APS 2018

From photons to the proton motive force (2)

If you know someone who has linked differences in the energy of photons from the proton motive force to the physiology of reproduction and all biophysically constrained biodiversity, ask if they will attend Schrödinger at 75-The Future of Biology
For contrast, touting genetic evolution is not the future of biology.
See: Abstract: K06.00013 : A Path Integral Method for Analytically Tractable Inference of Evolutionary Dynamics

Understanding the forces that shape genetic evolution is a subject of fundamental importance in biology and one with numerous practical applications. Modern experimental techniques give insight into these questions, but inferring evolutionary parameters from sequence data, such as how an organism’s genotype affects its fitness, remains challenging. Here we present a method to infer selection from genetic time-series data using a path integral approach based in statistical physics. Through extensive numerical tests we find that our method exceeds the current state of the art in the successful classification of mutations as beneficial or deleterious in a variety of scenarios, while also yielding orders of magnitude improvements in run time. Our approach can also be extended to jointly infer other evolutionary parameters such as the effective population size and mutation rates.

Serious scientists do not infer evolutionary parameters using sequence data. They link natural selection for energy-dependent codon optimality to biophysically constrained viral latency. Virus-driven energy theft is linked from mutations to all pathology. There is no such thing as a beneficial mutation.
See also: Abstract: K06.00001 : Coarse-grained models coupling cell cycle and gene expression*

During a cell cycle, cells grow and divide. Recent single-cell experiments show that gene expression levels depend on the cell cycle. Particularly important is the proportion of the number of mRNA and protein to the cell volume. It is not clear how cells maintain a constant mRNA and protein concentration as the cells grow. Here we propose a coarse-grained gene expression model incorporating ribosomes and RNA polymerases, which captures the exponential growth of mRNA and protein number. We show that the homeostasis of mRNA and protein concentrations during the cell cycle can be achieved in a robust manner independent of cell shape. Furthermore, we show that the fluctuations in ribosome and polymerase numbers do not propagate to protein concentrations while the fluctuation in cell density does. Furthermore, our model reconciles the discrepancy between the experimentally observed negligible correlations between mRNA and protein levels, and the predicted positive correlations from previous models

Energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated cell cycles to gene expression in more than 70,000 published works. See: microRNA
See also: Applications of ligation-mediated PCR

A nick in a strand is any place where there’s a missing covalent bond between a sugar and the next adjacent phosphate. Nicks can arise from DNA damage, during normal DNA replication, or from the action of nuclease enzymes. Since a nick breaks the continuity of the backbone of one strand, it must be repaired by re-forming the missing covalent bond in order to make the DNA molecule intact again. This job of sealing nicks (specifically, nicks that occur between a sugar 3′ -OH group and the adjacent phosphate attached to the preceding sugar’s 5′ -OH group) is the function of DNA ligase. Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.

The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.

Simply put: It’s all about that base and energy-dependent RNA-mediated DNA repair.
If you are still trying to put what is known about DNA repair and cell type differentiation back into the context of neo-Darwinian evolution, you are not a winner.
See: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

See also: The spread of true and false news online
Reported as: Researchers call for large-scale scientific investigation into fake news

Additionally, the article’s authors point out that false information affects not only the political sphere but also areas not previously regarded as political, such as public health topics like nutrition and vaccinations, as well as the stock market.

Do you know someone who has consistently touted the use of vaccinations compared to nutrition? Are they paid to do that or are they biologically uninformed?

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


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)
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).






Alternative splicing of pre-mRNA

George Church refutes theistic evolution

Wednesday Afternoon Lecture Series (WALS) – The future of genetic codes and BRAIN codes

The NIH Director’s Wednesday Afternoon Lecture Series, colloquially known as WALS, is the highest-profile lecture program at the NIH.

The future of genetic codes and BRAIN codes (video)
My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.
Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.
Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
They showed that a single set of light-activated reactions gave rise to most of life’s building blocks simultaneously. Simply put, that fact refutes every aspect of neo-Darwinian nonsense. It also eliminates consideration of any theories proposed by “big bang” cosmologists.
The irony of this is that not one of the young earth creationists I know would fail to link the hydrogen-atom energy-dependent de novo creation of nucleic acid precursors to all biodiversity on Earth via the physiology of biophysically constrained cell type differentiation.
For example, see: Multipurpose Plant Sensors Startle Scientists
Even if a young earth creationist knew nothing about energy-dependent cell type differentiation, he or she would not be likely to link minimal mutational differences, called mutations to the mutation-driven evolution of all biodiversity.
As you can see in the video, George Church has been forced to abide by the rules of serious scientists.
Here is an unavoidable rule: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.

