5th-6th Sept 2018 Dublin, Ireland

Ecological adaptations vs the randomness of evolution (3)

Summary: Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
Serious scientists will meet during Schrödinger at 75 – The Future of Biology – September 2018 to discuss the overwhelming amount of human idiocy exemplified in the works of theorists who failed to learn that life is “All about that base.”
Without the quantized energy-dependent creation of the base pairs, viral latency could not be biophysically constrained and entropy would be used to explain the evolution of biodiversity manifested in sympatric speciation.
See for comparison: The costs of living at the edge: Seasonal stress in wild savanna-dwelling chimpanzees

Adaptations associated with shifting from a predominately forested habitat to a more open environment are considered a crucial step in hominin evolution.

The adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. For example, higher levels of dehydroepiandrosterone in humans are an adaptation.
See:  Dehydroepiandrosterone – is the fountain of youth drying out?

…humans are unique in having adrenals that secrete large amounts of the prohormone, dehydroepiandrosterone (DHEA) and its sulfate, DHEA-S, into the bloodstream of males and females. Even non-human primates produce only ~10% of the DHEA found in humans

Carl Zimmer places everything known about how ecological variation must be linked to energy-dependent ecological adaptations into the context of human evolution.
See: Hints of Human Evolution in Chimpanzees That Endure a Savanna’s Heat

Millions of years ago, our apelike ancestors gradually moved from woodlands to savannas and began walking upright at some point. The Fongoli chimpanzees demonstrate just how difficult that transition would have been — and how that challenge may have driven some major changes in our evolution, from evolving sweat glands to losing fur and walking upright.

Before she graduated from her medical technologist course (circa 2014), I mentioned to Misty ______ the importance of  β-lactamase testing to understanding how the energy-dependent creation of microRNAs would soon be linked to all biophysically constrained biodiversity on Earth via antibiotic susceptibility testing in the hospital medical laboratory.
Shared strategies for β-lactam catabolism in the soil microbiome

A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product.

This clearly exemplifies how the virus-driven degradation of messenger RNA in β-lactamase positive organisms is linked to antibiotic resistance via what all serious scientists know about the molecular mechanisms of energy-dependent cell type differentiation.
The findings were reported in the ridiculous context of claims about How Bacteria Eat Penicillin

…some of the bacteria could, in fact, eat the drugs… As it turned out, they were everywhere. He also found examples of the phenomenon in the scientific literature going back to the 1960s.

In 1964, McEwen et al, linked the creation of the sun’s anti-entropic virucidal energy from Schrödinger’s claims in What is Life? (1944) to the creation of ATP and the creation of RNA. Now, others like McEwen know that RNA interference biophysically constrains viral latency.
In 1968, Frohlich speculated that the highly ordered storage of quantized energy in species from microbes to humans linked hydrogen-atom transfer to the functional structure of cell membranes via the hydrogen bonds of molecules, or other dipolar constituents, which he linked to the shared energy supply that biophysically constrains life.
Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
See also: UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML.

They linked the anti-entropic virucidal energy of sunlight from the creation of ATP to chromatin remodeling during the evolution of pathology, which all serious scientists know is biophysically constrained by the physiology of food energy-dependent pheromone-controlled reproduction.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

The interorganism systems of genetic regulation have since been placed into the context of sympatric speciation by all serious scientists.
See: Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

5th-6th Sept 2018 Dublin, Ireland

From photons to the proton motive force (1)

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

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

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

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

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

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

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

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

Schrödinger at 75 – The Future of Biology – September 2018

See also:  Here Comes Single-Cell Optogenetics

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

OLYMPUS experiment sheds light on structure of protons

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

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

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

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

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

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

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

Viruses in pathogenic variants disrupt alternative splicings (2)

Autophagy is activated by virus-driven energy theft. Click on the term “Autophagy” That fact is clear in the diagram of systems complexity and in my model.

See for contrast:  Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

A key question in virology, that is potentially answerable using paleovirological analyses, is what caused the elimination of extinct viral lineages?

Conclusion:

The selection pressures acting on hsaHTenv, its orthologs and progenitors might have been complex. Loss of fusogenicity but retention of receptor binding activity are, in a sense, opposing influences in terms of maintenance of the ORF and its function. Moreover, although some purifying selective pressure (low dN/dS) can be detected in hsaHTenv and its orangutan ortholog, a relaxation of those forces might be expected to have occurred after HERV-T extinction, perhaps leading to reduced antiviral activity observed in modern hsaHTenv. Finally, as MCT-1 is a moncaboxylate transporter that is upregulated in human cancers (Halestrap, 2013), the ability of hsaHTenv to deplete MCT1 from cell surfaces may suggest an additional or alternative metabolism-related cellular or even anti-tumor functions and selective pressures. Such an activity might have continued to shape hsaHTenv sequence independent of anti-HERV-T activity. In either case, this study highlights the potential importance of ERV proteins as raw material for the innovation of new functions in human ancestors.

All energy-dependent cell type differentiation is receptor-mediated. The nutrient energy-dependent de novo creation of receptors in cell types links metabolic networks to genetic networks via RNA-mediated protein folding chemistry, which biophysically constrains virus-driven energy theft. The energy theft links viral replication to the degradation of messenger RNA and mutations, which are linked to all pathology.

