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.
 

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Nature vs Science and Autophagy.pro

Conclusion: The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.


Until the day that I launched Autophagy.pro, I had only one or two Facebook posts that were marked as spam. Since December 11, 2017, I have had ~5 posts marked as spam.

See for example: This comment was marked as spam at Ciência Biomédica, when I responded to  Synthetic protein packages its own genetic material and evolves

Packaging is energy-dependent and biophysically constrained. Nothing evolves. The concept is foolish. See: A universal trend of amino acid gain and loss in protein evolution 
Excerpt: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
 
Laboratory co-oximeters determine the %HbO2 (%SaO2 ) by measuring the amount a specific frequency of light is absorbed as it passes through a known volume of blood. In contrast, pulse oximetry (SpO2) measures the change in light absorbed at systole and diastole. This allows the pulse oximeter to distinguish between the constant amount of light absorbed by the tissue, bone, venous blood, etc. from the arterial blood (the blood in the volume change due to the pulse).
 
The amount of light absorbed by the tissue, bone, venous blood etc., varies in the context of hydrogen-atom transfer in DNA base pairs in solution. Blood gas analysis in the medical laboratory links differences in hydrogen (H2) — as in H2O from quantized energy-dependent changes in the potential of hydrogen (pH) to all biophysically constrained biodiversity.
 

Measuring pH links what is known about nutritional epigenetics from the innate immune system to healthy longevity via everything known about autophagy. The measurements can be compared in the context of  what is known about virus-driven energy theft, which links stress from the replication of viruses to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

For example in a mammal, see: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin (June 14, 2013)

See Fig. 2 Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively.

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My comment to the Science site (submitted 6/14/13 published 6/20/13):

In my model species-specific epistasis is nutrient-dependent and pheromone-controlled. An additional example of this showed up earlier this week in the context of the epigenetically-effected microRNA/messenger RNA balance: “miR-124 controls male reproductive success in Drosophila”

miR-14 acts in neurosecretory cells in the adult brain to control metabolism and miR-124 acts in the context of brain-directed neuroendocrine control of sexual differentiation and male pheromone production, which is controlled in mammals by gonadotropin-releasing hormone (GnRH) neurosecretory cells of the hypothalamus.

We can anticipate extension to mammals of the Drosophila model from the abstract of a forthcoming Science article: “MiR-200b and miR-429 Function in Mouse Ovulation and Are Essential for Female Fertility.” Given our earlier work in the context of molecular epigenetics and the concept of alternative splicings and sexual differentiation in Drosophila and C. elegans, I suspect we will see evidence for nutrient-dependent adaptive evolution of GnRH pulse frequency-controlled LH secretion and pheromone-controlled female fertility in mice.

If I’m correct, this evidence will link glucose and pheromones to feedback loops that control reproduction in invertebrates and vertebrates. (See Nutrient–dependent / pheromone–controlled adaptive evolution: a model). Model organisms exemplify these feedback loops in microbes, nematodes, insects, and other mammals. The mouse to human example that Kamberov et al., and Grossman et al., detailed is the most telling.

A single amino acid substitution appears to result in what seem to be nutrient-dependent changes in the thermodynamics of intracellular signaling, intranuclear interactions, stochastic gene expression, and selection for phenotype via organism-level thermoregulation in a human population that arose in what is now central China during the past ~30K years.

Using a model that integrates what is known about the common molecular mechanisms may help establish whether adaptive mutations lead to thermodynamic effects on organism-level thermoregulation and epistasis, or whether epigenetic effects of nutrients and their metabolism to species-specific pheromones that control reproduction via changes in the microRNA/messenger RNA balance are the driving force behind adaptive evolution in species from microbes to man.

See: Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys
Reported as:  Estrogen discovery could shed new light on fertility problems December 12, 2017

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

The feedback loop is food energy-dependent and pheromone-controlled.
See: Feedback loops link odor and pheromone signaling with reproduction
Energy-dependent autophagy is the link from feedback loops to ecological adaptation. Science Magazine now has the opportunity to challenge the pseudoscientific nonsense of published works from the Nature Publishing Group. There is no need to consider mutations and evolution outside the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.
See also: Combating Evolution to Fight Disease

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

The retraction of Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication attests to the amount of pseudoscientific nonsense published by the “Nature Publications Group” during the past few decades.
See: Retraction Watch

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

How many others who published via the Nature Publishing Group were blinded by their belief in pseudoscientific nonsense that failed to link the food energy-dependent creation of enzymes and the creation of RNA from blood gas analyses to patient outcomes?
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

Who did not know that? How did non-enzymatic RNA replication become a non-energy-dependent consideration for anyone associated with the Nature Publishing Group?
See for comparison: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40

Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB–mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis.

