental evidence of energy-dependent biophysically constrained top-down causation suggests that flavor perception “evolved.”  See: Feedback loops link odor and pheromone signaling with reproduction

Exemplifying human idiocy

MicroRNAs biophysically constrain behavior (2)

Excerpt:

Researchers, like Shunsuke Suzuki, who cannot link photonic coupling from quantum physics to biophysically constrained atomic energy via classical physics and quantum chemistry prevent scientific progress, They are limited to asking questions that have already been answered by serious scientists.

MicroRNA 1-20 of more than 70,400
The fact that the energy-dependent creation of microRNAs links RNA-mediated cell type-differentiation to biophysically constrained viral latency and all morphological phenotypes has been established.
See: PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers

…using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets.

Reported as: RNA-based therapy cures lung cancer in mouse models

By turning down the activity of a specific RNA molecule researchers at Sahlgrenska Academy, Sweden, have cured lung tumors in mice by 40-50 percent. The results, published in Nature Communications, represent the tip of the iceberg in an extensive research project in which 633 new biomarkers for 14 types of cancer have been identified.

Ongoing support for my model of Energy as information and constrained endogenous RNA interference continues to link RNA-mediated differences in human populations to biophysically constrained viral latency and survival. Why haven’t others accepted the fact that there must be a link from the RNA-mediated differences to behavior? Morphological and behavioral phenotypes are energy-dependent and receptor-mediated.
See: Vital Signs: Racial Disparities in Age-Specific Mortality Among Blacks or African Americans — United States, 1999–2015
See also:
1) Vascular Endothelial Growth Factor Receptor 3 Controls Neural Stem Cell Activation in Mice and Humans (2015)
2) Delayed Dopamine Signaling of Energy Level Builds Appetitive Long-Term Memory in Drosophila (2015)
Reported as: Fruit flies remember a good meal, Blood growth factor activates neural stem cells

…the fruit fly brain is wired to remember and crave sweeter, energy-rich foods. After smelling and consuming a meal, such as a glob of sugar, information about the food’s energy content is relayed via dopaminergic neurons to a fruit fly’s olfactory long-term memory center.

The ability to remember a good meal is linked to a single amino acid substitution in one or more receptors.
3) A Single Amino Acid Substitution in the Activation Loop Defines the Decoy Characteristic of VEGFR-1/FLT-1 (2006)
The link from the food energy-dependent creation of microRNAs and the creation of enzymes to the single amino acid substitution that controls receptor-mediated neural step cell activation in mice and humans may not be obvious. For instance, the acronym VEGFR might not be linked to other reports on Vascular Endothelial Growth Factor Receptors.
The likelihood of establishing facts about top-down causation and biophysically constrained viral latency is reduced as each step towards neo-Darwinian pseudoscientific nonsense brings another level of obfuscation. See for example:

Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies (2016)

Duplicated genes are abundant in eukaryotic genomes and thus are presumed to play important roles in evolution.

Duplicated genes do not create themselves. The de novo creation of genes is energy-dependent and receptor-mediated. That fact establishes all the links from top-down causation to biophysically constrained viral latency and ecological adaptations via the creation of RNA and energy-dependent fixation of RNA-mediated amino acid substitutions.
If serious scientists understand the facts about food energy-dependent pheromone-controlled ecological adaptations in species from microbes to humans, questions like this are not likely to arise. VEGF165b elevation in pulmonary arterial hypertension patients, causative or adaptive? (4/1/18)
No reply is required. But see: VEGF165b elevation in pulmonary arterial hypertension patients, causative or adaptive? -Reply. (4/1/18)
Shunsuke Suzuki is a co-author of the reply. I am not interested in reading about questions or replies that are placed into the context of ridiculous theories, or attending meetings on Epigenetics & Chromatin where discussion of the emergence of novel CpG islands and genomic imprinting in mammalian evolution are discussed.
See for comparison: Direct Photonic Coupling of a Semiconductor Quantum Dot and a Trapped Ion (2015)
Understanding the key role played by single atoms and ions in the context of elementary quantum information processing protocols is required to answer questions about top-down causation and adaptation. Researchers, like Shunsuke Suzuki, who cannot link photonic coupling from quantum physics to biophysically constrained atomic energy via classical physics and quantum chemistry prevent scientific progress, They are limited to asking questions that have already been answered by serious scientists.
See Frohlich (1968) Long-range coherence and energy storage in biological systems

The supplied energy is thus not completely thermalized but stored in a highly ordered fashion.

