5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Conclusion:

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.
 

Watering Young Plant - Vintage Effect

The eternal significance of microRNAs (1)

Common Allele Linked to Sugar Consumption Leads to Lower Body Fat, Higher Blood Pressure
One energy-dependent change in a base pair is linked from the FGF21 rs838133 variant to microRNA-mediated changes in morphology and behavior. The quantized energy as information link from microRNAs to morphology and behavior is common to my mouse-to-human model of sympatric speciation.

By linking the common allele to sugar consumption, the authors attest to the fact that sympatric speciation is quantized energy-dependent. Energy as information biophysically constrains viral latency in the context of the game Cytosis for ages 10+.
See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Theorists have been reluctant to comment on this invited review of nutritional epigenetics, which I posted to Figshare.com on 4/10/14. As of today, the model of food energy-dependent pheromone-controlled ecological adaptations / sympatric speciation has been available for 4 years.
In my mouse-to-human model, the variant is rs3827760, aka 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
Summary: The energy-dependent creation of ATP synthase, ATP, microRNAs, messenger RNA, and supercoiled DNA biophysically constrains viral latency in the context of the “Levels of Biological Organization” I included in this presentation from 2010: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) See slide # 6.
See also, our award-winning 2001 review: Human pheromones: integrating neuroendocrinology and ethology

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.

Sympatric Speciation vs Pseudoscientific Nonsense (1)

Summary: The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
For a historical perspective, see:
1996 From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

For obfuscation of our claims about cause and effect, which have since been linked to all biodiveristy, see: Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)
Simply put, no new mechanisms were revealed. The well-known mechanisms of energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation were simply placed into the context of more unintelligible rhetoric.
See for comparison: 2013 Alternative splicings and amino acid substitutions (redux)
Tracking niche variation over millennial timescales in sympatric killer whale lineages

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

For more information on the current perspective, which is the same as the historical perspective, see:
2018 Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

…speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

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…

See also: May, 2015 Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

See also: August, 2015 Eibi Nevo: Evolution, Let’s Get It Right, It’s the “Basis of Everything”

Viruses are the dynamo of change that we see in the modern genome. . . .

Cytosis_Booklet_Science.pdf (63 KB) (Log in or Register [for free] to download.) The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
Cytosis is described as: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
The collaborative efforts of 20 serious scientists who validated the details in the game include the mention of Stephen J. Bush. See: Bush, SJ et al., (2017) Alternative splicing and the evolution of phenotypic novelty

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication
Reported as: RNA Replication Paper Retracted 
Szostak and others got busted for their pseudoscientific nonsense about non-enzymatic emergence by someone who understands quantized energy as information-dependent RNA-mediated top-down causation. People over age 10+ who play the cell biology game “Cytosis” may now force all biologically uninformed theorists to retract their claims, which typically have been placed into the context of mutation-driven evolution.

Watering Young Plant - Vintage Effect

What happened to Timothy J. Cunningham?

Missing CDC scientist: What happened to Tim Cunningham? Police release new details (video)

My comment:
He linked racial/ethnic disparities from epigenetically-effected RNA-mediated sex differences to all virus-driven pathology before anyone else did it.
His published works clearly refute all neo-Darwinian pseudoscientific nonsense and he also refuted all the claims made by Big Bang cosmologists.
See:
1) Racial/ethnic disparities in self-reported short sleep duration among US-born and foreign-born adults
2) Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states
3) miRNA-mediated ‘tug-of-war’ model reveals ceRNA propensity of genes in cancers
4) SRARP and HSPB7 are epigenetically-regulated gene pairs that function as tumor suppressors and predict clinical outcome in malignancies 
5) STAT1 is a sex-specific tumor suppressor in colitis-associated colorectal cancer
 
 

Watering Young Plant - Vintage Effect

Laws of Biology / Rules of Life

Summary: Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.
Understanding the Rules of Life: Predicting Phenotype

Rules of Life projects… may have these characteristics:

Addresses a fundamental question in the life sciences

Crosses different scales (spatial, temporal, levels of biological organization and complexity)

Generates results that will be broadly generalizable beyond the system under investigation, so that a rule can be formulated

Enables the forecasting or prediction of change in a biological system

The characteristics of the so-called “Rules of Life” were predicted in the context of Darwin’s “conditions of life,” and in What is Life? (1944)
Biologically uninformed science idiots took this claim from 1944 and placed it into the ridiculous context of mutation-driven evolution:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

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

Kohl’s Laws of Biology

…summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.

