Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Darwinian adaptation: a clear evolutionary trail?

Summary: The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that.
 

Origins of photosynthesis in plants dated to 1.25 billion years ago

The world’s oldest algae fossils are a billion years old, according to a new analysis by earth scientists. Based on this finding, the researchers also estimate that the basis for photosynthesis in today’s plants was set in place 1.25 billion years ago.

A universal trend of amino acid gain and loss in protein evolution

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

See for comparison:  Energy as information and constrained endogenous RNA interference (video)
For contrast, Philip Ball separates the origin of photosynthesis in plants from the origin of bioluminescence in bacteria in the ocean.
See: Water is an active matrix of life for cell and molecular biology

1) Water is a complex fluid in its own right (4, 5), and Darwinian adaptation to a complex milieu might be expected to generate much the same kind of enmeshing and interplay of the biological and environmental at the molecular scale that we find at higher levels of life’s organizational hierarchy.

Higher levels of organization are no different than other levels of organization. Organization is organization. But Philip Ball is a deceptive journalist. Neo-Darwinian evolution becomes Darwinian adaptation, which links the sun’s anti-entropic virucidal energy from feedback loops and the physiology of pheromone-controlled reproduction to microRNA-mediated autophagy and biophysically constrained viral latency in species from microbes to human. That causes the biologically uniformed journalist to claim:

2) All of this touches on the astrobiological question mentioned at the outset: should we, like Henderson (88) in 1913, regard water as uniquely “biophilic” and “fit” to act as life’s matrix?

There is no astrobiological question.  See the comments section on Understanding and accounting for relational context is critical for social neuroscience
George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
I wrote:  Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).
Philip Ball has since changed the clear evolutionary trail that links the sense of smell to ecological adaptation. Ecological variation links the creation of enzymes that metabolize food and drugs to his claim about  Darwinian adaptation.
See also for a recent representation of his word-play: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

There are stark difference in his claims about a Universe that is always looking that can be compared via claims about the creation of a universe in which viral latency is biophysically constrained by feedback loops. The feedback loops link food odors and pheromones from the physiology of reproduction in all living genera to all biodiversity via autophagy and the microRNA-mediated creation of supercoiled DNA.
In the spirit of the Christmas season and an attempt to stop the pseudoscientific nonsense touted by biologically uniformed theorists and journalists like Philip Ball, see: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2 (video excerpt <2 minutes long)
Remember, Santa Claus (or someone like him) is coming soon. Philip Ball may not be prepared for that. He has been a very bad boy. At the same time that President Trump, who tries his best to be good, has been accused of censorship and compared to Hitler.  I do not think that President Trump would try to change neo-Darwinian evolution to Darwinian adaptation without mentioning how the speed of light on contact with water changes everything.
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.
All the theories can be linked via facts to creationist science that has been supported with experimental evidence of biophysically constrained viral latency as presciently foretold by
1) Schrodinger,
2) Feynman,
3) Dobzhansky
4) McEwen,
and by
5) Eshel Ben-Jacob, who wrote: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment 
Note his use of the term adaptability. It may have led Philip Ball to change Darwinian evolution to Darwinian adaptation.
See also: Learning from Bacteria about Natural Information Processing

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

See also: QuEBS 2018: Workshop on Quantum Effects in Biological Systems  has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that. If Philip Ball just realized that, he knows he has a long-standing problem with misrepresentations of  top-down causation. In any case, it is important to know that he has forced all theorists and journalists to acknowledge the likelihood that Santa Claus is not just a figment of a child-like imagination, and that the creation of sunlight must be linked from its contact with water to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency in all living genera.
 

For God and Country

Trump challenges the CDC to remember 9/11

Synopsis: If you do not understand the experimentally established facts… use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condescending,  you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA (2015)
Federal Officials and Scientists Respond to Purported CDC Word Ban

…it seems that The Scientist has been highjacked by people that believes that science is fighting Republicans and promoting liberal ideas, right or wrong. For those that were not even born then, most of the advances in medicine and biology occurred during the war of cancer that President Richard Nixon initiated and supported. –dmarciani

Since then, the evolved use of meaningless words, such as evolved, and the use of meaningless phrases by the Center for Disease Control (CDC) has left the citizens of the United States of America (USA) comparatively unprotected from the forthcoming world-wide viral apocalypse. The last one (in 1918) killed ~50 million people.
See: Bill Gates warns that a new kind of terrorism could be coming, and the ‘potential damage is very, very huge’
The biologically uninformed masses know nothing about how viruses kill, or how fast they kill.  Most people know little or nothing about viruses in vaccines, which may be slow killers. That explains why, on the eve of the 100th anniversary of the year of the 1918 viral terror, the Trump administration is being criticized by non-scientists and pseudoscientists. Researchers who are biologically uniformed science idiots have helped to bankrupt the economy of the USA by submitting proposals for research that include meaningless words and phrases. The biologically uninformed masses (who are not idiots) have not learned the difference between pseudoscience and science, because they have been taught to believe in mutation-driven evolution. The difference between a scientific truth about ecological varaiation and ecological adaptation for comparison to pseudoscientific nonsense can be placed into the context of words, such as: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender”
With one exception, none of these words or phrases has anything to do with the purpose of the CDC, which is largely to protect the USA from virus-driven pathology. For comparison, the difference between food energy-dependent amino acid substitutions and mutations, which are caused by the virus-driven theft of quantized energy-as-information, clearly shows why USA Patriots for Donald Trump want to change what’s happening at the CDC.
See also: Trump administration forbids CDC officials from using 7 words and phrases

The claims of Trump-haters cut to the heart of the disrespect some people show for the President of the USA — and also the disrespect they show for the serious scientists who support him. As a medical laboratory scientist, I can point out the difference that one letter in one word makes to help other USA Patriots for Donald Trump understand what is known about how to protect us all from the next viral apocaplyse.
 
 
WORD→WORE→GORE→GONE→GENE. Implicit in this analogy is the idea that epistasis constrains evolution—for example, the original parent sequence does not tolerate three of the four eventual changes, as GORD, WERD and WOND are not words.
 
Serious scientists know that proteins do not evolve and that viruses do not automagically mutate! Similarly, the serious scientists known that new words, such as GORD, WERD and WOND are not created outside the context of biophysically constrained viral latency. Simply put, new words are not created, and new genes are not created from changes in base pairs outside the context of biophysically constrained viral latency at the level of energy-dependent base editing of food energy-dependent ACTG-linked changes in amino acid substitutions.
 
