5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

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

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

 

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.

Witzhany2018

The tipping point (revisited): 70,000 publications

Excerpt:

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”

The tipping point?: 50,000publications (May 16, 2016)
See also: The tipping point (revisited): 69,000 publications (January 20, 2018)
Nearly 1000 more published works have been added to the 69,000 on microRNAs that had already been published by last month.
All experimental evidence has been placed into the context of 12,000 more published works on microRNAs, since the time of this presentation (February 15, 2017):

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: Transposons: a blessing curse (open access) with my emphasis
Conclusion:

The circumstances of transposon bursts, preferences of insertion sites, and the life cycle of many elements are not fully understood. Like in classical mutagenesis with chemical or physical treatments, unwanted side effects are likely and cannot be excluded, and new TE-related phenotypes must be thoroughly tested for genetic and epigenetic stability. However, detrimental and beneficial events can teach us both principles, and well-established advantageous interactions between TEs and genes might serve as templates for more precise and targeted genome editing and breeding.

Pseudoscientists continue to put what is known into the context of their ridiculous theories about evolution:
See for comparison (from the same issue): Despacito: the slow evolutionary changes in plant microRNAs (paywalled) with my emphasis

…this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.

No experimental evidence of biophysically constrained biologically-based cause and effect suggest that microRNAs emerged or that plant genomes evolved. All experimental evidence consistently has shown that the anti-entropic virucidal energy of sunlight creates microRNAs in the context of photophosphorylation.
See: Energy limitation of cyanophage development: implications for marine carbon cycling
Photophosphorylation is obviously:

…a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).

Simply put, photophosphorylation links the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via oxidative phosphorylation and the physiology of reproduction in all living genera. That fact has been suspected or established in the context of all works published by serious scientists since the publication of 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.)

See also: Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage
For extension of the research from cyanobacteria to humans see:
Quantification of microRNA expression with next-generation sequencing 2013 (coauthored by George M. Church)
Differential expression of microRNAs in the normal skin of the Han and Uyghur populations in Xinjiang Province (2018)
Any additional claims about the emergence of microRNAs and the evolution of genomes can be placed into the context of what will be presented at the forthcoming conference on “Genetic Novelty/Genomic Variations by RNA Networks and Viruses,” or the cell biology board game “Cytosis” for ages 10+.

This new empirically based perspective on the evolution of genetic novelty will have more explanatory power in the future than the „error-replication“ narrative of the last century.

Simply put, all serious scientists have always known that the “error-replication” narrative of the 20th century was a ridiculous misrepresentation of what Darwin placed into the context of his “conditions of life.”
See for instance: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent. Experiments are described which show that the required ATP is produced by reactions associated with glycolysis, the citric acid cycle, and a type of oxidative phosphorylation.

An evolutionary theory killer

Subatomic: From thermophiles to humans

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. — Max Planck
Every great scientific truth goes through three stages. First, people say it conflicts with the Bible. Next they say it has been discovered before. Lastly they say they always believed it. — Louis Agassiz  (1807-1873)
The claims of neo-Darwininan theorists and big bang cosmologists bastardized the scientific truth that he included in his “conditions of life.” The theorists made it appear that the greatest of all scientific truths did not come from the Bible because their ridiculous theories were nowhere to be found in the context of links from the creation of energy to the physiology of reproduction and all morphological and behavioral diversity on Earth.
See for comparison:

Subatomic

Subatomic is themed around the intersection of particle physics and chemistry! At it’s core, Subatomic is a deck-building game with a light Area Majority mechanic for end game points. Players start with a hand of Up Quarks, Down Quarks and Particle/Wave Duality cards, which they use to form protons, neutrons, and electrons. Players combine these subatomic particles to either build available Elements or buy even more powerful cards for their deck.

See also: Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells (Nutrients, February 8, 2018)

We hypothesized that vitamin C mediates these biological processes partially through miRNA regulation.

MiRNA regulation is quantized energy-dependent. The energy comes from the sun. Their hypothesis appears to be based on my claims in my invited review of nutritional epigenetics, which was returned without review by the guest editors of the journal “Nutrients.”
I linked the anti-entropic virucidal energy of sunlight from the claims in Schrodinger (1944) “What is life?” via the quantized energy-dependent creation of microRNAs and vitamin C.
See  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

The likelihood that hemoglobin variants are associated with other beneficial nutrient energy-dependent changes in microbiota populations in the gut can be considered in the context of how balanced nutrition, which includes access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction (McNulty, et al., 2011).

Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional G protein-coupled genes such as olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).

Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).

Conclusion:

In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports (Grossman, et al., 2013; Kamberov, et al., 2013).

The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

See also: The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding

…our study demonstrates that NONO post-transcriptionally coordinates circadian mRNA expression of metabolic genes with the feeding/fasting cycle, thereby playing a critical role in energy homeostasis.

Reported as: Researchers discover how liver responds so quickly to food

“After mice eat, it looks as if NONO brings all these RNAs together and processes them so they can be used to make proteins,” says Panda.

Panda linked what serious scientists know about food energy-dependent RNA interference to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA and all mutations, which have been linked to all pathology.
See: Energy as information and constrained endogenous RNA interference (video 6.46 minutes)
See also: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy

Wednesday, February 7, 2018 12PM EST (available on demand with registration)

Everything I claimed about the need to link microRNAs to RNA-mediated amino acid substitution ins proteins was included in the context of this Webinar

Within the first 10 minutes, the speaker describes the ability to link specific amino acids to the structure of the protein strand, which allows for the differentiation of pathology from healthy longevity.

Within the first 17 minutes, he links energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution from microtubules to neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, Lewy Body Disease, and ALS.

He adds that others who are interested in his approach may contact him and he many help them to refine their approach.

Simply put, he does not seem to be among a group of competitors with interests that might prevent the dissemination of accurate information or to prevent rapid scientific advances linked from preventative medicine to Precision Medicine via cryo-EM technology.

Keep in mind the fact that Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973), and this claim:

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

Refine your approach to include this fact: Humans And Chimps Differ At Level Of Gene Splicing (2007)

Splicing is the process by which the coding regions of genes are joined to generate genetic messages that specify the production of proteins, the key structural and functional constituents of cells. Splicing can occur in alternative ways in the same genetic message to generate more than one type of protein. The new findings reveal that the alternative splicing process differs significantly between humans and chimpanzees.

See also: Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks (2012)
Stop touting ridiculous theories before everyone who understands the fact that cryo-EM links everything known to serious scientists about the creation of the sun’s anti-entropic virucidal energy from the physiology of reproduction to healthy longevity. Only then will you begin to understand how the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.
Teach your children well. If you teach them to believe in ridiculous theories, your hell will become theirs. Alzheimer’s is a form of hell on Earth, for example.

Crosby, Stills, Nash & Young – Teach Your Children

Here Comes the Sun: A Tribute to George Harrison by Paul Simon, Crosby and Grahm Nash

 

5th-6th Sept 2018 Dublin, Ireland

A mental health problem at the highest level (3)

Summary: It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)
The mental health of so-called science journalists must be addressed. Many of them seem to be pathological liars or, at best biologically uninformed science idiots who cannot link physics and chemistry from molecular epigenetics to all energy-dependent biodiversity on Earth.
The Biggest Myth In Quantum Physics by Ethan Siegel
Conclusion:

Take ourselves out of it, and all we have are the equations, the results, and the answers that the physical Universe gives. Physics cannot answer questions about “why” the Universe works the way it does; it can only explain how it works at all. If you’re interested in the fundamental nature of reality, ask the Universe questions about itself, and when it tells you its secrets, listen. Anything else that you layer atop it was put there by you, not by the Universe. Avoid that temptation, and you’ll never fall for the greatest myth about quantum physics: that it needs an interpretation at all.

The claim that quantum physics does not require a meaningful approach to explaining how energy is linked to all biodiversity in the context of interpretation of facts is ridiculous. Astrophysicist and author Ethan Siegel is the founder and primary writer of the blog “Starts With A Bang!” His books include Treknology and Beyond The Galaxy, Simply put, he is a biologically uniformed science idiot, like others who have failed to link their ridiculous theories to all biodiversity on Earth.
See for comparison: Refined control of cell stemness allowed animal evolution in the oxic realm
Reported as: Why animals diversified on Earth: Cancer research provides clues 

Just the presence of free oxygen is the result of some microbes finding a way of using sunlight to get energy. This was also a biological event.

The difference between how animals diversified and why they diversified is perfectly clear to all serious scientists. Energy is required!
McEwen et al (1964) linked the biological event from the creation of ATP to the creation of RNA and the creation of all biophysically constrained biodiversity. All other serious scientists have since followed his lead. Dobzhansky (1964) suggested that would happen.

