fruit-dove

The death of human ethology via ecology

Nutrient-dependent/pheromone-controlled adaptive evolution: a model Open access publication on June 14, 2013
Mutation-driven evolution also published on June 14, 2013
Variable habitat conditions drive species covariation in the human microbiota http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005435 Open access publication on April 27, 2017
Conclusion:

…we found that genetically related species respond to fluctuating habitat conditions in the same way, implying that they occupy similar ecological niches. Thus, current taxonomic groupings of bacteria are largely sufficient for explaining cross-sectional correlations in relative species abundances over the healthy human population. This result is not at odds with high rates of HGT; it simply implies ecologically derived constraints on evolution.

Reported on April 27, 2017 as: Resource availability drives person-to-person variations in microbes living in the body

Ecological model reveals relationships between resource availability and microbe species abundance

Historical perspective: “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)

From the forward to the reprint edition of “What is Life?” (1944)

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

All current extant literature attests only to the obvious role of ecological variation and food energy as information, which enables the ecological adaptations manifested in species diversity via the physiology of biophysically constrained pheromone-controlled reproduction. Nutrient energy-dependent changes in the microRNA/messenger RNA balance protect supercoiled DNA from virus-driven energy theft and the degradation of messenger RNA, which links mutations to all pathology. All serious scientists are now aware of these facts, but pseudoscientists are not convinced.
See for example:
7/24/13 James V. Kohl: “Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.
Despite the facts expressed by Schrodinger and emphasized by Penrose as well as my claim (above), neo-Darwinian theorists still seem willing to accept the claims of biologically uninformed science idiots, such as this one:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison:
Foote et al (2013)“Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
Chung et al (2014) “…ecological divergence and mate choice may produce reproductive isolation and speciation….
Plucain  et al (2014) “Ecological opportunities promote population divergence into coexisting lineages.
The pseudoscientific nonsense touted on this Yahoo group has not ended.

Human ethology is the study of the biology of human behavior, including the behavior’s phylogeny (evolutionary history), ontogeny (development), proximate causes, and adaptiveness (survival value). Postings relevant to these topics will be accepted.

Sonny Williams wrote:
Re: For the sake of all humanity, please ignore the shrill, uninformed cries of creationists and other types of supernaturalists.  Instead, talk to a regulatory geneticist.
I responded with a comment about the game: Cytosis: A Cell Biology Board Game

See: msg 86257

James Gray: Jay, I hope you can say that you missed the threat in this quote from Kohl. “What game will you be playing until your career as a researcher or philosopher or your life as as biologically uninformed atheist ends at the hands of those who are biologically informed young earth creationists?”

I know only two people who would take my comment about the game Cytosis, and perceive it as a threat that they would be killed by young earth creationists. James Gray is one; here is the other one:

Sonny Williams: Thanks for catching this, James…and warning me.  I consider Kohl a personal threat and think it is time he be banned from the group.

So far as I know, I am the only participant in the group that has published an award-winning review of human ethology.
See: Human pheromones: integrating neuroendocrinology and ethology (2001)
See also: msg 86274

Excerpt: “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.”

It will be interesting to see whether or not Sonny Williams and/or James Gray will claim that I threatened they would be killed by terrorists.
In any case, the regulatory geneticist Giacomo Cavalli and others have finally brought forth their claims about Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila
The claims were reported as: We are more than our DNA: Discovering a new mechanism of epigenetic inheritance

Cavalli and his team at the Institute of Human Genetics (University of Montpellier / CNRS) are the first to show that regulation of gene position can lead to transgenerational inheritance.

See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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

See also:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Anyone who claims they are the first to link the nutrient energy-dependent stability of polycombiic ecological adaptation via the transgenerational inheritance of chromatin states should be viewed with suspicion. Chromosomal inheritance was first linked to the transgenerational epigenetic inheritance of chromatin states by Thomas Hunt Morgan, who won the 1933 Nobel Prize in Physiology or Medicine for his works.
With all due respect Giacomo Cavalli may have come in third with publication in 2007 of  Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms.

The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal “gene kissing”. The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes (“epimutations”) with effects at a distance would then perdure over the number of generations required for “assimilation” of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of “junk DNA”, through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

I mayt never know if Giacomo Cavalli come in third with representations of intrachromosomally spreading teleregulation and interchromosomal “gene kissing” It is hard to evaluate his works, since he placed his finding into the context of epimutations and evolution via “junk DNA.”
For comparison, young earth creationists have been addressing the nonsense about “junk DNA” during the past two months.
See for instance: Major Evolutionary Blunders: Evolutionists Strike Out with Imaginary Junk DNA, Part 1

Scientists whose analysis is constrained to fit evolutionary theory will not see a brain, a digestive system, and other complicated biological phenomena as designed things but rather as conglomerations of parts cobbled together by nature. “We’re all here because of mutations,” claims molecular neuroscience professor Jernej Ule, who adds:

But most random mutations actually disrupt the functions of our genes and so are a common source of genetic diseases….How does nature resolve this conflict?…We’ve known for decades that evolution needs to tinker with genetic elements so they can accumulate mutations while minimising [sic] disruption to the fitness of a species.4