The global conformational change that allosterically realigns active-site residues (i.e., amino acids), accelerating catalysis, is an energy-dependent change.
Reported as:  Scientists unlock structure of mTOR, a key cancer cell signaling protein

1) Like many proteins, mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules.

The creation of the enzymatic activity of mTOR is quantized energy-dependent and it links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency via autophagy. The retractions of Jack Szostak’s nonsense about the magical creation of enzymes after the energy of life emerged and organisms subsequently evolved in the context of differences in H2 to all biodiversity on Earth, can be placed into the context works by serious scientists.

2)  …mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules. From that 2013 study, which took more than five years to complete, the team learned some key things about the protein, such as what the ATP-binding site looks like…

The study that took more than 5 years to complete was published as: mTOR kinase structure, mechanism and regulation

The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.

They had experimental evidence of energy-dependent changes in active-site residues (i.e., amino acids). They subsequently failed to link anything known to serious scientists about the energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction. They seemingly ignored all claims about RNA-mediated amino acid substitutions in the context of autophagy, which links base pair changes from changes in the microRNA/messenger RNA balance to RNA editing.
How could the Nature Publishing Group not know what all serious scientists know?
See for example: All Nobel Laureates in Physiology or Medicine

The Nobel Prize in Physiology or Medicine 2017

Jeffrey C. Hall, Michael Rosbash and Michael W. Young

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The molecular mechanisms are energy-dependent.
Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels  (1990) Hardin, Hall and Michael Rosbash
Who, besides Jack Szostak, does not know that the creation of energy must be linked to RNA-mediated cell type differentiation via messenger RNA levels?

The Nobel Prize in Physiology or Medicine 2009

Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”

Where did the enzyme telomerase come from?
Face the facts, Jack (Szostak) and others. Cell type differentiation is food energy-dependent and biophysically constrained at every level of examination. Biophysical constraints on viral latency are required for ecological adaptation. The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It’s all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.
See:  Structural diversity of supercoiled DNA

Alternative splicing of pre-mRNA

Methylation and the Innate Immune System

Free Webinar Training:

Methylation and the Innate Immune System

Please send your questions, comments and feedback to: support@qahomestudy.com

I sent these two questions in advance:

1) Does what organisms eat link food energy to RNA-directed DNA methylation and all healthy longevity via fixation of amino acid substitutions and transgenerational epigenetic inheritance in the context of the physiology of pheromone-controlled reproduction in species from microbes to humans?

2) Does the virus-driven theft of quantized energy link the loss of information from impaired methylation to all pathology?

——————————

See why I asked: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: Olfaction Warps Visual Time Perception



"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Robert Sapolsky's legacy of atheistic pseudoscientific nonsense

Summary: Not only does everything known to serious scientists about energy link RNA synthesis to life, everything McEwen and others have published links nutrient stress and/or social stress to the virus-driven degradation of messenger RNA and all pathology.
As moderator of the International Society for Human Ethology (ISHE), a not-for-profit scientific organization that consistently touts pseudoscientific nonsense in the context of neo-Darwinian evolution, Jay R. Feierman’s attacks on the works of serous scientists are increasing in frequency and in magnitude. Yesterday, he posted this link to a series of 25 lectures by Robert Sapolsky.  You could spend ~25 hours to learn what Sapolsky was teaching to students until 2011, or ignore everything he has claimed because he has been teaching atheistic pseudoscientific nonsense in the context of neo-Darwinian theory.

Today, Jay F. Feierman’s attacks on the works of serous scientists began with this:
Examining non-LTR retrotransposons in the context of the evolving primate brain

Although all mutational types have worked in concert with evolutionary forces to generate the current human brain, in this review we will explore the impact of mobile elements…