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.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

The claims made in the fake news about Donald Trump’s mental state can now be linked to the mental heath of his antagonists who have never seen Dozhansky’s “light of evolution.”
Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

The anti-entropic virucidal effect of sunlight was linked from ecological variation to ecological adaption in all living genera via the pheromone-controlled physiology of reproduction in soil bacteria 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.)

Seventy-four years later we have this example of human idiocy: Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
Reported as: Counting chromosomes: Plant scientists solve a century-old mystery about reproduction (2018)

Today, a team of geneticists reveals a remarkable mechanism that enables plants to count their chromosomes, solving a century-old mystery.

Molecular mechanisms are energy-dependent. That’s no mystery. See: How an RNA gene silences a whole chromosome (2015)
Most science journalists have refused to inform themselves. They have not linked sunlight on contact with water to all energy-dependent biodiversity via the physiology of reproduction. For example, John Hewitt wrote:

If anything we know the Sky Fathers totally forgot about selenium during most of the design phase and then had to write him in at the end as a walk-on.

I was surprised by his sarcastic attack on religion and wrote:

Let’s not do this. See instead: A third of Americans don’t believe in evolution 

Those who do not believe in evolution understand that energy-dependent RNA-mediated amino acid substitutions must be linked from the physiology of reproduction to chromosomal rearrangements that biophysically constrain viral latency. If you can place your claim about selenium into the context of protection of all life on Earth from the virus-driven degradation of messenger RNA, we could discuss your claim. What is it?

John Hewitt wrote:

Sky Daddy likes cranberries so much he gave them sequence-level machinery for producing selenocysteine in their mitochondrial genome

I could not get  him to make sense. I wrote:

This is the type of cryptic sarcastic claim that kills people. Thousands  of them. Quit playing your silly games. Who are you calling “Sky  Daddy?”  Sequence-level molecular machinery does not exist outside the context of the creation of the sun’s anti-entropic virucidal energy. 

For comparison, Roger M. Pearlman wrote:

name one person you know that can explain Neo-Darwinian Theory (NDT) so it adds up, and how you know it adds up otherwise don’t knock the NDT adherents here as they are equally inept at making NDT add up as are the leading NDT scientists

How can anyone who wants to discuss NDT not know about this published work from 1973? Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

The differences in the amino acid sequences are Koonin’s proof of evolution. See: 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.

If the differences in the amino acid sequences are energy-dependent and RNA-mediated, NDT is the most ridiculous example of pseudoscientific nonsense that has every been touted by people who claim to be more intelligent than their primate ancestors.

Proof of that fact was published as: Modern diversification of the amino acid repertoire driven by oxygen

..we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

Selective fixation of amino acid substitutions in organized genomes is energy-dependent and controlled by the physiology of reproduction.

That fact was reported as: Quantum Chemistry Solves The Question of Why Life Needs So Many Amino Acids 

If you were representing the amino acids as circles, they could be drawn as multiple concentric circles representing differing energy levels, rather than one single circle of the same chemical hardness and energy level – kind of like in the photo below.

Few people would make the connection from the amino acids as circles representing different energy levels to the claim that de Vries (1902) made when he invented the term mutation.

See:  What is Life? (1944)

But about forty years ago the Dutchman de Vries discovered that in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule. But quantum theory was but two years old when de Vries first published his discovery, in 1902. Small wonder that it took another generation to discover the intimate connection!

It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)

In the 1991 reprint edition, a forward by Roger Penrose who has co-authored with George F.R. Ellis, Stephen Hawking, Stuart Hameroff and others wrote:

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?

It is worth repeating the claim the food energy is required to link quantum physics from quantum chemistry to quantum biology and quantum souls until all pseudoscientists lean the difference between a mutation and an amino acid substitution. Until then, the mental health problem at the highest level will be maintained at the highest level by the highest level of human idiocy every known to have eliminated common sense from consideration in the context of biologically based cause and effect.

For example, Darwin’s claims were based on “conditions of life” that required all organisms to find food and reproduce. Nothing was known about mutations, and even then Darwin could not possibly have been foolish enough to put them first in the context of natural selection for mutation-driven pathology.

See also: Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics

Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism….

…through which monoallelic gene expression occurs in a parent-of-origin-specific manner.

