5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

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

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Conclusion:

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.
 

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

Autophagy is the antiphage defense strategy (2)

2/15/17 Energy as information and constrained endogenous RNA interference (video)
The 6.46 minute-long technical presentation (above) from the Precision Medicine Virtual Conference is difficult to understand.Thus, 10 months later, Nik Willmore asked:

12/24/17 What are your insights into CRISPR and mTOR, for a young audience? I’m not mocking you…yet, Humpty Dumpty. What is the basis of your unifying principle? Vibration? Bohmian morphogenetic fields? Modified Darwin? God? –Nik Willmore 

12/25/17 Replying to

God created the anti-entropic virucidal energy of sunlight and all energy-dependent biodiversity via the physiology of pheromone-controlled reproduction. I co-authored a book about that for a young audience in 1995/2002, and a 6-part series for today.

1/1/18 Replying to

Do you understand any aspect of how to model biophysically constrained biologically-based energy-dependent top-town causation and bottom-up effects on cell type differentiation via the physiology of reproduction and autophagy? The “walking fish” walks straight from quantum physics to quantum souls (2)

1/9/18 Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

My paraphrased summary:

RNA interference (RNAi) is our indispensable antiphage defense mechanism. Viruses escape the defense system by the theft of quantized energy, which encodes RNAi suppressors that prevent elimination of viral RNAs. The suppressors ensure energy-dependent virus accumulation.

1/12/18 Human cytomegalovirus-encoded miR-UL112 contributes to HCMV-mediated vascular diseases by inducing vascular endothelial cell dysfunction

The significantly altered pathways mainly include the mitogen-activated protein kinase signaling pathway, cell adhesion molecules, chemokine signaling pathway, cytokine-cytokine receptor interaction, circadian rhythm-mammal, mineral absorption, protein processing in the endoplasmic reticulum, proximal tubule bicarbonate reclamation, vasopressin-regulated water reabsorption, and arachidonic acid metabolism. In conclusion, hcmv-miR-UL112 could serve as a potential biomarker, and the miRNA-mediated regulation of signaling pathways might play significant roles in the physiological effects of hcmv-associated diseases.

1/12/18 H5N1 influenza virus-specific miRNA-like small RNA increases cytokine production and mouse mortality via targeting poly(rC)-binding protein 2

We conclude that miR-HA-3p is the first identified influenza virus-encoded microRNA-like functional RNA fragment and a novel virulence factor contributing to H5N1-induced ‘cytokine storm’ and mortality.

Virus-encoded microRNA-like functional RNA fragments are not novel virulence factors. They link the virus-driven degradation of messenger RNA to all pathology in all living genera via the theft of quanitzed energy, which typically links the fixation of RNA-mediated amino acid substitutions to healthy longevity.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs
All serious scientists know what goes wrong in the context of host microRNA-mediated regulation of viruses. They also know how it goes wrong. See Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

The serious scientists do not claim that viruses evolve. Scientists who make claims about evolution  typically do not know how to link the creation of sunlight from ecological variation to food energy-dependent pheromone-controlled ecological adaptation via the physiology of biophysically constrained reproduction and biophysically constrained viral latency. Indeed, most pseudoscientists do not know the difference between a mutation and an RNA-mediated amino acid substitution.
See for comparison: Mechanisms of Recombination conference Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Description

Genetic recombination provides an important mechanism for the repair of chromosome breaks caused by DNA damage or replication fork demise. Defects in the recombination process have been linked to cancer predisposition, in particular breast cancers caused by mutations in BRCA1, BRCA2 and PALB2, and also acute leukemias associated with the rare genetic disease Fanconi anemia. Understanding precisely how recombination occurs is of interest to workers in the fields of meiosis, DNA repair, replication, chromosome architecture and interactions, and chromatin biology.