Robert Sapolsky may be responsible for many of these ridiculous reports on the evolving primate brain. Sapolsky studied under Bruce McEwen, but Sapolsky failed to link energy as information from an endogenous substrate in all cell types to the light-activated creation of ATP and the creation of RNA in microbes like P. fluorescens.
With exposure to ultraviolet light, this species (P. fluorescens) fluoresces. The weekend resurrection of the bacterial flagellum was also reported in this species. The energy-dependent physiology of pheromone-controlled reproduction links the creation of the sun from the creation of ATP and the creation of RNA to the weekend resurrection of an irreducibly complex functional structure and all biophysically constrained biodiversity on Earth via McEwen et al., (1964). Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Not only does everything known to serious scientists about energy link RNA synthesis to life, everything McEwen and others have published links nutrient stress and/or social stress to the virus-driven degradation of messenger RNA and all pathology.
Sapolsky is reported to be an atheist in a Wikipedia entry. That should not matter to anyone who is capable of linking quantized energy from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum. See: Olfaction Warps Visual Time Perception But, for those of us who have followed McEwen’s lead, and done that, Sapolsky’s lectures attest to his atheistic ignorance of biologically-based cause and effect.
His lectures can be viewed as examples of the human idiocy that Feynman mentioned in the context of the different measures used to make claims about energy as information. The origin of information still appears to come from the sun despite the fact that Feynman used the example of food energy. The history of publications on how the virus-driven energy theft of quantized energy has been linked from mutations to all pathology now includes information about how human endogenous retroviruses must be biophysically constrained.
The information is linked from energy as information to the physiology of pheromone-controlled reproduction in Bombyx mori to the control of cellular processing in mammals by everything I have published since 1995 and everything known about the creation of the innate immune system in bacteria (CRISPR). The works of those who claim that the emergence of energy and “evolution did it” can be compared to the works of serious scientists.
See for examples: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors (2012)
Transposable-element associated small RNAs in Bombyx mori genome (2012)
Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses (2012)
Control of mammalian retrotransposons by cellular RNA processing activities (2014)
Protein-Coding Genes’ Retrocopies and Their Functions (2017)
Identification and characterization of two putative microRNAs encoded by Bombyx mori cypovirus (2017)

This is the first report that an insect double stranded RNA virus may generate miRNAs and the results obtained will benefit the future study of the functions of BmCPV-encoded miRNAs on viral replication and virus-host interaction.

Pheromones (Ectohormones) in Insects (1959)

Independently of Butenandt & Hecker (14, 50), the fractionation of Bombyx extracts and purification of the pheromone was also reported on by Makino et at. (71).

Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) by FRITZ, IRVING B. and MCEWEN, BRUCE
Since 1959, McEwen and many others have linked food energy and pheromones to the biophysically constrained viral latency that ensures the survival of all species.  See also: Feedback loops link odor and pheromone signaling with reproduction
Since the time I met him in 1995, Jay R. Feierman has contributed to the unnecessary suffering and premature death of thousands via his misrepresentations of the facts about food energy-dependent pheromone-controlled RNA-mediated cell type differentiation.
See: Environment and Neurodegenerative Diseases: an Update on miRNA Role
I’m beginning to think that the most obvious way to prevent the deaths by suicide of our veterans is not something that will be discussed in any scientific forum or on most forms of social media.
See for comparison:
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.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (6)

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology.

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

See first: Energy-dependent physical and biophysical constraints (5)
See next: Design of a synthetic yeast genome
They use what occurs in the context of natural selection for quantized energy-dependent changes in base pairs and link RNA-mediated amino acid substitutions from changes in enzymes and feedback loops. The feedback loops link the pheromone-controlled de novo creation of more receptors via the physiology of reproduction, which biophysically constrains viral latency in all organized genomes.
Their work was reported today, July 26, 2017 in the context of Scientists build DNA from scratch to alter life’s blueprint with my emphasis

Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to “rewrite” the yeast genome, following a detailed plan they published in March.

The research may reveal basic, hidden rules that govern the structure and functioning of genomes.

All serious scientists known that the structure and function of all organized genomes is energy-dependent and RNA-mediated. For example, in all animals the functional structure of supercoiled DNA is controlled by food odors and pheromones in the context of the physiology of energy-dependent reproduction that links food energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Alternatively, virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.

See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The question arises: Does Boeke or anyone like him know that the organized genome of yeast is rewritten only in the context of the food energy-dependent pheromone-controlled biophysical constraints on viral latency? I ask because he may be hiding something. Anyone who does not know how chirality and autophagy biophysically constrain viral latency is not likely to have written a book chapter like this, which was co-authored by J.D. Boeke in 1988.

See: Yeast Ty Elements as Retroviruses in  Viruses of Fungi and Simple Eukaryotes

The title of J.D. Boeke’s latest effort: Design of a synthetic yeast genome, would make any young earth creationist proud of his Boeke’s accomplishment. It attests to facts about “design” that atheistic hate mongers like Richard Dawkins and other pseudoscientists have linked from mutations and natural selection to evolution.

See: Mutation-Driven Evolution

See also for example: Magnus S. Magnusson’s comments on Richard Dawkins event cancelled over his ‘abusive speech against Islam’ Magunsson started removing my responses a few hours ago.

I attempted to discuss the fact that Boeke and others use base substitutions within ORFs to introduce or remove enzyme recognition sites. That is how they facilitate the energy-dependent assembly of synthetic chromosomes.