Reported as: Virology: Pushing the envelope

My comment:
Rarely do we see this degree of prescient raw insight displayed by a non-scientist who predicted the claims about viruses in the manuscript reviewed.
Please see: Evolution rising from the grave http://dx.doi.org/10.1038/3… Excerpt: “Reactivation of a dormant message signals the dawn of a new humanity.”
See also: Living with the Neanderthals http://www.nature.com/natur…

My competing interests include ownership of domains that disseminate accurate information about energy-dependent biologically-based cause and effect, which is biophysically constrained. My publication history extends across twenty years during which I have refuted every aspect of neo-Darwinian nonsense.
The nonsense places claims about evolution into the context of what is known to serious scientists about the links from angstroms to ecosystems in all living genera. Serious scientists start with hydrogen-atom transfer in DNA base pairs in solution.
The potential of hydrogen is referred to as pH. Virus driven energy theft links changes in pH to the degradation of messenger RNA and the mutations that are linked to pathology in all living genera.
My comments are rarely published here.
—————————————————-
See, for comparison, my comment to Greg Bear’s FB page:
Darwin’s Radio and Darwin’s Children (revisited)
“Viral Fossils Reveal Immune Capabilities of Our Ancestors”
http://buff.ly/2nT1osY
Hi Greg. Nutrient energy-dependent pheromone-controlled RNA-mediated viral latency became the focus of my published works and presentations after you linked pheromones to ecological adaptations in a new human subspecies.
My 2017 Labroots Precision Medicine presentation is an extension of facts you helped to detail for your target audience.
https://www.youtube.com/watch?v=cdtsfweO5SQ
“Energy as information and constrained endogenous RNA interference” is being ignored because it refutes every aspect of pseudoscientific nonsense that has ever been touted by neo-Darwinian theorists. I continue to be amazed by those who claim to be scientists who cannot begin to understand what you understood at the time you wrote “Blood Music.” Like others, I am also somewhat scared of what you predicted in “Quantico.”

Biology to a Physicist

Sal Giardina: apologetics revisited

March 26, 2017 Sal Giardina wrote:

“James, I appreciate your responding to my posts but I would prefer that your input would be related to the content of the post.”

My reply: If you do not want people to learn how my claims are linked to yours, please tell me that you intend to continue with apologetics rather the concept of energy as information.

Apologetics:

… the religious discipline of defending or proving the truth of religious doctrines through systematic argumentation and discourse.[1][2][3] Early Christian writers (c. 120–220) who defended their beliefs against critics and recommended their faith to outsiders were called Christian apologists.[4] In 21st century usage, ‘apologetics’ is often identified with debates over religion and theology.

In the context of debates over religion and theology, Sal Giardina opened discussion of physics, chemistry, and the conserved molecular epigenetics of RNA-mediated cell type differentiation. Secular humanists are scared by the ghosts of their biologically uninformed past and their ongoing ignorance. Fortunately for them, Sal Giardina and others like him cannot prove anything via the use of apologetics. So far as I know, the apologeticists have never convinced anyone to believe in any of their claims.
See for example: What does DNA have to do with the Origin of Life ?
Unfortunately, you must join this “false flag” group go find this post: https://www.facebook.com/groups/231023426993207/permalink/1119981528097388/?comment_id=1120290524733155&reply_comment_id=1120913471337527&notif_t=group_comment&notif_id=1477870268849582 I’ve been banned from the group twice, but just submitted a request to re-join.
My comments: Secular humanists seem willing to believe that the origin of life could somehow lead to consciousness as a side effect.
See for example: Consciousness could be a side effect of ‘entropy’, say researchers
My comment: Serious scientists do not make such ridiculous claims. These researchers are theorists who tout meaningless pseudoscientific nonsense. Their ridiculous claims makes news when biologically uninformed journalists, like Fiona Macdonald pass the unsupported claims on to others who do not know that the theorists are touting meaningless pseudoscientific nonsense.
See also: Virus evolution and this special issue on Orgasms:  Introductory editorial to ‘Orgasm: Neurophysiological, Psychological, and Evolutionary Perspectives
My comment: Who are the people trying to convince others that virus evolution links prairie vole monogamy to the evolution of human love via organsm? One of them is James Pfaus.
Excerpt:

In ‘The Role of Orgasm in the Development and Shaping of Partner Preferences’, Coria-Avila, Herrera-Covarrubias, Ismail, and Pfaus (2016) explore the relationship between orgasm and sexual preference-formation in animals. Of particular significance with respect to human orgasm, Coria-Avila et al. describe the pre- and post-ejaculatory factors contributing to male rats forming conditioned sexual preferences.

See this article by Rachel Feltman, who placed the ridiculous claims of Pfaus before my detailed model of nutrient-dependent pheromone-controlled biologically-based cause and effect.
What Do We Actually Know About Pheromones?
Excerpt:

But Kohl’s products, which he likens to food spices (“They give you an extra kick!”), make some researchers roll their eyes. Dr. Jim Pfaus, professor of psychology at Concordia University in Montreal, is one of them.

See for comparison: Ecologically relevant neurobehavioral assessment of the development of threat learning
Summary: “Informed Conditioning” is linked to the differences between wolves and dogs and biophysically constrained cell type differentiation in all living genera.
See for example: A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris)
See also (link opens pdf): Early life experiences: enduring behavioral, neurological and endocrinological consequences

See also: Sexual Differentiation of the Brain: A Fresh Look at Mode, Mechanisms, and Meaning

…no study has yet shown an effect of manipulating the expression of a particular microRNA on a behavioral or brain sex difference. In other words, we are still awaiting the demonstration that microRNAs contribute to sexual differentiation of the brain.