 
Trump knows that the CDC has virtually ignored the facts about food energy-dependent amino acid substitutions via the use of these meaningless words: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender.”

In the language of serious scientists, these words cannot be linked to what happens when the virus-driven theft of quantized energy causes a change in one base pair that leads to one amino acid substitution in a virus. Simply put, the change in the virus is linked to constraint breaking mutations. And the change in a virus causes all pathology in all cells of all hosts. Eventually, all human hosts die from the virus-driven degradation of messenger RNA.

Trump knows that. He also knows that viruses cause suicide and glioblastoma in veterans who have served overseas. (SARCASM ALERT: That does not mean he is required to tell John McCain.)  But, the facts have been discussed in the context of articles published in the American Legion Magazine.

It is a wonder that everyone does not know about the virus-driven activation of the death gene, since the death gene was discovered about 20 years ago by researchers at Abcam. Since then the discovery has been linked to this report:  Redox-sensitive alteration of replisome architecture safeguards genome integrity.

See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene.

Whose going to explain how John McCain gets cured — if he is not sacrificed for the sake of the CDC?

If you are easily bored by details but want to learn about what science advisors are telling President Trump, see: Epigenetic modifications poster (Just kidding. If you are bored by the details you won’t look at the details in the poster.) Instead, you are more likely to compare the President of the United States to Hitler, when Trump knows enough about epigenetics to try and help all serious scientists to protect us from the next viral apocalypse, and to protect us from the practice of corporate medicine, which is an assault on our freedom.

Epistasis biophysically constrains viral latency. The constraints are food energy-dependent and pheromone-controlled. All serious scientists have known that since this article was published in 1994. [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

Two of Eugene Daev’s subsequent works cited my award-winning publications, yet I have been unfriended on Facebook by many who will continue to not face the facts known to Trump and to all serious scientists in the world.

See for example: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014)

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also:  Effect of two pyrazine-containing chemosignals on cells of bone marrow and testes in male house mice (Mus musculus L.)

The induction of genetic instability leading to a higher genetic heterogeneity in cells of vital tissues and organs may differentially change
the fitness of animals and their progeny. Such olfactory effects can affect rates of microevolutionary transformations [5]. With regard to the conservatism and the significant role of the chemical communication in a wide range of mammals, including Homo sapiens [25], we believe extremely promising the study of genetic mechanisms underlying regulation of reproduction and immunity by volatiles that work through the olfactory system.

25 is Kohl, J.V., The Mind’s Eyes, J. Psychol. Human Sexual., 2007, vol. 18, pp. 313–369. (Concurrently published as this award-winning book chapter from the Handbook of the Evolution of Human Sexuality: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences.)
My former FB friends and others have the freedom to claim that I am a crank, because veterans suffered and died to protect your freedom.
See for contrast:  One crank dies, another rises to take his place
I have the freedom to continue to defend the country from the claims of biologically uniformed science idiots (i.e., PZ Myers) and anyone who compares Trump to Hitler.

BANNED: CDC Gets List Of ‘Forbidden Words’ From The Trump Administration

Activists immediately accused the Administration of censorship, even hysterically comparing the Administration’s move to Orwell’s “1984” and Adolf Hitler’s efforts to control information in Nazi Germany.

Despite the CDC’s own director, Dr. Brenda Fitzgerald, insisting the ban did not extend beyond the scope of a handful of budget documents, it was immediately clear to Democrats that the Trump Administration was moving to throttle all scientific research.

Find out who might benefit from a move to throttle all scientific research.
See: Alphagenomix.com and download this sample report. On page 19, the interpretation of results is placed into the context of the food energy-dependent creation of enzymes that are altered by drug therapies. The Trump administration was virtually forced to alter the funding process at CDC by the fact that Jack Szostak’s works with others led to retractions. They thought enzymes could create themselves. Two retractions in 10 years led to the embarrassment of all biologically uninformed theorists.
See “Retraction watch”

  1. A Nobel Laureate has retracted a 2016 paper in Nature Chemistry that explored the origins of life on earth, after discovering the main conclusions were not correct.
  2. 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.

The problem with ridiculous complacency-based beliefs has plagued serious scientists for decades. It was recently placed into the context of claims made by the former President of the USA.

Obama warns of complacency, notes rise of Hitler

Despite the democracy of the Weimar Republic, Adolph Hitler rose to power, he continued.

“Sixty million people died. … So, you’ve got to pay attention. And vote.”

While some could see the remark as a veiled jab at President Trump, Obama did not mention Trump by name during the event, according to the newspaper.

Now, the claims others are making link Obama’s claims to complaints about the fact that Trump took actions against the misinformation coming from the CDC. The complaints are predictably linked to Hitler’s censorship via: Godwin’s Law 

(or Godwin’s rule of Hitler analogies)[1][2] is an Internet adage that asserts that “As an online discussion grows longer, the probability of a comparison involving Hitler approaches 1”;[2][3] that is, if an online discussion (regardless of topic or scope) goes on long enough, sooner or later someone will compare someone or something to Adolf Hitler or his deeds.

The former President of the USA was caught in a thinly veiled attack on President Trump, and that attack was based on Obama’s ignorance — or based on his motives. What motives? Godwin’s Law existe only the context of pseudoscientific nonsense. That nonsense includes nothing known to the serious scientists who are physicists, chemists, biologists, or polymaths ( e.g., some medical laboratory scientists).
See for comparison: Caught in the act: Papillomaviruses promote non-melanoma skin cancer November 30, 2017

…papillomaviruses associated with UV light promote the development of non-melanoma skin cancer. The investigators provide an explanation why the viruses can be detected in benign human cancer precursors but not in advanced carcinoma.

Everyone is infected with skin-typical (“cutaneous”) human papillomaviruses (HPV) at some point in their lives, usually in early childhood already. In healthy people, the immune system can fight off the viruses, but this often changes in older age.

Those claims about biophysically constrained viral latency were used as the basis for development and use of the HPV vaccine at a time when all serious scientists knew this: “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.” Did I mention that before more than 60 times? See: Search Results for “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site”
The anti-entropic effect of virucidal sunlight links RNA-mediated amino acid substitutions to healthy longevity. That fact was presciently detailed in “What is Life?” (1944).

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

The fact that virucidal light links the food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction to epistasis was placed into the context of this 2016 video representation:
What is life when it is not protected from virus driven entropy (6:37) Published on 30 Mar 2016

Abstract:

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

If you do not understand the experimentally established facts from this presentation, please use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condesending,  you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA.
All structural diversity is energy-dependent and the pheromone-controlled physiology of reproduction links feedback loops from biophysically constrained viral latency to healthy longevity in all living genera.