But there’s more! Boeke’s history of publications links nearly 30 years of pseudoscientific nonsense to an impressive refutation of neo-Darwinian theory. The design of the synthetic yeast genome via the energy-dependent assembly of synthetic chromosomes attests to the fact that natural selection for energy-dependent codon optimality is the link to the design of all biophysically constrained biodiversity.

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

Some people might think that pseudoscientists can recover from refutation linked to the stability of messenger RNA (mRNA), but the recovery time ended two decades ago with publication of From Fertilization to Adult Sexual Behavior

See our section on molecular epigenetics.

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…

The proteins do not automagically create themselves. Energy-dependent changes in chirality must be linked from autophagy to biophysically constrained viral latency. In that context, this report is another clear refutation of mutation-driven evolution.

See: Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing

These data reveal the immense promise of in situ albumin targeting for development of translational, carrier-free RNAi-based cancer therapies.

The increased amount of information on naturally occurring energy-dependent RNA interference (RNAi) linked to cancer treatment was reported as: Molecular hitchhiker on human protein signals tumors to self-destruct

“What fascinates and excites me most about this approach, in addition to improved tumor penetration, is lack of toxicity at a relatively high dose,” she said. “We could potentially use our siRNA delivery system to target several genes simultaneously or sequentially. Most cancers are driven by multiple abnormal genes, so targeting one often leads to activation of others as the tumor adapts.”

Tumors do not adapt. Viruses quickly adapt via energy theft and the substitutions of amino acids in their genomes. The amino acid substitutions in the tumors cause the tumors to adapt to the lack of energy-dependent microRNAs carried by albumin. That is how virus-driven energy theft is linked to the proliferation of undifferentiated cell types in all tissues of all organisms.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The energy-dependent microRNA flanking sequences do not evolve and genes do not assemble themselves.  Quantized energy as information biophysically constrains virus-driven energy theft, which would otherwise link mutations to all pathology.

Young earth creationists recently placed the virus-driven theft of quantized energy into the context of Cancer Research Confirms the Curse.

…the cancer-suppressing molecule NAD+ diminishes with age appeared in the same Science issue.3Harvard Medical School News summarized the findings. As NAD+ lessens, “DNA breaks go unrepaired and, as these breaks accumulate over time, precipitate cell damage, cell mutations, cell death and loss of organ function.”4 It seems the only way to cure cancer would be to somehow reach into and constantly correct every cell’s mutations.

Carrier-free gene silencing links femtosecond blasts of UV light from the anti-entropic virucidal effects of sunlight on contact with water to everything serious scientists know about food energy-dependent top-down causation and changes in the microRNA/messenger RNA balance, which have been linked to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

A femtosecond is the SI unit of time equal to 10−15 or 1/1,000,000,000,000,000 of a second; that is, one quadrillionth, or one millionth of one billionth, of a second.[1] For context, a femtosecond is to a second as a second is to about 31.71 million years; a ray of light travels approximately 0.3 µm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.[2]

For comparison: One picosecond is equal to 1000 femtoseconds (fs). Theoretical physicists who thought they knew something about the nature of quantum coherence based their theories on measurements of timescales up to 1.5 picoseconds (ps), but they have since learned that decoherence occurs within 60 fs. The transfer of energy in the context of photosynthesis clearly links the anti-entropic virucidal energy of UV light to RNA-mediated DNA repair in much less time than theorists realized.

See: Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

See also: OLYMPUS experiment sheds light on structure of protons

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The differences in the energy of photons and the amount of time it takes for energy-dependent RNA-mediated DNA repair link displays of ignorance by Magnus S. Magnusson and other atheistic hate-mongers that can be compared to any display by anyone who has ever been involved in linking pattern recognition to biophysically constrained life on Earth.

For comparison, that is what young earth creationists have done with the information about energy as information from Biblical Genesis.

See also: One billion suns: World’s brightest laser sparks new behavior in light

The light’s coming off at different angles, with different colors, depending on how bright it is.

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

See: The Reality of Color Is Perception

Color is one of the longstanding puzzles in philosophy, raising doubts about the truthfulness of our sensory grasp on things, and provoking concerns as to the metaphysical compatibility of scientific, perceptual, and common sense representations of the world. Most philosophers have argued that colors are either real or not real, physical or psychological. The greater challenge is to theorize the subtle way that color stands between our understanding of the physical and the psychological.

See for comparison: Olfaction Warps Visual Time Perception

The fact that olfaction warps visual time perception links the speed of light on contact with water from the visual appeal of a rainbow to the integration of all sensory input and our appreciation of how energy and mass are linked across the time-space continuum via what is known about the sense of smell in bacteria and the food energy-dependent pheromone-controlled physiology of reproduction in all living genera.