Olfaction is important to humans as well, but visual stimuli are far more potent and the arousal potential of same-sex versus opposite-sex images depends on the partner preference of the observer (see for review Baum, 2006).

Michael Baum and others still make ridiculous claims about visual input compared to the epigenetic effect of food odors and pheromones on energy-dependent microRNA-mediated cell type differentiation in species from microbes to humans. That fact supports my claim that people like him are biologically uninformed.

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

See also: Crosstalk between epigenetics and metabolism—Yin and Yang of histone demethylases and methyltransferases in cancer

Pioneering experiments by Allfrey and Mirsky >50 years ago identified methylation and acetylation of histones by isotope incorporation and showed that histone modification can influence whether RNA synthesis of genes is switched on or off [3].

See also: 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.

If you knew nothing about the energy-dependent de novo creation of nucleic acid precursors, you still could start from the energy-dependent creation of RNA and link RNA-directed DNA methylation to all biophysically constrained biologically-based cause and effect in all living genera to their physiology of pheromone-controlled reproduction in the context of learning and memory at the cellular level of intracellular and extracellular communications.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
My comment: The conserved molecular mechanisms of experience-dependent learning and memory have been linked from energy-dependent RNA-mediated cell type differentiation to all biodiversity via quantised energy and all subsequent levels of examination the must begin with the origins of information, the sun’s anti-entropic virucidal energy.

See for comparison:  Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

My comment: Femtosecond blasts of UV light link the sun’s virucidal energy to RNA-mediated DNA repair in all living genera. People who do not know that should simply admit that they biologically uninformed. Most of them are theorists who know nothing about anything that must be linked from angstroms to ecosystems. They should not antagonize those who are biologically informed serious scientists. Serious scientists publish experimental evidence in reports such as this one.

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

Excerpt:

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.

My comment: The sequences cannot be selected outside the context of natural selection for energy-dependent codon optimality, which is the basis for the control of hydrogen-atom transfer in DNA base pairs in solution. Control is manifested in the measurement of pH.

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

Excerpt:

Coulombic interactions between the histidine residues modulate protonation and subsequent conformational transitions required for peptide mediated gene transfer activity and are an important factor to consider in future peptide design.

My comment: Coulomb barrier:The Coulomb repulsion which tends to keep positively charged bombarding particles out of the nucleus. Specifically, the Coulomb potential associated with this force.

Energy-dependent Coulombic interactions link autophagy to polycombic ecological adaptations for comparison to what happens when virus-driven energy theft is linked to the hecatombic evolution of all pathology.

See also: Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions (published in 1995)

See for comparison: Jonas Edward Salk (October 28, 1914 – June 23, 1995) was an American medical researcher and virologist. He discovered and developed one of the first successful polio vaccines.

My comment: The fact that Jonas Edward Salk died in the same year that information about Coulombic interactions was published exemplifies the fact that we still need people like Salk to lead the way towards more scientific progress.

Is everyone who could do that already dead? Have people like Sal Giardina and other apologeticists replaced them. Will any of the works from the early 1990s to 1964 be resurrected before all of humanity is irreversibly impacted?

See for example: Biology, molecular and organismic (1964)

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.

Links from the creation of nucleic acid precursors to entropy and mutation-driven evolution are still being addressed by apologeticists who know nothing about physics, chemistry, or molecular epigenetics.
See also:  Biblical Creation / Entropy
http://godordirt.com/wp-content/uploads/2013/11/hsz-biblical-entropy.jpg
See for comparison: What is life when it is not protected from virus driven entropy (6 minutes)
I think most people can understand the concept of Creation by God of all biophysically constrained life on Earth. If not, they should be told about the examples, since all examples show that all organisms must eat or die. If they die, they do not reproduce, which means they never became an extant species. Instead, the individuals and/or species became part of the fossil record or they became nothing recognizable to serious scientists as anything more than dirt.
See also: godordirt.org
See also: Virus Documentary | Discovering & Understanding Viruses || How Viruses Work ? (60 minutes)

My comment: Terra Firma is the battlefield mentioned in the video (a village in central Brazil). Stephen Morse, virologist at Rockefeller is fighting on the side of virus-driven entropy, which he attributes to emergence and evolution. For example, His book, Emerging Viruses (Oxford University Press) was selected by “American Scientist” for its list of “100 Top Science Books of the 20th Century”.

My comment: According to the book, our innate immune system emerged and evolved to become the source of all pathology. If the innate immune system is referred to as our “immune system” the word innate changes to evolved, and mutations are linked to evolution in the context of ridiculous neo-Darwinian theories. That is how emerging viruses are automagically linked to all healthy longevity via polycombic ecocological adaptation and to all pathology via hecatombic evolution.
We have come full circle back to the definitions that are used and discussed in Polycombic ecological adaptation as a science, not a theory (2):
See also:  The Human Virome

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome. It does not link virus-driven energy theft toi mutations and all pathology.

Excerpt:

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.