See also:
Workshop on Quantum Effects in Biological Systems has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
The CDC has failed to link light-harvesting in biological systems from excitons to protection of organized genomes from the virus-driven degradation of messenger RNA in species from bacteria to humans.
That is why Trump is again being compared to Hitler. The biologically uninformed masses failed to perceive the CDC’s censorship. The CDC censorship of works published by serious scientists who have linked physics, chemistry and biology to healthy longevity via the anti-entropic energy-dependent creation of RNA and enzymes has nearly bankrupted the USA due to the costs of health care.
Who will admit that they were fooled by the use of words? Most people think they are more intelligent than that. But most intelligent people can be fooled by pseudoscientists if the pseudoscientists claim to have reached a consensus. But, what other countries base their healthcare policies on the consensus about theories of neo-Darwinists and “Big Bang” cosmologists? What other agencies can be compared to the CDC and our NIH?
See also: Science’s credibility crisis: why it will get worse before it can get better 

Several other instances of bad science have gained attention in the media. The problems in “priming research”, relevant to marketing and advertising, prompted Nobel Prize winner Daniel Kahneman to issue a publicised statement of concern about the wave of failed replication.

And a study on “power poses”, which claimed that body posture influences a person’s hormones level and “feelings of power” went first viral on TED when it was published – then again when its replication failed.

We are observing two new phenomena. On the one hand doubt is shed on the quality of entire scientific fields or sub-fields. On the other this doubt is played out in the open, in the media and blogosphere.

I dedicate this effort from the blogosphere to an attempt to reduce the tensions among those who have offered their overwhelming support for the efforts of the American Legion and the American Legion Riders who ride for God and Country.
See also The American Legion Magazine. The December 2017 issue contains another article about the stress-linked reactivation of viruses. This time its about the virus that causes shingles. When the issue is available online, see “Reactivation” by Beth W. Orenstein, and link biophysically constrained viral latency to healthy longevity via the food you eat and the pheromone-controlled physiology of reproduction.  Ask yourself “What would President Trump do?” And remember, your donations to the American Legion don not support corporate medical practices. They are used to help those who served their country and lived to continue protecting your freedom. Remember them, and everyone who has ever died trying to protect others.
 
–by Wade Youmans (Read 9/09/17 before the 9/11 Memorial Ride of the American Legion Riders–pictured above)
Remembrance
It is a moral obligation, yea indeed, a most solemn moral and spiritual duty.
To remember.
To remember is to hold fast to that which is truly important, that which is precious in the wisdom of the heart and mind.
By remembering and reflecting, upon things, objects, individual persons, anything material and physical, Which is no more, that which is no more in the mortal sense is yet sustained and can endure.
Far better to remember and reflect, even if that is painful for the heart and mind.
To forget, to blissfully disregard and discard, is a disservice to that which is gone, and ’tis a disservice to one’s own heart and mind.
For remembrance is a needful, essential endeavor for the vitality of the heart and mind, for the whole of the human spirit.

See also: ‘Whatever it took to save lives’ 

Black chicken wire over the bus windows. The odor, the heat, the tropical humidity.

“All the wounded are in the emergency room. They’re sending these sick guys to my unit. They were dehydrated. They were dirty. There was vomit. Wounds weren’t visible, but their suffering was acute and there wouldn’t be any Purple Hearts passed out for their near-death experience.

Nature’s magic helps veterans in transition

Nature’s magic” was placed into the context of the evolution of differences in H2. See: https://phys.org/news/2017-11-chemists-reveal-mechanism-dihydrogen-production.html

 
Excerpt: “This work is a critical step toward a mechanistic understanding of the nitrogenase enzyme. There is still work to be done to understand the mechanism of the other H2 evolution process that leads to N2 binding, activation, and reduction to NH3.”
 
Please help serious scientists stop those who are still touting the magic of evolution by learning how autophagy helps to protect all organized genomes from the virus-driven degradation of messenger RNA.
 

Autophagy is the link from the sun’s anti-entropic virucidal energy to the creation of enzymes and the physiology of pheromone-controlled reproduction, which has been linked to all biophysically constrained biodiversity.  For example, food energy links error-free DNA repair to all healthy longevity and the virus-driven theft of quantized energy links mutations to all pathology.

Keep in mind that as a member of the American Legion Riders, I ride for God and Country, not for Nature’s magic. Also, with 40 years experience as a medical laboratory scientist, I learned enough about the potential of hydrogen (pH) to realize that the potential did not “evolve.”

See also: https://aeon.co/essays/science-and-metaphysics-must-work-together-to-answer-lifes-deepest-questions
Metaphysics of metamorphosis

The swarming, ever-changing character of the living world challenges our deepest assumptions about the nature of reality

Excerpt: …‘physiologists in general never trouble themselves about such things because they suppose themselves to be above “metaphysics” when in fact they are only a very little above it – being up to the neck in it’.
Those who have failed to link the metaphysics of energy to biophysically constrained viral latency, have failed to link the virus-driven theft of quantized energy to the death gene by what is known to serious scientists.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166303/
When a member of the American Legion suffers and prematurely dies from the same virus-caused pathology that has not yet claimed the life of John McCain, ask yourself what is known about the life and death of all veterans who served overseas. Stop letting politics kill more veterans.
Support the Trump administrations efforts to make America great, again. They can do it without your support, but that probably will not end well for you. This is not about Trump’s behavior or about the behavior of anyone else.

An antagonist from Canada complained about Trump’s so-called censorship of the CDC and said his “tactics” didn’t work in Canada. I claim that similar tactics are always effective. The truth hurts but it only hurts those who believed they could keep touting pseudoscientific nonsense. Not only did Canadians get rid of the “transgender” nonsense, they helped to nearly stop James Cantor from promoting pedophilia as another form of sexual orientation.
 

See: Infamous Reparative Therapy Clinic For Transgender Youth Set To Close
Two years ago, I wrote:

The misrepresentations of the issues are out of control.

Excerpt: GIC’s “developmental model” was backwards. It blamed symptoms like depression and anxiety on the gender non-conforming behavior itself, rather than on the stigma attached to it or the conflict of not being able to fulfill one’s gender identity. This philosophy allowed the clinic to claim it was treating these negative mental health outcomes without affirming the trans behavior.”