See also: Schrödinger at 75 – The Future of Biology – September 5-6, 2018
The future of biology lies in the understanding of how the creation of the sun’s anti-entropic energy links RNA-mediated top-down causation via natural selection for energy-dependent codon optimality in the context of novel CpG islands and genomic imprinting. The RNA-mediated genomic imprinting must be linked to biophysically constrained viral latency. It is ridiculous to link the systems complexity of cell type differentiation and cancer prevention to mammalian evolution without consideration of how behavior could be linked to biophysically constrained cell type differentiation.
See for instance: CpG islands microRNA

Exemplifying human idiocy

MicroRNAs biophysically constrain behavior

The link from the quantized energy of sunlight to the creation of microRNAs and biophysically constrained morphological phenotypes has been clear since 1944, when Schroedinger placed it into the context of “What is Life?”.
In the reprint edition, Roger Penrose added: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)
Unfortunately for those who have suffered unnecessarily and died prematurely since then, biologically uninformed theorists failed to link the creation of food energy-dependent microRNAs to behavior.
But see: MicroRNA degradation by a conserved target RNA regulates animal behavior 2/26/18

…we show that a genome-encoded transcript harboring a near-perfect and deeply conserved miRNA-binding site for miR-29 controls zebrafish and mouse behavior. This transcript originated in basal vertebrates as a long noncoding RNA (lncRNA) and evolved to the protein-coding gene NREP in mammals… Thus, we demonstrate an endogenous target-RNA-directed miRNA degradation event and its requirement for animal behavior.

Claims that microRNAs regulate animal behavior were expected. The claims about the origination of a transcript and/or evolution of a protein coding gene via an endogenous near-perfect deeply conserved miRNA-binding site has not been supported by any experimental evidence.
Similar claims about evolved differences in amino acids and proteins have not been linked to behavior. In this case, however, the claim about the evolution of a near-perfect miRNA-binding site dismisses everything known to serious scientists about the food energy-dependent pheromone-controlled physiology of reproduction that we detailed in our section on molecular epigenetics from this 1996 review: From Fertilization to Adult Sexual Behavior.
In 1996, microRNAs were called pre-mRNAs and we linked them to alternative splicings of RNA and behavior in species from microbes to humans. The cell biology game “Cytosis” linked the alternative splicings of RNA to food energy-dependent pheromone-controlled biophysically constrained viral latency in the context of the creation of enzymes, hormones, and receptors.
The link from the energy-dependent creation of microRNAs to behavior still must be placed into the context of what is known to all serious scientists. See: RNA: Structure meets function conference and 4th International Congress on Epigenetics & Chromatin,  which was announced as if it was a conference on emergence and evolution.

Emergence and evolution are not discussed by serious scientists who read the extant literature such as this: Consequences of RNA oxidation on protein synthesis rate and fidelity: implications for the pathophysiology of neuropsychiatric disorders 10/15/17

…a discovery of oxidized microRNA has been recently reported. The oxidized microRNA causes misrecognizing the target mRNAs and subsequent down-regulation in the protein synthesis. It is noteworthy that oxidative modification to RNA not only interferes with the translational machinery but also with regulatory mechanisms of noncoding RNAs that contribute toward the biological complexity of the mammalian brain.

See also:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (2014)

Molecular genetic mechanisms of allelic specific regulation of murine Comt expression (2015)

…our data demonstrate that the Comt+ transcript contains regulatory miRNA signals in its 3′-untranslated region leading to mRNA degradation; these signals, however, are absent in the shorter transcript, resulting in higher mRNA expression and activity levels.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia (2016)
Catechol O-methyltransferase (COMT) functional haplotype is associated with recurrence of affective symptoms: A prospective birth cohort study (2018)

Combination of the COMT functional haplotype model and inverted-U model may shed light on the effect of dopaminergic regulation on the trajectory of affective symptoms over the life course.

Analysis of COMT Val158Met polymorphisms and methylation in Chinese male schizophrenia patients with homicidal behavior (2018)

…we showed that the Val allele at Val158Met (rs4680) may be associated with the homicidal behavior of schizophrenia patients as well as that the methylation level of Val158Met (rs4680) could be affected by the variation of Val158Met (rs4680) and eventually contribute to the violent behavior of schizophrenia patients.