My comment: The facts about nutrient energy-dependent single nucleotide substitutions and RNA-mediated amino acid substitutions link hemoglobin variants to healthy longevity and the facts link molecular defects to the pathology of α-, β- or δ-thalassemia, respectively.

See for comparison: 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: Peptides design based on transmembrane Escherichia coli’s OmpA protein through molecular dynamics simulations in water-dodecane interfaces
See for comparison: Understanding abundance and diversity using ghosts and goblins: a spooky ecology lesson!
Conclusion:

If we wanted to compare the diversity of two forests, we would want to look at climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. Diversity can be impacted by a slew of factors. While this is a fun and rather ridiculous example of how species counts and diversity works, the leap to how this can inform ecology, management, and conservation is clear.

My comment: The fact that nothing known about virus-driven energy theft is included in their comparisons makes the most important of all comparisons irrelevant to their claims about how climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. link ecological variation to polycombic ecological adaptation via the physiology of reproduction in all living genera.
See for comparison: An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells

G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2–ESE interaction. The NS1 protein directly interacts with SF2 in the nucleus and modulates splicing of NS mRNAs during virus replication.

Reported as: Single nucleotide change responsible for allowing H7N9 flu to jump from birds to humans found
The identification of the G540A links the single nucleotide polymorphism (SNP) from a biomarker in fowl infected with a flu variant to what was reported as mutation.
Researchers assumed that “…the mutation played a role in allowing the virus to spread between humans once it made the leap from an avian source.”
As usual, they found no evidence to support that ridiculous claim. That ridiculous claim is among many others that theorists thought could be used to link mutations to evolution via mathematical models instead of facts about nutrient energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.

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.

terrarium-eco-system

Trump's appeal to common sense (2)

See: Trump’s appeal to common sense
Orphan Gpr182 suppresses ERK-mediated intestinal proliferation during regeneration and adenoma formation

To our knowledge, this is the first study to use a genetic mouse model to simultaneously map Gpr182 localization patterns and elucidate novel physiological functions for the negative regulation of intestinal proliferative capacity, especially during regeneration and adenoma formation. Future studies to identify the ligand for this exciting and physiologically relevant orphan GPCR [G protein-coupled receptor] will shed light on its tractability as a potential therapeutic target.

Reported as: Unmasking previously misunderstood gene, scientists discover potential drug target for gastrointestinal cancers

The study also shows that science is as much about asking questions as finding answers.

The de novo creation of G protein-coupled receptors (GPCRs) and GPCR-mediated cell type differentiation is energy-dependent and RNA-mediated.
Nutrient energy-dependent microRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution to all morphological and behavioral phenotypes via the de novo creation of GPCRs. See: The phylogenetic utility and functional constraint of microRNA flanking sequences
For example, the potential of hydrogen is expressed as pH and all biophysically constrained RNA-mediated energy-dependent protein folding chemistry is pH-dependent.

The questions that these researchers failed to ask are:
1) Where did the energy come from for the creation of this GPCR?
2) Where did the energy go when the GPCR mutated?
Until they understand the importance of the answers to those two questions, they will not know enough about GPCRs. It is important to link their creation from all energy-dependent chemotaxis and phototaxis to all biologically-based biodiversity on Earth via amino acid substitutions in supercoiled DNA, which protect all organized genomes from virus-driven energy theft and genomic entropy. Anyone who does not have enough common sense to link energy from ecological variation to ecological adaptation is not likely to learn that virus-driven energy theft causes all pathology via the loss of GPCRs.
See for comparison: Family-wide structural characterization and genomic comparisons decode diversity-oriented biosynthesis of thalassospiramides by marine proteobacteria

…comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction and compound efflux.

Amino acid metabolism is nutrient energy-dependent.
See also: Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

The issue begins with articles about various aspects of genomics, with Holland et al. [26] discussing gene duplication and Urrutia and co-workers [51] alternative splicing and their contributions to phenotypic innovation while Orlando and co-workers [47] outline the latest methodologies that allow analysis of fossil genomes.

Alternative splicing is nutrient energy-dependent and it links RNA-mediated amino acid substitutions from the de novo creation of genes to the functional structures of all proteins and the morphological and behavioral phenotypes of all living genera via feedback loops that link what they eat to their physiology of pheromone-controlled reproduction.

Stability of the hybrid epithelial/mesenchymal phenotype

…we propose three particular network topologies that can be used to mine for other similar ‘phenotypic stability factors’ (PSFs) – (a) a double negative feedback loop with ZEB, (b) inhibition on both miR-200 and ZEB, and (c) a double negative feedback loop with ZEB as well as inhibiting miR-200. In all these three cases, the PSF can self-regulate positively or negatively. With a surging interest in mapping and modeling the signaling pathways regulating metastasis [45, 63, 101–104], the theoretical approach presented here can serve as a template to elucidate the effect of many intracellular and extracellular signals in regulating EMT dynamics and governing the relative stability of the E, M and E/M phenotypes.

Viruses send chemical messages 

Virus-driven energy theft allows the metabolism of energy in viruses to be linked from viral microRNAs to all pathology. It does not allow anyone to link viruses to the evolution of heterosexual love.

Researcher investigates the science behind love
Larry Young already did this and decided that viruses must cause the evolution of human love.