For comparison, Magnus S. Magnusson co-authored “Complex spike patterns in olfactory bulb neuronal networks”  He and his colleagues failed to link fast decoherence from the anti-entropic virucidal energy of sunlight to all biodiversity via the physiology of reproduction and RNA-mediated DNA repair.

In the world of those who have consistently linked olfaction to our visual perception of energy and mass in the context of the space-time continuum, Magnusson can be referred to as a biologically uninformed science idiot — if only because he has no expertise in any scientific discipline.

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology via the difference between “Nature” and God’s perfect “Creation.”

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

Although that fact has been repeatedly revealed in the extant scientific literature, which includes texts like the Holy Bible, atheistic hate-mongers refuse to read anything that challenges their beliefs at the same time they either claim to believe in nothing or attack the beliefs of intelligent scientists.

See for examples of what pseudoscientists are likely to believe.

This New Equation Could Unite The Two Biggest Theories in Physics

Quantum entanglement… describes the way that two particles can interact in such a way that they become inexorably linked, and essentially ‘share’ an existence.

The Universe According to Emmy Noethe

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

That claim forced others to make their ridiculous theories fit into the context of “…the idea that the Universe expanded just like a balloon shortly after the Big Bang.”

Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

…three physicists heavily criticised inflation theory – the idea that the Universe expanded just like a balloon shortly after the Big Bang. The article went as far as claiming that the model “cannot be evaluated using the scientific method” – the academic equivalent of saying it isn’t even real science.

Cytosis

From E. coli to monkeys and mankind: Theories vs models (2)

Dedicated to Dr. Tom Jordan and Priscilla Jordan on the day of their retirement from the Baptist ministry, May 28, 2017. They always encouraged me to learn more about the “Laws of Biology” and link the Laws from energy as information to all biodiversity on Earth via the physiology of reproduction.

See also: From E. coli to monkeys and mankind: Theories vs models

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding (5/23/127)

…changes in observed association and dissociation, suggesting the possibility of kinetic and thermodynamic tuning of Cas9 behavior.

Simply put, the technology didn’t work. That’s a problem for CRISPR/Cas9 advocates (see the incessant barrage of CRISPR/Cas9 promotion on the closed FB group CRISPR Cas9).

Advocates will be forced to accept the fact that natural selection for energy-dependent codon optimality has always been the link from ecological variation to ecological adaptation via food odors and pheromones.

Suggesting the possibility of kinetic and thermodynamic tuning is akin to telling all serious scientists that, until now, the innate immune system of bacteria and the CRISPR Cas technology has not been examined inside the context of the Laws of Physics and the Basic Principles of chemistry. The Laws and the Basic Principles must link RNA-mediated protein folding chemistry from the physiology of reproduction to all food energy-dependent pheromone-controlled behavior in species from microbes to humans via amino acid substitutions in supercoiled DNA.
 

That fact separates the serious scientists from the pseudoscientists who have refused to examine other facts about biologically-based biophysically constrained protein folding chemistry. The facts start with the sun’s anti-entropic virucidal energy as information and the energy as information has been linked to all cell type differentiation by these researchers.

See: Mechanism of transmembrane signaling by sensor histidine kinases (5/18/17)

Reported as: Scientists investigate how the sense of smell works in bacteria

The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

My summary of the signalling mechanism, which links subatomic particles to cell type differentiation in all living genera via the sense of smell in bacteria:

The active and inactive signaling states link energy-dependent changes from angstroms to ecosystems via slight variations at the nitrate-binding site. When the ion binds to the sensor, a change in 0.5-1 angstroms (approximately one fifth of the size of the ion itself) causes a change in the protein that links input from the sensor to a change in the output that varies by as much as 7 angstroms.

In the context of what is known about food energy-dependent pheromone-controlled quorum sensing in bacteria, the change in 0.5-1 angstroms can be linked from the changes in 7 angstroms to base pair changes and amino acid substitutions that stabilize the organized genomes of species from E. coli to primates in the context of all energy-dependent interactive ecosystems, which appear to have existed from the dawn of Creation.

For example, the link from energy-dependent changes in angstroms to ecosystems in all vertebrates is mentioned in the title of this published work: The zinc spark is an inorganic signature of human egg activation. 

The spark that links inorganic material to organic life was placed into the context of our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. See our section on molecular distance in: From Fertilization to Adult Sexual Behavior.

Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993). While ramifications of these centimorgan sexual dimorphisms are not yet clearly established, in recent years cis- and trans-acting factors contributing to these recombination length differences have been reported for a specific part of the murine major histocompatibility complex (MHC) (Shiroishi, Sagai, Hanzawa, Gotoh, and Moriwaki, 1991).

Simply put, the cited works linked energy-dependent changes from angstroms to ecosystems via the innate immune system of bacteria, which was linked to sex differences in chromosomes. Note the difference between our accurate representation of biophysically constrained energy-dependent chromosomal inheritance and the claims in: Sex chromosome evolution: historical insights and future perspectives

Conclusion:

…a direct experimental test of the steps in sex chromosome evolution constitutes more robust evidence than a comparative study, especially considering the new manipulative possibilities opened up by the CRISPR/Cas9 system [105]. In any case, the field of sex chromosome evolution seems likely to remain active and dynamic for many years to come.

Reported as: Knowledge gap on the origin of sex

The review shows that the significance of ecology has not been sufficiently noted. Therefore, the biologists in Lund call for more research on how the living environment of a population affects the development and evolution of sex chromosomes. This could include factors such as access to food, age variations within a population or the consequences for sex chromosomes when populations that have lived separately meet and mix.

The fact that others still claim that the origin of sex has not already been linked from factors such as access to food, age variations within a population or the consequences for sex chromosomes attests to the ignorance of theorists. The fact that theorists want to attempt to evoke aspects of the CRISPR Cas9 technology in attempts to explain sexual differentiation attests to the ignorance of those who think more research is required to link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction and chromosomal inheritance.

Energy-dependent changes were linked from angstroms to ecosystems in all living genera in this published work: Structural diversity of supercoiled DNA (10/12/15) and in this parody from 12/10/14.

See also: Origins of Life: A Problem for Physics

The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

See for comparison: The Chirality Of Life: From Phase Transitions To Astrobiology

A key missing piece is the origin of biomolecular homochirality: permeating almost every life-form on Earth is the presence of exclusively levorotary amino acids and dextrorotary sugars.

Watch as Jeremy England eliminates any discussion of light activated endogenous substrates in the context of microRNAs linked to the energy-dependent creation of exclusively levorotary amino acids and dextrorotary sugars.

A New Physics Theory of Life

You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.

If another ridiculous theory emerged, will it explain anything outside the context of experimental evidence that links energy as information to biophysically constrained cell type differentiation via the physiology of reproduction in all living genera? For example, what theory might emerge to explain how an infection in the throat is linked to mental disorders in adults.

See: Streptococcal throat infection linked to mental disorders

The researchers found that the risk of any mental disorder was increased for individuals with a positive streptococcal test compared to those without a streptococcal test…

Watch a biologist fail to link physics and chemistry from the strep infection to brain development via the innate immune system and molecular epigenetics as he explains CRISPR at 5 different levels of his ignorance. 5/24/17

 

The speaker is a co-author of: Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis 3/5/15

In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.

Reported as: In vivo CRISPR-Cas9 screen sheds light on cancer metastasis and tumor evolution

The results highlighted some well-known tumor suppressor genes in human cancer, including Pten, Cdkn2a, and Nf2, but included some genes not previously linked to cancer. Unexpectedly, the screen also implicated several microRNAs — small RNA segments that are functional in the cell.

Neville E Sanjana, has now linked his ignorance from 2015 to assays that link energy-dependent microRNAs to healthy longevity or from virus-driven energy theft to all pathology. Kaveli Kull attests to the fact about what loser must do, when facts replace their ridiculous theories about genome editing.

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

Anyone who has tried to explain what humans are made of without linking energy from the light activated endogenous substrate that links ATP to the creation of RNA via microRNAs in the context of what is now being referred to as endogenous RNA interference may not recognize how desperate evolutionary theorists have become in their attempt to make others think that all neo-Darwinian theorists are not losers.

See (link opens .pdf) Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

Amino acid modification FA_Epigenetics_Table1

Theistic evolutionists fight back and lose (3)

See also: Theistic evolutionists fight back and lose
See also: Theistic evolutionists fight back and lose (2)
For succinct representations of the claims made by people who are obviously biologically uninformed, see:

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.
See for comparison:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? — Roger Penrose (8 August 1991)

7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison:

…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.) — Erwin Schrodinger (1944)

See also: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation (August 3, 2013)
Abstract excerpt:

Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history…

The amino acid substitutions are not accumulated during evolutionary history. The substitutions link nutrient energy-dependent RNA-mediated top down causationk from ecological variation to ecological adaptation via the creation of heat shock proteins. The heat shock proteins “buffer” organized genomes to protect them from virus-driven energy theft and genomic entropy via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.
See also this discussion attempt: An epigenetics gold rush: new controls for gene expression
Sonny:

The other day, I read a new paper from a sociologist who wrote that epigenetics reveals that the environment is “more important than genes” in constructing the phenotype.  That is an egregiously misleading statement.

James Kohl

m6A is the link from energy-dependent changes in angstroms to ecosystems via learning and memory, which links ecological variation to ecological adaptation in the context of the physiology of pheromone-controlled reproduction.

Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

Excerpt: “The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).” p. 6776

James Kohl: Ultimately, the biggest embarrassment to scientists who have linked energy-dependent changes from angstroms to ecosystems via chirality, autophagy, and supercoiled DNA is that other scientists start with the de novo creation of copy variants.

Sinclair et al., (January 25, 2017) Nucleic and amino acid sequences support structure-based viral classification

They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others to challenge their claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
 
They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.
 
The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
 

Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model and this presentation. Energy as information and constrained endogenous RNA interference

Keeping up-to-date with the primary literature just got a little easier

Today, Springer Nature is pleased to announce the launch of an innovative service which we believe will significantly improve the workflows of researchers by saving time and enabling access to the most relevant content, allowing users to access a new way to keep up to date without visiting any new websites.

Recommended is a service which we believe will help all primary researchers in the natural sciences keep up to date with the literature that really matters to them.  It is a personalised service that suggests relevant papers for users, regardless of publisher, based on what they have previously read across all Springer Nature services.

The “Nature Publications Group” banned me from commenting on their publications several months ago.
Comments on this news are disabled for everyone, which means the Nature Publications Group knows how to hide from any accountability for the lies they have told in the context of gene-centric theories.
See: The RNA code comes into focus Published online
See also:

The presence of an N1 methyl group on adenine bases in DNA and RNA was thought to be a form of damage. Results now show that it also occurs at specific sites in messenger RNAs, where it affects protein expression.

This nutrient energy-dependent methyl mark link RNA methylation from learning and memory to biophysically constrained RNA-directed DNA methylation, which is now represented in the context of endogenous RNA interference (RNAi). The link from the epigenetic landscape to RNAi and to the physical landscape of supercoiled DNA has repeatedly been placed into the context of via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all living genera via the physiology of reproduction.
Typically, the physiology of reproduction prevents the transgenerational epigenetic inheritance of virus-driven pathology in all living genera — until the landscape changes to one in which energy-dependent RNA-mediated DNA repair can no longer keep up with the virus-driven energy theft.

Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose

A giant neuron found wrapped around entire mouse brain

Yuste and Eberwine would like to see 3D reconstructions of individual neurons compared to analyses of the genes expressed in those neurons. This may offer clues as to the type and function of each cell.

The nutrient energy-dependent structure and function of all cell types in all living genera links biodiversity from the physiology of pheromone-controlled reproduction in C. elegans to the predatory behavior of P. pacificus, a predatory nematode with teeth.

See: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

All ecological adaptations, such as teeth, exemplify what is required to link energy-dependent endogenous RNA interference to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Predictably, Paul Allen will be the next to start funding works that might help to prevent the viral apocalypse, now that Bill Gates is mentally prepared to do so.

See: Bill Gates refutes theistic evolution

Malnourished children can be getting enough calories, but not the right nutrients.

See for comparison: Mathematics supports a new way to classify viruses based on structure

“Our work is the first to tie structural lineages to sequences so comprehensively,” says Professor Sinclair.

See for comparison: Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses

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

The antigenic changes are clearly nutrient energy-dependent, as are all changes in all cell types of all living genera. Their results link virus-driven energy theft to all pathology, which is why Sinclair et al (2017) must put his mathematical model back into the context of evolution across billions to millions of years.

 
They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others with critical thinking skills to challenge their ridiculous claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
 

They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.

The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
 

Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.

The energy-dependent coding sequence links the physiology of reproduction to RNA-mediated amino acid substitutions and cell type differentiation in all living genera.

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

…the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes (Bumbarger, Riebesell, Rödelsperger, & Sommer, 2013), and in flies (Swarup et al., 2013).

See for comparison:

What Came First—the Virus or the Egg? 

Three recent studies find that the single-pass transmembrane protein HAP2 mediates gamete fusion and is remarkably similar to class II fusion proteins found in viruses such as dengue and Zika.

Mutational Processes Shaping the Genome in Early Human Embryos

In-vitro-fertilized human embryos often acquire large structural and numerical chromosomal abnormalities. Liu et al. now show that multiple smaller copy number variations may also arise in in-vivo-conceived embryos. Analysis of these variations provides insight into the DNA mutational processes occurring in early embryos and the mechanisms underlying them.

I repeat: “…evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.” Similarly, “DNA mutational processes occurring in early embryos…” cannot shape the genome because mutations prevent biophysically constrained protein folding chemistry.

For comparison: Linking Protein and RNA Function within the Same Gene

Exposure to ultraviolet light leads to a cell-wide DNA damage response that includes a global reduction in transcription. Williamson et al., identify a protein involved in this process as well as a noncoding RNA produced by alternative processing of RNA transcribed from the same gene that promotes recovery from the repressed state.