See: An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
This explains why John Hewitt claims I’m providing BS. He is a biologically uninformed science journalist who does not understand the facts about light energy-dependent changes in organized genomes.
Any journalist who publishes anything like The vibrational theory of olfaction for the win should prepare to defend his claims in the context of serious scientists who know how energy must be linked to the vibrations and how the vibrations link quantum physics from quantum chemistry to quantum souls via the physiology of pheromone-controlled reproduction and fixation of RNA-mediated amino acid substitutions.

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.

A Mathematical Model Links Quantum Physics to Quantum Souls (1)

Historical facts: All energy-dependent cell type differentiation is biophysically constrained by the de novo creation of microRNAs and enzymes that metabolize food and drugs. All food energy-dependent metabolism occurs in the context of microRNA-mediated cause and effect and the physiology of pheromone-controlled reproduction. The food energy-dependent pheromone controlled physiology of reproduction in bacteria links what organisms eat to the transgenerational epigenetic inheritance of their morphological and behavioral phenotypes. The virus-driven degradation of messenger RNA has been linked to all pathology in the context of the National Microbiome Initiative, the Precision Medicine Initiative, Alpha Genomix profiling of pathways linked to the creation of CYP enzymes and test results that differentiate the most likely response to some medications based on fixation of  RNA-mediated amino acid substitutions in the organized genomes of different people and different populations of modern humans.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
The ingestion of sago palm-like leaves linked increased endogenous vitamin C from the stability of the mouse genome to the stability of the organized genome in a modern human population via one base pair change and the fixation of one RNA-mediated amino acid substitution.
See also: Towards a systemic paradigm in carcinogenesis: linking epigenetics and genetics (2015)

The SMT’s [Somatic mutation theory’s] fundamental assumption is that there is no cancer without genetic or chromosomal harm.

See for comparison: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
Watch as 2 of 3 co-authors of the article about can prevention tell the world that cancer is caused by “bad luck.”

Now see one of the 3 co-authors admit to his overwhelming ignorance in: Why Is This Bacterium Hiding in Human Tumors?

“The whole idea of bacteria in tumors is fascinating and unexpected,” said Dr. Bert Vogelstein, a colon cancer researcher at Johns Hopkins.

  1. The fundamental assumption that there is no cancer without genetic or chromosomal harm links the virus-driven degradation of messenger RNA in bacteria to the food energy-dependent pheromone-controlled physiology of reproduction in bacteria and healthy longevity via error-free DNA repair.
  2. The fundamental assumption that there is no cancer without genetic or chromosomal harm links virus-driven pathology to cell type-specific and species-specific pathology in all cell types of all individuals of all living genera via the failure of microRNA-mediated error-free DNA repair.

There is now a mathematical model of top-down causation that links the sun’s anti-entropic virucidal energy on contact with water to the physiology of pheromone-controlled reproduction and all biodiversity via RNA-mediated error-free DNA repair. The mathematical model refutes the pseudoscientific nonsense touted by neo-Darwinian theorists because it starts with the creation of the sun, which biophysically constrains viral latency. The importance of linking this mathematical model to all models of biologically-based cause and effect cannot be overstated.
See: Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules

After the Schrodinger’s intuition, expressed in his book “What is life?” [12], the first systematic approach to a quantum interpretation of biological process dated back to the model proposed by Frohlich [13] several years ago. He suggested the occurrence, in biological matter, of macroscopic quantum phenomena able to explain the energy transport without loss in the living organisms and signal transfer based on collective coherent oscillations associated to a branch of longitudinal
electric modes in the frequency range [ ] also known as Frohlich frequency. So in living systems, according to Frohlich’s model, energy could be stored in a thin two – dimensional layer placed beneath the cell membrane, that in this way would act as a biological superconducting medium, under dipolar propagating waves without thermal loss [13].

The ridiculous assumptions about thermal loss and evolution were placed into the context of other ridiculous assumptions that failed to start from the creation of the sun and link the anti-entropic virucidal energy of the sun from food energy to all biodiversity via the physiology of pheromone-controlled reproduction.
For comparison see: Reversing the thermodynamic arrow of time using quantum correlations

We observe a spontaneous heat flow from the cold to the hot system. This process is enabled by a trade off between correlations and entropy that we quantify with information-theoretical quantities.