How Trump Could Unravel Obama’s Science Legacy

Funding science involves a delicate balance. Science in the Obama years tilted the needle towards applied research—from the launch of the ambitious Precision Medicine Initiative to sequence the genomes of one million people, to the creation of a string of institutes to foster robotics and other innovative manufacturing technologies in partnership with private industry.

The Precision Medicine Initiative preceded the National Microbiome Initiative. Pseudoscientists finally realized that energy-dependent metabolic networks must be linked to genetic networks in attempts to understand the difference between healthy longevity and the pathology, which is caused by virus-driven energy theft.  For comparison, “…the creation of a string of institutes to foster robotics and other innovative manufacturing technologies in partnership with private industry” was a way to provide corporations with more taxpayer funded research as the amount of suffering from disease increased and the death toll continued to rise.
 
 

Alternative splicing of pre-mRNA

Autophagy: from pre-mRNAs to microRNAs, enhancers, QTLs et al.

Nothing known to serious scientists links anything except energy-dependent changes in chirality to autophagy and biodiversity via RNA-mediated amino acid substitutions that differentiate all cell types in all living genera. That fact forces pseudoscientists to invent new terms to confuse the biologically uninformed masses who were taught to believe in the neo-Darwinian pseudoscientific nonsense of mutation-driven evolution.
Autophagy in the liver: functions in health and disease 
See the section: Regulation of autophagy by amino acids

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt from our section on molecular epigenetics.

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

My family members and friends of Robin Williams might be appalled to learn that death from Parkinson’s and death from Lewy Body Disease both include instances of suicide that is caused by untreated virus-driven energy theft. The virus-driven energy theft also is the cause of all pathology in species from archaea to humans. It is manifested as energy-dependent changes in alternative splicings of otherwise identical genes.

The prevention of unnecessary suffering and death could be as simple as restoring the balance of amino acids and sugar to prevent all pathology via RNA-mediated cell type differentiation.

That’s not going to happen without some discussion of what is known to serious scientists about the links from angstroms to ecosystems. All of them are energy-dependent. So, “go ahead,  make my day!”

Ask your professors where the energy came from and how it is linked to the changes in pH that predict when difference in healthy longevity become differences in the types of pathology via links from autophagy to supercoiled DNA or to negative supercoiling.

See also: Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end

This review suggests the term “pre-mRNA” changed to “microRNA” as serious scientists learned more about how energy-dependent cell type differentiation was biophysically constrained.

We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.

This was ~20 years after we linked alternative splicings of pre-mRNA to all cell type diversity via the pheromone-controlled physiology of reproduction in yeasts at the advent of energy-dependent sexual reproduction.

See also: Implications of polyadenylation in health and disease

This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3′ end formation.

Watch as researchers continue to invent new names for the molecular effectors in attempts to obfuscated the facts about biophysically-contrained protein folding chemistry that have been known to all serious scientists since Schrodinger (1944) linked the anti-entropic energy of the sun to all biodiversity.

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

Abstract excerpt:

Eusocial insects organize themselves into behavioral castes whose regulation has been proposed to involve epigenetic processes…

Research article summary excerpt:

…behavioral plasticity can be manipulated in the ant C. floridanus by pharmacological and genetic tools that target chromatin regulatory enzymes to stimulate, inhibit, and reprogram behavior. These findings reveal the epigenome as a likely substrate  underlying caste-based division of labor in eusocial insects.

Conclusion:

…our ability to alter a canonical altruistic behavior in a truly social organism by experimental perturbation of a single gene suggests that the application of increasingly versatile reverse genetic approaches in eusocial insects will allow us to expose the general organizational principles underlying complex social systems (10).

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
All general organizational principles underlying complex social systems are nutrient-dependent and pheromone-controlled in the context of the regulation of gene expression that enables the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

‘Mysterious’ non-protein-coding RNAs play important roles in gene expression

Berger and Daniel Bose, PhD, a postdoctoral fellow in her lab, study the regulation of gene expression from enhancers, non-coding regions of the genome more distant from protein-coding regions.

The only mystery should focus on why they thought they could continue to suppress the facts by referring to natural selection for energy-dependent codon optimality in terms like “enhancers.” Since 2013, everything known to serious scientists about nutrient-dependent microRNAs has been linked to all healthy longevity and virus-driven energy theft has been linked to to all pathology. Serious scientists are not using the term “enhancer.” See for example any of the 56,000 published works that use the term “MicroRNA

Ask why Phys.org / Medical Xpress must report old news from 2013 in the context of unpublished research by two people who cannot be found on the PubMed indexed list of research that links sunlight from chirality to autophagy and chromosomal rearrangements to all biodiversity via energy-dependent changes in the microRNA/messenger balance, which link supercoiled DNA to the protection of all organized genomes from virus-driven entropy.

See: Enhancer RNAs alter gene expression: New class of molecules may be key emerging ‘enhancer therapy’

Enhancers are sequences in the genome that act to boost or “enhance” the activity or expression of nearby genes. They “often behave in a cell-specific manner and play an important role in establishing a cell’s identity and functional potential,” said Christopher Glass, MD, PhD, a professor in the department of Medicine and Cellular and Molecular Medicine at UC San Diego and principal investigator of one of the papers.