Facts about interethnic differences and similarities that link now microRNAs to behavior were discussed in the context of Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles (1999)
The COMT val158met polymorphism was not found in seven nonhuman primates. One gorilla, two chimpanzees, two bonobos, and two orangutans had the G nucleotide at the variable position in the COMT gene, which codes for the amino acid valine in the COMT protein. The difference in non-human primates and modern humans was not linked to interethnic similarities or differences in COMT val158met polymorphisms. That may explain why the differences were not linked from dietary differences to behavior via the creation of food energy-dependent microRNAs.
But see: The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders
Reported as: Microbiota-gut-brain axis is at epicenter of new approach to mental health
The approach is not new. See: Feedback loops link odor and pheromone signaling with reproduction (2005)
Remember: Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
Place that claim into the context of the comment by Roger Penrose: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?
If the human idiocy touted by neo-Darwinian theorists and big bang cosmologists is not perfectly clear, see:

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

Creating biophysically constrained viral latency (2)

Creating biophysically constrained viral latency (2)
Serious scientists have reached the point where they are finally ready to expose the pseudoscientific nonsense during Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses and also during Schrödinger at 75 – The Future of Biology – September 2018.
Until then, pseudoscientists may want to see these examples of accurate information about top-down causation.
MicroRNA Processing Gene Methylation and Cancer Risk

Methylation of three CpGs (DROSHA: cg23230564, TNRC6B: cg06751583, and TNRC6B: cg21034183) was prospectively associated with time to cancer development (positively for cg06751583, inversely for cg23230564 and cg21034183) whereas methylation of one CpG site (DROSHA: cg16131300) was positively associated with cancer prevalence.

Oncogene-induced regulation of microRNA expression: Implications for cancer initiation, progression and therapy

microRNAs are small non-coding RNAs that negatively regulate gene expression, assisting or antagonizing oncogenic signalling. The differential expression of microRNAs in cancer is well-documented and is considered a fundamental aspect of tumourigenesis.

Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs

This study showed a preliminary support to suggest that the herbal medicine RDN combined with LRD can reduce both susceptibility and the severity of DENV.

Dampened STING-Dependent Interferon Activation in Bats
Reported as: How bats carry viruses without getting sick
There is a clear link from the gut bacteria of insects to food energy-dependent pheromone-controlled biophysically constrained viral latency in mammals.
See: Regulation of midgut cell proliferation impacts Aedes aegypti susceptibility to dengue virus

Our study demonstrates that the intestinal epithelium of the blood fed mosquito is able to respond and defend against different challenges, including virus infection. In addition, we provide unprecedented evidence that the activation of a cellular regenerative program in the midgut is important for the determination of the mosquito vectorial competence.

Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex
Our work suggests that the Or-Orco complex has two important characteristics. First, the biophysical properties of the channel vary according to subunit composition, even with highly similar proteins such as BmOr-1-Orco and BmOr-3-Orco. Second, because ligand-selective Or sequences within and between insect species are extremely divergent, the primary amino acid sequence of the ion-conducting pore is likely to differ according to the subunit composition of the Or-Orco complex.

Figure 1) Targeted mutagenesis of Ae. aegypti orco

a, Snake plot of Ae. aegypti Orco with amino acids colour-coded to indicate conservation with Drosophila melanogaster.

It should have been perfectly clear to Leslie Vosshall and others like her that the energy-dependent creation of microRNAs was the key to ecological adaptation via RNA-mediated biophysically constrained viral latency in all living genera. Instead, she attempted to make scientific progress by genetically engineering changes to the fertility of mosquitoes.
She appears to think that genetic engineering of the mosquitoes is the way forward.
Genetic engineering alters mosquitoes’ sense of smell 5/29/13

…the mosquitoes with orco mutations showed reduced preference for the smell of humans over guinea pigs, even in the presence of carbon dioxide, which is thought to help mosquitoes respond to human scent. “By disrupting a single gene, we can fundamentally confuse the mosquito from its task of seeking humans”…

Genetic engineering is gene-centric pseudoscientific nonsense. See: Nothing in cancer makes sense except…

An evolutionary logic pervades all major areas of cancer sciences including causation, cancer clone development and resistance to therapies [10] (Fig. 1).

What some people call evolutionary logic failed to link mutations to beneficial changes in behavior.

 

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

Creating biophysically constrained viral latency (1)

When a theorist or so-called science journalist claims that not enough is known about how quantum physics must be linked from energy-dependent top-down causation to quantum chemistry or how energy-dependent bottom-up quantum chemistry is linked to biophysically constrained viral latency, ask if they have seen this.

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.