See also: Major Evolutionary Blunders: Evolutionists Strike Out with Imaginary Junk DNA, Part 2

I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century….The failure to recognize the full implications of this [important parallel information derived from non-coding DNA] may well go down as one of the biggest mistakes in the history of molecular biology

For more information on parallel information, which appears to be linked to non-coding DNA see: A universal trend of amino acid gain and loss in protein evolution

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

See also: The death of human ethology via ecology (2)

rp_PO9583119-frontl.png

The Virus-Driven Suicide March for Science

Genetic analysis of α-synuclein 3′ untranslated region and its corresponding microRNAs in relation to Parkinson’s compared to dementia with Lewy bodies
My summary: Genetic predispositions and energy-dependent microRNA biogenesis link top-down causation to the biophysically constrained transgenerational epigenetic inheritance of neuronal type-specific expression.  Energy-dependent variability in endogenous RNA interference and the SNCA gene contribute to synucleinopathies in the context of two different human pathologies.
Virus-driven energy theft is linked to the regulation of the α-synuclein (SNCA) gene and the etiology of Parkinson’s disease (PD) and to (DLB) dementia with Lewy bodies. RNA-directed DNA methylation is clearly linked from the negative supercoiling of DNA to DLB.
See: DNA methylation changes at SNCA intron 1 in patients with dementia with Lewy bodies
My summary: Lower methylation rates are a biomarker for dementia with Lewy bodies (DLB)
After Robin Williams death was attributed to suicide, he was diagnosed with DLB. The misdiagnosis of Parkinson’s disease contributed to his death.  Virus-driven pathology will continue to contribute to the unnecessary suffering and death of many more victims who have been misdiagnosed by biologically uniformed psychiatrists and other so called “medical professionals.”
See also: Up-regulation of SNCA gene expression: implications to synucleinopathies

…this model system will enable us to compare different neuronal and glial lineages involved in synucleinopathies representing an attractive strategy to elucidate-common and specific-SNCA-genetic variants, regulatory mechanisms, and vulnerable expression levels underlying synucleinopathy spectrum disorders. This forthcoming knowledge will support the development of precision medicine for synucleinopathies.

Synucleinopathies

Because each of the synucleinopathies has a distinct set of symptoms, prognosis and management issues, it has been suggested that the term “has little practical value as a diagnostic term for the clinician.

When did any term used by medical professionals in any model of pathology link nutrient energy-dependent pheromone-controlled ecological adaptations to all healthy longevity and link virus-driven energy theft from synuclinopathologies to all pathology?
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: Hypothesis free pseudoscience vs facts (4) 10/3/16

Someone should tell Robin Williams’ widow that these guidelines could apply to the use of antibiotics to treat gut discomfort before virus-driven energy theft causes Lewy Body Disease to be misdiagnosed and leads to death by suicide.

See also: Hypothesis free pseudoscience vs facts (5) (10/4/16)

If others had learned that virus-driven energy theft is the cause of the RNA-mediated changes in gut microbes, the publication of results in 1985 might have prevented the death of Robin Williams from Lewy Body Disease. His first symptom was gut discomfort.

Had the viruses in the bacteria been killed by killing the bacteria with an effective antibiotic, Robin Williams and many others would still be alive — like Barry Marshall. Instead, many researchers are still stuck with the irrelevant theories touted by neo-Darwinists.

See also: Combating evolution: Battlefield medicine vs politicized science (12/4/16)

1) He died from constraint-breaking mutations because his physician’s did not know how to link the National Microbiome Initiative to the Precision Medicine Initiative by what is known to all serious scientists about RNA-mediated biophysically constrained viral latency.

2) Anything more I could say has been said in the context of Nobel Prize-winning works from 1936 to this year’s award to Ohsumi. It is not possible to break it down into language that a layperson will understand, unless the layperson understands why Ohsumi won the award, which was based on all works that have every linked energy-dependent changes in angstroms to ecosystems via autophagy. And yet, Ohsumi has not linked virus-driven energy theft to Lewy Body Disease and all other pathology.

See also: Autophagy: from pre-mRNAs to microRNAs, enhancers, QTLs et al. (1/4/17)

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

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

Every aspect of preventative medicine links the National Microbiome Initiative to the Precision Medicine Initiative via energy-dependent changes. The changes link angstroms to ecosystems in all living genera. When do you think you will be told that the obvious link from the changes to healthy longevity is the pheromone-controlled biophysically constrained chemistry of RNA-mediated protein folding. I hope you learn that fact before you die from virus-driven energy theft.

Heading into Today’s March, Here’s When to Doubt a Scientific “Consensus

…the “power of the paradigm” often blinds scientists to alternatives to their view. Question the paradigm, and some respond with anger.

But here’s a checklist to decide when you can, even should, doubt a scientific “consensus,” whatever the subject. One of these signs may be enough to give pause. If they start to pile up, then it’s wise to be leery.