Reported as: Experiment shows that arrow of time is a relative concept, not an absolute one

The second law of thermodynamics says that entropy, or disorder, tends to increase over time, which is why everything in the world around us appears to unfold forward in time. But it also explains why hot tea grows cold rather than hot. In this new effort, the researchers found an exception to this rule that works in a way that doesn’t violate the rules of physics as they have been defined.
The idea of entangled particles has been in the news a lot lately as researchers around the world attempt to use it for various purposes—but there is another lesser-known property of particles that is similar in nature, but slightly different. It is when particles become correlated, which means they become linked in ways that do not happen in the larger world. Like entanglement, correlated particles share information, though it is not as strong of a bond. In this new experiment, the researchers used this property to change the direction of the arrow of time.

Succinctly stated as:

This observation did not violate the second law of thermodynamics, the group explains, because the second law assumes there are no correlations between particles.

The ridiculous assumption that there are no correlations between subatomic particles led to assumptions that energy emerged and that all life evolved in the context of mutations and natural selection, which led to the “bad luck” theory of cancer.
Frohlich’s model was dismissed and so was the the fact that “…energy could be stored in a thin two – dimensional layer placed beneath the cell membrane, that in this way would act as a biological superconducting medium, under dipolar propagating waves without thermal loss [13].
[13.] Long-range coherence and energy storage in biological systems (1968)

Biological systems are expected to have a branch of longitudinal electric modes in a frequency region between 1011 and 1012 sec−1. They are based on the dipolar properties of cell membranes; of certain bonds recurring in giant molecules (such as H bonds) and possibly on pockets of non-localized electrons. In Section 2 it is shown quit generally that if energy is supplied above a certain mean rate to such a branch, then a steady state will be reached in which a single mode of this branch is very strongly excited. The supplied energy is thus not completely thermalized but stored in a highly ordered fashion. This order expresses itself in long-range phase correlations; the phenomenon has considerable similarity with the low-temperature condensation of a Bose gas. General consequences and proposals of experiments are discussed in section 3.

Four years earlier, McEwen et al., (1964) linked the creation of the sun’s anti-entropic virucidal energy to the creation of ATP and the creation of RNA.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

That same year, Dobzhansky (1964) first asserted this claim:

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.

In 1973, Dobzhansky again mocked all the pseudoscientists whose mathematical model failed to link the creation of the sun’s anti-entropic energy from the physiology of pheromone-controlled reproduction to RNA-mediated fixation of amino acid substitutions that differentiate all cell types in all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
He assumed that all serious scientists would recognize that the light of evolution linked Schrodinger’s claims about sunlight to all biodiversity via the food energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions.
He claimed

“…one can calculate the minimum numbers of single mutations needed to change the cytochrome C of one organism into that of another.”

He linked that calculation to this fact:

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

The levels of complexity that must be addressed by the calculations have since been addressed and reported in: Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules
Nothing has changed about the facts that all serious scientists have linked from biophysically constrained viral latency to all biodiversity via the physiology of pheromone-controlled reproduction.
For example, see: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

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

Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

See also:

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

In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “What is Life?”

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?

For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:

The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level).  Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues.  This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.

Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor.  HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions.  That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.

I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

CONCLUSIONS:

We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors.  A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:

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.

Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done.
See for instance:

3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.

My comment:  After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:

Complex spike patterns in olfactory bulb neuronal networks

Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.

Abstract excerpt:

BACKGROUND:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My conclusion: People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.

Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.

See also 3/18/17: [MODERATOR NOTE: I’m posting this submission even though it misquotes Feierman, who did not ever say or imply that “adaptations randomly occur.” jrf]
See alson 3/18/17: [MODERATOR NOTE: Adaptations and mutations are not synonyms. An adaptation is a mutation acted upon by natural selection to configure a population to the current environment. It would be an oxymoron to say that “adaptations randomly occur.” By definition, adaptations are mutations that have been acted upon by natural selection by which their frequency is increased in a population over time in a specific environment. jrf]

amino acid homeostasis

Energy-dependent pheromone-controlled entropy (4)

Solar-driven reforming of lignocellulose to H2 with a CdS/CdOx photocatalyst
Reported as: Scientists harness solar power to produce clean hydrogen from biomass
They claim that the rigid structure of nature’s equivalent to armored concrete evolved to protect plants and trees from degradation. They don’t make claims about what might cause the degradation.
They start with the likelihood that degradation automagically occurs. That led them to design a combination of catalyst and solution that mimics how the anti-entropic energy of sunlight is linked to the potential of hydrogen, which is referred to as pH. Their design allowed them to extract the potential of hydrogen in the context of naturally occurring hydrogen-atom transfer in DNA base pairs in solution. They placed their simple design into the context of the evolution of armored concrete.