Download provisional conference program
Excerpts:

Douglas Bishop (University of Chicago, US)
A primary function of the ATPase activity of E. coli RecA is to prevent accumulation of a toxic form of the protein bound to undamaged chromosomal sites

Maria Jasin (Memorial Sloan Kettering Cancer Center, US)
Protecting the genome by homologous recombination

The energy-dependent microRNA-mediated creation of enyzmes protects all organized genomes from the virus-driven degradation of messenger RNA that links the theft of quantized energy from mutations to all pathology.  Pseudoscientists who do not start with the creation of energy, have bastardized Darwin’s claims. His claims were based on placing “conditions of life” before natural selection. Conditions of life are energy-dependent and biophysically constrained by the mechanisms of pheromone-controlled recombination, which have been linked to autophagy by all serious scientists since 1925.
See also my RNA-mediated Facebook page and/or my RNA-mediated Facebook group and other tweets @jvkohl
The number of my tweet impressions since December 21, 2017 has climbed to more than 68,000 as the number of published works that mention “microRNA” has climbed to nearly 69,000. See for comparison: The tipping point (revisited): 68,000 publications, which was published to my other blog site on December 21, 2017.
See also: What Darwinists Fail to Consider (discussion attempt)
See also, this discussion attempt about the “spark of life.”
See also: Noncoding RNA Helps Cells Recover from DNA Damage

“The most logical, simple explanation is that the [noncoding RNA] counteracts the protein encoding form…”

My comment to the Scientist:

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the 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: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

See also: Search Results for “autophagy”

Alternative splicing of pre-mRNA

The Origin of Information (4)

Summary: Others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See: The Origin of Information (3)
Finally, someone is asking questions that can be summarized in one question (see below). Until now, on the International Society for Human Ethology’s Yahoo group, and elsewhere, the moderator: Jay R. Feierman has prevented the dissemination of accurate information on this topic. Now others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See the discussion attempt at: 88233 Re: DNA Begins As a Quantum Wave, According to New Science

Excerpt: Much of the information in this article came from The Synchronicity Key: The Hidden Intelligence Guiding The Universe and You

Conclusion: Clearly though, our view of the universe and life itself is changing as these concepts are understood by more people each day.

The fact that DNA begins as a quantum wave linked to biophysically constrained amino acid substitutions was addressed in the context of: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Natural selection for quantized energy-dependent codon optimality and the stability of messenger RNA during transgenerational epigenetic inheritance has since been placed into the context of experimental evidence reported as Olfaction Warps Visual Time Perception.
See also the series of presentations at virtual conferences that began with: The Origin of Information: How to Solve It.
When I realized that people might not understand that the origin of information must be linked from quantum waves to RNA-mediated healthy longevity and from virus-driven energy theft to all pathology, I split the original presentation submission into two parts. The revised title was RNA mediated molecular epigenetics and virus driven entropy.
From hydrogen atom transfer in DNA base pairs to ecosystems was presented during the same virtual conference.
Several more presentations added information about top-down energy-dependent RNA-mediated biologically-based biodiversity. For example, this may be my final presentation at Labroots virtual conferences Energy as Information and Constrained Endogenous RNA Interference
The journalists from Labroots have ignored my presentations despite a series of my comments on their attempt to continue touting pseudoscientific nonsense about neo-Darwinian theories.  It seems unlikely that any science journalist will admit to their overwhelming ignorance.
See for comparison:168949 From the evolutionary psychology Yahoo group. Re: DNA Begins As a Quantum Wave, According to New Science
Jay R. Feierman admits:

This claim is above my level of expertise to refute. It comes from a peer reviewed article in The American Chemical Society’s Journal of Physical Chemistry B. See below, which is taken from https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html.
“Scientists are reporting evidence that intact, double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. And then like friends with similar interests, the bits of genetic material hangout or congregate together. The recognition — of similar sequences in DNA’s chemical subunits — occurs in a way once regarded as impossible, the researchers suggest in a study scheduled for the Jan. 31 issue of ACS’ Journal of Physical Chemistry B”.
Read more at: https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html#jCp

There are many things in physics and physical chemistry that seem incredulous to me. That includes some of the claims of quantum mechanics. What about the Penrose Hameroff Theory of Quantum Consciousness. See http://www.quantumconsciousness.org/sites/default/files/1998%20Hameroff%20Quantum%20Computation%20in%20Brain%20Microtubules%20The%20Penrose%20Hameroff%20Orch%20OR%20model%20of%20consciousness%20-%20Royal%20Society_0.pdf.