(1) When different claims get bundled together

(2) When ad hominem attacks against dissenters predominate

(3) When scientists are pressured to toe the party line

(4) When publishing and peer review in the discipline is cliquish

(5) When dissenters are excluded from the peer-reviewed journals not because of weak evidence or bad arguments but to marginalize them.

(6) When the actual peer-reviewed literature is misrepresented

(7) When consensus is declared before it even exists

(8) When the subject matter seems, by its nature, to resist consensus

(9) When “scientists say” or “science says” is a common locution

(10) When it is being used to justify dramatic political or economic policies

(11) When the “consensus” is maintained by an army of water-carrying journalists who defend it with partisan zeal, and seem intent on helping certain scientists with their messaging rather than reporting on the field as fairly as possible

(12) When we keep being told that there’s a scientific consensus

Is there any consensus for comparison to one that most people believe in about the fact that they must eat or they will starve to death?

See for comparison: Could genetics influence what we like to eat?

…little is known about how natural variation in these genes could affect eating behaviors in healthy people. Gene variation is a result of subtle DNA differences among individuals that make each person unique.

What is Life? (reprint edition)

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

See also:  Anesthesia points to deeper level ‘quantum channels’ as origins of consciousness

OR theory is not theory. They linked the anti-entropic virucidal quantised energy of sunlight from ecological variation to ecological adaptation in all living genera via nutrient energy-dependent viral latency as Penrose did in his forward to the reprint of “What is Life?”  Theorists who typically do not understand any aspect of biophysically constrained RNA-mediated protein folding chemistry may continue to tout their pseudoscientific nonsense about mutations and evolution, but all serious scientists know that energy-dependent codon optimality is the key to human consciousness. For example, they know that people who do not eat lose consciousness and die.

Scientist Confirms the Quantum Soul

Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

Quantum Souls

The Quantum Souls blog explores how the sun’s anti-entropic virucidal energy is linked to quantum biology, consciousness and in the soul of humans and animals. Contrary to evolutionary theorists, we are not mutants who evolved after energy emerged from nothing.

Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose (2)

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

See also: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015
“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and 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.

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

Physics

Young earth creationists refute theistic evolution

Every great scientific truth goes through three stages. First, people say it conflicts with the Bible. Next they say it has been discovered before. Lastly they say they always believed it. –Louis Agassiz

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

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

Excerpt:

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

Are all evolutionists atheists?

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

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

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

See also: The RNA code comes into focus

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

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

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

Excerpt:

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

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

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

George Church refutes theistic evolution (3)

Fifty years of illumination about the natural levels of adaptation

… George C. Williams developed in his 1966 book Adaptation and Natural Selection the essentials of a unifying theory of adaptation that remains robust today and has inspired immense progress in understanding how natural selection works.

Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

See also: George Church refutes theistic evolution and George Church refutes theistic evolution (2)
Why did so many pseudoscientists fail to link ecological variation to ecological adaptation via natural selection for energy-dependent changes in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy? Why have they continued to tout ridiculous theories for comparison to what is being reported about adaptation by serious scientists. Almost every day there is something old reported as if it was new information to be considered before it is again ignored by theorists.
See for examples from this past week:
Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Interplay between miRNAs and Human Diseases: A Review
400 pilot whales stranded on New Zealand’s ‘whale trap’ beach

Other factors include whales’ incredibly tight social bonding, which is especially strong within groups of pilot whales.
 
Social bonding is nutrient energy-dependent and controlled by the physiology of reproduction. In species from microbes to humans, the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones.
 

Rather than tout theories about solar storms and geographical traps, serious scientists investigate the facts that link the sun’s anti-entropic virucidal energy to endogenous RNA interference via olfaction and the innate immune system. Serious scientists link food odors and pheromones to behavior in all living genera.

2005 Feedback loops link odor and pheromone signaling with reproduction

2015 Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. 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).

Ecological variation that is not manifested in ecological adaptation links virus-driven energy theft to the stranded whales. The energy theft prevents nutrient energy-dependent ecological adaptation. Unfortunately, theorists do not understand any aspect of natural selection for energy-dependent codon optimality.The prefer to use definitions and assumptions for comparison to the experimental evidence of biologically-based cause and effect that serious scientists must use in the context of their religion.

Pseudoscientists claim that atheism is not a religion. Atheism is a religion by definition.

See: atheism

  1. 1a :  a lack of belief or a strong disbelief in the existence of a god or any godsb :  a philosophical or religious position characterized by disbelief in the existence of a god or any gods

See for comparison:  How an obscure oriental cult in a corner of Roman Palestine grew to become the dominant religion of the Western world
Even historians know that the history of a religion can influence the faith of believers today. For example, atheism today arose in the context of de Vries 1902 definition of “mutation” and acceptance of assumptions that accumulated mutations could lead from natural selection to the evolution of one species from another species.

Christianity can clearly be linked from events that start from the creation of energy as information in Biblical Genesis to the weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces with exposure to UV light.

Atheism as a religion cannot stand up to the overwhelming amount of experimental evidence that supports claims in the Old Testament, which were linked to claims in the New Testament. There is nothing that appears to link the emergence of everything from nothing or the evolution of one species from another. That fact links three more definitions to all biodiversity on Earth.

The emergence of atheism as a world religion can now be placed into the context of definitions that recently were added to the Merriam-Webster dictionary.

Phytoremediation

the treatment of pollutants or waste (as in contaminated soil or groundwater) by the use of green plants that remove, degrade, or stabilize the undesirable substances (such as toxic metals)

CRISPR

The CRISPR segment encodes, via transcription, short RNA sequences that pair with complementary sequences of viral DNA. The pairing is used to guide an enzyme to cleave the viral DNA and prevent further infection.

 Microbiome

  1. 1 :  a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body <Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. — Carl Zimmer> < … what’s arguably become the hottest area of medicine: microbiome research, an emerging field that’s investigating how the bacteria that live in and on our bodies affect our health. — Sunny Sea Gold>
    1. 2 :  the collective genomes of microorganisms inhabiting a particular environment and especially the human body <They form one community among the many that make up the human microbiome: the full genetic complement of bacteria and other organisms at home on your skin, gums, and teeth, in your genital tract, and especially in your gut. — Nathan Wolfe>

The definitions that were recently added to the Merriam-Webster dictionary link the energy-dependent pheromone-controlled physiology of reproduction in bacteria from the National Microbiome Initiative to the Precision Medicine Initiative via endogenous RNA interference, which prevents the virus-driven energy theft that links mutations to all pathology.

For comparison, see: How algorithms (secretly) run the world

“Algorithms are not inherently fair, because the person who builds the model defines success,” she said.
See also: Digital Star Chamber

Following the advice of Jeff Jarvis’s What Would Google Do, they are collecting data from both workers and customers, using algorithmic tools to make decisions, to sort the desirable from the disposable.

What would Jesus do about the use of algorithms to predict outcomes?

Algorithms can be made more accountable, respecting rights of fairness and dignity for which generations have fought. The challenge is not technical, but political, and the first step is law that empowers people to see and challenge what the algorithms are saying about us.

Did Jesus know the creation of energy and virus-driven energy theft are predictable links to outcomes that pseudoscientists think can be linked via algorithms? Did He ever mention the fact that pseudoscientists might be called theorists by serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about the physiology of reproduction and the functional structure of supercoiled DNA.

See for example: Structural diversity of supercoiled DNA
The functional structure of supercoiled DNA links what organisms eat to endogenous RNA interference and the physiology of reproduction, which links chromosomal inheritance from chirality to autophagy and all biodiversity on Earth. That cannot be done with definitions and/or algorithms.

See also: microRNA
How will you continue to avoid discussing the energy-dependent link from nutrient-dependent changes in the microRNA/messenger RNA balance to all healthy longevity, as everything known about virus-driven energy theft continues to be linked to all pathology?

Alternative splicing of pre-mRNA

George Church refutes theistic evolution (2)

See: George Church refutes theistic evolution

George Church may not know that he refuted every aspect of theistic evolution in his presentation on February 8, 2017. Hopefully, someone will tell him how he linked quantum physics from chemistry to biophysically constrained protein folding and all biodiversity, or explain to others how he did that. Here is my explanation of his admissions. I placed the explanation into the context of this poster session submission.

Title: Energy as information and constrained endogenous RNA interference
Abstract:

Sunlight-induces energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Changes in the potential of hydrogen (pH) link quantum physics to classical physics via chirality (manifested in chemistry). Energy-dependent biophysically constrained protein folding chemistry links what is known about molecular epigenetics to what is known about autophagy.  For instance, energy-dependent changes in pH link ecological variation from angstroms to ecosystems via base pair changes and RNA-directed DNA methylation (endogenous RNA interference).  That is how the sun’s anti-entropic virucidal energy is linked from the physiology of reproduction to all life on Earth.

Base pair changes link microbial quorum sensing from the nutrient energy-dependent pheromone-controlled physiology of reproduction to the National Microbiome Initiative. Endogenous RNA interference (RNAi) links the base pair changes from the innate immune system to supercoiled DNA and chromosomal inheritance. Sunlight is linked from the National Microbiome Initiative to the Precision Medicine Initiative via genome wide inferences of natural selection for nutrients and the pheromone-controlled energy-dependent fixation of amino acid substitutions in all organized genomes.

This presentation explains how natural selection for energy-dependent codon optimality links biologically-based cause and effect from the de novo creation of G protein-coupled receptors (GPCRs) to fixation of RNA-mediated amino acid substitutions. GPCRs link metabolic networks and genetic networks to the amino acid substitutions that differentiate all cell types in all individuals of all species.

Ecological variation is linked to energy-dependent metabolic networks and genetic networks, which link alternative RNA splicings from supercoiled DNA to polycombic ecological adaptations.  Ecological adaptations, which are manifested in morphology, are linked from supercoiled DNA and chromosomal inheritance to healthy longevity via energy-dependent differences in behavior.

For contrast, virus-driven energy theft links messenger RNA degradation to negative supercoiling and constraint-breaking mutations. Virus-driven hecatombic evolution links energy theft from biophysical constraint-breaking mutations to all pathology. For example, the viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA in human infants, which typically is repaired by energy-dependent endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

A link to the poster session and narrative summary should be available within the next two weeks.

terrarium-eco-system

Trump's appeal to common sense (2)

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

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

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

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

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

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

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

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

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

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

Stability of the hybrid epithelial/mesenchymal phenotype

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

Viruses send chemical messages 

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

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

How Trump Could Unravel Obama’s Science Legacy

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

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

rp_levels-of-organization.jpg

Energy-dependent chirality (2)

See Energy-dependent chirality
2013 MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination
See also E. Ben-Jacob
Ben-Jacob et al., have linked everything currently known about natural information processing from natural selection for energy-dependent codon optimality to healthy longevity and from virus-driven energy theft to mutations that cause cancer.
See for comparison: LH Tsai
Tsai laboratory

Our primary goal is to elucidate the mechanisms underlying neurological disorders affecting learning & memory. The major research areas include age disorders, autism, and Alzheimer’s disease.

2012 MicroRNAs in learning, memory, and neurological diseases

Recent advances in methods of next-generation sequencing, such as RNA-seq, offer the means to quantitatively evaluate the functions of miRNAs in a genome-wide manner in large cohorts of samples. These new technologies have already yielded valuable information and are expanding our understanding of miRNA-based mechanisms in higher-order brain processing, including learning and memory and cognition, as well as in neuropsychiatric disorders.

2015 Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

The exposure to a new sensory experience, for instance, profoundly alters the morphology and connectivity of neural circuits, and these changes are thought to be instrumental in the formation of long-lasting memories and adaptive responses (Goelet et al., 1986).

They linked ecological variation to experience-dependent changes in the connectome and ecological adaptations.
2016 Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior
They linked the ecological adaptation to social behavior.
Reported as: Researchers identify genome-modifying enzyme linked to Rett Syndrome

To understand how the HDAC3 protein regulates the genes, the researchers then analysed them further. In particular, they hoped to identify any motifs, or patterns of DNA sequence, to which regulatory proteins, known as transcription factors, could bind. Transcription factors are proteins that control which genes are turned on or off within the genome.

They linked ecological variation to gene regulation via energy-dependent transcription
2016 Gamma frequency entrainment attenuates amyloid load and modifies microglia
Abstract conclusion:

Our findings uncover a previously unappreciated function of gamma rhythms in recruiting both neuronal and glial responses to attenuate Alzheimer’s-disease-associated pathology.

They linked light-induced changes in gamma oscillations (20-50 Hz) to pathology via levels of amyloid-beta (Abeta)1-40 and Abeta 1-42 isoforms in the context of energy-dependent changes in the onset of plaque formation and cognitive decline in the mouse model of Alzheimer’s disease.
isoform: any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence.
Tsai et al., have linked everything currently known about natural information processing from natural selection for energy-dependent codon optimality to RNA-mediated amino acid substitutions and healthy longevity and from virus-driven energy theft to mutations that cause neurodegenerative diseases. They place what is known about amino acid substitutions into the context of isoforms.
See also: 2017 In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory
Everything known about natural selection for energy-dependent codon optimality and healthy longevity for comparison to virus-driven energy theft and the mutations linked to all pathology is placed into this context:

“… neuronal activity induces relocalization of gene loci to ‘transcription factories’, and specific enhancer–promoter looping contacts allow for precise transcriptional regulation.

Learning and memory appear to depend on specific enhancer–promoter looping instead of energy-dependent changes that link microRNAs from amino acid substitutions to healthy longevity and virus-driven energy theft to cancer via the works of Eshel Ben-Jacob et al.

Enhancer–promoter looping interactions are an important event in transcriptional initiation, but looping is not always sufficient to drive expression per se. This is exemplified by the finding that many looping contacts are established prior to gene activation [66].

Claims about enhancer–promoter looping interactions obfuscate facts about energy-dependent transcription, which is established in the context of energy-dependent changes in the microRNA/messenger RNA balance. The works of LH Tsai et al., go a long way towards obfuscating the facts serious scientists have learned form the works of the late Eshel Ben-Jacob et al.
See also: Language and Communication as Universal Requirements for Life (link opens pdf)

If stem-loop consortia build complex consortia, they initiate social interactions not present in a pure chemical world, that is, biological selection emerges. This designates the crucial step from inanimate world to life (Figure 16.8).

No matter how much obfuscation of facts about energy-dependent chromatin remodeling is introduced via use of different terms, such as chromatin topology, stem-loop and enhancer–promoter looping, the word play can always be viewed in the context of funding attempts that are the primary concern of politicized science.

Alternative splicing of pre-mRNA

Re-inventing mutation-driven evolution (2)

… we suspected that splicing efficiency, as defined by the fraction of pre-mRNA converted into mature mRNA, must have contributed to temperature-dependent Cirbp mRNA accumulation

Splicing efficiency is energy-dependent in the context of temperature-dependent oscillations that link the sun’s anti-entropic virucidal energy to all biodiversity via Turing’s claims and my model.

In 1951, the brilliant British scientist Alan Turing published a paper proposing a theory in chemistry called morphogenesis, which explains how cells are grouped together within an organism.

According to Turing, oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.

Could Turing’s claim be linked to Peter Berean‘s claims about differences between “bio-functional information” and energy as information?

See also: Cellular Clocks and Metabolism

..each tissue and organ appears to have unique 24 hour cycles related to the specific functions of the organ and the unique metabolic functions. Also, cycles of available material and cellular activity appears to ubiquitous.

The cellular clock mechanisms are nutrient energy-dependent and linked RNA-mediated amino acid substitutions in supercoiled DNA to the differentiation of all tissues in all organs in all living genera via biophysically constrained protein-folding chemistry in the context of the physiology of reproduction.

See also: Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal

Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora.

There are no deep evolutionary traits because all traits are energy-dependent. All traits must link RNA-mediated autophagy from the innate immune system to supercoiled DNA in the context of the physiology of reproduction. That fact links everything known to serious scientists about nutritional epigenetics from autophagy to the biophysically constrained protein folding chemistry of all genera.

For example, nutrient energy-dependent supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. Phylogenetic trees may be established by patterns of viral latency.

Viral latency recapitulates the past effects of virus-driven energy theft on gene activation via what is known about energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution that link angstroms to ecosystems in all living genera. Nutrient energy-dependent gene activation links the mitochondria to effects that viruses had on hydrogen-atom transfer before the anti-entropic virucidal effects of ultraviolet light linked ecological variation to ecological adaptation of organized genomes in species from bacteria to archaea.

Placing bacteria and archaea into different domains of life was a mistake made by Carl Woese who did not link the nutrient energy-dependent physiology of reproduction from autophagy to supercoiled DNA because he failed to consider the role of virus-driven energy theft in all pathology. That pathology is exhibited in the number of viruses in archaea compared to the number of viruses in ecologically adapted bacteria  and in ecologically adapted humans.

See also: Stanford manufactures gene-engineered cells to cure the incurable

1) To fix this, Stanford researchers use a virus to deliver a correct version of the gene onto batches of skin cells, then coax them to form sheets of healthy skin.

2) Cells are nurtured in a broth of sugars, carbohydrates, fats, growth factors and hormones, warmed at body temperature: 98.6 degrees Fahrenheit.

The virus links the natural information processing of all cell types from the innate immune system to autophagy and the nurturing helps to ensure that the pluripotent state leads to energy-dependent biophysically constrained protein folding chemistry that typically links the pheromone-controlled physiology of reproduction to all biodiversity via RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genome from virus-driven entropy.
See also: Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

In addition, over the past 15 years, a myriad of non-coding, but functional RNAs have been discovered, including microRNAs and long non-coding RNAs that can regulate transcription [42] but more commonly translation [43] of protein coding genes. Mutations affecting non-coding genes can thus lead to changes in the repertoire of proteins that determines cell behaviour in developmental programmes, resulting in phenotypic evolution. Long non-coding RNAs have been associated with development and evolution but they are less well studied than shorter microRNAs and small RNAs [44].

During the past 15 years nutrient energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated protein folding chemistry to all biophysically constrained biodiversity via autophagy and supercoiled DNA in the context of the physiology of reproduction. There are now more than 56,000 published works that link energy as information from changes in hydrogen-atom transfer in DNA base pairs in solution to all extant biodiversity via the physiology of reproduction.
See: microRNA (56,324 citations)
See also: Long noncoding RNAs in the p53 network

p53 regulates the expression of a repertoire of lncRNAs, and some of these lncRNAs are critical regulators of cell cycle arrest, DNA damage repair, chromosomal stability and apoptosis, altogether contributing to tumor-suppressor function of p53. LncRNAs are dysregulated in a variety of cancers and therefore can be utilized as biomarkers for disease progression and as therapeutic targets.98

Energy-dependent changes in the microRNA/messenger RNA balance are linked from every aspect of biophysically constrained protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans. The sun’s anti-entropic virucidal energy has been linked to DNA damage repair, chromosomal rearrangements and chromosomal stability. Rather than continue to ignore the facts about energy-dependent healthy longevity for comparison to virus-driven energy theft and all pathology, some people may still be interested in seeing this:
What is life when it is not protected from virus driven entropy

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.

 

Physics

Anti-entropic virucidal energy as information

 How Can Physics Underlie the Mind? Top-Down Causation in the Human Context by George Ellis (p. 404)

Repeated thousands of times over geological timescales, it is this relentless repetition of the top-down process of adaptive selection [29] that gives Darwinian evolution its enormous power.

Theorists never seem to ask questions about where the enormous power came from or where it goes when organisms die. They seem to think that relentless repetition of biophysically constrained energy-dependent protein biosynthesis and degradation automagically emerged so that organisms could begin to evolve via adaptive selection in the context of Darwinian evolution, which has no power source outside the context of Darwin’s “conditions of life.”