George Church has, until yesterday, focused his efforts on exogenous RNA interference rather than what is known about endogenous RNA interference, which links supercoiled DNA to the prevention of all virus-driven pathology in all living genera. Most people will not recognize what President Trump has forced the NIH to do before the theistic evolutionist, Francis Collins is replaced. They may read this, but not understand what it means.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The likelihood that NIH funding will be used for any studies that do not link prevention from the National Microbiome Initiative to the Precision Medicine Initiative via the microRNAome and energy-dependent microRNA expression can be placed into the context of failed mathematical models, which have not addressed any aspect of energy-dependent biologically-based cause and effect.
Let me help others decipher the content of George Church’s claims in: The future of genetic codes and BRAIN codes
The question (at 54:22) about teratomas is answered with a classic attempt to obfuscate what is known about virus-driven energy theft and all pathology.
How organs assemble in the context of virus-driven energy theft has been placed into the context of energy-dependent viral latency since the time that Sinclair Lewis published “Arrowsmith” in 1925 and Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance.
At 59.00 the question about natural selection for energy-dependent codon optimality leads to another attempt to obfuscate what is known about top-down causation.
At 1:00 he begins to talks about adding a built-in sequencer in your phone.  At this point, you may need some comic relief, which Jon Stewart provided with his question about whether the new technology would be integrated with a camera. See: Jon Stewart interviews Greg Bear.
At 1:04, the question and answer about Alzheimer’s vs cognitive enhancement can be placed into the context of Greg Bear’s works, which were published in 1999 and 2003. They were reviewed by Michael A. Goldman in “Nature.”
Evolution rising from the grave
Living with the Neanderthals
See also: Newly found mechanism for protecting neurons could underlie brain disease

The neurons expel large (4- micron diameter) membrane-bound vesicles (dubbed “exophers”) that are filled with clumped protein and damaged cellular organelles including mitochondria.

The only mention of exopher in the extant literature indexed on PubMed is in the article published yesterday, C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress.  The authors seem to be trying to make everything known to all serious scientists appear to be new information about the biophysically constrained RNA-mediated transgenerational epigenetic inheritance of morphological and behavioral phenotypes.
This is roughly the equivalent of inventing de Vries 1902 term “mutation,” which was used by theorists to dismiss Darwin’s “conditions of life.”
For comparison, there are now 58,887 indexed articles on PubMed that mention microRNA.  For example, see: MCMDA: Matrix Completion for MiRNA-Disease Association prediction
If you do not object to the level of obfuscation that is required for pseudoscientists to continue touting their ridiculous theories, you may not be allowed to join those who are Combating Evolution to Fight Disease.
What career goals will you pursue after the Trump administration ensures that pseudoscientific nonsense is no longer funded?
Activity-dependent spatially-localized miRNA maturation in neuronal dendrites
Reported as: Bright Spots in Brain Cells

Thanks to Anna Di Cosmo for calling attention to more detailed facts about cell type differentiation that link energy-dependent changes in fluorescence from the weekend resurrection of the bacterial flagellum to endogenous RNA interference and the maturation of brain cells in rats.
Everything known appears to link the conserved molecular mechanisms of nutrient-dependent pheromone-controlled physiology of reproduction in species from archaea to humans.
In any case, no one is challenging the perspective that serious scientists like Anna Di Cosmo have added to what is known about everything that links quantum physics to quantum consciousness via energy-dependent “bright spots in brain cells.”
And there is still no other model for comparison to this model of biologically-based cause and effect. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
A good model predicts, and people who understand the need for a good model of biologically-based cause and effect predictably make the most scientific progress.
In 2013 I wrote:

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.”

In 2015, Role of olfaction in Octopus vulgaris reproduction, Anna Di Cosmo’s group concluded:

The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). The knowledge of the nature of the factor released by the optic gland could shed light on the role played by this gland in the reproduction: is it a gonadotropin or a trophic factor? Intriguingly, even though the mechanisms and molecules regulating reproduction are the same in both male and female, O’Dor and Wells (1978) observed mature sperms in young O. vulgaris males independently from optic gland hypertrophy.