On several occasions, Feierman has threatened to ban me from the Human Ethology Yahoo Group. Then, he simply fails to post my comments when they do not support his nonsense.
I’ve added some comments to this discussion because it seems to be progressing nicely at a time after Feierman has admitted he knows virtually nothing about biophysically constrained biologically based RNA-mediated cell type differentiation.
See: Discus for discussion of

How to teach evolution when students hold creationist views


Feierman, and others like him, have been teaching neo-Darwinian theories either directly or indirectly. But Feierman’s nonsense has consistently been the most offensive to me personally. After publication of my 2013 review, I attempted to discuss the refutation of neo-Darwinian nonsense he had been touting since I first met him at a conference in 1995.
His responses to Nutrient-dependent/pheromone-controlled adaptive evolution: a model include:
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.
Now, he admits, albeit elsewhere, that he knows nothing about how food energy as quantized information must be linked to healthy longevity via the pheromone-controlled physiology of reproduction, or be linked from the virus-driven degradation of messenger RNA to mutations and all pathology.
See also this example of a false dichotomy: Scholars who believe nurture trumps nature also tend to doubt the scientific method

One group, made up of psychologists, economists, philosophers and political scientists believes more strongly in the genetic influences on behaviour, beliefs and culture. The other group, consisting sociologists, non-evolutionary anthropologists, women’s and gender studies scholars and all humanities scholars (except philosophy), believes in the primacy of environmental influences.

No Genetics without Epigenetics? No Biology without Systems Biology?

…there has never been a genetics without an epigenetics.

Energy-dependent changes link the epigenetic landscape to the physical landscape of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that all serious scientists have linked from mutations to all pathology in all living genera.
See: microRNA  for more than 63,000 examples of that fact.

Cytosis

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Conclusion:

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

Reported as: Knowledge gap on the origin of sex

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

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

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

See also: Origins of Life: A Problem for Physics

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

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

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

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

A New Physics Theory of Life

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

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

See: Streptococcal throat infection linked to mental disorders

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

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

 

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

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

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

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

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

Kalevi Kull: Censorship & Royal Society Evo Event

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

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

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

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

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

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

Alternative splicing of pre-mRNA

UV light and non-coding RNA

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene

…these events underlie a switch to expression of short mRNA isoforms and preferential use of alternative last exons in a number of genes, including ASCC3. Intriguingly, the switch between ASCC3 isoforms occurs on more than one level, in that the long mRNA isoform encodes a protein, functioning in the context of the ASCC complex and required for maintaining transcriptional suppression in the late stages of the DNA damage response, whereas the short isoform functions as a nuclear non-coding RNA that is required for transcription to recover. Intriguingly, the short and long isoforms constitute an autonomous regulatory module and functionally interrelate, so that the effect of deleting one can be at least partially compensated for by deleting the other (Figure 7H).

There is no such thing as an autonomous regulatory module. All RNA-mediated protein folding chemistry is energy dependent and functional interrelations link differences in the energy of photons from natural selection for energy-dependent codon optimality to all biodiversity on Earth via the physiology of reproduction.
Reported as: Noncoding RNA Helps Cells Recover from DNA Damage

“If the protein is made from the long pre-mRNA, then global transcription is repressed. But if the short RNA is made, it helps recover transcription hours after damage.”
Uncovering mechanisms
How the short isoform aids repair remains unknown.

My comment to The Scientist: There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the 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: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

Biology to a Physicist

Sal Giardina: apologetics revisited

March 26, 2017 Sal Giardina wrote:

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

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

Apologetics:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Excerpt:

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

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

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

Excerpt:

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

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

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

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

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

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

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

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

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

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

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

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

For comparison, see: Mutation-Driven Evolution

Excerpt:

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

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

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

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

See for comparison: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

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

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

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

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

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

Physics

Confusing effects and affects of visual input

Their report indicates that these researchers never learned to differentiate between epigenetic effects on RNA-mediated cell type differentiation compared to the experience-dependent affects on behavior of amino acid substitutions.

Experience Affects Critical Period Plasticity in the Visual Cortex through an Epigenetic Regulation of Histone Post-Translational Modifications

Excerpt:

We show that the early exposure of rat pups to enriching environmental conditions accelerates the critical period for plasticity in the primary visual cortex, linking this effect to increased histone acetylation, specifically at the BDNF gene level. Moreover, we report that the exposure of adult animals to environmental enrichment enhances histone acetylation and reopens juvenile-like plasticity.”