My comment: They never had a developmental model. At best they had a philosophy based on ridiculous theories that never included anything known to serious scientists about the biological basis of cell type differentiation. These clinicians, like most sex researchers, never learned anything about links from nutrient-dependent RNA-mediated events to behavior.

For example, RNA-directed DNA methylation and RNA-mediated amino acid substitutions link sexual orientation in yeasts to sex differences in the morphological and the behavioral phenotypes of humans via conserved molecular mechanisms. We detailed that fact in the context of our 1996 Hormones and Behavior review.

Despite the extension of our molecular epigenetics section and the model of hormone-organized and hormone-activated developmental differences across species from insects to other primates, psychologists and many psychiatrists continued to link their philosophies and theories to damaging practices.

Like the practice of medicine, outcomes are more predictable if they are based on what is known about RNA-mediated cell type differences. Fixation of nutrient-dependent RNA-mediated amino acid substitutions in some patient populations compared to others allows clinicians to predict whether a medication will do more harm than good in the context of what is known about pharmacogenomics and precision medicine. Fixation of RNA-amino acid substitutions in individuals of different species is also linked to their nutrient-dependent pheromone-controlled physiology of reproductive sexual behavior in species from microbes to man.

That fact has been known to serious scientists for several decades. It is the reason that other careers will be ruined until people like Ken Zucker accept the our model of RNA-mediated cell type differentiation instead of continuing to ignore details of the biologically-based development of personal preferences published in From Fertilization to Adult Sexual Behavior (1996).

 

 

 
 
 
 

 

 

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

The overwhelming ignorance of sex researchers (2)

Conclusion: There is a clear link from Estrogen receptor α polymorphism in individuals and in species with differences in behavioral phenotypes. The differences are food energy-dependent and RNA-mediated. The differences link the sense of smell and the pheromone-controlled physiology of reproduction in soil bacteria from The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the report on the Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys

Reported on December 12, 2017 as: Estrogen discovery could shed new light on fertility problems

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…

From our section on “Neurosteroids” in this December 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Perhaps significantly, neuron-specific transcription regulation of neurosteroidogenic enzymes and subsequent neurosteroids production suggest clues to mechanisms that allow some persons to develop in accord with typical gonadal male-pattern or female-pattern hormones and have appropriate male-typical or female-typical physiques nonetheless have parameters of their sexual behavior profile quite opposite to their physical phenotype. For instance, it might be possible for local neurosteroid action in CNS loci specific for sexual orientation to operate independently of other hormonal production and separately from gross body morphology in general. This could, for instance, account for different manifestations of transsexualism and homosexuality.

The “gay agenda” served its proponents well as they attempted to bury the facts that link feedback loops from odors and pheromones to biophysically constrained viral latency.

See: Feedback loops link odor and pheromone signaling with reproduction

Most sex researchers still live in fear that the biologically uninformed masses will learn that homosexual orientation is nothing more than another variation of what happens in the context of transgenerational epigenetic inheritance.

See: The overwhelming ignorance of sex researchers (December 8, 2016)

All serious scientists link food energy to the pheromone-controlled physiology of reproduction and autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links mutations to all pathology in species from microbes to humans.

If you try to make any aspect of pathology specific to any group of individuals in any human population, you challenge the totality of experimental evidence that links top-down causation to healthy longevity. You be forced to admit that you are not perfectly healthy, which means you are not qualified to judge the mental health or judge the physical health of others. The take home message is stop judging anyone based on your ignorance.

See also the author’s copy of this award-winning review: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

Abstract:

The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self. Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response. The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior. Psychophysiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships. Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences. Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.

Conclusion:

ISSUES FOR FURTHER CONSIDERATION

    Rarely do sex researchers address the ongoing philosophical debate between canonical neo-Darwinism and Biblical creation.  Perhaps this is because any debate between scientific theory and religion arises from distinctly different domains of cognitive thought.  Does the acceptance of Darwin’s theory represent the glorification of Science pitted against religion, or is it a means by which Science and religion might be integrated?  Integration of Science and religion might be achieved by recognizing that the key components of this olfactory/pheromonal model appear to be as irreducibly complex as the basic tenets of evolution and the basic tenets of religion.

    From an evolutionary perspective, highly conserved GnRH peptide ligand/receptor signaling mechanisms are the molecular biochemical mechanisms for sexual reproduction in all organisms.  These signaling mechanisms also appear to play an integral role in the development of sexual preferences.  From a religious perspective, these signaling mechanisms dictate that the creation of life, which begets life, also allows for the creation of diversified life through the same mechanisms.  These mechanisms allow life to recognize the difference between self and non-self and to respond to this difference.

    Perhaps the creation of diversified human life gave us the ability to recognize differences between our sexual behavior and the sexual behavior of others.  Since all life does not beget diversified life, those who judge sexual preferences that do not seem to result in diversified life may be judging creation itself.

    It is easy to understand how someone could judge a particular sexual preference, without thought.  Unconscious affects that are manifest in the development of human sexual preferences are, by their nature, a part of diversified life that few people think about.  What we think about human sexual preferences becomes less meaningful when we realize that most of sexual behavior is not what we cognitively think it should be.  Indeed, the largest contributor to sexual preferences that are manifest in the sexual behavior of any species appears to be unconscious affect.  This also appears to be the basis for diversified life.

See this claim about diversified life for comparison: New Zealand discovery of fossilised ‘monster bird’ bones reveals a colossal, ancient penguin

Insights into penguin evolution

The other startling thing about the new colossal fossil is its ancient age. At 55 to 60 million years old, it is nearly as old as the earliest penguin ancestors ever found. It would have lived during a geological period known as the Paleocene, just after the mass extinction 66 million years ago that wiped out non-bird dinosaurs.

The most startling thing about this ridiculous claim is that it cannot be linked from anything known to serious scientists about biophysically constrained viral latency to all biodiversity on Earth via the pheromone-controlled physiology of reproduction and chromosomal rearrangements in birds.

See for comparison: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes 

Two fixed differences among 597 amino acids drive a Val73Ile and Ala552Thr (valine to alanine) polymorphism in ZAL2m that distinguish its morphological and behavioral phenotype from ZAL2.

See also: Autophagy.pro

There is a clear link from Estrogen receptor α polymorphism in individuals and in species with differences in behavioral phenotypes. The differences are food energy-dependent and RNA-mediated. The differences link the sense of smell and the pheromone-controlled physiology of reproduction in soil bacteria from The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the report on theObligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys

No automatic alt text available.