Alternative splicing of pre-mRNA

Demoncrats fight polycombic ecological adaptation

Comey sent Congress letter on Clinton emails despite DOJ warning it would breach policy


…we don’t ordinarily tell Congress about ongoing investigations, but here I feel an obligation to do so given that I testified repeatedly in recent months that our investigation was completed,” Comey wrote, referring to the Bureau’s previous investigation into Clinton’s private email server. “I also think it would be misleading to the American people were we not to supplement the record.

See also: 96. ‘The Huffington Post’ colluding with Hillary


“I am committed to make sure she is elected as the next President of United States. I am reaching out to my friends to raise money for her campaign. Please let me know if I can be of any service to you.”

No doubt the entirety of Huffington Post is in it for Hillary when they display their “disclaimer” (“Donald Trump is a racist, sexist, homophobe Hitler” or something along these lines) under every “article.”

The author of this email once an “article” on the Huffington Post that Trump was “a sorcerer and a wizard”. Yes… Huffington Post actually  published this.  That’s why no one takes The Huffington Post seriously.

See for comparison: 04/17/16 PART 2: A Wide-Ranging Conversation with Physicist Geoffrey West on Life, Evolution and US Presidential Politics


I don’t think Bill Clinton has any interest in, or knowledge of science, and I suspect Hillary is the same.

Did The Huffington Post stop Suzan Mazur from reporting more facts about virus-driven energy theft in the context of neo-Darwinian pseudoscientific nonsense touted by supporters of those who some people suspect have no interest in, or knowledge of science?

Are those people called Demoncrats? Does pattern recognition allow others to see who is supporting the pathology that has led us to the forthcoming viral apocalypse?


Major scientists from a dozen countries present evidence that a paradigm shift is underway or has already taken place, replacing neo-Darwinism (the standard model of evolution based on natural selection following the accumulation of random genetic mutations) with a vastly richer evolutionary synthesis than previously thought possible.

See also: 8/6/15  Günther Witzany: Modern Synthesis “Must Be Replaced,” Communication Key to Evolution

My comment: Witzany is the author of: Life is physics and chemistry and communication


Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language.

My comment: What is known about virus-driven energy theft has already shifted the paradigm during the past few decades and the possibility of a new “evolutionary synthesis” has been eliminated by facts about energy-dependent ecological adaptation.

Excerpt from my comment:

…watch closely as they squirm under the weight of experimental evidence that collectively refutes their ridiculous theories and philosophy.

See also: 8/6/16 A Chat with Information Scientist Pedro Marijuán

….the cell communicates with the environment via specific signaling pathways. This is the essence of all prokaryotic activity. And this is the essence of multicellular development.

My comment: Nothing more  has been published by Suzan Mazur about the biological regularities that show there is only one domain of life, not two or three. She must know by now that Carl Woese was wrong.

It has become perfectly clear that the organized genome of bacteria protects them from virus-driven energy theft that occurs at a higher rate in archaea. The energy-dependent link from the organized genomes of bacteria to the organized genomes of eukaryotes is also perfectly clear in the context of autophagy and the 2016 Nobel Prize in Physiology or Reproduction.

However, after months of installments that attacked the censorship of next week’s meeting of the Royal Society, it appears as if someone at the Huffington Post or someone they were colluding with told Suzan Mazur to stop her attacks on the Clinton’s lack of interest in, or lack of knowledge of science.

For one year, Suzan Mazur has been on the trail of lying pseudoscientists and one month before next week’s meeting, she published this book. Royal Society: The Public Evolution Summit 

Page 70 … There are interesting thoughts about the forming of RNA…

Bateson: interesting thoughts about the forming of RNA and its replication

Page 3 … Larry Moran — Sandwalk James Kohl — RNA-mediated.com…

Page 52 …invading DNA. Whether they do it at the DNA level or the RNA level…

Shapiro: we were told that DNA uptake was not possible in the context of the Luria-Delbrueck experiment.
See Comparing mutation rates under the Luria-Delbrück protocol

Page 10 Coincidentally, we have come to recognize that “non-coding” RNAs …

Page 11 These agents have been since ever and still are interacting RNA con…

Page 12 … evolution of genome invading RNA networks that edit host g…

Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”

Page 126 …of Francis Crick, i.e., that information flows from DNA to RNA to …

Energy as information does not flow from DNA to RNA. It flows from RNA to supercoiled DNA via autophagy in the context of the de novo creation of genes and increasing organismal complexity via the physiology of reproduction in all living genera.

See also:


Energy-dependent biodiversity (4)

Quorum Sensing Determines the Choice of Antiphage Defense Strategy in Vibrio anguillarum

The strategy links the innate immune system to energy-dependent healthy longevity or from virus-driven energy theft to all pathology.