M. Lynch (2007) is The frailty of adaptive hypotheses for the origins of organismal complexity

…emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization.

See for comparison:  Evolutionary determinants of genome-wide nucleotide composition (2018) with senior author Michael Lynch
Reported as: Scientists explore mysteries behind diversity of DNA composition among species

…mutation drives the overall pattern, but selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.

Natural selection for energy-dependent codon optimality is the driving force that links the sun’s anti-entropic virucidal energy to  biophysically constrained viral latency and all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I reiterate:

“…selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.”

Selection is quantized energy-dependent and RNA-mediated. The energy comes from sunlight!
See also: Cytosis and Subatomic
See also: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) (2010)
Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.

5th-6th Sept 2018 Dublin, Ireland

Less evolvable RNA-mediated ecological adaptations

No experimental evidence of biophysically constrained RNA-mediated cell type differentiation supports the claim about “…the evolutionary plasticity of the regulatory regions involved in transcriptional regulation…” The overwhelming systems complexity of energy-dependent RNA-mediated cause and effect can no longer be placed into the context of the pseudoscientific nonsense touted by theorists. Watch Andrea Wagner’s group try to escape from the claims made by losers.
But first 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

RNA-mediated gene regulation is less evolvable than transcriptional regulation

…nucleic acid binding sites of RNA-mediated gene regulation are less evolvable than those of transcriptional regulation. This observation is consistent with the high levels of mRNA target conservation for RBPs (10, 82, 83) and the evolutionary plasticity of the regulatory regions involved in transcriptional regulation (84⇓–86) as well as their role in the evolution of myriad adaptations and innovations (11, 87, 88).

It is obvious to anyone who has followed the works of Andreas Wagner that his group has reached an impasse.
See: Evolution of Viral Proteins Originated De Novo by Overprinting (2012)

We found that young de novo genes have a different codon usage from the rest of the genome.

There is no such thing as a de novo gene.
See: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

I collectively refer to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.

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

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality links what organisms eat to their pheromone-controlled physiology of reproduction in species from microbes to humans. Ecological variation is linked to ecological adaptations only in the context of biophysically constrained viral latency. That fact is now perfectly clear in the context of more than 71,000 indexed published works that link the energy-dependent creation of ATP synthase to the creation of ATP and the creation of RNA in the context of McEwen et al., (1964) and Frohlich (1968).
People like Andreas Wagner are stuck with their ridiculous claims about evolution, when all serious scientists know that only the hecatombic evolution of virus-driven pathology is possible. Healthy longevity requires food energy-dependent biophysically constrained polycombic ecological adaptations. The metabolism of food to species-specific pheromones links RNA-mediated autophagy to all biodiversity. The virus-driven degradation of messenger RNA is linked to all pathology.
Andreas Wagner reversed every aspect of what is known in: Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014)

…he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

See for comparison: Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Andreas Wagner, and others like him, will probably continue to misrepresent what is known about how the creation of sunlight must be linked to food energy-dependent pheromone-controlled reproduction by natural selection for codon optimality. But the facts about how energy must be linked to increasing organismal complexity are not going to change.
See: Schrödinger at 75 – The Future of Biology – September 2018
and/or Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

 
 
 

5th-6th Sept 2018 Dublin, Ireland

Let there be anti-entropic virucidal light

Summary: This is a lie!

…theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

Fuelling the future

In his short story ‘Let There Be Light’, the science-fiction author Robert A Heinlein introduced the energy source that would power his Future History series of stories and novels.

In The Darwin Code, Greg Bear helped to explain how he linked biophysically constrained light energy to the creation of a superior human species in “Darwin’s Radio” (1999) and “Darwin’s Children” (2003).
On June 21, 2017, Philip C. Ball ignored the science fiction and all facts that link the quantized energy of sunlight to biophysically constrained viral latency.
See: Quantum common sense

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

His pseudoscientific nonsense led me to ridicule him on June 24, 2017.
See:

See for comparison: Genesis 1:3

And God said, “Let there be light,” and there was light.

For a historical perspective on the creation of anti-entropic virucidal light see Schrodinger’s claims in “What is LIfe?” (1944),

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See for comparison: Ecological and evolutionary consequences of viral plasticity 3/27/18

For bacteriophages, this host-viral performance link has been characterized empirically and with intracellular theories. Such theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

My comment on the preprint:

The “importance of viral plasticity to unravel host-phage interactions” has been modeled in the context of everything known about the creation of anti-entropic virucidal light (e.g., ultraviolet light), and how sunlight is linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA and fixation of RNA-mediated amino acid substitutions that biophysically constrain viral latency in all cell types of all living genera.