Energy-dependent base editing and correction of mutations (2)


On 12/10/17, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals.
QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. […] discussion of notable scientists and pioneers of Quantum Biology… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
Decades later, researchers reported on: Signatures of exciton condensation in a transition metal dichalcogenide. The mass media news representation is:  Physicists excited by discovery of new form of matter, excitonium.

…when an electron, seated at the edge of a crowded-with-electrons valence band in a semiconductor, gets excited and jumps over the energy gap to the otherwise empty conduction band, it leaves behind a “hole” in the valence band. That hole behaves as though it were a particle with positive charge, and it attracts the escaped electron. When the escaped electron with its negative charge, pairs up with the hole, the two remarkably form a composite particle, a boson—an exciton.

Wikipedia

“An exciton is a bound state of an electron and an electron hole which are attracted to each other by the electrostatic Coulomb force. It is an electrically neutral quasiparticle that exists in insulators, semiconductors and in some liquids.”

If excitons are found in water, the speed of light on contact with water could be linked to the quantized energy-dependent de novo creation of all biodiversity on Earth via the pheromone-controlled physiology of reproduction in all living genera. That fact led me to find information that links thermodynamic cycles of energy-dependent RNA-mediated protein folding chemistry to hydrophobicity in supercoiled DNA.

The Water-Food-Energy Nexus: Processes, Technologies, and Challenges

The book is organized into 4 sections on water, food, energy, and the future of sustainability, highlighting the interplay among these topics. The first section emphasizes water desalination, water management, and wastewater treatment. The second section discusses cereal processing, sustainable food security, bioenergy in food production, water and energy consumption in food processing, and mathematical modeling for food undergoing phase changes. The third section discusses fossil fuels, biofuels, synthetic fuels, renewable energy, and carbon capture. Finally, the book concludes with a discussion of the future of sustainability, including coverage of the role of molecular thermodynamics…

See for comparison. There is no coverage of the role of molecular thermodynamics in the symbols used to represent different religions. It’s as if the differences exist outside the context of what is known about the creation of the sun’s anti-entropic virucidal energy.

No automatic alt text available.

The role of molecular thermodynamics in energy-dependent RNA-mediated cell type differentiation was detailed in the context of: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

Energy-dependent changes in base pairs have since been linked from changes in the microRNA/messenger RNA balance and RNA editing to fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all living genera. However, there appears to be no mention of how the virus-driven degradation of messenger RNA has been linked from mutations to all pathology in Guidelines for Genome-Scale Analysis of Biological Rhythms (2017).

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms.

Could ignoring this fact be a problem? See: Virus-mediated archaeal hecatomb in the deep seafloor

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

If the guidelines for linking the anti-entropic virucidal energy of sunlight to all biodiversity on earth via the physiology of pheromone-controlled reproduction in species from microbes to humans were applied, the guidelines could be extended to claims about the Molecular and cellular reorganization of neural circuits in the human lineage

…the dopaminergic interneurons found in the human neocortex were absent from the neocortex of nonhuman African apes. Such differences in neuronal transcriptional programs may underlie a variety of neurodevelopmental disorders.

Small but distinct differences among species mark evolution of human brain

Researchers found one gene, ZP2, was active in only human cerebellum — a surprise, said the researchers, because the same gene had been linked to sperm selection by human ova.

That claim can be placed into the context of what we detailed about energy-dependent RNA-mediated cell type differentiation in the molecular epigenetics section of our 1996 Hormones and Behavior review.
See: From Fertilization to Adult Sexual Behavior (1996)

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…

The alternative splicings of pre-mRNA have since been place into the context of energy-dependent changes in microRNAs (aka pre-mRNAs), which have been linked to differentiation of all cell types in all individuals of all living genera.
See: Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription

In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles.

The tractable changes in organized genomes can be viewed in the context of The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)
The link to sperm selection by human ova establishes the role of quantized energy as information in the context of the physiology of reproduction, which protects all species from the virus-driven degradation of messenger RNA. 
The link from the dopaminergic neuronal system to feedback loops that biophysically constrain behavior have been placed into the context of the transition from adolescence to adulthood.
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The authors fail to mention that Val158Met function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).
The degrading enzyme catechol-O-methyltransferase (COMT), determines dopamine availability in the prefrontal cortex. Thermostablility and exploratory behavior link the difference in the valine allele and the methionine allele to difference in primate brain development and behavior. That fact links the Second Law of Thermodynamics to one energy-dependent base pair change and the creation of one enzyme to changes in the microRNA/messenger RNA balance that link natural selection for energy-dependent codon optimality to one amino acid substitution that differentiates the cell types of the brain in different species of primates.
Dobzhansky (1973) presciently placed that fact into this context:

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

See also: Humans And Chimps Differ At Level Of Gene Splicing (2007)
See also: Tissue-specific alternative splicing remodels protein-protein interaction networks (2012)
Smocovitis (2006): Keeping up with Dobzhansky (link opens pdf):

The direction and speed of the evolution of any group of organisms at any given time is the resultant of the interaction of a series of reasonably well known factors and processes, both hereditary and environmental. The task of the evolutionist, therefore, is to seek out and evaluate all these factors and processes in respect to as many different organisms as possible, and from the specific information thus acquired construct such generalizations and hypotheses as he can. This requires the broadest possible knowledge of biology, which, if it cannot be acquired through direct contact with original research, must be built up vicariously through communication with biologists in different fields. — G. Ledyard Stebbins, Jr., ‘Preface’, Variation and Evolution in Plants, 1950.

Communication with biologists in different fields has revealed facts about the direction and speed of ecological adaptations linked to longevity.
See: The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us (2017)
The facts must be placed into the context of enzyme-dependent error-free DNA repair.
The secret to safe DNA repair (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

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.

They touted their belief in the emergence and the evolution of all biodiversity on Earth.

As I was preparing this post, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals. Not enough people understand biologically-based cause and effect, which limits the market for anything that protects the organized genomes of people from the virus-driven degradation of messenger RNA.

See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

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.

My business partner and I discussed the obvious fact that most people do not want to learn anything about preventative medicine or effective treatments for all pathology, and that most are willing to accept what they are told by “pill-pushing” medical practitioners. The medical practitioners will not tell them that feedback loops link food odors and pheromones to the biophysically constrained pathways of healthy longevity. The medical practitioners will not tell people that vaccines and drug therapies alter the feedback loops. The vaccines and drug therapies act on the energy-dependent creation of the same enzymes linked from the creation of sunlight to all biodiversity on Earth.