My comment: Nutrient-dependent microRNAs link chemotaxis to phototaxis in species from microbes like Pseudomonas florescens to mammals. MicroRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution from the nutrient-dependent physiology of reproduction in all living genera to supercoiled DNA, which protects organized genomes from virus-driven entropy.

For example, the BNDF Val66Met and COMT Val158Met amino acid substitutions alter the stability of organized genomes during life history transitions in the mouse to human model.

Also, the bull sperm microRNAome links soil bacteria to plant growth and nutrient-dependent microRNAs in mammalian milk that alter brain development in human infants by protecting them from Zika virus-damaged DNA.

See also: Increased vitamin C in the diet could help protect against cataracts

Excerpt:

…participants who had a higher intake of vitamin C were associated with a 33 per cent risk reduction of cataract progression and had ‘clearer’ lenses after the 10 years than those who had consumed less vitamin C as part of their diet.

My comment: They add this caveat:  “… the participants are predominantly of UK-origin and female, reflecting cataract progression between the ages of 60 and 70 years on average, so may not be generalisable.” The caveat suggests that everything known to serious scientists about the links from the nutrient-dependent stability and virus-driven entropy of all organized genomes in species from microbes to humans may not include their results.

human-evolution

Neuroscience Virtual Event vs AAAS Symposium

Neuroscience Virtual Event Abstract Submission

Poster title: From hydrogen-atom transfer in DNA base pairs to ecosystems (March 16-17, 2016)
Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.
Today [2/3/16] at 3:05 pm
Thank you for submitting your abstract to the LabRoots Neuroscience 2016 conference. You will be notified of acceptance within one week and will be given further guidelines at that time. Please visit the labroots.com site for more information.
Thank you!
The LabRoots Team
See also: RNA-mediated regulatory mechanisms link microbes to humans (3)

Excerpt:

Elaine Y. Hsiao, University of California, Los Angeles (UCLA) February 14, 2016
The Role of Gut Microbiomes in Neurodevelopmental Disorders

Bruce McEwen, Rockefeller University February 14, 2016
Mother-Infant Interactions Influence Both Cognitive and Physical Development

Moshe Szyf, McGill University February 14, 2016
Nurture Alters Nature through Epigenetic Modifications of DNA

Excerpt:

…will present evidence that the “social environment” early in life can alter DNA methylation, the basis for the emerging field of “social epigenetics”. By highlighting the impact that external factors and the social environment can have on gene expression, he will provide a mechanistic basis for the long term effects of early childhood experience.

My comment: It will be interesting to compare notes from the Virtual Event to notes from the AAAS Symposium in the context of these publications.

From Fertilization to Adult Sexual Behavior (1996)
Excerpt: 

…the nature/nurture debate is much more than simply a scientific argument. It is a clash of cultures, of ideologies and of politics.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2015)
Excerpt:

The impact of epigenetic effects of chemical ecology on behavioral affects is now relatively well-known (Ledón-Rettig et al., 2012). Effects on hormones and their affects on behavior have been detailed in the honeybee model organism. ‘The concept that is extended is the epigenetic tweaking of immense gene networks in “superorganisms” that “solve problems through the exchange and the selective cancellation and modification of signals”’ (references in Kohl, 2012).

Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress (2015)
Excerpt:

In this emerging paradigm, mitochondria lie at the interface of genetic and environmental factors contributing to disease trajectories.

Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)
Excerpt:

Using both WT mice and a humanized mouse model of reduced BDNF function (Val66Met SNP), we found that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 expression in the hippocampus in response to chronic and acute novel and familiar stressors.

 
 

rp_levels-of-organization.jpg

Despicable fools?

Excerpt:

Light is generally accepted to travel at a constant speed, but its group velocity can be slowed by passing through refractive materials. Compared to its top speed in a vacuum, light travels slightly slower in air and slightly slower still in water. These changes in speed are fairly insignificant, however.

My comment: I doubt that any member of the RNA society thinks that the changes that link the de novo creation of nucleic acids to cell type differentiation in all living genera are insignificant changes in the speed of light.