Pieces of wood, paper and leaves were placed in test tubes and exposed to solar light.

Their sunlight-powered extraction technology reminds me Schrodinger’s (1944) inference. Schrodinger seemed to suggest that someone designed an anti-entropic force, when he attempted to support the answer to his question: “What is Life.”
Theosophically, the God of the Holy Bible and Schrodinger both seemed to be saying that God might have used “the force” as if it came from the “Star Wars” series of movies. The sun could be like other stars and brave souls used “the force” to protect other people from harm.
In the context of the movies series, God, Schrodinger, and all serious scientists have detailed every aspect of how the conserved molecular mechanisms of RNA-mediated protein folding chemistry protect all organized genomes from virus-driven energy theft and genomic entropy.
For comparison, their design enables the production of clean hydrogen from unprocessed biomass. They think they have created a viable alternative to high temperature gasification, which appears to be a renewable means of hydrogen production. It could be compared to God’s way of ensuring that food energy is linked to the physiology of reproduction via endogenous RNA interference and to all biodiversity via energy-dependent biophysically constrained supercoiled DNA. The supercoiled DNA is the linked to chromosomal rearrangements that protect organisms from evolving into something different than their ancestors.
However, their design runs in reverse. They are taking the hydrogen energy out instead of putting it into supercoiled DNA via what is known about quantum physics and how subatomic particles must be linked to the energy-dependent de novo creation of all biodiversity and/or the virus-driven energy theft that appears to be destroying it.

For comparison, this claim links the anti-entropic virucidal energy of sunlight on contact with water from the creation of nucleic acid precursors to all healthy longevity and biodiversity on Earth via the physiology of reproduction.
Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

Viruses proliferate at the expense of their hosts. …approximately 25% of viruses released by lysed prokaryotic cells are decomposed at fast rates. We show that… virus decomposition provides a major source of labile organic compounds able to sustain the microbial food webs and nutrient cycling at a global scale.

If you are a theorist who still does not know where the anti-entropic force comes from that prevents virus-driven energy theft from destroying all life on earth, find out more about how the virucidal effect of sunlight feeds the world in the context of the nutrient energy-dependent pheromone controlled physiology of reproduction.
It may be too late for you to become a serious scientist, but at least you will not continue to be one of the pseudoscientists who had us outnumbered since the time neo-Darwinism was invented.
See for an example of a pseudoscientist:
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.

Biology to a Physicist

Theorists sell hidden energy (2)

Theorists sell hidden energy (Jan 5, 2017)

January 6, 2017 Giant atoms could help unveil ‘dark matter’ and other cosmic secrets

The universe is an astonishingly secretive place. Mysterious substances known as dark matter and dark energy account for some 95% of it. Despite huge effort to find out what they are, we simply don’t know.

Our model is based on the fact that weakly interacting particles must bounce from the nucleus of the atom it collides with and exchange a small amount of energy with it – similar to the collision between two pool balls. The energy exchange will produce a sudden displacement of the nucleus that will eventually be felt by the electron. This means the entire energy of the atom changes, which can be analysed to obtain information about the properties of the colliding particle.

They do not have a model that is based on any facts. They have a theory that is based on other theories. For comparison, this is a model of biologically-based cause and effect.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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

Many theorists recognize the problem with my model of adaptively evolved behavior. There is no such thing as an evolved behavior!
Ecological variation must link nutrient energy-dependent biophysically constrained RNA-mediated protein folding chemistry to supercoiled DNA or it must link virus-driven energy theft to all pathology.  Serious scientists have linked energy-dependent changes from angstroms to ecosystems. They started with Schrodinger’s anti-entropic energy of sunlight and linked it to the physiology of pheromone-controlled reproduction.
Pseudoscientists who have ignored all the claims made by Schrodinger (1944) in “What is Life?” are making desperate attempts to convince others that they know the difference between life and death, even though they do not know the difference between healthy longevity and all pathology is virus-driven energy theft.
See: CDC forced to release documents showing they Knew Vaccine Preservative Causes Autism
Thimerosal, is metabolized (converted) into the toxic and “harmful” methylmercury. And then in turn, the harmful methylmercury is metabolized (converted) into the most harmful, long-term-toxic, “inorganic” mercury that is retained in bodily tissue.