Although enhancers have been recognized for more than 25 years, scientists have labored to fully flesh out the breadth and complexity of what enhancers do and how they do it. In 2010, it was discovered that enhancers directed expression of RNA on a broad scale in neurons and macrophages, a type of immune system cell. Dubbed eRNAs…

I do not know any serious scientists who accepts the term invented to replace pre-mRNAs after the term microRNAs was introduced at the turn of this century and more than 56,000 published papers now use the term microRNA in the context of links from metabolic networks to genetic networks in all living genera via non-coding RNAs..

SnapShot: Non-coding RNAs and Metabolism

In recent years, understanding the crucial role played by cellular homeostasis in disease initiation and progression became the focus of scientists and clinicians. This SnapShot sketches the involvement of both short microRNAs and long ncRNAs in the major metabolic pathways altered in diseases.

Functional Importance of eRNAs for Estrogen-dependent Transcriptional Activation Events

Who do they think does not know that the functional importance of microRNAs and the functional difference of eRNAs is the same. eRNAs are the term theorists use for microRNAs.

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also: SPECIAL ISSUE—THE ZIKA VIRUS GLOBAL PANDEMIC: THE LATEST EMERGING INFECTION
Placental Pathology of Zika Virus: Viral Infection of the Placenta Induces Villous Stromal Macrophage (Hofbauer Cell) Proliferation and Hyperplasia

It is still not well understood what role(s) the Hofbauer cell has in facilitating or inhibiting transplacental transmission of infectious agents such as the Zika virus. However, based on the demonstration in this communication of proliferation and prominent hyperplasia of Hofbauer cells in the placenta from a microcephalic fetus infected early in gestation, the identification of residual Zika virus in villous stromal cells, using an RNA probe, and the previously published results of in vitro infection and replication of Zika virus in human Hofbauer cells, it appears highly probable that the Hofbauer cell has an important, or even primary, role in those cases where transplacental transmission of the Zika virus does occur. The unexpected absence in placental tissues of any necrosis or leukocytic response by the mother or fetus to transplacental Zika virus infection is also interesting and of unknown significance.

The absence of a response in the organized genomes of the host clearly indicates ecological adaptation to the virus has already occurred and the supercoiled DNA of the host helps to protect a host from DNA damage. The infants are comparatively unprotected. If they survive to reproduce, and their bones turn up in what a future paleontologist thinks is a fossil record that spans hundreds of thousands of years, the paleontologist would almost undoubtedly claim to have found a new species of non-human primate.
For comparison, all serious scientists known that energy-dependent autophagy is the link to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

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

terrarium-eco-system

Critical values expose virus-driven energy theft (2)

Why Don’t The Amish Get Cancer?

…the Amish commitment to simple, productive lives and clean, local food is benefiting their health in ways that the rest of America can only dream about.

They exemplify what it means to be an ecologically adapted human population.

See also: Past 5,000 years prolific for changes to human genome

The facts support the beliefs of young earth creationists. That invites ridicule and denigration of my published works. But the experimental evidence of biologically-based cause and effect shows that 86.4% of the putatively deleterious protein-coding SNVs arose in the last 5,000 to 10,000 years.

Ridiculous ideas about mutations, natural selection and evolution have never been supported, and “selection” has not purged the mutations from the population. Instead, we have the Amish as well as Seventh Day Adventists (with their networks of hospitals and medical professionals) as examples of how ecological variation must be linked to ecological adaptation via epigenetic effects on the genetic code.
 
The fact that you “must have a code that you can live by” extends to everyone else and across all living genera. It is the genetic code, but no experimental evidence suggests that it automagically created itself or that we evolved after that.

See for comparison:

For comparison see: Critical values expose virus-driven energy theft

Autophagy cannot be discussed outside the context of how sunlight is linked from chirality to the de novo creation of G protein-coupled receptors and to all energy-dependent biodiversity, or from virus-driven energy theft to all pathology.

Measurement of pH in cord blood and measurement of bilirubin in neonates link the anti-entropic virucidal epigenetic effect of ultraviolet (UV) light to the treatment of infants who are in distress. Respiratory distress is linked from pH to the treatment and bilirubin is linked to the treatment with virucidal UV light.

 Autophagy in the liver: functions in health and disease

Regulation of autophagy by amino acids.

Amino acid sensing and integration
Amino acid signalling is integrated by the RAG–Ragulator–v-ATPase complex on lysosomes to activate mTORC1 (REF. 98) (FIG. 4). Although consensus has not yet been reached, it is believed that the RAG heterodimer, composed of a RAS-related GTP-binding protein (RAG) A or RAGB monomer and a RAGC or RAGD monomer, contributes to mTORC1 activation98. mTORC1 is particularly sensitive to decreases in the levels of leucine, arginine and glutamine 88,99,100
Metabolic recycling of amino acids
The final stage of hepatic autophagy contributes to the amino acid supply through the breakdown of proteins. Hepatic autophagy is critical for maintaining systemic blood glucose levels during fasting by providing amino acids for the generation of glucose via hepatic gluconeogenesis
As autophagy has important roles in both quality control of organelles and the supply of amino acids and fatty acids to cancer cells, this degradation system is thought to support cancer survival and proliferation199. Selective autophagy enables the liver to efficiently and precisely control the quality and quantity of cytoplasmic organelles, including mitochondria, peroxisomes and lipid droplets, as well as the proper functioning of NRF2. Thus, selective autophagy is one strategy hepatocytes can utilize to adjust their cellular metabolic capacity. Conversely, inactivation of selective autophagy, which results in elevated oxidativestress and accumulation of SQSTM1-positive aggregates and lipid peroxides, is connected to chronic hepatitis virus infection, alcoholic steatohepatitis, NAFLD and HCC.
Metabolic adaptation through liver autophagy during fasting therefore proceeds via utilization of glycogen and fatty acids in the early phase and amino acids in the later phase.
See for comparison: Life is physics and chemistry and communication

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

See also: The Strange Inevitability of Evolution

These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself. That is a view long championed by Schuster’s sometime collaborator, Nobel laureate chemist Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that’s right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability.