See also: Counting viruses and bacteria in photosynthetic microbial mats.

The ratio has been linked from the sun’s quantized anti-entropic virucidal energy to RNA-mediated DNA repair via hydrogen-atom transfer in DNA base pairs in solution. The energy transfer links the innate immune system and microRNA flanking sequences from angstroms to ecosytems in the context of the physiology of reproduction and supercoiled DNA.

The facts are neo-Darwinian theory killers that have been ignored for more than 20 years. Whose lives did they think they were toying with — besides their own? The Precision Medicine Initative and National Microbiome Initiative have already linked the metabolic networks and genetic networks of all living genera with facts about RNA-mediated protein folding chemistry. It’s biophysically constrained! Surprise! Contraint-breaking mutations cannot be linked to Mutation-Driven Evolution outside the context of mathematical models, definitions and ridiculous assumptions (reported by you with exquisite consistency and clarity).

So now, they plan a meeting; try to quell discussion of virus-driven energy theft and disease and then want to discuss damage control with you.

Get ’em, Suzan!

See also: Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape
Reported as:

Missense mutations (that change one amino acid for another) in histone H3 can produce a so-called oncohistone and are found in a number of pediatric cancers. For example, the lysine-36–to-methionine (K36M) mutation is seen in almost all chondroblastomas. Lu et al. show that K36M mutant histones are oncogenic, and they inhibit the normal methylation of this same residue in wild-type H3 histones. The mutant histones also interfere with the normal development of bone-related cells and the deposition of inhibitory chromatin marks.

My  comment: I cannot keep up with the amount of pseudoscientific nonsense that is being touted in the last few attempt to save the careers of those who have placed all virus-driven energy theft into the context of mutations and/or natural selection and evolution.
Today, I found this domain: Oncohistone.com  I suspect it was established to compete with information dissemination at RNA-mediated.com
But why? They are not linking energy-dependent changes in angstroms to ecosystems via RNA-mediated amino acid substitutions. They are not linking virus-driven energy theft to all pathology. They are linking a definition of missense mutations (that change one amino acid for another) to what they expect others to call oncohistones. That will help them continue to link mutations to pathology without linking virus-driven energy theft to the mutations.
I can’t remember if I already posted about that to this blog. But I wanted to ensure I placed it into the context of the domain they established and Suzan Mazur’s update on the Royal Society meeting.
The desperation is showing in every area of research where scientists have clung to definitions and assumptions for far too long.
See for comparison:  MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
Energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution link microRNA-based regulation of all cell type fate determination to healthy longevity or from virus-driven energy theft to pathology.

In Energy-dependent biodiversity (2) I mentioned this:

All the confusion about linking the mouse model to humans via energy-dependent hydrogen-atom transfer in DNA base pairs, which are linked to supercoiled DNA and protection of organized genomes from virus-driven energy theft and genomic entropy is missing.

My comment: The confusion must be viewed in the context of this article: Structure of the T4 baseplate and its function in triggering sheath contraction

Reported as: How viruses infect bacteria: A tale of a tail

The scientists were also able to identify a minimal set of molecular components in the baseplate that work together like miniature gears to control the activity of the virus’s tail. These components, and the underlying functional mechanism, are the same across many viruses and even bacteria that use similar tail-like structures to inject toxins into neighboring cells.
“These findings are important for our understanding of how these contractile tail-like systems work,” says Leiman. “But they also set a benchmark for the complexity of biological systems that can be described at the atomic level.” The human body contains almost as many bacteria as human cells (30-40 trillion), and the human gut microbiota will likely represent an important target for personalized medicine in the future. “It is clear that we need to understand the detailed mechanisms by which these bacteria interact with each other and how phages are involved in these interactions.”

See also: Evolutionary ‘probables’ a positive step


The new method samples evolutionary histories, called phylogenetic networks, and makes suggested connections between closely related species, or even multiple individuals within species.
“That’s one of the nice things about the Bayesian approach and why we went in that direction,” he said. “We don’t give biologists a single answer. We don’t say, ‘Here’s your optimal evolutionary history.’ We say, ‘Here’s a sample of evolutionary histories the method found while walking the space of possible evolutionary histories.'”
My comment: They don’t say anything about the fact that the history of any species is nutrient energy-dependent and controlled by the physiology of reproduction. If you asked them, they might claim that Mother Nature caused everything to happen automagically.