In fact, I don’t know anyone who thinks that changes in the speed of light are insignificant. Do you? Is someone inadvertently teaching students that changes in the speed of light are insignificant? Serious scientists want to know who is teaching pseudoscientific nonsense. Please tell a serious scientist if you know any biologically uninformed science teachers who think that changes in the speed of light are insignificant.

Were you taught to believe in pseudoscientific nonsense and taught nothing about the links from atoms to ecosystems via the physiology of reproduction? If so, I could probably teach you to believe in anything, couldn’t I?

Guinea pigs beat climate change by tweaking their own DNA

Excerpt:
Evolution by genetic mutation and natural selection can be slow. But epigenetic changes that affect how genes are expressed, such as attaching methyl molecules onto DNA, are much faster and more flexible. Experiments in a type of brine shrimp and the plant Arabidopsis thaliana have shown that such heat-induced epigenetic responses can even be inherited by the next generation.
My comment: No experimental evidence of biologically-based cause and effect links evolution from genetic mutation and natural selection.
See for comparison: microRNA All experimental evidence of biologically-based cause and effect links microRNAs to RNA-mediated cell type differentiation.

See also: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

Excerpt:

The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ (Lockett, Kucharski, & Maleszka, 2012) that ‘solve problems through the exchange and the selective cancellation and modification of signals (Bear, 2004, p. 330)’.

Michael Skinner is mentioned in the news article linked above.

“This suggests global changes in the environment like climate change will affect all species through environmental epigenetics,” says Michael Skinner at Washington State University in Pullman.

See also: Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations

Excerpt: 

…the transgenerational phenomenon is initially induced through epigenetic inheritance but, in later generations, the transgenerational phenotype may involve a combination of the effects of epimutations and derived genetic mutations.

My comment: Skinner et al., (2015) were still trying to claim that the nutrient-dependent RNA-mediated events linked through transgenerational epigenetic inheritance should be viewed in the context of “epimutations” and “genetic mutations.” They are the paradigm shift preventers who refuse to acknowledge my claims about how thermodynamic cycles of protein biosynthesis and degradation are linked from atoms to ecosystems in all genera.

See: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)
Published abstract:

Chemical ecology drives adaptive evolution via 1) ecological niche construction, 2) social niche construction, 3) neurogenic niche construction, and 4) socio-cognitive niche construction (Kohl, 2012). Nutrients are metabolized to pheromones that condition effects on hormones that affect behavior in the same way that food odors condition behavior associated with food preferences. For example: glucose (Roland and Moenter, 2011) and pheromones alter the secretion of gonadotropin releasing hormone (GnRH) and luteinizing hormone (LH). Across species comparisons of epigenetic effects on genetically predisposed nutrient-dependent and hormone-driven invertebrate and vertebrate social and sexual behavior indicate that human pheromones alter the development of the brain and behavior via the same molecular mechanisms (Krubitzer & Seelke, 2012), which are conserved across all species.

Cited works:
1.    Nei, M., Mutation-Driven Evolution. 2013, Oxford, UK: Oxford Univesity Press.
2.    Noble, D., Physiology is rocking the foundations of evolutionary biology. Experimental Physiology, 2013: 10.1113/expphysiol.2012.071134.
3.    Wilson, L., et al., Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42. BMC Dev Biol 2011. 11(1): 10.
4.    Bumbarger, Daniel J., et al., System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes. Cell, 2013. 152(1): 109-119.
5.    Kohl, J.V., Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2012. 2(17338).
6.    Meiklejohn, C.D., et al., An Incompatibility between a Mitochondrial tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and Fitness in Drosophila. PLoS Genet, 2013. 9(1): e1003238.
7.    Yadav, J.S., B.V. Joshi, and M.K. Gurjar, An enantiospecific synthesis of (4R,5R)-5-hydroxy-4-decanolide from d-glucose. Carbohydr Res, 1987. 165(1): 116-119.
8.    Niehuis, O., et al., Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones. Nature, 2013. 494: 345–348.
9.    Lassance, J.-M., et al., Functional consequences of sequence variation in the pheromone biosynthetic gene pgFAR for Ostrinia moths. Proceedings of the National Academy of Sciences, 2013. in press.
10.    Stensmyr, M. and F. Maderspacher, Olfactory Evolution: Mice Rethink Stink. Curr Biol, 2013. 23(2): R59-R61.
11.    Kohl, J.V., Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation. http://dx.doi.org/10.6084/m9.figshare.643393, 2013.
12.    Kondrashov, F.A., Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci, 2012. 279 (1749): 5048-5057.
13.    Grossman, Sharon R., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell, 2013. 152(4): 703-713.
14.    Kamberov, Yana G., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell, 2013. 152(4): 691-702.
15.    Kohl, J.V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 2013. 3(20553).

Video representation

human-evolution

Hydrogen-atom transfer in DNA base pairs (5)

In an invited review of nutritional epigenetics, I linked atoms to ecosystems without the pseudoscientific nonsense touted by neo-Darwinists.
Kohl, James V. (2014): Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
The invited submission was returned without review.
When I provide all the details for the origin of the DNA code, what prevents the submission from being rejected without comment?

January 18, 2016 at 11:13 pm 

Can Anybody Actually Win The Evolution 2.0 Prize?

Thanks. I agree that the atoms to ecosystems model did not answer the questions. But your approach seems to limit any attempt to link the source of the code from information to hydrogen-atom transfer in DNA base pairs.

I’m not sure what “values of both encoding table and decoding table” have to do with linking the origin of the code to cell type differentiation via the code or via what is currently known about biophysically constrained protein folding chemistry.
You seem to be asking for someone to address the problem from the perspective of an engineer instead of from the perspective of a biophysicist who can link biologically-based cause and effect from the origin of the code to chromosomal rearrangements and biodiversity with examples from testing already performed in every hospital medical laboratory.

Are you clarifying the fact that the de novo creation of the code is not to be considered in the context of the prize? Is that what you mean by the statement: “…the prize excludes any life form or any code introduced at the outset of the experiment.”

Are you attempting to limit an explanation of how the origin of the code links atoms to ecosystems via DNA repair?I’m somewhat confused about the purpose of your book. Did you intend to exclude any explanations of biologically-based cause and effect that would come from creationists or anyone who could link Sheldrake’s works from morphic resonance to Lipton’s works via Stuart Kauffman’s claims about the need for an anti-entropic force?

January 20, 2016 at 4:17 pm

Thanks. I start with the de novo creation of nucleic acids. Are you able to answer questions about the links from quantum physics to chemistry and the conserved molecular mechanisms that link atoms to ecosystems in all living genera?

Thanks. I have demonstrated the well-known need for an anti-entropic force, which must be linked from Schrodinger’s claims to Stuart Kauffman’s claims. I have detailed the links from the anti-entropic force to RNA-mediated DNA repair at a time when Kauffman and Sheldrake are not discussing Lipton’s works and you are not discussing the works that refute Shapiro’s theories.
You have led many others to a point where they can dismiss “Evolution 2.0” as nothing more than another opinion. That’s what folks like PZ Myers want them to do, and that’s why he attacked me for my accurate representation of chromosomal rearrangements.
Others have linked the anti-entropic force from microbes in the guts of octopuses to chromosomal rearrangements and to human cognition via the conserved molecular mechanisms I have helped to detail during the past 20 years.
Simply put, you’re still trying to address the ridiculous claims of people like PZ Myers when it’s time to dismiss their nonsense and move forward using experimental evidence of biologically- based cause and effect.
For example: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit http://www.cell.com/cell/abstract/S0092-8674%2815%2900184-1 and Feedback loops link odor and pheromone signaling with reproduction http://www.ncbi.nlm.nih.gov/pubmed/16290036 are ‘cut from the same cloth.’
The metaphorical cloth emerged in the context of Dobzhansky’s “light of evolution,” which turned out to be the light that linked ecological variation to ecological adaptation in all living genera via nutrient-dependent RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living genera.

I agree you have demonstrated the well-known need for an anti-entropic force. One comes to the same conclusion from many different approaches. But my priority is getting from chemicals to code, empirically.
Finally, Perry Marshall and I agree on the first part of what I wanted to include in two part prize submission.

Thanks. Dobzhansky’s “light of evolution” (1973) is sunlight. See also, Dobzhansky (1964). Apparently, he had a bizarre sense of humor. He linked ecological variation to ecological adaptation in all living genera via the chemistry of RNA-mediated amino acid substitutions and nutrient-dependent protein folding.
At that point, the physiology of reproduction replaces ideas about random mutations and evolution. Experimental evidence of chromosomal rearrangements and ecological speciation trump neo-Darwinian theories (separately and collectively).
Anyone who excludes the epigenetic effects of sunlight cannot get from chemicals to code. Thus, if you keep me from submitting details that link top-down causation to all cell type differentiation in all individuals of all living genera, your prize money is safe.
No serious scientist will attempt to claim the prize money without first linking Schrodinger’s sunlight and Dobzhansky’s “light of evolution” to current representations, which must be placed into the light of what is known about supercoiled DNA.

Thanks. You are speculatively interpreting my works when you have not accepted part 1 or part 2 of the submission.  Why do you think I have not addressed the creation of the first cell?
Today, others reported everything I reported in what could have been part 1 of a 2 part submission.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
Now see: “Team uses internet network theory to decipher the first epigenetic communication network” January 28, 2016
In part 2 of my submission, I will detail the origin of the code and explain how information leads to the de novo creation of receptors and all cell types in all living genera.
If you want part 2, accept part 1. If not, others will keep reporting the details I want to report in the context of mutations and evolution.

Evolution 2.0’s blind spot

Perhaps the problem is that my model challenges Perry Marshall’s representations in Evolution 2.0. For comparison, some biophysicists and molecular biologists will link the following 4 published works:

1) Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder 

2) The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

3) Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress and

4) Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

My comment: There is only one way to link transgenerational epigenetic inheritance from the nutrient-dependent pheromone-controlled physiology of reproduction in soil bacteria to ingestion of plants and toxicosis via the sperm microRNAome in a mammal. Serious scientists must start with nutrient energy-dependent Hydrogen-Atom Transfer in DNA Base Pairs. That is the way that’s exclude in Evolution 2.0. Sunlight is not a code, but I have already repeated linked it to the origin of the code and the biophysically constrained molecular mechanisms that link chemistry to all cell type differentiation.
The problem for neo-Darwinian evolutionary theorists and for Perry Marshall has since been succinctly reported in:
Researchers observe one of the world’s fastest chemical reactions for the first time
Excerpt:

Extremely fast reactions are often covered up by slower ones.

My comment: The fact that theorists have never before observed the world’s fastest chemical reactions explains why Perry Marshall claims the origin of the DNA code is unknown. Serious scientists know that, whether or not the reactions are observed, the origin of the DNA code must link atoms to ecosystems in all living genera.
No new labels are required, no new calculations. Nothing new under the sun is required. Others need only look further into Perry Marshall’s claims and link them to the claims of serious scientists who know how ecological variation leads to ecological adaptation in the context of the sun’s biological energy and hydrogen-atom transfer in DNA base pairs.
See also:

See also: Published on 25 Aug 2014 with my emphasis

Base pairs, which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs (G-C and A-U) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g., G-U or A-A) allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins.

My comment: In my model, hydrogen-atom transfer in DNA base pairs link the nutrient energy-dependent amino acid sequence to the the physiology of reproduction and to all biodiversity.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.

My comment: I’ve since added the molecular mechanisms that link base-pairing to supercoiled DNA and chromosomal rearrangements that link the physiology of reproduction to ecological speciation. By starting with the sun’s anti-entropic biological virucidal energy, terms like mutations and evolution can be replaced with the terms used by ecologists.
See for example: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA, which was reported as Base-pairing protects DNA from UV damage.
Excerpt:

… the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy.

My comment: Protection from UV damage via the Watson-Crick base-pairing mechanisms also links the virucidal property of UV light to antibiotic resistance.
See: Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation
Excerpt:

Bacteria use these systems to sense and respond to their environment, which include stresses and nutrient conditions, but also include other bacteria and their antagonistic enzymes and specialized metabolites.

My comment: The systems are nutrient-dependent and they link ecological variation to ecological adaptation via specialized metabolites called pheromones. The pheromones control the nutrient-dependent physiology of reproduction in species from microbes to mammals. Again, please note the fact that there is no need to mention any theoretical links from mutations to evolution.  The Antibiotic Resistance was reported as: Bacteria battle: How one changes appearance, moves away to resist the other

Excerpt:

Straight said the common understanding of the usefulness of antibiotics, however, sidestepped the ecological dynamics of the bacteria themselves in how they form communities, and interact with each other.

My comment: The ecological dynamics of social niche construction are nutrient-dependent and pheromone-controlled in species from microbes to mammals. In this example of that fact, biophysically constrained cell type differentiation was linked from UV light to the DNA base pairing protection mechanism.  The facts about cell type differentiation were revealed in context of UV absorbances at 319, 333, and 351 nm. The differences in the UV absorbances link RNA-mediated amino acid substitutions to a conjugated pentaene moiety.
Every level of investigation that links UV light from energy dependent changes in base pairs to cell type differentiation becomes increasingly complex. None of de Vries “jump-like” changes are required, so there is no reason to mention his definition of “mutation.”
Definitions and assumptions about how long it might take one species to evolve into another are irrelevant. No experimental evidence of biologically-based cause and effect suggests that any species has ever mutated and evolved into any other species.

See also: [Antiviral action of carbonyl-conjugated pentaene macrolides] Abstract excerpt:

Clear antiviral activity of carbonyl-conjugated pentaene macrolides, such as flavofungin, mycothicin, brunefungin and flavopentin was shown on models with infectious and oncogenic viruses.

See also the indexed articles in a search for: UV light toll-like receptor
For example with my emphasis: A Light-Controlled TLR4 Agonist and Selectable Activation of Cell Subpopulations; Ultraviolet radiation signaling through TLR4/MyD88 constrains DNA repair and plays a role in cutaneous immunosuppression; TLR3: a receptor that recognizes cell injury is essential for permeability barrier homeostasis following UV irradiation
My comment: There are now clear links to controlled and contrained DNA repair and homeostasis from UV light via the innate immune system and cell type differentiation. Differences in somatic cell types also have been linked from the germ lines of plants (like fescues) to the germlines of mammals (like bulls).
See: Soma-to-Germline Transmission of RNA in Mice Xenografted with Human Tumour Cells: Possible Transport by Exosomes reported again on January 14, 2016 as No Sex Required: Body Cells Transfer Genetic Info Directly Into Sperm Cells, Amazing Study Finds and Previously thought impossible: Body cells transfer genetic information directly into sperm cells
Again, see also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
My comment: Everything known to serious scientists about cell type differentiation links nutrient energy-dependent changes in base pairs from Darwin’s “conditions of life” and Schrodinger’s “What is Life?” to Dobzhansky’s “light of evolution.”  Nothing in Biology Makes Any Sense Except in the Light of Evolution. However, nothing about evolution makes sense outside the context of nutrient energy-dependent changes in base pairs that Dobzhansky mentioned in this context:
Excerpt:

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

See also: Combating Evolution to Fight Disease
Excerpt:

The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.

My comment: The current molecular understanding of the genesis of variation links the availability of nutrients to ecological adaptation via hydrogen-atom transfer in DNA base pairs linked to RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
See also: 2003 Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
See also: 2009 Bacterial Quorum-Sensing Network Architectures
See also: 2014 Life is physics and chemistry and communication
See also: (unpublished) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
I suspect that by now all serious scientists understand that hydrogen-atom transfer in DNA base pairs must be linked to RNA-mediated amino acid substitutions in the context of biophysically constrained chemistry of protein folding. They should also understand why I have not re-submitted my invited review of nutritional epigenetics to another publisher.
Having arrived at the additional complexity that links quantum physics to cell type differentiation via hydrogen-atom transfer in DNA base pairs, I doubt that I will ever again publish in a peer-reviewed journal. My peers can, however, direct their comments and criticisms of my atoms to ecosystems model in the comments section here, or comment on my FB group.
Until then, I will keep reporting news, like this. CERN scientists ‘break the speed of light’
Whether or not this is confirmed makes no difference. The speed of light on contact with water has not yet been linked by anyone else from hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via the physiology of reproduction in all living genera.
Until others are willing to look at the anti-entropic epigenetic effects of the sun’s virucidal biological energy, learning about cell type differentiation in the context of pathology or healthy longevity will be more difficult. The obvious requirement is to start with the de novo creation of genes and link gene activation to biodiversity without the pseudoscientific nonsense of mutations and evolution.
See also: Cancer: Evolution 2.0’s Blind Spot