“Inorganic” mercury is the end product of mercury metabolism. Methylmercury subject groups confirm that the metabolic pathway for mercury in the human and animal body consists in the reduction/conversion of the harmful methylmercury into a more harmful “inorganic” mercury which is tissue-bound, and long-term-toxic. Hence, both the originating substance (methylmercury) and its conversion/reduction, inorganic mercury are found.

Based on published findings by Dr. Paul King, the metabolic pathway for organic mercury involves the conversion of Ethylmercury (Thimerosal) into “methylmercury” and then the further reduction of “methylmercury” into inorganic mercury.

This is why it is important to link chirality to autophagy and RNA-mediated protein folding chemistry to supercoiled DNA. Those who cannot link metabolic networks to genetic networks via the conserved molecular mechanisms that start from the creation of hydrogen, will fail to link pH from single nucleotide polymorphisms an natural selection for energy-dependent codon optimality. They will fail to link supercoiled DNA to protection from virus-driven energy theft and genomic entropy. They will fail to protect you from disease and tell you that all pathology is caused by random mutations and evolution. They cannot find where the energy came from in Schrodinger’s equation, and they will try anything to make you think they are experts on all aspects of emergence and evolution.
See for follow-up: Thimerosal Hooker
See also: Monks in High Towers: A Plea to Our Fellow Academics

We should remember that the creation of knowledge is generally a positive sum game. When practitioners in one field make progress and gain insight, all fields stand to benefit. Our fates are intertwined. Border patrolling and tower guarding will hurt everyone. The monks in high towers should recognize that apprenticeships in other towers are not only helpful, they are essential for both the creation and conservation of understanding and knowledge.

On January 5, 2017 I published this to my blog site: “Theorists sell hidden energy” Simply put, natural selection for energy-dependent codon optimality is obviously the link to healthy longevity, and virus-driven energy theft is obviously the link to all pathology.
The facts that link energy-dependent chirality to autophagy and the transgenerational epigenetic inheritance of supercoiled DNA, which protects all organized genomes from virus-driven entropy, are no longer disputed by serious scientists. The serious scientists have linked Thomas Hunt Morgan’s claims about chromosomal inheritance from Schrodinger’s claims to Dobzhansky’s claims about RNA-mediated amino acid substitutions as the source of all energy-dependent biodiversity.
Clearly, the monks in their towers have all but died out to make room for the inevitable — a decades-old paradigm shift that started with two outsiders who were helped by a insider. The insider, Milton Diamond, was subsequently forced outside because he challenged the nature vs nurture nonsense touted by John Money.
See “From Fertilization to Adult Sexual Behavior” (1996) and “follow the Money” from then to the claims still made now by the old monks whose towers are collapsing in their ignorance of biologically-based cause and effect.

See also: Bacteria deployed to destroy mosquito-borne dengue can’t take the heat

Mr Ross’s findings may lead to the deployment of temperature-resistant strains of Wolbachia in Aedes aegypti and other mosquito species in the field.

The fact that temperature-resistant stains have only recently been considered attests to the fact that most researchers do not understand enough about physics, chemistry, and molecular epigenetics to predict that biologically-based life must consistently adapt to ecological change or species become extinct. Bacteria and other living genera do not mutate for the purpose of natural selection which reportedly linked natural selection to the evolution of all biodiversity without consideration for thermodynamic cycles of protein biosynthesis and degradation.
See: Mutation-Driven Evolution (p. 196)

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.

See for comparison: Virus-driven mutation or amino acid substitution 

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] 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.

See also: Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Physics

Invisible dark matter

Scientists looking for invisible dark matter can’t find any

Excerpt: “Over 80 percent of our matter is in this dark matter form. You and I are the flotsam and jetsam; dark matter is the sea,” Gaitskell said. “That’s why one doesn’t give up. We’ve got to figure out what this dark matter component is.”

When pressed, Gaitskell acknowledged the possibility, however slight and unlikely, that scientists are looking for something that isn’t there.

See also: Architecture of the symmetric core of the nuclear pore
Uniting Cryo-ET and Cryo-EM places what’s known about ecological variation and ecological adaptation on Earth into the context of what is known about links from angstroms to ecosystems via the structure and function of macromolecular assemblies.
When researchers fail to discover anything new about dark matter but discover new interactions between quantized energy (sunlight) and water molecules that were unexpected, they inadvertently support the claims of serious scientists that can be interpreted in the context of facts. The shows that most theorists cannot answer even the most basic questions that Schrodinger (1944) addressed in “What is Life?”