In mammals, this is manifested in links from what offspring ingest to their food energy-dependent pheromone-controlled survival. See for example: MicroRNAs: Milk’s epigenetic regulators

The deficiency of exosomal miRNAs in infant formula and the persistent uptake of milk miRNAs after the nursing period via consumption of cow’s milk are two epigenetic aberrations that may induce adverse long-term effects on human health.

It has been more that two decades since publication of The Scent of Eros: Mysteries of Odor in Human Sexuality. We linked the pheromones from mother’s milk to the mother-infant bond and to adult behaviors. I am disappointed to admit that all experimental evidence of biologically-based cause and effect has been ignored by theorists who tout emergence and mutation-driven evolution.
Apparently, Nothing can stop them! They do not seem to realize that Dobzhansky’s “light of evolution” was sunlight and it linked ecological variation to ecological adaptation in all living genera via the pheromone-controlled physiology of reproduction.

Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

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

See for comparison: Cytosis – The Science Behind the Game (free pdf download)

This is the four page booklet that explains the science in Cytosis. It was written and edited collaboratively by 20 PhD’s and Doctors through the world.
 
Please take some time to learn what happens to biologically uninformed theorists when serious scientists collaborate.
 
The collaborators achieved their common goal. The link from the creation of the sun’s anti-entropic virucidal energy to ATP and the creation of RNA is clear to players 10y/o +. The link from the virus-driven degradation of messenger RNA to all pathology in species from microbes to humans is equally clear..
 
Simply put 1) What organisms eat links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency.
 
Simply put 2) Food odors and species-specific pheromones biophysically constrain viral latency.
 
Simply put 3) Feedback loops typically prevent the hecatombic evolution of pathology that starts with viruses in seawater or the viruses in bacteria that eat electrons and produce uranium isotopes.
 

You may not believe that the sun was created and may not think that electrons were created to be eaten. Winners of this game will not care what losers believe. Losers can compare what they believe about the evolution of hydrogen and all biodiversity to the facts known to serious scientists who helped to create this game.

See also:

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

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Exposing the 2nd Law to more ridicule (1)

Summary: Experiment demonstrates quantum mechanical effects from biological system

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him – if ever again he reasserted the facts.

After 1944, Richard P. Feynman took a stand against the human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

New Genes and Functional Innovation in Mammals 21 July 2017

We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

Reported as: Genes identified that distinguish mammals from other animals  4 December 2017

They have also identified antimicrobial peptides, which participate in the body’s defence against pathogens.

The energy-dependent creation of “…antimicrobial peptides, which participate in the body’s defence against pathogens” already was linked from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency, which protects all organized genomes from the degradation of messenger RNA. False assumptions about entropy for comparison to experimental evidence of the de novo creation of genes have been placed into the context of the “arrow of time.”

Scientists Experimentally Demonstrate the “Reversal of the Arrow of Time” 
4 December 2017

Through a remarkable experiment, an international team of scientists has found that it is possible to reverse the arrow of time without violating the second law of thermodynamics.

Pseudoscientists need no longer consider anything that cannot be linked to this experimental evidence of top-down energy-dependent causation and biophysically constrained viral latency/genomic entropy. Thank God, nothing but experimental evidence of the anti-entropic virucidal energy of sunlight has ever been considered by those who have linked feedback loops from odors and pheromones to all biodiversity on Earth.
See: QuEBS workshop

…has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Quantum effects in biological light-harvesting systems have been linked from the de novo creation of sunlight to answers about all biophysically constrained biodiversity via Schrodinger’s What is Life? (1944).

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

See for comparison: 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 also: What is life when it is not protected from virus driven entropy (video) 30 Mar 2016

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

See for comparison: On causal roles and selected effects: our genome is mostly junk December 5, 2017

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable.

Conclusion:

That is to say, many of our uniquely human traits are probably the contingent products of drift and historical accidents—they make us us, but were not selected to have that, or necessarily any, effect. So we are back to Ohno’s conundrum. If lungfishes have junk, or at the least extraordinarily weakly or diffusely functional DNA in their genomes, why is it that we think we do not?

The concept of “junk DNA” is inconsistent with anything known to serious scientists about energy-dependent biophysically constrained viral latency.  Feedback loops link top-down causation to the pheromone-controlled physiology of reproduction via RNA-mediated fixation of amino acid substitutions in the organized genomes of all living genera.
See: Understanding and accounting for relational context is critical for social neuroscience
My comment: New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: [Top-down causation: an integrating theme within and across the sciences?] http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
See also: What Bacteria Can Tell Us About Human Evolution December 5, 2017

See for comparison: Learning from Bacteria about Natural Information Processing
The link from biological light-harvesting systems to the pheromone-controlled physiology of reproduction in species from microbes to humans exemplifies everything known to serious scientists about biophysically constrained viral latency, which links ecological variation to ecological adaptations in the context of physics, chemistry, and molecular epigenetics. The facts refute all neo-Darwinian nonsense and the nonsense touted by “Big Bang” cosmologists.
Sunlight is quantized energy as information and it is virucidal.
See also: Generation of photonic entanglement in green fluorescent proteins

…our prepared state is free from environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. Our photonic entanglement generation and characterization indicate that the SFWM process in EGFP is a promising quantum process for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials.

Reported as: Experiment demonstrates quantum mechanical effects from biological system

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology.

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him.
After 1944, Richard P. Feynman took a stand against human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

See for comparison: Microbiome-Centric Human Health: A Call for Systems Biology
Stop calling for more microbiome-centric systems biology and link what is known about energy-dependent changes in electrons to ecosystems in all living genera via pheromone-controlled biophysically constrained viral latency.
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.

Science after peer review

Light-activated error-free DNA repair (4)

Summary: Most of what you probably thought was about science is based on the pseudoscientific nonsense touted by biologically uninformed theorists. Attempts to mine data from any peer-reviewed article that has been published by a theorist should start with the first article that linked energy-dependent life to the creation of uranium isotopes.

See: PLOS & The Hacker Within: mining scientific articles tutorial & hackathon

See for comparison: microRNA

See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

This was reported as: Biologists discover electric bacteria that eat pure electrons rather than sugar, redefining the tenacity of life

Editor’s Note: This article originally appeared in the October 2005 issue of Scientific American.