Femtosecond blasts of UV light have already been linked to DNA repair via alternative processing of RNA transcribed from the same gene.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

See also: Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer

The fact that UV-light induced charge transfer states in DNA control pH responsive RNA-mediated DNA repair seems to have escaped the notice of those who tout selective repair via effective gene transfer without mentioning the source of energy for the transfer.

It’s the anti-entropic virucidal energy of sunlight!

What is Life? 

…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.)

————————

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (Roger Penrose 8 August 1991)

See also: Theistic evolutionists fight back and lose (2)

Physics

Young earth creationists refute theistic evolution

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

The series about refutations of theistic evolution continues. Creationists and two publications in “Nature” support the claims of young earth creationists who cited: Holmes (1996)  Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors

See: Holmes E. C. 2003. Molecular Clocks and the Puzzle of RNA Virus Origins. Journal of Virology. 77 (7): 3893–3897.

Excerpt:

“Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”

Are all evolutionists atheists?

As we point out in our article about peer-review, scientists are human beings, complete with the motivations and conflicts of interest all of us have. And it seems the secularization of the sciences has made things worse, as there is currently an epidemic of fraud in science.

My comment: Re: Richard Dawkins called theistic evolutionists ‘deluded’.
I agree. All serious scientists have linked the anti-entropic virucidal energy of sunlight on contact with water from chirality and autophagy to supercoiled DNA via the innate immune system and the physiology of reproduction. Serious scientists also have linked virus-driven energy theft to all pathology.
The accurate representations in Biblical Genesis of what is known about energy-dependent RNA-mediated cell type differentiation have forced pseudoscientists to finally admit to the facts about RNA, which refute their DNA-centric theories.
See for example: An epigenetics gold rush: new controls for gene expression
Excerpt:

“We are only in the beginning of the story,” Rechavi says.

See also: The RNA code comes into focus

…in October 2016, the US National Institutes of Health awarded He and Pan a 5-year, US$10.6-million grant to establish a centre to develop methods for identifying and mapping RNA modifications.

See for comparison:
Chronic treatment of non-small-cell lung cancer cells with gefitinib leads to an epigenetic loss of epithelial properties associated with reductions in microRNA-155 and -200c.
Combined small RNA and degradome sequencing reveals complex microRNA regulation of catechin biosynthesis in tea (Camellia sinensis).
More than 58,000 published works link nutrient energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity or they link virus-driven energy theft to all pathology in all living genera.
Young earth creationists have called attention to the facts about sunlight as the link from energy as information to biophysically constrained viral latency for ~15 years. Evolutionary theorists waited too long to admit to the facts. It is not only the theistic evolutionists who were ‘deluded.’ It was anyone who was taught to believe in mutation-driven evolution. The biologically uniformed masses in the United States do not know that the US National Institutes of Health award millions of dollars in grants to establish nothing that is not already known to serious scientists about energy-dependent RNA-mediated cell type differentiation.
If the US National Institutes of Health did not spend millions, no one could attempt to deliver a “billion dollar baby” like this one: Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy
Excerpt: RNAi has targeted exogenous genes in models of viral infection…
Instead, millions of dollars will be spent to “…develop methods for identifying and mapping RNA modifications…” before the biologically uniformed masses are told that the modifications are nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in species from microbes to humans.
Ecological variation must be linked to energy-dependent ecological adaptations via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all individuals of all living genera. The differences in bacteria and archaea can be compared to the transgenerational epigenetic inheritance of Zika virus-damaged DNA as examples of the continuum of energy-dependent creation and maintenance of all organized genomes in all living genera.
If unethical researchers continue to misrepresent what is know to young earth creationists and to all serious scientists, they can continue to steal millions of dollars to fund their ridiculous claims about mutations and evolution. Money is the motivator. Do not expect those who are motivated by it to tell the Truth. That’s what young earth creationists do.

See also: Researchers uncover a role for HSP90 in gene-environment interactions in humans

Excerpt:

By helping proteins fold and function, HSP90 influences a range of characteristics in simple organisms on which natural selection can act, and thus alters the course of evolution,” says Georgios Karras, lead author of the study and a post-doctoral researcher at Whitehead Institute.

My comment: He claims a Heat Shock Protein can be linked from natural selection to evolution.

Natural selection for energy-dependent codon optimality links pH-taxis, thermotaxis, chemotaxis, and phototaxis to the creation of the Heat Shock Protein, which helps to protect organized genomes from virus-driven energy theft and genomic entropy in the context of the pheromone-controlled physiology of reproduction in species from microbes to humans.