See for comparison: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors (1996)

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: Virus-mediated archaeal hecatomb in the deep seafloor (2016)

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.

The nonsense about the non-existant power of evolution touted by George Ellis appears to have led to this report. Nonlinear self-adapting wave patterns  by David Kessler and Herbert Levine

We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded.

They propose that an emergent wave pattern of light energy self-adapts to the size of a biophysically constrained system. Their proposal must link energy as information to all cell type differentiation and all biodiversity via the physiology of reproduction.

Their proposal is not consistent with anything known to serious scientists, or even to George Ellis, about top-down causation. Serious scientists have linked the anti-entropic virucidal energy of sunlight from ecological variation to ecological adaptation. This has been done in the context of links from angstroms to ecosystems in all living genera See for example: Structural diversity of supercoiled DNA.

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Simply put, DNA supercoiling is energy-dependent. The energy does not create itself, which suggests it is not likely to self-adapt to any biophysical constraints. Indeed, the fact that energy as information in cell types is biophysically constrained suggests that the energy is epigenetically trapped and/or released as is required for metabolic networks to be linked to genetic networks. Simply put, there are likely to be thermodynamic cycles of energy transfer that link femotosecond blasts of ultraviolet light to DNA damage repair.

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

See also: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

Although sequence-specific association of co-regulated genomic loci is appealing, random interactions between loci with shared chromatin properties might be an equally effective way of modulating transcription levels.

Sequence-specific association of co-regulated genomic loci is energy-dependent. Serious scientists have showed that none of the interactions between loci with shared chromatin properties randomly occur. For example, two epigenetic traps link the sun’s anti-entropic virucidal energy from the energy-dependent interactions to the de novo creation of G protein-coupled receptors (GPCRs). The epigenetically-effected de novo creation of the GPCRs links chemotaxis and phototaxis to all morphological and behavioral phenotypes via the physiology of reproduction and transgenerational epigenetic inheritance of supercoiled DNA.

For comparison, the proposal from Nonlinear self-adapting wave patterns  was framed outside the context of how thermodynamics must be linked to chemotaxis and/or phototaxis. The authors told us that an adiabatic process apprears to occur without the transfer of heat or matter. In an adiabatic process, the energy transfer between a thermodynamic system and its surroundings works in only one direction. The automagically created energy exists and gets the work done without the transfer of heat or matter.
That unidirectional process seems to exclude everything known about biophotonics, which provides the conceptual basis for a theory that extends the first law of thermodynamics to energy-dependent RNA-mediated cell type differentiation via what is known about protein folding chemistry. By pretending that self-adapting wave patterns exist outside the context of biophotonics, and by pretending that the author’s proposal fits into the context of a key concept in thermodynamics that is not linked to chemotaxis or phototaxis, we are led to believe that some chemical and physical processes occur so rapidly that they may be conveniently described by the “adiabatic approximation.” That means there is not enough time for the transfer of energy as information or as heat to go to or from the system.

But what about the energy as information carried by the light? Roger Penrose presciently addressed claims about light in non-technical terms when he asked: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991) See the forward to the reprint of Schrodinger’s: What is Life?

New type of traveling wave pattern could contain biological coordinates is the report on the most recent findings that link the traveling energy to biological coordinates in the context of the biophysically constrained chemistry of RNA-mediated protein folding. The most recent finding can be placed into the context of what serious scientists already know.

See for example: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination (2013), which also was co-authored by Herbert Levine. (I noticed that Eshel Ben-Jacob is the senior author because I am more familiar with Eshel’s works.)

See also: Stability of the hybrid epithelial/mesenchymal phenotype (2016) Two of the co-authors are Eshel Ben-Jacob and Herbert Levine, but Eshel Ben-Jacob died prior to publication.

See: In Memory of Professor Eshel Ben Jacob

Image may contain: 1 person, text

Note: There is no indication of whether Herbert Levine attended and I do not know if he knows anything about RNA-mediated cell type stability. I do not want to speculate about this. I will mention that all the claims made by Eshel Ben-Jacob about energy-dependent natural information processing and biophysically constrained cell type differentiation have been placed into the context of accurate information about RNA-mediated biologically-based cause and effect.

See for example:Phyto-Medicine in Gene(s) Targeting Future Direction for Sickle Cell Disease Management 6/13/16 Reported by Journals and Conferences on Genetics & Molecular Biology on 12/15/16

Biochemically, SCD occurs due to a non- conservative substitution of a #polarglutamate (Glu) by non-polar valine (Val) in an invariant region, the sixth position of Hb-β chain-subunit (GAG/GTG; Glu (E) Val (V); rs334). Replacement of this single non-polar amino acid ‘valine’ results in a biochemical difference that leads to formation of a sticky patch on the surface of the β-chains. The sticky patch is observed on both the #oxygenated (“R” Form) and deoxygenated (“T” Form) of HbS. This distort folding and binding pattern of the Hb molecule, due to altered properties. Other known mechanism of #polymerization of Hb in SCD involves nucleation, which is due to the aggregation of HbS molecules.