See also: Is it Time to Upgrade Your Health Routine? Diet. Exercise. Cellular Health.

Healthy cells “communicate” to carry out processes in our body

Cells are called the building blocks of life because that’s precisely what they are: the smallest unit of life, with between 30 and 50 trillion of them making up the average human body. Within each tiny cell are components called organelles, including familiar names like the mitochondria and the nucleus, that work together, or communicate, to carry out all of the processes in our body. They convert food to energy, help our muscles contract when we walk, and secrete serotonin that gives us the sense of well-being.

Communication is essential to proper cell function

Cells function properly with consistent communication between organelles like the mitochondria and nucleus, which are dependent on each other. Healthy communication leads to optimal performance in hundreds of functions. One of the most important communication-dependent processes is mitochondrial function, since the mitochondria turn nutrition into energy. Proper communication is the key to having sufficient energy to carry out all of the cells’ functions.

Basis is a proprietary formulation of two compounds — nicotinamide riboside (a unique form of vitamin B3) and pterostilbene (a powerful antioxidant) — in capsule form. It’s designed to support healthy levels of NAD+, which is essential to fundamental cellular function in over 500 areas, including creating energy and maintaining the integrity of our DNA.

Why Don’t The Amish Get Cancer? (revisited)

They are ecologically adapted. That’s why. Most people are not ecologically adapted. That’s why they suffer and die from virus-driven energy theft, which causes all pathology.

fruit-dove

Critical values expose virus-driven energy theft

Critical Values: is ASCP’s quarterly magazine with news and features covering trends of interest to pathologists and laboratory professionals alike.

See for example: Attentive Clinical Laboratory Scientist Discovers First Human Case of Borrelia turicatae

Critical Values spoke with technologist Dolli Lane, MLT(ASCP)CMCsCM, and the chief of the hematology section, Chris Boyd, MLT(ASCP)CM, about their findings. Their story demonstrates how attention to detail saves lives.

Every serious scientist I know is on the verge of linking the creation of the sun’s anti-entropic virucidal energy from hydrogen-atom transfer in DNA base pairs in solution to autophagy and supercoiled DNA via the physiology of reproduction in all living genera.

See for example: Cephalopod Olfaction

Several behavioral and functional studies have been conducted on nautiluses and decapods, demonstrating the role of olfactory organs in mate choice, predation improvement, defense strategy, and spatial orientation. Recent functional and morphological studies of octopods have revealed new perspectives about the role played by olfaction in the complex behavioral patterns shown by these fascinating animals.

Many of the serious scientists could explain what biologically uninformed theorists routinely ignore.  For example, every pseudoscientist and atheist is still touting the religious dogma associated with neo-Darwinian theories. Their theories failed to include a link from Darwin’s energy-dependent “conditions of life” to all biophysically constrained biodiversity. That link is the nutrient energy-dependent physiology of pH-dependent pheromone-controlled reproduction.

Most of the military-trained medical laboratory scientists I know were trained to troubleshoot procedures and instruments to avoid the errors that theorists from the evolution industry or big bang cosmology industry have continued to make. For example, the most important critical value linked to health or pathology is pH.
 

The scientific term “pH” is an abbreviation that stands for “potential of hydrogen,” which is a measure of the acidity or alkalinity of a solution.The term, which first came into use in 1909, is Germanic in origin and is derived from the word “potenz,” meaning power, plus “H,” which is the symbol for hydrogen on the periodic table.

The energy levels in a hydrogen atom can be obtained by solving Schrödinger’s equation in three dimensions. Because most people cannot do that, it may be more important for them to know that energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution must be linked to “conditions of life.”

When too much of the potential energy is used by a living organism or a virus, the organism dies. Theorists typically do not know that, or perhaps they simply don’t care where the energy came from.  Darwin claimed it must be linked from his “conditions of life” to all biodiversity via the physiology of energy-dependent reproduction.

That explains why theorists cannot trouble-shoot their ridiculous theories. If they were required to perform a blood gas analysis in a hospital medical laboratory, they probably would not understand that human life exists only in the biophysically constrained pH that ranges from ≤7.25 or ≥ 7.6. Theorists could not link calibrations and controls that are required to report accurate results to patient outcomes. Theorists are told that the outcomes are due to mutations and evolution.

See instead:Stat Profile Prime CCS Blood Gas Analyzer from Nova Biomedical

Measuring pH links nutritional epigenetics from the innate immune system to healthy longevity via everything known about virus-driven energy theft, which links nutrient stress and social stress to the replication of viruses, which link mutations 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.

See also: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water

The energy-dependent interaction between water and ions is omnipresent in biological processes related to enzymes, ion channels and protein folding.