For an example of the anti-entropic energy-dependent RNA-mediated complexity of cell metabolism and cell type differentiation, see: Sulforaphane mobilizes cellular defenses that protect skin against damage by UV radiation

Topical application of sulforaphane-rich extracts of 3-day-old broccoli sprouts up-regulated phase 2 enzymes in the mouse and human skin, protected against UVR-induced inflammation and edema in mice, and reduced susceptibility to erythema arising from narrow-band 311-nm UVR in humans.

See also: Skin microbiota–host interactions

The skin is a complex and dynamic ecosystem that is inhabited by bacteria, archaea, fungi and viruses. These microbes—collectively referred to as the skin microbiota—are fundamental to skin physiology and immunity. Interactions between skin microbes and the host can fall anywhere along the continuum between mutualism and pathogenicity. In this Review, we highlight how host–microbe interactions depend heavily on context, including the state of immune activation, host genetic predisposition, barrier status, microbe localization, and microbe–microbe interactions. We focus on how context shapes the complex dialogue between skin microbes and the host, and the consequences of this dialogue for health and disease.‏

Study: Vitamin B3 might help against skin cancer

Nicotinamide, an amide form of vitamin B3, boosts cellular energy and regulates poly-ADP-ribose-polymerase 1, an enzyme with important roles in DNA repair and the expression of inflammatory cytokines. Nicotinamide shows promise for the treatment of a wide range of dermatological conditions, including autoimmune blistering disorders, acne, rosacea, ageing skin and atopic dermatitis. In particular, recent studies have also shown it to be a potential agent for reducing actinic keratoses and preventing skin cancers.

Nicotinamide: Mechanism of action and indications in dermatology

The existing clinical data and literature on nicotinamide suggests that it is an inexpensive, safe drug with beneficial effects as an adjunct in many dermatological diseases because of its anti-inflammatory, anti-oxidant, barrier repair and protective effects. It can be used both as a topical and oral drug without any major adverse effects.

For the link from topical application that protects human skin from excess UVR-induced inflammation to diet-driven protection from cancer, see also: Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention

The engineered commensal Escherichia coli bound specifically to the heparan sulphate proteoglycan on colorectal cancer cells and secreted the enzyme myrosinase to transform host-ingested glucosinolates—natural components of cruciferous vegetables—to sulphoraphane, an organic small molecule with known anticancer activity. The engineered microbes coupled with glucosinolates resulted in >95% proliferation inhibition of murine, human and colorectal adenocarcinoma cell lines in vitro. We also show that murine models of colorectal carcinoma fed with the engineered microbes and the cruciferous vegetable diet displayed significant tumour regression and reduced tumour occurrence.

Reported as: With these special bacteria, a broccoli a day can keep the cancer doctor away

For comparison, see: Sulforaphane-Induced Cell Cycle Arrest and Senescence are accompanied by DNA Hypomethylation and Changes in microRNA Profile in Breast Cancer Cells

Rarely does anyone see an example of how conserved across-kingdom molecular mechanisms protect all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.

So far as I know, evolutionary biologists still claim that energy-dependent protection emerged so that species could evolve their increasing organismal complexity over-the-weekend.

See for comparison: Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors

This work enables predictable control over the dynamic range of regulatory components.

Article excerpt:

1) Because the lac and tet systems evolved separately, the promoters that respond to LacI and TetR are tuned to transcribe downstream genes at rates appropriate to their original setting.

2) We also developed a thermodynamic model that predicted the contribution of free energy of binding to the overall transcriptional initiation rate, which we measured in a fluorescence-based plate reader experiment.

The two excerpts can be linked to the overwhelming amount of pseudoscientific nonsense touted by neo-Darwinian theorists via the example of the energy-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces with exposure to UV light.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

The energy-dependent fixation of two RNA-mediated amino acid substitutions was reported in the context of how evolution “rewired” the nitrogen regulation system over-the-weekend via two mutations.

From the Editor’s Summary
Losing and then regaining flagella

The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor et al. mutated a central regulator for the formation of flagella in the bacterium Pseudomonas fluorescens. They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.

The ability to adapt to ecological variation via the de novo creation of amino acids should not be placed back into the context of neo-Darwinian nonsense about mutations and evolution. The neo-Darwinists have failed to link mutations to beneficial changes in behavior. In bacteria and in humans the behavior is biophysically constrained in the context of viral latency via energy-dependent changes in microRNAs and autophagy.

5th-6th Sept 2018 Dublin, Ireland

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

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


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

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

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

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

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