They linked one nutrient energy-dependent RNA-mediated amino acid substitution to the stability of a hemoglobin variant that protects some human populations from malaria. It is one of ~1264 human hemoglobin variants that exemplify how ecological variation is linked from biophysically constrained energy-dependent RNA-mediated protein folding chemistry to ecological adaptations.

That fact can be placed into the context of Dobzansky’s claims in 1964 and in his 1973 expose of the evolution industry. He showed that the cure for all pathology must begin from the understanding of energy-dependent hydrogen-atom transfer in DNA base pairs in solution. Energy-dependent changes in base pairs link the sun’s quantized anti-entropic virucidal energy from autophagy to single nucleotide polymorphisms and fixation of RNA-mediated amino acid substitutions. The fixation of the substitutions helps to ensure healthy longevity in all living genera via the physiology of reproduction and supercoiled DNA, which prevents the virus-driven entropy of all organized genomes.
Dobzhansky 1964

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

Dobzhansky 1973

…the socalled 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: Combating Evolution to Fight Disease 9/13/14

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.

See also: Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans
Conclusion:

Substitutions in other lineages have proven to be highly informative for understanding deleterious effects in the contemporary human genome; among numerous features that have been considered, the strongest predictors of the pathogenicity of a mutation are species divergence features [83–86]. Nevertheless, methods used to predict the deleteriousness of a mutation at a site typically rely on a single summary of how variable a site is across the phylogenetic tree. Our analysis suggests that the location of a mutation on the evolutionary tree is informative of how deleterious the same mutation is for humans. It is our hope that the integration of divergence patterns and sequence context into methods that predict the fitness or health effects of human mutations could increase accuracy and predictive power.

Do not trust anyone who does not know the difference between a mutation and a fixed amino acid substitution to explain any aspect of RNA-mediated biologically-based cause and effect. The number of theorists who want you to believe in their pseudoscientic nonsense is hundreds of times more than the number of serious scientists with experimental evidence of how energy-dependent RNA-mediated protein folding chemistry must be linked to morphological and behavioral phenotypes in all living genera by keeping virus-driven energy theft in check.

See also: Keeping CRISPR in Check
Excerpt 1)

Notably, the work is “going specifically after Cas9 and then applying the discoveries in human cells,” Harvard’s George Church, who was not involved in the study, wrote in an email to The Scientist.

Excerpt 2)

Knowing how the viral enemy evades CRISPR-based immunity will provide valuable insights into ways to better fight [viruses],” wrote Horvath.

This is a complete reversal of claims by George Church that were put into the context of this report:
Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy
Excerpt:

…the design, stability and degradation of RNAi based effective molecules appears to be the major lime light to challenge the conventional drug safety concerns and ensures to be the most powerful gene recovery in future which execute billion dollar business hope.

See for comparison: Obama Advisers Urge Action Against CRISPR Bioterror Threat
See also: Jon Stewart interviews Greg Bear It’s not very funny anymore, is it?
Also: March 9, 2016 See Gene intelligence: The risks and rewards of genome editing resonate beyond the clinic.

Last month, one of the top intelligence officials in the United States warned that genome-editing technology is now a potential weapon of mass destruction.

CRISPR—a weapon of mass destruction?

James Clapper placed “genome editing” among six threats listed in the section on weapons of mass destruction.

See also 12/9/16 The B/Z reaction, and the problem with peer review 

…oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.

The predictable oscillating chemical reactions have now been placed into the context of  Nonlinear self-adapting wave patterns  by David Kessler and Herbert Levine, who I mentioned near the beginning of this blog post.
Abstract (with my emphasis):

We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability for a range of wavevectors, k , that extends down to k = 0, connecting at that point to two symmetry modes of the underlying dynamical system. The Min system of proteins in E. coli is such a system with the symmetry emerging from the global conservation of two proteins, MinD and MinE. For this and related systems, traveling waves can adiabatically deform as the system is increased in size without the increase in node number that would be expected for an oscillatory version of a Turing instability containing an allowed wavenumber band with a finite minimum.

None of the serious scientists I have ever known would take Schrodinger’s claims about the anti-entropic energy of sunlight and link everything from the creation of energy to an oscillatory version of a Turing instability without addressing the loss of energy as information, which links virus-driven energy theft to genomic entropy. The fact that someone who has co-authored with Eshel Ben-Jacob left out the role of virus-driven energy theft probably never occurred to anyone who read the article. And so, here we are.
See also: Herbert Levine

Research Statement

Biological systems operate in nonequilibrium states, using free energy derived from metabolism to run all the various processes needed for survival. Understanding the chemical and physical mechanisms that govern these processes is an essential component for advancing our quantitative understanding biological systems. Ultimately, this new level of understanding should prove crucial for tackling currently intractable diseases such as metastatic cancer.

The energy derived from metabolism is nutrient-dependent. The physical and chemical mechanisms that link RNA-mediated amino acid substitutions to cell type differentiation in all living genera are linked from the sun’s anti-entropic virucidal energy via the claims of serious scientists like Gunter Witzany.
See also: Life is physics and chemistry and communication