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 [energy] 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. These pathways can be selectively inhibited by iodoacetate, fluoroacetate, and antymycin A, and RNA synthesis is blocked in the presence of these inhibitors. However, CO, which inhibits mitochondrial oxidative phosphorylation but does not block nuclear ATP synthesis, does not affect RNA synthesis in isolated nuclei or in whole cells. The use of CO as a selective inhibitor of mitochondrial ATP synthesis has made it possible to suppress cytoplasmic protein synthesis while allowing nuclear protein synthesis to continue.

See for comparison: A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome

Serine/threonine phosphorylation also has important effects on RTK signaling. We consistently found numerous PSP hits in our screens, although most of their functions remain unknown.

Reported as: First complete interactome map of human receptor tyrosine kinases and phosphatases

The researchers were surprised to find that some PTPs defy convention and act to promote RTK signalling suggesting that their roles are more complex than previously thought. For example, a phosphatase called PTPRA activates the EGFR, which is mutated in many cancers, revealing a new way in which cancer might spread. They also found two new phosphatases, PTPRB and PTPRH, which work as expected by grinding EGFR signalling to a halt, with potential anti-tumour properties.

Phosphorylation has long been suspected or known to be the energy-dependent molecular mechanism that enables the fixation of RNA-mediated amino acid substitutions. Ffixation of amino acid substitutions in supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. That fact is placed back into the context of evolution of the  protein phosphatases from genes in this example of gene-centric theory.

… protein phosphatases evolved from distinct genes and employ different enzymatic mechanisms (Li et al., 2013). They are traditionally divided into two classes, protein Ser/Thr phosphatases (PSPs) and protein tyrosine phosphatases (PTPs). PSPs include the PPP, PPM, and FCP/SCP families (Li et al., 2013). The cysteine-based PTP superfamily includes about 100 members (Alonso et al., 2004; Tonks, 2006) grouped into classical PTPs and dual specificity phosphatases (DUSPs). Classical PTPs play critical roles in tyrosine kinase signaling (Neel and Tonks, 1997), whereas DUSPs can dephosphorylate Tyr and Ser/Thr residues. Some DUSPs function as lipid or glycogen phosphatases. The EYA family comprises a small set with an aspartate-based catalyticdomain (Alonso et al., 2004; Jemc and Rebay, 2007).

This is a potent obfuscation of the facts known to all serious scientists who have linked ecological variation to energy-dependent ecological adaptation via what is known about biophysically constrained protein folding chemistry.

PPPs are typically multi-subunit proteins, composed of a catalytic subunit and scaffold/regulatory subunits that serve to determine their substrate specificities.

The regulatory subunits are energy-dependent RNA-mediated amino acid substitutions. Theorists know that refutes their neo-Darwinian nonsense so they pretend not to know that substrate specificities are energy-dependent and that the energy is linked to species-specific differences in morphological and behavioral phenotypes by what organisms eat.

Here’s another misrepresentation of that fact.

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

The human brain is a complex and highly evolved structure. Mouse models do not fully recapitulate cell-type diversity or lineage trajectories of the human brain (Florio et al., 2015; Konopka et al., 2012; Pollen et al., 2015; Reilly et al., 2015; Silbereis et al., 2016; Thomsen et al., 2016). Furthermore, human neurodevelopmental diseases such as autism spectrum disorders and schizophrenia are incompletely modeled in mouse.

The only way to keep fooling people into believing that the human brain evolved, is to keep teaching them to ignore what is known about energy-dependent autophagy.

See for example: Autophagy fan club

Sena Latagan We would prefer not to censor our members, but we do ask that members be respectful and try to remain on topic.
Sena Latagan James, for the purposes of this group’s discussions autophagy is defined as an intracellular bulk degradative process whereby intracellular contents are engulfed in a double membrane structure that then fuses with lysosomes. We ask our members to restrict their discussions to issues related to this definition of autophagy.
James Kohl Thanks. In other words, you are claiming that autophagy is energy-dependent. Please tell me which post was not about autophagy and advise the group of your determination on the validity of any complaints. My publication history spans 20 years, and I hate to see complaints from those who are biologically uniformed force me to leave because of a definition.
Olfaction is the link from autophagy to supercoiled DNA and pseudoscientists have failed to recognize that fact since the time that de Vries defined the term mutation.
See what’s next, and try to stop the dissemination of accurate information if you like. Cephalopod Olfacton
Censors can only do so much damage, and the time has come when serious scientists are doing damage repair, whether or not anyone in this group likes it. Similarly, chirality links the sun’s biological energy from the speed of light to autophagy and RNA-mediated DNA repair. If you would rather others not know that fact, change the name of the group to something that does not infer it is a group for discussion of autophagy.
Perhaps, “Definition Fan Club” would be more appropriate.

Sena Latagan Member James Kohl has been removed for posting unrelated topics. We the admins would like to remind everyone to please stay on topic in respect to the other members who are here to discuss autophagy as it is currently defined in the literature. Thank you.

Autophagy cannot be discussed outside the context of how sunlight is linked from chirality to the de novo creation of G protein-coupled receptors and to all energy-dependent biodiversity, or from virus-driven energy theft to all pathology. Definitions, such as de Vries 1902 definition of mutation are used only by the biologically uninformed who chose to stay uninformed. They will never know what it takes to know something about biologically-based cause and effect.

See: Critical values expose virus-driven energy theft (2)