See also the reappearance in 2009: The Workings of an Ancient Nuclear Reactor 

In 2005, this was published: Feedback loops link odor and pheromone signaling with reproduction

 

The  food energy-dependent link from electrons to ecosystems in all living genera escaped from the ridiculous misrepresentations of theorists who linked emergence to evolution. Serious scientists clarified the fact that all organism must eat or their pheromone-controlled physiology of reproduction does not represent healthy longevity. For comparison, ecological variation and ecological adaptation have consistently been placed into the context of what organisms eat — even if they eat electrons — and the physiology of pheromone-controlled reproduction that biophysically constrains viral latency.

See for comparison: Discussion of Seeing the Beautiful Intelligence of Microbes

Issaiah Wallace Why is it that the only info I can find on “virus-driven energy theft” is yours?No one else is smart enough?

Issaiah Wallace If you’re saying every pathology has a viral etiology, then you’re simply wrong.

People who tell me I’m wrong typically do not tell me what I am wrong about. That makes me think they know nothing about the topic. See for comparison: Chemists reveal one mechanism of dihydrogen production by nitrogenase

The results of the experiments suggested that only one hydrogen was actually involved in the rate-limiting step of H2 formation, and not two as the stoichiometry of the reaction indicates.
This experimental evidence fits well with the fact that the energy-dependent creation of only one enzyme is required to link the anti-entropic virucidal energy of sunlight to biophysically constrained RNA-mediated cell type differentiation in all living genera via hydrogen-atom transfer in DNA base pairs in solution and the physiology of pheromone-controlled reproduction. In this report, however, they claim:

There is still work to be done to understand the mechanism of the other H2 evolution process that leads to N2 binding, activation, and reduction to NH3.

I do not believe that two different types of hydrogen evolved.SARCASM ALERT: But maybe that’s what I’m wrong about.But see: Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity (with my emphasis)

Figure 1. Biocatalytic cascade for optical detection of three amino acids, using two detection pathways: A) measurement of NADH at 340 nm, and B) conversion of NADH to a visible color (formazan) via NBT/PMS which is observable at 580 nm.As shown in Figure 1, amino acids (glutamate, in this case) can be analyzed in two ways. Pathway A utilizes the UV properties of NADH alone, which can be observed[47] at 340 nm. Pathway B implements phenazine methosulfate (PMS) and Nitroblue tetrazolium (NBT). Here, PMS mediates the reaction of NADH reducing NBT to a colored product, formazan, which can be measured spectrophotometrically at 580 nm. Changing the starting enzyme and other chemicals as appropriate, the system can be adapted for the detection of alanine and phenylalanine using the same method. Alanine can be analyzed using an enzyme system containing alanine dehydrogenase (AlaDH; E. C. 1.4.1.1). AlaDH consumes alanine and NAD+ to produce pyruvate (Pyr), NH3nine and NAD+, and NADH. Phenylalanine dehydrogenase (PheDH; E. C. 1.4.1.20) produces phenylpyruvate (PhPyr), NH3, and NADH in the presence of phenylala. These two systems can be devised similarly to the glutamate cascade, with either pathway A, direct observation of NADH at 340 nm,[47] or pathway B, conversion of NADH to formazan via NBT/PMS which is observable at 580 nm.[48]

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

The next reformation: 500 years too late? (1)

Summary: The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
The vibrational theory of olfaction for the win

Although there is nothing comparable to this kind of insight into the molecular world of scent within the shapist mentality, we should probably thank its supporters for making this battle of ideas so epic. There may yet be time for two more big events in the field, one a Nobel party [for Luca Turin], and the other, a funeral [for shape theory].

Shape theory has been touted in the context of the Watson and Crick model of the static DNA double helix. All serious scientists have since dismissed that ridiculous model. I admit, however, that in my review of the book, The Emperor of Scent, which was about Luca Turin, I was critical of his correct approach. But Wen Zhou’s group has since linked Turin’s claims from the creation of sunlight to the creation of ATP and the creation of RNA. The extension from the creation of RNA to the creation of olfactory receptors links the time-space continuum to the pheromone-controlled physiology of reproduction and all biodiversity via feedback loops.
That was expected by every serious scientist I know. The serious scientists know that gene activation is energy-dependent. They do not link sudden energy jumps from de Vries (1902) definition of mutation to all biodiversity. The next reformation links the creation of the sense of smell to all biodiversity in the context of biophysically constrained viral latency.
See: The next reformation: 500 years too late? (2)

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

The next reformation: 500 years too late? (2)

The problem for those who use definitions is that everything known about the links from food energy-dependent changes in electrons to ecosystems must now be ignored. Last week, publications in Nature and in Science linked energy-dependent changes in base editing to RNA editing, which means that all the ignorance of biologically uninformed theorists can be placed into the context of Feynman’s claims about “human idiocy.”
See also: RNA editing and alternative splicing: the importance of co-transcriptional coordination
Apparently, the theorists did not think the facts about energy-dependent RNA editing and alternative splicings of pre-mRNA would be detailed.
But see for comparison: James Kohl reviews: The Emperor of Scent: A Story of Perfume, Obsession and the Last Mystery of the Senses

More than a century ago, in 1900, Max Planck, one of the greatest physicists of all time, announced his revolutionary new scientific theory of an energy constant in quantum mechanics. Eighteen years later he was awarded a Nobel Prize.

As Luca Turin waits for his rewards/award, he and others may benefit from knowing more about Planck’s attitude: “…a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

See also the review by Avery Gilbert: a human pheromone-denier (per Leslie Vosshall). The link opens the .pdf
Gilbert, A.N. 2003. The emperor’s new theory. Review of “The emperor of scent: A story of perfume, obsession, and the last mystery of the senses”, by Chandler Burr. Nature Neuroscience 6:335.
Gilbert’s conclusion:

Against this reality, Emperor of Scent represents a triumphalist account of an unproven alternate theory. In ancient Rome, the honor of a triumph was reserved for an emperor who achieved a glorious victory. Should Turin’s conjecture prove correct, he will of course deserve one. But until then, this appears to be a case of premature adulation.

Gilbert’s claims about premature adulation can be compared to the claims of other pseudoscientists. Serious scientists have not been afraid to link claims of adulation from the creation of energy to the creation of all biodiversity via the physiology of reproduction. The serious scientists linked Turin’s theory to every aspect of energy-dependent biophysically constrained biodiversity via the feedback loops that link the sense of smell from the pheromone-controlled physiology of reproduction to viral latency.
See: Feedback loops link odor and pheromone signaling with reproduction
Even those who might not have believed that Luca Turin correctly represented energy-dependent top-down causation in the context of links from quantum physics to chemistry and all biologically-based diversity had little doubt that food odors and pheromones are the obvious link from olfaction to survival of all species.
The next reformation: 500 years too late? (3)

Cytosis

From base editing to RNA editing (2)

Summary: The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation

A “fresh” (i.e., not yet “fossil”) bone can be plastically deformed before it breaks because it is still rich in collagen and because the calcium crystals that constitute large part of the bony matrix are not yet substituted by other minerals, as happens during the process of mineralization34. Such a diagenetic process may occur in environments that are rich in water, like a riverbed or a perilacustrine paleosol; the latter was probably the case in the Ceprano area5.