A google search for “virus-driven energy theft” would be a good place to start looking for information that you appear to have missed in its entirety.

See also, for example: Virus-mediated archaeal hecatomb in the deep seafloor http://advances.sciencemag.org/content/2/10/e1600492.full

“We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.”

See for comparison: Riding the Evolution Paradigm Shift With Eugene Koonin May 7, 2015

…the new understanding of evolution needs to integrate what we now know about viruses and virus-host interactions which, from my own perspective, has been absolutely one of the key factors of all evolution since the emergence of cells — well, actually even before the emergence of cells.

Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

To learn more about ecology and dismiss the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists, see:
Phase Transitions in the Assembly and Function of Human miRISC March 16, 2018

…may explain how miRISC silences mRNAs … and provide[s] experimental evidence that protein-mediated phase separation…

Probably facilitates biophysically constrained RNA-mediated achiral glycine-controlled energy processing in all jawless vertebrates.

Alternative splicing of pre-mRNA

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Psychophysical Laws and the Superorganism  (open access)

…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.

Reported on Jun 14, 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model

and again on: Mar 27, 2018 as Honeybees may unlock the secrets of how the human brain works

The study… found that superorganisms may obey the same laws as the human brain.

Kohl’s “Laws of Biology” and Darwin’s “conditions of life” can now be compared in the context of how quantized energy as information was linked to biodiversity in this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
See also for review:

Functional and evolutionary aspects of chemoreceptors (2012)
Sensory receptors—design principles revisited (2013)
Moving forward: See: Tuning Insect Odorant Receptors (in press)

Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.

Future attempts to place psychophysical laws of biology back into the context of neo-Darwinian pseudoscientific nonsense will continue to pit ridiculous theories about experience-dependent tuning of odor receptors against everything known to serious scientists about RNA-mediated biophysically constrained viral latency and supercoiled DNA.
See for comparison:
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)
Learning from Bacteria about Natural Information Processing (2009)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)

Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.

Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity.

See also: Schrödinger at 75 – The Future of Biology – September 2018
The scheduled speakers will undoubtedly link the Science Behind the Game “Cytosis” to the Science Behind the Game “Subatomic” via everything known to all serious scientists based on Schrodinger’s prescient claims in What is Life? (1944).
See also: What is life when it is not protected from virus driven entropy

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

See also: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also “Outer Membrane Vesicles” microRNA (4 of 4 from a 3/27/18 search)

How Our Other Genome Controls Our Epi-Genome (2016)

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens (2017)

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA (2017)

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections (2018)

See also: March 28, 2018 sponsored by System Biosciences
Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect
 
Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.
Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.
5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry (2)

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

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

Odor activation of ATP (2)

Metabolic Regulation of Cytoplasmic DNA Synthesis (1974)

The curve that results when the rate of DNA synthesis is plotted as a function of ATP concentration is sigmoidal, suggesting that more than one site on the enzyme interacts with ATP and that these sites are acting cooperatively.

Odor activation of ATP is the obvious link to RNA-mediated feedback loops that control the food energy-dependent pheromone-controlled physiology of reproduction via the rate of DNA repair in species from microbes to humans.
See: “ATP activation
See for comparison: Feedback loops link odor and pheromone signaling with reproduction (2005)
See also: “ATP activation” microRNA
See also: Mapping malaria by combining parasite genomic and epidemiologic data

Here, we discuss the spatial epidemiology of malaria in the context of transmission-reduction interventions, and the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate data sets to measure both connectivity and transmission.

The sun’s anti-entropic virucidal energy has been linked to protective food energy-dependent hemoglobin variants via 1700+ examples. The variants link interethnic similarities and differences to all extant human populations.
HbVar: A Database of Human Hemoglobin Variants and Thalassemias
SNPs or indels [insertions/deletions] link amino acid substitutions to hemoglobin variants. Molecular defects [mutations] in regulatory or coding regions of the human genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.
What can be said about so-called scientists and so-called science journalists who do not know the difference between how a food energy-dependent amino acid substitution is linked to ecological adaptations and how a mutation is linked to diseases?
Who was the first to say it?

Who will be the next to disagree:
7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

Darwin repeatedly asserted that “conditions of life” must be placed before natural selection. Without the sun’s anti-entropic energy, no species on Earth can adapt to ecological variation.