Alternative splicing of pre-mRNA

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

Hard Science: The Measure of All Things Natural w/Dr. J Michael Bailey (video) Published on 24 May 2017

First in a series of interviews DocAmitay had with Dr. J. Michael Bailey, controversial researcher who dares to ask questions that most do not dare to ask and that many do not want answered. The next few videos present a candid look at the man behind “the monster” created by Trans advocates, the media and those who oppose critical thinking and scientific inquiry when the results do not conform to their own ideologies, wishes or needs. Please stay tuned for Parts 2 and beyond, coming soon!

Critical thinking and scientific inquiry are not linked by ideologies. The human condition is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of pheromone-controlled reproduction. My experience with the ideologies of Dr. J. Michael Bailey, and many others like him, led me to attack his claims about critical thinking and others have since shown that he lacks any critical thinking skills.

See for example: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing
The critical thinking skills of serious scientists linked different SNPs to risk factors among human populations that confer risk for inefficacy or toxicity among African Americans, Asians, Hispanics and other populations. For comparison, this problem appears to be common to all social scientists.
See: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, social scientists take everything known about the human condition and predict that it evolved to be manifested as differences in African Americans, Asians, Hispanics and other populations. Serious scientists must take exact and general formulations and support their claims with experimental evidence of biologically based cause and effect.
The problem that serious scientists have in any attempts to discuss anything with social scientists is that all social scientists are pseudoscientists. See: Feynman on social science and Feynman Chaser – The Key to Science
Social scientists  have not learned enough about life on Earth to link physics and chemistry from molecular epigenetics to energy-dependent biophysically constrained cell type differentiation. In a fight for the soul of science, pseudoscientists are unarmed opponents of established facts.
See also: A Fight for the Soul of Science

…one year after George Ellis and Joe Silk, two white-haired physicists now sitting in the front row, called for such a conference in an incendiary opinion piece in Nature. One hundred attendees had descended on a land with a celebrated tradition in both physics and the philosophy of science to wage what Ellis and Silk declared a “battle for the heart and soul of physics.”

The “heart and soul” of biologically-based behavior cannot be considered outside the context of energy-dependent changes in angstroms to ecosystems. Anyone who claims to be able to think critically should start by asking the question: “Where did the energy come from?”
They must then use their critical thinking skills to link energy-dependent changes from angstroms to ecosystems in all living genera and to also explain why entropy has not caused the death of all life on Earth. One way to do that is via a model of biophysically constrained cause and effect that pits the snake-centric theory of human brain evolution against nutrient-dependent pheromone-controlled ecological adaptation.
The following review of 5 publications allows comparison of a model of top-down causation, which links energy-dependent changes from angstroms to ecosystems in E. coli to non-human primates, for comparison to a theory of how past selection for snake detection links monkeys to mankind.
Snake-centric theory
Pulvinar neurons reveal neurobiological evidence of past selection for rapid detection of snakes 2013

Compared with three other categories of stimuli (monkey faces, monkey hands, and geometrical shapes), snakes elicited the strongest, fastest responses, and the responses were not reduced by low spatial filtering. These findings integrate neuroscience with evolutionary biology, anthropology, psychology, herpetology, and primatology by identifying a neurobiological basis for primates’ heightened visual sensitivity to snakes, and adding a crucial component to the growing evolutionary perspective that snakes have long shaped our primate lineage.

With no experimental evidence of biologically-based cause and effect snake-centric theory was extended to the concept of the evolution of the social brain
Social and asocial prefrontal cortex neurons: a new look at social facilitation and the social brain 2017

Two populations of neurons were discovered: “social neurons”, preferentially active under social presence, and “asocial neurons”, preferentially active under social isolation. The activity of these neurons correlated positively with performance only in their preferred context (social neurons under social presence; asocial neurons under social isolation), thereby providing a potential neuronal mechanism of social facilitation. More generally, the fact that identical tasks recruited either social or asocial neurons depending on the presence or absence of a conspecific also brings a new look at the social brain hypothesis.

Simply put, they discovered social neurons in monkeys that other theorists predicted might be found in the context of snake-centric theory. For comparison, here is a model of biophysically constrained biologically based energy-dependent cell type differentiation in species from microbes to monkeys.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model 2013
In the context of the model, the molecular mechanisms of energy-dependent cell type differentiation in E. coli can be linked to the mind of the monkey.
See for comparison: Mechanism of transmembrane signaling by sensor histidine kinases 2017

One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases (HKs), parts of two-component signaling systems (TCS). The structural mechanisms of transmembrane signaling by these sensors are poorly understood. We present here crystal structures of the periplasmic sensor domain, the TM domain and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor HK NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces significant rearrangements and piston-like shifts of TM helices. The HAMP domain protomers undergo lever-like motions and convert the piston-like motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCS.

Understanding the two-component signaling system that links what organisms eat from multisensory perception to their biophysically constrained pheromone-controlled physiology of reproduction in E.coli and in other bacteria links ligand-receptor binding to choices for healthy longevity via transgenerational epigenetic inheritance, or sickness and all pathology in humans.
For an example of how researchers express their inability to understand the complexities of systems biology that link the behavior of microbes to the behavior of humans, see:
Behavioral and neural correlates to multisensory detection of sick humans (2017)

In the perpetual race between evolving organisms and pathogens, the human immune system has evolved to reduce the harm of infections.

In the ridiculous misrepresentations made by these researchers who have studied human olfaction, they failed to link energy-dependent RNA-mediated cell type differentiation in any other species to energy-dependent RNA-mediated cell type differentiation in humans. The magic and pseudoscientific nonsense of neo-Darwinian theories does not require pseudoscientists to do anything except make claims that are based on the claims of other pseudoscientists who failed to include anything known about energy as the anti-entropic source for all biodiversity.
See for comparison:

See also: This 2016 publication eliminates the evolutionary perspective from any further consideration whatsoever in all model organisms. One of the co-authors is a co-author of the already outdated 2015 publication.The origin and evolution of social insect queen pheromones, which antagonist Jay R. Feierman introduced to the ISHE’s human ethology group this morning. I will continue to mention that his antagonism has caused the death of millions to billions of people during the past two decades because he insists on reintroducing the pseudoscientific nonsense of the past each time new experimental evidence of biophysically constrained cause and effect refutes another aspect of his neo-Darwinian pseudoscientific nonsense.
See for comparison: Expression of key components of the RNAi machinery are suppressed in Apis mellifera that suffer a high virus infection
Endogenous RNA interference protects all organized genomes from the virus-driven energy theft that causes the degradation of messenger RNA, which links mutations to all pathology
To place that fact into the context of the honeybee model organism, see: MicroRNAs in Honey Bee Caste Determination
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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

It makes no difference whether or not you accept the facts about energy-dependent changes in microRNAs, unless you speak only to other theorists. This exemplifies how theorists speak to each other.
Nuclear codon reassignments in the genomics era and mechanisms behind their evolution
The nuclear codon reassignments are food energy-dependent and they control the physiology of reproduction, which links chromosomal inheritance to all biodiversity on Earth. There is no experimental evidence of biologically-based cause and effect that supports claims that molecular mechanisms evolved to control nuclear codon reassignments, or that anything else evolved to link biophysically constrained RNA-mediated cell type differentiation from angstroms to ecosystems in species from microbes to humans.
If you ignore everything known to all serious scientists about energy as information, you can continue to link mutations to evolution until everyone else on Earth is laughing at you, whether or not you live to see that day.
Until then, see also: How to make a sterile helper
Metaphorically, theorists make sterile helpers out of those who would rather believe in ridiculous theories that provide no Earthly good to humanity.  To avoid arguments from metaphors, serious scientists publish articles like this.
Serum microRNA signatures as “liquid biopsies” for interrogating hepatotoxic mechanisms and liver pathogenesis in human
At an appointment with a primary care physician yesterday, I discussed the fact that microRNA signatures have rapidly become the most predictive test of pathology. Nutrient energy-dependent microRNAs can be compared to viral microRNAs. The viral microRNA content of fluids and tissues is a measure of DNA damage. That damage must be repaired to restore healthy longevity at the level of hydrogen atom transfer in DNA base pairs in solution. Damage repair is energy-dependent. Viruses steal that energy, which is why the mutations that virus-driven energy theft causes cannot be linked to the evolution of anything except more hecatombic pathology. The physician is an exceptionally talented triathlete. I do not know anyone who knows how, when, or where the abilities of triathletes evolved.
Sarcasm alert: Perhaps, they evolved from behaviors in E. coli that linked the fear of snakes in monkeys to the evolution of similar structures in primate brains.

rp_levels-of-organization.jpg

Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

3/27/17 My comment:

On March 24, 2017 this article was published in ‘Science.’ A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

The article linked virus-driven energy theft from hydrogen-atom transfer in DNA base pairs in solution to all pathology.

On March 24, 2017 this article also was published in ‘Science.’ Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

The authors failed to link the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via protection of organized genomes manifested in supercoiled DNA.

It seems likely that without “Cytosis,” another generation of biologically uninformed researchers would fail to link top-down causation from quantum physics to all energy-dependent healthy longevity via endogenous RNA interference.

Without “Cytosis” the unnecessary suffering and premature deaths caused by the virus-driven degradation of messenger RNA might never be stopped by serious scientists who known how cell type differentiation occurs.

Are you planning to develop a game about “Photosynthesis” to show others how to link physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation via the physiology of reproduction? If so, I could help with some of the more technical aspects.

Sunlight as information

Proof: Sunlight is energy as information

Hypothesis: Kallmann’s syndrome is proof that virus-driven energy theft causes all pathology in species from archaea to humans via the degradation of messenger RNA and the loss of one allele.
 

Thought experiment:

Step 1) The loss of one allele and the transgenerational epigenetic inheritance of Zika virus-damaged DNA can be compared to the degradation of messenger RNA in bacteria that is manifested in archaea and L-forms.

Step 2) The degradation of messenger RNA in primates differentiates healthy longevity from pathology via a single amino acid substitution in gorillas compared to chimpanzees and modern humans.

Discussion:

Unless someone shows how mutation-driven evolution leads to increasing organismal complexity in species from microbes to humans, the speed of light on contact with water clearly establishes the link from the de novo creation of microRNA flanking sequences to hydrogen-atom transfer in DNA base pairs in solution and all energy-dependent morphological and behavioral phenotypes.

Conclusion:

Unless there is another model for comparison to Kohl (2013), energy as information will be established as the link from endogenous RNA interference to all biodiversity.  Until then, a natural law appears to link food odors and the pheromone-controlled physiology of reproduction from biophysically constrained RNA-mediated protein folding chemistry to feedback loops.

The feedback loops clearly link physics and chemistry to biodiversity from energy as information and food odors to pheromones that control the physiology of reproduction. Pheromones are the chemical signals that prevent virus-driven energy theft and genomic entropy in all living genera.

amino acid homeostasis

The essence of precision medicine: drug targets or healthy longevity?

The molecular epigenetics of healthy longevity
Trichome, a Functional Diversity Phenotype in Plant
Abstract:

Trichomes play a very important role in the process of evolution for plant which are epidermal appendages covering the surface of plants. In this paper, some progress concerning the genes responsible for trichome formation is presented for monocots and dicotyledons plants. Meanwhile, the special structures and physiological functions of trichome are briefly introduced, such as reflectance, energy balance, ultraviolet protection, drought resistance, gas exchange, insect resistance and disease resistance. The review provides a theoretical basis for the further study of other trichome related traits in plants.

The review links the process of evolution from the energy balance to ultraviolet protection without mention of where the energy came from or how the energy balance is biophysically constrained by the chemistry of RNA-mediated protein folding in the context of fixed amino acid substitutions in supercoiled DNA. They should simply claim that evolution is an automagical process that they cannot explain in terms that might be used by serious scientists to link physics and chemistry to molecular epigenetics and all biologically-based cause and effect.
Article excerpts

Trichomes, as a plant protective barrier against natural hazards such as herbivores, ultraviolet (UV) irradiation, pathogen attacks and excessive transpiration, play a key role in development of plants and occur widely in various plants.

Trichomes are a model system for cell differentiation, cell cycle regulation, cell polarity and cell expansion…

Trichomes cannot be a model system because cell differentiation it is energy-dependent and biophysically constrained by the physiology of reproduction in all living genera.

Light reflectors and energy balance

Studies have shown that trichomes can be reflectors of broadspectrum radiation, and play a physiologically significant role in modulating the plant energy balance [57,65,66]. When leaves are exposed in environments, this can regulate heat balance via transpiration cooling, which requires an adequate water supply or through reduced leaf absorption [66].

All physiologically significant roles played in the context of thermodynamic cycles of protein biosynthesis and degradation in all living genera must link energy-dependent changes from angstroms to ecosystems. Now that those links have been established, they can be used to virus-driven energy theft to all pathology.
Clearly, nothing evolves without an anti-entropic virucidal energy source, which means that no species has ever evolved into another species via natural selection for anything except energy-dependent codon optimality.
Natural selection for energy-dependent codon optimality is the essence of precision medicine. See:
See for comparison: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

Methylation of histone lysine residues is a significant component of epigenetics and is associated with control of gene expression [1]. Specifically, methylation of lysine 9 of histone H3 (H3K9) has been recognized as hallmark of transcriptionally suppressed genes [2].

“The essence of precision medicine is to understand, which drug targets are effective given each person’s unique genetic and epigenetic makeup,” Filipp said.

Methylation is energy-dependent and RNA-mediated. Nutrient energy-dependent viral latency links lysine residues (amino acid substitutions) to all healthy longevity in all living genera via natural selection for differences in the energy of photons, which has been linked from hydrogen-atom transfer in DNA base pairs in solution to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Each person’s unique genetic makeup arises only in the context of epigenetic effects on supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. Different levels of energy link energy as information in photons from changes in the microRNA/messenger RNA balance and hydrogen-atom transfer in DNA base pairs in solution to the pheromone-controlled physiology of reproduction in all living genera.

Virus-driven energy theft links mutations to all pathology.
For more pseudoscientific nonsense about cancers and metastases, see: Cancer Cells Conversations About Metastasis
My comment: Different levels of energy link energy as information in photons from changes in the microRNA/messenger RNA balance and hydrogen-atom transfer in DNA base pairs in solution to the pheromone-controlled physiology of reproduction in all living genera.
Virus-driven energy theft links mutations to all pathology.
See also:
Mitochondria as a Favourite Organelle for Invading Viruses

ER-alpha 36, A Novel Biomarker for ER-Negative Breast Cancer
DNA Repair Mechanisms in ESCs and iPSCs
If pseudoscientists consistently fail to link the sun’s anti-entropic virucidal energy to all biophysically constrained RNA-mediated cell type differentiation via fixation of amino acid substitutions, do not expect them do discover that the energy for DNA repair is essence of precision medicine.
See also my comments on: Ben Carson and the Power of the Hippocampus
For example:
Do you realize that Ben Carson and others like him have linked energy to the experience-dependent near-infinite capacity of the brain, and linked virus-driven energy theft to all pathology via Schrodinger’s claims in “What is Life?” (1944)
All of Carson’s claims about the hippocampus link what is known to all serious scientists about energy-dependent RNA methylation and experience-dependent cell type differentiation, which is biophysically constrained by the physiology of reproduction in all living genera.
See: “Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice” June 22, 2016
The repository of non serious scientists is found among neo-Darwinian theorists. Also, Dobzhansky (1964) made claims about the difference between serious scientists and “serious intellectuals,” who he would probably also refer to as biologically uninformed.
For example, Neuroskeptic concludes that “It’s not a totally crazy approach, but it makes a lot of assumptions.”
Ben Carson did not make any assumptions about the claims that link ATP from the energy-dependent de novo creation of RNA to all biodiversity via links from RNA methylation to learning and memory in all living genera. See: Dobzhansky’s claims (1973) about RNA-mediated amino acid substitutions and cell type differentiation in all living genera. The energy clearly must be linked from what organisms eat to the physiology of reproduction. See for comparison:
Biology, molecular and organismic (1964) Excerpt: “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. ”
For an example of some intelligent men, see: DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION” (1964)

The essence of precision medicine: drug targets or healthy longevity?

fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… 

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have 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.

Alternative splicing of pre-mRNA

Explorers who do not know what is known (2)

See: Explorers who do not know what is known
See also: Energy-dependent polycombic ecological adaptation

Now see: The B/Z reaction, and the problem with peer review December 9. 2016 by John Leonard

  1. … oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.
  2. Alan Turing didn’t live to see the publication of evidence that would have validated his theory almost immediately.
  3. …when Belousov attempted to have his research published in 1951, the leading scientific journals flatly rejected his work, based on the assumption that the experiment results were “impossible.”
  4. Only a single paragraph from Belousov’s analysis was finally published four years later, in 1955. Alan Turing was already dead. And so was the career of Boris Belousov,  so disgusted the editors of the leading journals had flatly rejected his work without even trying to replicate the results that he stopped performing scientific research.
  5. A horribly flawed peer review process utterly failed Boris Belousov. The editors of science journals successfully asserted themselves as the arbiters of what may be considered acceptable science, and their power remains largely unchecked even today.
  6. Rather than simply assuming that some process or claim  is “impossible,” perhaps we should seriously consider at minimum a cursory investigation of the alleged evidence.
  7. Peer review is a horribly flawed system, but unfortunately, it remains the best system we have.
Peer-review fuels plagiarism. Plagiarism fuels ignorance when what is known about physics, chemistry, and conserved molecular mechanisms is placed back into the context of ridiculous theories. People and plagiarists like John L. Leonard fuel ignorance when they refer to me as an ill-mannered idiot.
October 24, 2016 at 1:15 pm he wrote:

And I don’t like ill-mannered idiots.

Less than two months later, John L. Leonard plagiarizes my detailed model and referenced claims about energy-dependent cell type differentiation. He put them into the context of failed peer review, Turing’s suicide, and the reason why Boris Belousov stopped his research.  I think that if Facebook groups had been available so that people like John L.Leonard could criticize his works, Boris Belousov might also have committed suicide.
Clearly, the amount of overwhelming ignorance displayed in the context of peer review now extends across many more forms of communication in which the opinions of the biologically uninformed prevail. See for example my invited review of nutritional epigenetics, which was returned without review. Then see the subsequent publications from two guest editors of the journal “Nutrients” who requested my review: Lynnette Ferguson and Justin O’Sullivan.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition
Insights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes

See for comparison: A protein conjugation system essential for autophagy (1998)

This process is crucial for survival during starvation and cell differentiation.

See also: A Harvard scientist just won $3 million for discovering the hidden ‘intelligence’ that defends our cells (2016)
He discovered nutrient energy-dependent autophagy, again.
See for instance: How autophagy both activates and inhibits cellular senescence (2016)

Although autophagy was originally recognized as a nonspecific lysosomal degradation pathway (general autophagy), increasing evidence supports a selective form of autophagy that mediates the degradation of specific targets (selective autophagy).

Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine for experimental evidence that links selective autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft.
See: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates (2016)

Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis.

Others have helped to establish the fact that energy-dependent receptor-mediated selective autophagy is RNA-mediated.
Schrodinger (1944)  What is life?

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)

Diamond et al. (1996) From Fertilization to Adult Sexual Behavior

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.

Ben-Jacob et al. (2006) Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information

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

Ben Jacob (2009) Learning from Bacteria about Natural Information Processing

It seems that bacteria have some sort of collective memory by which they keep track of how they handled their previous encounters with antibiotics. They know how to collectively glean information from the environment, “talk” with each other, distribute tasks, generate collective memory, and turn their colony into a “cybernetic system”—a massive “brain” that can perform natural distributed information processing, learn from past experience, and possibly alter the genome organization or even create new genes to better cope with novel challenges.8–13,17,18

Fortunately, serious scientists are now limiting attempt by pseudoscientists and opinionated laypeople to present more pseudoscientific nonsense about mutations, natural selection, and evolution. Those attempts may stop here.
See: The complex evolutionary history of aminoacyl-tRNA synthetases November 29, 2016
This article includes ongoing misrepresentations of how biophysically constrained protein folding chemistry is linked from RNA-mediated amino acid substitutions to the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum.
Everything known to serious scientists is again placed back into the context of theories and “complex evolutionary histories.”
But the resurrection of the flagellum occurred within 96 hours in an organism (P. fluorescens) that fluoresces with exposure to ultraviolet light.
The failure to link the anti-entropic virucidal energy of sunlight to healthy longevity is the reason some researchers still frame their results in the context of ridiculous theories. In this article, they could refute the theories by the mere mention of the energy source that powers all cell type differentiation in all cell types of all individuals of all living genera.
Instead of the explanatory power of energy as information, an “evolutionary history” approach is used, which ignores the weekend evolution of the irreducibly complex bacterial flagellum.
The journal article was reported as: Ancient enzyme morphed shape to carry out new functions in humans

 Schimmel compared it to reshaping an airplane’s wing to serve as the airplane’s tail instead. “Nature has provided ways for reshaping objects, like C-Ala, and when that happens, new functions occur,” he said.

Selective autophagy is akin to the complete destruction of the airplane, which is rebuilt in its entirety via energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution in all living genera. All the reassembled parts must be linked from energy transfer to functional structures at every level of examination. In the context of biologically-based cause and effect, angstroms must be linked to ecosystems in all living genera via conserved molecular mechanisms.
Attributing all that to “Nature” is an example of the pervasive ignorance that is common among theorists. That ignorance should probably never be displayed by creationists, especially if they attempt to argue with theorists.
Instead, all creationists can stay silent or they can learn about the experimental evidence that has linked selective autophagy to chromosomal rearrangements since the time of the 1933 Nobel Prizes for Physiology or Medicine (Thomas Morgan Hunt) and for Physics (Schrodinger/Dirac).
See also: “aminoacyl-tRNA synthetase” microRNA
miR-15a and miR-16-1 down-regulation in pituitary adenomas (2005)
Feedback loops link odor and pheromone signaling with reproduction (2005)

From Fertilization to Adult Sexual Behavior December 1996

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

The alternative splicings are energy-dependent. Virus-driven energy theft causes all pathology by using the energy to stabilize the genomes of viruses. If not for the atheists, plagiarists, and other creationists who would rather steal the information or fight against its dissemination, the neo-Darwinists would never have stood a chance.Watch for more reports that link energy-dependent RNA-mediated amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

Someone else will also soon expose the fact that what theorists are calling ancient aminoacyl tRNA synthetases are the enzymes in bacteria that decode genetic information to help produce amino acids in all living genera. The nutrient energy-dependent fixation of the RNA-mediated amino acid substitutions links selective autophagy from nutritional epigenetics to healthy longevity via the physiology of reproduction in all genera.

fruit-dove

Tasting light links energy from creation to adaptation

Biology to a Physicist
The C. elegans Taste Receptor Homolog LITE-1 Is a Photoreceptor

“In Brief: A taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”

Excerpt: Light sensation is critical for all phyla of life, ranging from bacteria to humans (Wang and Montell, 2007; Yau and Hardie, 2009). Organisms have evolved various types of photoreceptor proteins…

Photoreceptors are G protein-coupled receptors (GPCRs). No experimental evidence of biologically-based cause and effect links the evolution of any type of photoreceptor to any other type of G protein-coupled receptor (GPCR). Nothing except energy-dependent hydrogen-atom transfer in DNA base pairs in solutions like sea water and blood links the de novo creation of olfactory receptor genes, which are GPCRs, to all biodiversity via the physiology of reproduction and supercoiled DNA in all living genera.
The facts about supercoiled DNA link energy-dependent RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all living genera via the claim that “…a taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”
That claim can be readily linked to the energy-dependent experience-dependent nutrient-dependent RNA-mediated de novo creation of all GPCRs and experience-dependent behavior that links chemotaxis from the de novo creation of olfactory receptor genes to phototaxis via the nutrient energy-dependent de novo creation of photoreceptors and/or all other receptors.
Reported as: Tasting light: New type of photoreceptor is 50 times more efficient than the human eye

1) …within the protein, having the amino acid tryptophan in two places was critical to its function.

2) Breaking it apart, or “denaturing” it, completely stops its ability to absorb light, rather than just diminishing it — showing that it really is a different model, Xu said.

The two nutrient energy-dependent RNA-mediated amino acid substitutions link UV light from DNA repair to all biophysically constrained pheromone-controlled biodiversity via the innate immune system and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. The claim that the are using a different model to do that should be placed into the context of the only model that links angstroms to ecosystems in all living genera to all nutrient energy-dependent RNA-mediated amino acid substitutions and pheromone-controlled biodiversity.
Also reported as: Powerful New Photoreceptor Found in Roundworms

Because the “genetic code” of these photoreceptor proteins are so much different than that of other photoreceptors found in the animal kingdom, there is a ton of untapped potential in this discovery.

There is only one genetic code. It links the epigenetic landscape to the physical landscape of supercoiled DNA via energy-dependent changes in base pairs, which link natural selection for codon optimality to the physiology of reproduction by protecting the organized genomes of all living genera from virus-driven energy theft.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See also: Meaning = Information + Evolution

Notions like meaning, signal, intentionality, are difficult to relate to a physical word. I study a purely physical definition of “meaningful information”, from which these notions can be derived. It is inspired by a model recently illustrated by Kolchinsky and Wolpert, and improves on Dretske classic work on the relation between knowledge and information. I discuss what makes a physical process into a “signal”.

Energy as information becomes a signal via its effect on hydrogen-atom transfer in DNA base pairs in solution. The information links the anti-entropic virucidal energy of sunlight to all biophysically constrained cell type differentiation in all living genera via the innate immune system, which links the physiology of reproduction to supercoiled DNA.
For more experimental evidence of this established link to biologically-based cause and effect, which was not presented in the context of my model from 2013, see:
Dynamic control of chirality and self-assembly of double-stranded helicates with light
Physicochemical mechanism of light-driven DNA repair by (6-4) photolyases

Clearly, if one photon provides just enough energy to perform repair, two photons are even better. However,
these are speculations…

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer
Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells
A Framework for integrating multiple biological networks to predict microRNA-disease associations
Without a framework that links energy-dependent changes from angstroms to ecosystems in all living genera via their physiology of reproduction and fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protects organisms from virus-driven energy theft and genomic entropy, all that’s left is the pseudoscientific nonsense of neo-Darwinian theories.
For comparison, with a framework that links the sun’s anti-entropic virucidal energy to cell type differentiation in all genera, it is likely that the cure for all pathology is within sight. For example all pathology appears to be is epigenetically controlled at the level of quantized energy.
See also: Melanocytic Nevi and the Genetic and Epigenetic Control of Oncogene-Induced Senescence
Melanocytic nevi represent benign clonal proliferations of the melanocytes in the skin that usually remain stable in size and behavior or disappear during life. Infrequently, melanocytic nevi undergo malignant transformation to melanoma. Understanding molecular and cellular mechanisms underlying oncogene-induced senescence should help identify pathways underlying melanoma development, leading to the development of new strategies for melanoma prevention and early detection.
See also: microRNA
More than 55,000 published works link energy-dependent changes in the microRNA/messenger RNA balance to the framework that links amino acid substitutions to cell type differentiation and healthy longevity compared to virus-driven energy theft, which has been linked to all pathology by amino acid substitutions that stabilize viruses.
Here is some background on the concept of sunlight as energy that links information to all biodiversity via natural selection for energy-dependent RNA-mediated codon optimaility.
Light Absorption, Reflection, and Transmission

If a light wave of a given frequency strikes a material with electrons having the same vibrational frequencies, then those electrons will absorb the energy of the light wave and transform it into vibrational motion. During its vibration, the electrons interact with neighboring atoms in such a manner as to convert its vibrational energy into thermal energy. Subsequently, the light wave with that given frequency is absorbed by the object, never again to be released in the form of light. So the selective absorption of light by a particular material occurs because the selected frequency of the light wave matches the frequency at which electrons in the atoms of that material vibrate. Since different atoms and molecules have different natural frequencies of vibration, they will selectively absorb different frequencies of visible light.

The absorption of ultraviolet light links the anti-entropic virucidal energy of the sun to all biophysically constrained biodiversity.

What is life when it is not protected from virus driven entropy

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

See also: Royal Society: The Public Evolution Summit  Page 12
Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”
The title may change to “You are what you eat.” He has already linked energy and information-dependent changes from physics to chemistry and all the biodiversity of life.
See also: Life is physics and chemistry and communication

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

Biological facts about life link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. Why hasn’t everyone already accepted the facts that Schrodinger helped to detail in What is Life?

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

See also from the forward to 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)

Eliminating energy-dependent creation and Darwin’s “conditions of life” was probably not de Vries intention when he defined the term mutation in 1902. But, neo-Darwinian theorists took his claims about sudden energy jumps and assumed the jumps could explain what would happen if accumulated random mutations had somehow caused one species to evolve into another.
In that view of evolution, millions of years are required to link the sudden energy jumps to all morphological and behavioral diversity. Serious scientists have since learned that all energy-dependent changes in organized genomes link what organisms eat to their physiology of reproduction. That is how biodiversity is biophysically constrained by the availability of food and how food odors and pheromones are linked to the physiology of reproduction by feedback loops.
See: Feedback loops link odor and pheromone signaling with reproduction
Neo-Darwinian theorists eliminated energy and the nutrient energy-dependent feedback loops that link odors and pheromones to biophysically constrained biologically based cause and effect.
See for comparison: Scientists Seek to Update Evolution and Genetic and mechanistic diversity of piRNA 3′-end formation.
The news article by Carl Zimmer and the journal article ignore all accumulated experimental evidence of biologically-based energy-dependent top-down causation. The authors of the journal article invent the term “egoistic genes” as if no one had refuted the pseudoscientific nonsense of Richard Dawkins’ “The Selfish Gene.”
Pseudoscientists seem to think that serious scientists must prove their pseudoscientific nonsense is nonsense. Serious scientists do not try to do that because they are not taught to believe in theories. Serious scientists are taught to find experimental evidence of biologically-based cause and effect that supports their claims.

See for an example of the energy-dependent de novo creation of G protein-coupled receptors: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

See for comparison: Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

See also: 30 Reasons to Never Put Another M&M in Your Mouth Ever Again
See also: The Sea Slug That Eats The Sun
See also: Sci-hub  Our mission is to remove any barrier which impeding the widest possible distribution of knowledge in human society!
See also: Purkinje effect: Physiology:
The effect occurs because the color-sensitive cones in the retina are most sensitive to green light, whereas the rods, which are more light-sensitive (and thus more important in low light) but which do not distinguish colors, respond best to green-blue light.[4] This is why humans become virtually color-blind under low levels of illumination, for instance moonlight.
The effect links the sun’s anti-enrtopic virucidal biological energy to all biophysically constrained cell type differentiation via the physiology of reproduction in all living genera.
Light and Color – Detailed Help

Jack is wearing a red shirt. The shirt is illuminated with white light. Jill views Jack’s shirt while looking through a magenta filter. To Jill, Jack’s shirt will appear ____.

If you look at a red shirt through a red filter, you will most likely claim that the shirt is white. If you eliminate the sun’s biological energy from your claims about evolution, you will eliminate everything known to serious scientists about the energy-dependent creation of all biodiversity.
The fact that light and color are clearly linked to the morphological and behavioral phenotypes of the fruit dove, pictured above, is hard to dismiss, no matter how biologically uninformed others are.

Alternative splicing of pre-mRNA

The futility of The Battlefield FB group

Apparently, Paul Hartley blocked me from further discussion of his OP about dinosaurs and gladiators before I could ask if he thought “The Battlefield” is a “false flag” group. Does anyone else think that?
 

If so, do you think it can survive publication of experimental evidence that links responsive supramolecular systems to stepwise changes in the assembly of metal complexes via induction of a light-driven rotary motor scaffold akin to the bacterial flagellum of P. fluorescens?

See: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Others are claiming that partial unwrapping of the supercoiled DNA complex precedes the photoisomerization steps, which link energy-dependent autophagy to inversion of the chirality in helicates. That explains how energy-dependent RNA-mediated isomerization establishes the difference between metastable and stable helicates, which links amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy. For example, supercoiled DNA protects the organized genomes of dinosaurs and gladiators from stress-linked pathology until stress-linked changes in pH overcome the ability of the innate immune systems to protect the organized genomes via the light-induced changes in hydrogen-atom transfer in DNA base pairs in solution.
See for comparison: Team combines quantum physics and photosynthesis to make discovery that could lead to highly efficient solar cells

They claim plants evolved to control responses to the sun’s biological energy. As proof of concept their “…design incorporates a heat engine photocell that absorbs photons from the sun and converts the photon energy into electricity.”

Via the comparison of two simple quantum mechanical photocell systems, they found that “…by simply incorporating two photon-absorbing channels, rather than only one, the regulation of energy flow emerges naturally within the photocell.”

They linked the natural emergence of the energy flow in their design to the natural energy of photosynthesis in plants in an attempt to explain how green became the predominant color of plants on Earth. Others found molecular structures that prevent death via the accumulation of excess energy in plants.

The design of the molecular structure of their quantum heat engine photocell is similar to “…the structure of photosynthetic molecules that incorporate pairs of chlorophyll.” But wait. They claimed that the plants evolved molecular mechanisms after the natural emergence of energy flow was linked to photosynthesis and molecular structures that prevent death caused by the accumulation of excess energy.When I see such a convoluted representation of energy-dependent biologically-based cause and effect that does not include any mention of virus-driven energy theft or the physiology of reproduction, I am inclined to call researchers like this “biologically uninformed science idiots.”Many people hate it when I do that. What would you call them? But some of them are plagiarists, too.

See: Modern Science refutes the Evolutionary theory

Tomi Aalto’s blog is a continuation of his plagiarism. His posts can be compared to more than 800 of mine on my domain.

The difference is that Suzan Mazur acknowledged RNA-mediated.com as an information source in her book: Royal Society: The Public Evolution Summit

From page 3: “Some of the social momentum over the last year, in particular, has come via coverage of the evolution discourse in a flurry of books and from these diverse venues…”

James Kohl — RNA-mediated.com

In “Darwin’s Children” (2003) Greg Bear also acknowledged me and the International Paleopsychology Project, where I first encountered him and Eshel Ben-Jacob, who died last year. See this tribute to Eshel’s works.

He mastered the concept of energy-dependent autophagy and linked everything known about Schrodinger’s anti-entropic virucidal energy of sunlight to the nutrient-dependent physiology of pheromone-controlled reproduction in species from microbes to humans.
Theorists still hate it when that happens, and they continue to tell others who are biologically uninformed that not enough is known to link virus-driven energy theft to all pathology.

What does Tomi Aalto, or any other plagiarist hope to accomplish by taking bits and pieces of my works, or the works of others, without the ability to link the energy-dependent de novo creation of G protein-coupled receptors from energy as information to all biodiversity and also link virus-driven energy theft to all pathology? That inability to link top-down causation to any model of biologically-based cause and effect led to this criticism of my 2013 review.

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Would it not be more appropriate for others who are not atheistic antagonists to support my claims by citing and discussing my works, rather than make ongoing attempts to establish themselves as experts?

See for examples of what is expected of other serious scientists.

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).

Two fatty acyl reductases involved in moth pheromone biosynthesis also cites Kohl (2013) see #10

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

Re: Tomi Aalto’s plagiarism and the plagiarism of others.


Larry Kisner Sr. suggested I contact Kevin Anderson in an attempt to publish what I have already published. He also refused — and Mark Armitage ignored my requests — to provide the slide that shows fluorescence in dinosaur osteocytes.

See my comment on the video by Mark Armitage. See also: Future Projects
 
The Influence of Carbon Dioxide Enhancement on Plant Growth
Thermoregulation in Honey Bees
Fossils of the Coconino Sandstone
Biochemistry and Taxonomy in Pine Trees
The Formation of Multiple Tree Rings in Bristlecone Pine Trees
 

Each of these projects focuses on aspects of my published and unpublished works that link the sun’s anti-entropic virucidal energy to RNA-mediated amino acid substitutions and biophysically constrained cell type differentiation in species from microbes to humans.

See for example: What is life when it is not protected from virus driven entropy  (video 6:37 minutes)

Abstract:

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

See also: Metabolic Phenotyping Research

Excerpt: SARCASM ALERT

7. They will claim that the Extended Evolutionary Synthesis will have explanatory power when it automagically evolves into a model of top-down causation that links physics and chemistry to the conserved molecular mechanisms of biologically-based cause and effect, which serious scientists have detailed during the past century.

See for comparison:

Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells

Dual genomes: exposing the evolution industry

Pheromones and longevity in worms (and flies)

I posted this to one of my OPs on “The Battlefield,” which means I may be the next to go. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks
 

For comparison to what is known about the de novo creation of genes in mollusks, Anna Di Cosmo’s group cited my most recent review in 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). — p. 61

The facts link my model to biologically-based cause and effect from energy-dependent changes in angstroms to ecosystems in all living genera via the de novo creation of the genetic code. See also: Junk DNA’ Used To Sort Species

Now watch Lenski’s group claim that different species of viruses evolved in one month. Biologists watch speciation in a laboratory flask
Nutrient energy-dependent pheromone-controlled speciation can now be observed in the context of fluorescence, which links ecological variation to morphological and behavioral diversity to chromosomal rearrangements in C. elegans compared to P. pacificus, a predatory nematode with teeth. Researchers find chemical tag that locks chromosomes together during meiosis 

The ENEA study proposed that the image may have been created by an intense source of light, but no man-made light would produce the required strength.

Serious scientists have linked femotosecond blasts of UV light to RNA-mediated DNA repair and the repair has been linked via the natural fluorescence in DNA from dinosaur osteocytes to the weekend resurrection of the bacterial flagellum. One could look at the evidence in the discovery at Christ’s tomb from that perspective given the intensity of light energy as information that might be required to Resurrect Him.
For comparison, Lenski’s group has placed everything he knows into the context of evolved species of viruses during a month-long experiment that failed to include anything known about biophysically constrained energy-dependent RNA-mediated cell type differentiation in any living species. Again, see: Biologists watch speciation in a laboratory flask
The bottom line is always whether you choose to believe in theorists or in the evidence of biologically-based cause and effect — no matter when that evidence is discovered or where it is found.

See: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

Natural selection for energy-dependent codon optimality is the only obvious link to the de novo creation of olfactory receptor genes. And Svante Paabo is the senior author. Here he is again, supporting my model with others who understand the role of microRNAs. MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Does everyone understand why Bill Ludlow blocked me after I commented on his OP from “The Battlefield?” about this:

Scientists Seek to Update Evolution

See also: Tertiary alphabet for the observable protein structural universe
From the journal article: “…the frequency of amino acids in different secondary-structural environments is closely related to thermodynamic propensities (20–24).”
From the news report: “Since protein structural states are really conformational ensembles, the language of statistical mechanics is most appropriate for describing their behavior.”
This is the language they use: “…we find that the emergent sequence variability is often in close agreement to the evolutionary variability…”
Instead of linking sunlight from thermodynamic cycles of energy-dependent protein biosynthesis and degradation to biophysically constrained cell type differentiation and all RNA-mediated biodiversity, they link emergence to evolution.
Welcome again to the world of biologically uninformed theorists. This time, “…we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs).”
The ability to take everything known to serious scientists and put it back into the context of unintelligible theories via use of terms like tertiary structural motifs far surpasses the ability of serious scientists to make sense of their pseudoscientific nonsense. Thus, the pseudoscientific nonsense will continue to kill us all.
See for comparison: The Pangenome: Are Single Reference Genomes Dead?

…when Tettelin, then at the Institute for Genomic Research (TIGR), and his colleagues compared eight isolates of Streptococcus agalactiae (or group B Streptococcus, GBS), they found not only the small, within-gene variations predicted by conventional genetics, but an average of 33 completely new genes with every new genome sequenced. “It was a shock,” says Tettelin. “We saw there were many regions—relatively large regions—of diversity.”

All that diversity is energy-dependent and linked from the pheromone-controlled physiology of reproduction to all  morphological and behavioral phenotypes in all living genera.

Thanks to Anna Di Cosmo for sharing this example of energy-dependent de novo transcriptome assembly.

Abstract conclusion:

The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.

No serious scientist I know examines morphogenesis outside the context of feedback loops that link odor and pheromones to the physiology of reproduction in species from microbes to humans via the de novo creation of G protein-coupled receptors (GPCRs). How many pseudoscientists do you know who skip past the de novo creation of GPCRs and proceed to link mutations from natural selection to evolution outside the context of everything known to serious scientists about biologically-based cause and effect (i.e., energy-dependent biodiversity)?The lack of discussion and/or support from other creationists for my presentations of accurate information like this may suggest to others that this is a “false flag” group. Note that after I blocked those who I know participate in other “false flag” groups, there has been no discussion of my OPs. If you tried to evaluate the content presented here, would you get the impression that this is a group in which the admins are Creationists? When did you realize the de novo creation of genes for olfactory receptors must precede the de novo creation of photoreceptors to link chemotaxis and phototaxis to energy-dependent cell type differentiation, which is our only protection from the viral apocalypse?

See: Pterosaurs Hijack Royal Society Evo Meeting

See also: Royal Society: The Public Evolution Summit

Page 11- 12 Re: … evolution of genome invading RNA networks that edit host genomes.

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

He is the author of Life is physics and chemistry and communication.

Abstract:

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

The claims about quasispecies and hypercyclesthat dominate molecular biology and virology should have long ago long before now have been placed into the context of all reviews of neo-Darwinian pseudoscientific nonsense.

See for example: Major Evolutionary Blunders: Imagining That Life Is Only Chemistry

See also: “I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732).  — Lewis Thomas as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

Alternative splicing of pre-mRNA

Metabolic Phenotyping Research

Global Consortium to Conduct Metabolic Phenotyping Research

Consortium members in six countries will use chromatography, mass spectrometry, and other technologies to conduct metabolic phenotyping research that examines the dynamic interactions between genes, environments, microbiomes, diets, and lifestyles, and their collective impact on disease.

My Predictions.
1. They will link energy as information to healthy longevity.
2. They will report their findings as if they discovered new molecular mechanisms.
3. The mechanisms will link the anti-entropic virucidal energy of ultraviolet light to all biophysically constrained RNA-mediated cell type differentiation in all living genera via the innate immune system and supercoiled DNA, which protects all organized genome from virus-driven entropy.
4. They will not link virus-driven energy theft to all pathology.
5. They will claim that the energy emerged and that all biodiversity on Earth evolved.
6. They will continue to be funded by the evolution industry and big bang cosmology industry, which ignore the obvious link from food energy to the physiology of reproduction and ecological adaptation.
SARCASM ALERT
7. They will claim that the Extended Evolutionary Synthesis will have explanatory power when it automagically evolves into a model of top-down causation that links physics and chemistry to the conserved molecular mechanisms of biologically-based cause and effect, which serious scientists have detailed during the past century.
See for comparison:

Diagram with abstract
Full text with references
See also: Dual microRNA Screens Reveal That the Immune-Responsive miR-181 Promotes Henipavirus Entry and Cell-Cell Fusion

… these dual screens further the understanding of the role of host-derived small noncoding RNAs in the infection cycle of henipaviruses, and provide a miRNA-based resource for the study of viruses from the order mononegavirales, including members of both the filovirus and paramyxovirus families, which presents significant threats to human and animal health. This study implicates miR-181 and certain class A Eph receptors as critical modulators of henipavirus membrane fusion, and highlights how the natural innate immune response of the host can be exploited by a RNA virus to promote cell-to-cell spread.

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

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