The virus-driven degradation of messenger RNA links the diagenetic process in living tissue links to the fossil record via changes that appear to have occurred during the past 5-10,000 years.
See for instance: MicroRNA-32 promotes calcification in vascular smooth muscle cells: Implications as a novel marker for coronary artery calcification
The increased level of calcification in smooth muscle cells, which is associated with increased rates of coronary artery calcification is a clear indicator that the proliferation of viruses in organized genomes causes the negative supercoiling of DNA, which serious scientists have linked to all pathology.
See also: A Post Mortem Case Study: Diffuse Pulmonary Ossification and Sudden Death
Case studies have no explanatory power outside the context of models that link electrons to ecosystems in all living genera. In this case study, it is clear that the pulmonary ossification and sudden death can be placed into the context of my model of nutritional epigenetics.
See: 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.

Attempts to support theories about random mutations and evolution have failed miserably and have largely been replaced with facts about energy-dependent RNA-mediated cell type differentiation.
See: RNA Editing Possible with CRISPR-Cas13

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

This paper is the end of the road for pseudoscientists and biologically uninformed theorists, like Eugene Koonin, who made this ridiculous claim in 2005:
Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. –Jordan et al., (2005) A universal trend of amino acid gain and loss in protein evolution
See for comparison: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… (2015) — Eugene Koonin
See also Koonin’s attack on all models of ecological adaptation: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016)

…population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Each time a new claim attests to the facts about energy-dependent RNA-mediated biophysically constrained cause and effect, remember how long those facts have been placed on hold by people like Eugene Koonin and Jay R. Fiereman, who is the moderator of the International Society for Human Ethology’s Yahoo Group.
See this attempt to discuss mysterious DNA changes with Jay R. Feierman who on 7/25/13 wrote:

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.

All DNA modifications are energy-dependent and RNA-mediated. Publications in Science and Nature attest to the foolishness of those who have tried to link base editing and RNA editing to human cell type differentiation without starting with the fact that RNA-mediated amino acid substitutions are food energy-dependent.
Clearly there are no mysterious stress-linked DNA modifications. Nutrient stress and/or social stress cause the proliferation of viruses. Typically the proliferation of viruses is biophysically constrained by food energy and the pheromone-controlled physiology of reproduction in species from microbes to humans.
See “Cytosis” for the game-ending details that placed the nonsense about neutral null falsification back into the historical perspective of the “Dark Ages.”
See also: Tempo and mode of genome evolution in a 50,000-generation experiment (with my emphasis)

Evidence for beneficial mutations

We sought to understand what proportion of the genomic changes in the non-mutator populations was adaptive, and how that proportion changed over time. One line of evidence derives from the expectation that synonymous substitutions—point mutations in protein-coding genes that do not affect the amino-acid sequence—are neutral and should therefore accumulate at a rate equal to the underlying mutation rate20,35. This expectation is not strictly true owing to selection on codon usage, RNA folding, and other effects, but it is generally thought that such selection is extremely weak, affects only a small fraction of sites at risk for synonymous mutations, or both 36,37.

RNA-mediated protein folding chemistry is biophysically constrained. It is nutrient energy-dependent and biodiversity is controlled by the energy-dependent physiology of reproduction. In 2015, Lenski’s group admitted to their lie about the beneficial mutations, with the claim “This expectation is not strictly true owing to selection on codon usage…”
No beneficial mutations have been found by serious scientists. But Lenski’s group clearly indicated they would continue to lie about all aspects of energy-dependent biodiversity. They hoped to make it appear that all energy-dependent biodiversity emerged and then automagically evolved. If they could do that, they knew that their idiot minions were not likely to examine selection for energy-dependent codon usage. But then,
See for comparison: The dynamics of molecular evolution over 60,000 generations
After 10,000 more generations, Lenski’s group reported that standard models of mutation-driven evolution has not been supported by their experimental evidence. Instead, they placed their results into the context of natural selection for energy-dependent codon usage and long-term adaptation, which obviously occurred outside the context of mutation–selection balance and neutral mutation accumulation.
They clearly indicated that the complexity of ecological variation and energy-dependent ecological adaptation must be considered before reporting anything in the context of natural genetic variation. Simply put, they refuted all the pseudoscientific nonsense their past claims caused to be touted by other biologically uninformed theorists. They reported that ecological adaptation occurs outside the context of the mutations and evolution.
But see: Molecular evolution: No escape from the tangled bank

Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection.

The claim that there is no escape from the tangled bank is true. Joshua B. Plotkin took Lenki’s group’s refutation of mutation-driven evolution and placed it back into the context of the spontaneous emergence of energy-dependent ecological interactions. And then, he again touted the nonsense about evolution by natural selection.
See also: Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli (2017)

…we developed a toolkit for characterizing any Escherichia coli OTS that reassigns the amber stop codon (TAG). It assesses OTS performance by comparing how the fluorescence of strains carrying plasmids encoding a fused RFP-GFP reading frame, either with or without an intervening TAG codon, depends on the presence of the nsAA. We used this kit to (1) examine nsAA incorporation by seven different OTSs, (2) optimize nsAA concentration in growth media, (3) define the polyspecificity of an OTS, and (4) characterize evolved variants of amberless E. coli with improved growth rates.

Even with the tools available, which have refuted all ridiculous theories of mutation-driven evolution, the claims that variants “evolved” continues to plague all serious scientists. It seems that placing the claims that variants evolved into the context of natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction in all living genera serves no purpose. However, even if biologically uninformed science idiots are not willing to admit that top-down causation requires first consideration for the energy source, there is hope for the future. Most people intuitively understand that the food energy from what organisms eat must be linked to the metabolism of food and the metabolism of food to species-specific pheromones is the only known link from the physiology of reproduction to all biophysically constrained biodiversity in the context of viral latency.
Epigenetic effects must be linked to affects on behavior and the difference between an effect on hormones and an affect of hormones on behavior must be considered in the context of how food odors and pheromones are linked to the physiology of human reproduction by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction