5th-6th Sept 2018 Dublin, Ireland

MicroRNA-mediated denuclearization (2)

Summary:
The virus-driven theft of quantized energy creates a cellular environment that promotes the survival and self-proliferation of viruses by encoding viral miRNAs or miRNA-like molecules. The viral miRNAs or miRNA-like molecules target different types of host cells.
The sun’s anti-entropic virucidal energy biophysically constrains viral latency in the context of global control of human ES cell differentiation via circRNAs derived from lncRNAs. That fact refutes all neo-Darwinian gene-centric pseudoscientific nonsense. That fact also attests to the link from Chinese philosophy to scientific creationism in South Korea.
Scientific creationism appears to have defeated communism in the context of the electron cloud superimposed over the yin yang symbol of constrained energy.
For scientific support of the claims that appear to have defeated communism, see:
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes.

CONCLUSIONS:

Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled.

Global control of human ES cell differentiation via circRNAs derived from lncRNAs refutes neo-Darwinian gene-centric pseudoscientific nonsense. The level of control comes as no surprise to serious scientists who start with the energy-dependent creation of microRNAs and link the energy to the RNA-mediated creation from genome assembly to the creation of all cell types.

The global control-based refutation is merely one more example of pattern recognition.

See: Three invariant Hi-C interaction patterns: applications to genome assembly

We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.

Schrödinger suggested that genome assembly was energy-dependent in What is Life? (1944)

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

See also: What is life when it is not protected from virus driven entropy (video)

See also: Rotavirus-encoded virus-like small RNA triggers autophagy by targeting IGF1R via the PI3K/Akt/mTOR pathway

Examining virus-host cell interaction is important for elucidating mechanisms of virus proliferation in host cells. Viruses can create an environment that promotes their survival and self-proliferation by encoding miRNAs or miRNA-like molecules that target various host cell.

See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

…fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

See also: Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

See also: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses. When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets.

The energy-dependent fine-tuning of the base-pair stability in plants prevents the emergence of rotaviruses via multiple interspecies re-assortment events linked to healthy longevity in post-vaccination era South Korea.

See for comparison: Engineered virus has artificial amino acid allowing it to serve as a vaccine

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus. In their paper published in the journal Science, the team outlines the means by which they modified an influenza virus causing it to incite an immune response without a risk of infection.

Scientific creationists in South Korea have showed that the Chinese cannot protect themselves from a viral apocalypse via vaccinations. The viruses adapt too quickly.

Knowing that also allows the scientific creationists to create a virus that damages the DNA of specific human populations who are less well-adapted to their food energy-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niches.

Would you threaten nuclear war after you learn that the population of your country could be decimated by a genetically engineered virus produced in a neighboring country. Or, would you denuclearize and de-escalate the tensions as soon as you learned that all niche construction is food energy-dependent and that the pheromone-controlled physiology of reproduction biophysically constrains viral latency.

That fact cannot be placed back into the context of atheism or communism. It is a neo-Darwinian theory killer and is the most likely reason for denuclearization in a reasonable world.

The facts about biophysically constrained viral latency and energy-dependent life will be discussed during Schrödinger at 75 – The Future of Biology – September 2018

See for comparison: Organ-specific metastases obtained by culturing colorectal cancer cells on tissue-specific decellularized scaffolds

…lung and liver decellularized scaffolds retained their tissue-specific tropism when injected in mice.

Reported as: Scientists create better laboratory tools to study cancer’s spread

The hypothesis is this is caused by both ‘seed and soil’ – that the cancer cells have something in them that drive them to a particular organ, and the soil has to be right for them to grow. Most of the focus has been on studying the cancer cell, or the seed, and not as closely looking at the soil, which is the organs that they go to. Our models will help us understand to better understand the conditions of the soil that help promote cancer metastasis.

The use of Schrödinger’s sunlight-to-soil metaphor of degraded organic matter and biophysically constrained viral latency is not likely to be a coincidence. It also appears in the context of the energy-dependent weekend resurrection of the bacterial flagellum and in the context of the weekend Resurrection of Christ.

See also:  Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

See also:  Thou fool, that which thou sowest is not quickened, except it die:”

See also: Science, state, and spirituality: Stories of four creationists in South Korea

Scientific creationism in South Korea supposedly began with the support of the US government in their attempt to fight against communism and atheism. Pseudoscientists have not linked energy-dependent RNA-mediated biophysically constrained viral latency to all healthy longevity in the context of Communism and atheism.

For comparison, all serious scientists who understand the role that the creation of energy plays in the creation of supercoiled DNA have won the war against communism by combating evolution to fight disease.

All disease has been linked to the virus-driven energy theft that causes the degradation of messenger RNA, which has been linked to all pathology.

The energy-dependent creation of microRNAs has been linked from the creation of the innate immune system to all biophysically constrained behaviors via what is known about how the physiology of pheromone-controlled reproduction must be linked from soil bacteria to the growth of seeds and all food energy-dependent life on Earth.

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.
 

5th-6th Sept 2018 Dublin, Ireland

Let there be anti-entropic virucidal light

Summary: This is a lie!

…theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

Fuelling the future

In his short story ‘Let There Be Light’, the science-fiction author Robert A Heinlein introduced the energy source that would power his Future History series of stories and novels.

In The Darwin Code, Greg Bear helped to explain how he linked biophysically constrained light energy to the creation of a superior human species in “Darwin’s Radio” (1999) and “Darwin’s Children” (2003).
On June 21, 2017, Philip C. Ball ignored the science fiction and all facts that link the quantized energy of sunlight to biophysically constrained viral latency.
See: Quantum common sense

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

His pseudoscientific nonsense led me to ridicule him on June 24, 2017.
See:

See for comparison: Genesis 1:3

And God said, “Let there be light,” and there was light.

For a historical perspective on the creation of anti-entropic virucidal light see Schrodinger’s claims in “What is LIfe?” (1944),

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

See for comparison: Ecological and evolutionary consequences of viral plasticity 3/27/18

For bacteriophages, this host-viral performance link has been characterized empirically and with intracellular theories. Such theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

My comment on the preprint:

The “importance of viral plasticity to unravel host-phage interactions” has been modeled in the context of everything known about the creation of anti-entropic virucidal light (e.g., ultraviolet light), and how sunlight is linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA and fixation of RNA-mediated amino acid substitutions that biophysically constrain viral latency in all cell types of all living genera.

A google search for “virus-driven energy theft” would be a good place to start looking for information that you appear to have missed in its entirety.

See also, for example: Virus-mediated archaeal hecatomb in the deep seafloor http://advances.sciencemag.org/content/2/10/e1600492.full

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

See for comparison: Riding the Evolution Paradigm Shift With Eugene Koonin May 7, 2015

…the new understanding of evolution needs to integrate what we now know about viruses and virus-host interactions which, from my own perspective, has been absolutely one of the key factors of all evolution since the emergence of cells — well, actually even before the emergence of cells.

Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

To learn more about ecology and dismiss the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists, see:
Phase Transitions in the Assembly and Function of Human miRISC March 16, 2018

…may explain how miRISC silences mRNAs … and provide[s] experimental evidence that protein-mediated phase separation…

Probably facilitates biophysically constrained RNA-mediated achiral glycine-controlled energy processing in all jawless vertebrates.

Alternative splicing of pre-mRNA

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Psychophysical Laws and the Superorganism  (open access)

…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.

Reported on Jun 14, 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model

and again on: Mar 27, 2018 as Honeybees may unlock the secrets of how the human brain works

The study… found that superorganisms may obey the same laws as the human brain.

Kohl’s “Laws of Biology” and Darwin’s “conditions of life” can now be compared in the context of how quantized energy as information was linked to biodiversity in this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
See also for review:

Functional and evolutionary aspects of chemoreceptors (2012)
Sensory receptors—design principles revisited (2013)
Moving forward: See: Tuning Insect Odorant Receptors (in press)

Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.

Future attempts to place psychophysical laws of biology back into the context of neo-Darwinian pseudoscientific nonsense will continue to pit ridiculous theories about experience-dependent tuning of odor receptors against everything known to serious scientists about RNA-mediated biophysically constrained viral latency and supercoiled DNA.
See for comparison:
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)
Learning from Bacteria about Natural Information Processing (2009)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)

Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.

Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity.

See also: Schrödinger at 75 – The Future of Biology – September 2018
The scheduled speakers will undoubtedly link the Science Behind the Game “Cytosis” to the Science Behind the Game “Subatomic” via everything known to all serious scientists based on Schrodinger’s prescient claims in What is Life? (1944).
See also: What is life when it is not protected from virus driven entropy

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

See also: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also “Outer Membrane Vesicles” microRNA (4 of 4 from a 3/27/18 search)

How Our Other Genome Controls Our Epi-Genome (2016)

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens (2017)

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA (2017)

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections (2018)

See also: March 28, 2018 sponsored by System Biosciences
Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect
 
Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.
Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.
Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Polymaths and paradigm shifts: from Asimov to Bear (3)

Polymaths and paradigm shifts: from Asimov to Bear (2)

Teilhardism And The New Religion: A Thorough Analysis of the Teachings of Pierre Teilhard de Chardin”, p.18, TAN Books

The evolutionist thesis has become more stringently unthinkable than ever before. — Dr. Wolfgang Smith (2015).

A Chat with Information Scientist Pedro Marijuán (2017)

I’ve based my informational scheme of the cell on this thinking of “distinction on the adjacent” — where molecular recognition is the essential phenomenon over which biological complexity has been developed.

Biological complexity develops in the context of the olfactory code. Molecular recognition of food odors and pheromones biophysically constrains viral latency.

See: Fundamental principles of the olfactory code  Volume 164, February 2018, Pages 94-101 open access

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response.

Alternative splicing of microRNAs (aka pre-mRNAs) are required for a behavior response.

The splicing code  Volume 164, February 2018, Pages 39-48

…the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Algorithms define nothing. The availability of quantized energy as information must be linked to biophysically constrained viral latency and all biologically based cause and effect.

What is code biology?  Volume 164, February 2018, Pages 1-10

The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes.

New codes do not automagically occur. The new codes are energy-dependent and RNA-mediated in the context of the fixation of amino acid substitutions that differentiate the cell types of all living genera.

On universal coding events in protein biogenesis  Volume 164, February 2018, Pages 16-25

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases…

The energy-dependent creation of the tRNA synthetases links hydrogen-atom transfer in DNA base pairs in solution to all energy-dependent biodiversity.

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow  Volume 164, February 2018, Pages 26-38

An important issue related to code biology concerns the cell’s informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows.

Quantized energy is the information that flows through every cell type in all prokaryotes.

Causation, constructors and codes  Volume 164, February 2018, Pages 121-127

A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The diverse range of processes starts with the creation of energy-dependent enzyme action. The anti-entropic virucidal energy of sunlight was first linked to the creation of all biodiversity on Earth in 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)

If you think you can link anything except sunlight to all biodiversity on Earth, see: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
If you know that serious scientists do not link viruses to the evolution of anything except pathology, see:
Schrödinger at 75 – The Future of Biology – September 2018
The future of biology will not be left in the hands of biologically uninformed theorists.

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)

Summary: Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
A whirling plane of satellite galaxies around Centaurus A challenges cold dark matter cosmology Feb 2, 2018
Reported as:

This is inconsistent with more than 99% of comparable galaxies in simulations. Centaurus A, the Milky Way, and Andromeda all have highly statistically unlikely satellite systems. This observational evidence suggests that something is wrong with standard cosmological simulations.Science, this issue p. 534; see also p. 520

See also: Synchronized Galactic Orbit Challenges Our Best Theory of How the Universe Works Feb 1, 2018
Thanks to Dan Winter for his comment.

“… kind of funny when they fail to recognize a simple picture of phase conjugate (opposing cones) doing ‘4 wave mixing’ – which is how gravity is stabilized- AND emerges into self organization (negentropy)-those who are basically clueless to why objects fall to the ground- have no hope of understanding that the phase conjugate cause of gravity- (www.fractalfield.com/conjugategravity ) is ITSELF the path out of the entropy (belief in inevitable chaos) those fatalists try to infect us with…”

See also: A measurement of the z = 0 UV background from Hα fluorescence

This value is consistent with transmission statistics of the Lyα forest and with recent models of a UVB that is dominated by quasars.

Reported as: Universe’s ultraviolet background could provide clues about missing galaxies

Simulations show that there should be more small galaxies in the Universe, but UV radiation essentially stopped them from developing by depriving them of the gas they need to form stars.

Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
Serious scientists are beginning to wonder when pseudoscientists and all science journalists will report findings in the context of top-down causation and energy-dependent constraints. Thankfully, we are about to see constraints placed on the amount of pseudoscientific nonsense reported.
See for examples: 
Co-author, John E. Walker is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy

Living cells need fuel in the form of adenosine triphosphate, or ATP, to stay alive. This fuel is generated by a molecular machine made of two motors joined by a rotor. One generates rotation by using energy provided by oxidative metabolism or photosynthesis; the other uses energy transmitted by the rotor to make ATP molecules from its building blocks, adenosine diphosphate, or ADP, and inorganic phosphate. The structure has been determined of a fungal machine, isolated from its cellular power stations, the mitochondria, where the machine operates. It provides unsuspected details of the blueprint of the machine and how it works. The working principles of the fungal machine apply to similar machines in all species.

Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Mitochondria generate the cellular fuel ATP to sustain complex life. Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM). Disruption of the IMM, dissipation of the pmf, and cell death occur if the concentration of calcium ions inside mitochondria is sufficiently elevated to open a pore in the IMM. The identity of the pore is disputed. One proposal is that the pore is in the enzyme that makes ATP. Here, we show that proteins in the enzyme’s peripheral stalk are not involved in the formation or regulation of the pore.

Co-author, Susumu Tonegawa is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

Tagging activated neurons with light

Two new protein tools translate neuronal activity into gene expression during a light-defined time window.

Co-author,Ada E. Yonath is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

…we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.

Co-author, John O’Keefe is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The honeycomb maze provides a novel test to study hippocampal-dependent spatial navigation

Rats learn rapidly and their choices are influenced by three factors: the angle between the two choice platforms, the distance from the goal, and the angle between the correct platform and the direction of the goal. Rats with hippocampal damage are impaired in learning and their performance is affected by all three factors.

Co-author, Linda Buck is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Feedback loops link odor and pheromone signaling with reproduction

These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

The levels of complexity include everything known to serious scientists about energy-dependent niche construction and changes in the fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all species.
See for example: Hypothalamic microRNAs flip the switch for fertility (2017); The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014); and the section on molecular epigenetics from our 1996 Hormones and Behavior review: 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.

See for contrasting ignorance:Universal Alternative Splicing of Noncoding Exons (2018)

We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

See also: (Co-author, Linda Partridge is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018)
Drosophila as a model for ageing

Drosophila melanogaster has been a key model in developing our current understanding of the molecular mechanisms of ageing. Of particular note is its role in establishing the evolutionary conservation of reduced insulin and IGF-1-like signaling in promoting healthy ageing.

Sense and antisense RNA are not toxic in Drosophila models of C9orf72-associated ALS/FTD

We confirmed that these RNA foci are capable of sequestering endogenous Drosophila RNA-binding proteins, and that the production of dipeptide proteins (poly-glycine-proline, and poly-glycine-arginine) is suppressed in our models. We find that neither cytoplasmic nor nuclear sense or antisense RNA are toxic when expressed in adult Drosophila neurons, suggesting they have a limited role in disease pathogenesis.

Schrödinger (1944) “What is LIfe?”  placed energy-dependent biophysical constraints on viral latency into the context of light-activated endogenous substrates and ecological adaptations via the physiology of reproduction in species from soil microbes to humans.

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: Mutation-Driven Evolution (2013) and my refutation of that pseudoscientific nonsense in Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day.
See also for a brief video review: “What is life when it is not protected from virus driven entropy”

 

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Reporting new scientific truths is not allowed in the USA (2)

Summary: Genetic mutations do not drive evolution.  Energy-dependent RNA-mediated fixation of amino acid substitutions links the physiology of reproduction to biophysically constrained viral latency.
With minimal effort, you can peruse the science news each day to see how many pseudoscientists report their findings outside the context of food energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.
See for example:
Type 2 diabetes has hepatic origins

The researchers are now working on identifying the endogenous ligand produced by the body, or on developing molecules that could mimic its function.

Clearly, they are aware of the fact that they must link food energy to the endogenous substrate without claiming that gene activation and the creation of the protein automagically occur.
Diabetes, obesity behind 800,000 cancers worldwide: study

“Our study shows that diabetes—either on its own or combined with being overweight—is responsible for hundreds of thousands of cancer cases each year across the world.”

Who did not know that?
New study finds mycobacteria can sense presence of proteins that cause disease

The transcription factor regulates the levels of the protein cargo transported by the machinery. When the bacteria sense the machinery is absent, the levels of the protein substrates are reduced.

Fat distribution in women and men provides clues to heart attack risk

“We hypothesized that there are gender-based differences in body composition and ectopic fat depots and that these could be associated with gender-specific risk profiles for diseases like diabetes, heart disease and stroke,” said lead author Miriam A. Bredella, M.D., radiologist at Massachusetts General Hospital and associate professor of radiology at Harvard Medical School in Boston.

Sex-differences in cell types link the food energy-dependent pheromone-controlled physiology of reproduction to RNA-mediated cell type stability in all living genera.
Women may be more vulnerable to concussions because of ‘leaner’ nerve fibers

The paper shows us that there is a fundamental, anatomical difference between male and female axons,” Smith said. “In the male axon, there are a great number of microtubules, which make the entire structure stronger, whereas in female axons, it’s more of a leaner type of architecture, so it’s not as strong.

This representation of energy-dependent RNA-mediated cell type differentiation is sexist. If researchers claimed there were racial differences in biophysically constrained cell type differentiation, the claim would be racist.

That’s the problem that all pseudoscientists have with cryo-EM. It makes everything that will be reported in the context of energy-dependent links from electrons to ecosystems appear to be racist in the context of A Civic Biology: Presented in Problems (New York, 1914)

Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

Exploratory whole-exome analysis revealed higher expression of humanin-like 8 (MTRNR2L8, or HN8) in both suicide and depression (Figure 1, Supplementary Table 2). MTRNR2L8 is an isoform of the humanin gene (HN) (), a newly discovered mitochondrial-derived 24 amino acid peptide (), which is coded by nuclear DNA.

See also:

These effects appear to be driven primarily by depression, with the exception of genes involved in ‘DNA-dependent ATPase activity’, which appear to be greater in suicide but not depression. Results suggest cortical gene expression related to microglial, endothelial and glial cell functions may contribute toward or be altered in MDD and suicide, and identify the putative genes and pathways which may play a functional role in these disorders.

This claim makes it obvious that the researchers do not know the difference between an epigenetic effect on hormones and the affect of hormones on behavior. That explains their failure to link energy-dependent epigenetic effects from ATPase activity to changes in the microRNA/messenger RNA balance. That means they cannot link RNA-mediated differences in the cell types that protect organized genomes from the virus-driven degradation of messenger RNA to mutations and all pathology.

Heat, Hydrogen, and Togas

Ther­mo­to­gae are strict an­aero­bes and gram ne­ga­ti­ve. Their pep­ti­do­gly­can is uni­que in hav­ing as much D-ly­sine as the usu­al L-ly­sine. And, no LPS (or, at least, no LPS-ma­king en­zym­es), de­spi­te be­ing gram-ne­ga­ti­ve.

The stability of all organized genomes is energy-dependent and biophysically constrained by the fixation of amino acid substitutions in organized genomes. The amount of D-ly­sine compared to the amount of L-ly­sine links the dynamic control of chirality to the quantized energy-dependent creation of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.

 

The fact that hydrogen-atom transfer in DNA base pairs in solution links quantized energy as information from the creation of sunlight to the quality of RNA, which must be linked to energy-dependent DNA repair, seems to have escaped the attention of theorists.

Chemists reveal one mechanism of dihydrogen production by nitrogenase (with my emphasis)

There are 2 types of hydrogens in the catalytic cofactor (called FeMo-co): one located in a bridging position where it binds to two iron atoms (a bridging hydride), and one on a nearby sulfur atom ligands (basically a protonated sulfur atom: S-H). It turns out that during H2 evolution, the latter is the active partner. The S-H bond breaks and the resulting H+ moves toward the bridging hydride and protonates it forming H2: The calculations provide an explanation of the experimental observation that only one hydrogen is “active,” while the other is a mere spectator waiting for the arrival of its partner.
 

Can anyone help to link the calculations to the evolution of the two types of hydrogens in the context of Feynman’s claims about food energy and human idiocy?

A correspondent wrote:

Interesting chirality issues, however I know of no biological system where light directly changes polymer helicity, and this paper is not a biological system. Vines can change their macroscopic helicity, incredibly, just by single amino acid substitutions in different cytoskeltal monomer proteins.

Thanks. A single amino acid substitution at position 6 of the GnRH decapeptide in all vertebrates links the sense of smell in bacteria to the pheromone-controlled physiology of reproduction and all biophysically constrained biodiversity via achiral glycine. 

See also: Photoinduced charge transfer occurs naturally in DNA
Scientists identify the segmentation and consolidation mechanism of long-term memories

According to the research, published in the scientific journal Current Biology, the brain identifies context changes as “frontiers” in the flow of our experience and uses them to fragment the course of events into small units of memory that can be stored long-term. The study shows that this process takes place during the identification of a boundary event thanks to the rapid reactivation of the flow of information that precedes it.

The flow of information is energy-dependent and serious scientists have link the energy-dependent changes from RNA-methylation to RNA-directed DNA methylation and all biodiversity via the pheromone-controlled physiology of reproduction.
The article does not mention RNA-methylation, which means it is a compilation of pseudoscientific nonsense.
See for comparison: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).

When physics gives evolution a leg up by breaking one

Genetic mutation may drive evolution, but not all by itself.

Genetic mutations do not drive evolution.  Energy-dependent RNA-mediated fixation of amino acid substitutions links the physiology of reproduction to biophysically constrained viral latency.
See Schrodinger (1944): and link the anti-entropic virucidal energy of sunlight to all biodiversity via the creation of RNA and the physiology of pheromone-controlled reproduction.

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 the reprint edition with the forward by Roger Penrose.
“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)
‘Mind’s eye blink’ proves ‘paying attention’ is not just a figure of speech

Mind’s eye blink is closely related to “attentional blink” that has been studied by Cornelius Vanderbilt Professor of Psychology David Zald and Professor of Psychology René Marois. Attentional blink is a phenomenon that occurs when a person is presented with a rapid series of images. If the spacing between two images is too short, the observer doesn’t detect the second image. In 2005, Zald determined that the time of temporary blindness following violent or erotic images was significantly longer than it is for emotionally neutral images.

Olfaction spontaneously highlights visual saliency map
Fear-related chemosignals modulate recognition of fear in ambiguous facial expressions
Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
 

Light-induced-conformer-intercoversion-of-hydrogen-bond

Eating electrons and excreting degraded energy

Summary: The tenacity of energy-dependent life extends from quantum physics to quantum souls via what is known about the birds and the bees (and bacteria). Simply put, if they don’t eat, they die.

Neuroscience—and the new weapons of the mind

Dietary modification also shows increasing promise for the exogenous manipulation of neurotransmitter signaling. Recent research into the effects on brain chemistry of the microbiome—the bacterial flora located in the human gut traditionally thought to aid in digestion—shows significant potential for covert alterations of neurotransmission.

Energy-dependent changes in electrons to ecosystems link the covert alterations of neurotransmission to behavior.

See Schrodinger (1944)

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

If you do not know where nuclear energy comes from or do not know how it got into the mitochondria of every cell of every eukaryote ever created See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

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

The tenacity of energy-dependent life extends from quantum physics to quantum souls via what is known about the birds and the bees (and bacteria). Simply put, if they don’t eat, they die.  If they eat right, their pheromone-controlled physiology of reproduction can be linked to survival of every species from archaea to humans. In that context, there is no room for any nonsense about mutations and evolution.

See: What We Can Learn From the Quantum Calculations of Birds and Bacteria

…green sulphur bacteria can synthesize sugar from light by biologically controlling quantum mechanical effects at temperatures up to 80 degrees Fahrenheit.

The physiology of pheromone-controlled reproduction biophysically constrains the virus-driven degradation of messenger RNA that links the facts about vibrations and olfaction from quantum physics to all biologically-based biodiversity on Earth.

In his 1944 book, “What is Life?,” Schrödinger focused on how organisms, such as fruit flies, employ quantum mechanical effects to combat entropy by producing order from disorder.
‘Humans have not yet figured out how it is that nature can stabilize a coherent electronic quantum state in such complex systems for such long periods of time.’

Luca Turin figured that out more than 2 decades ago.
See: The vibrational theory of olfaction for the win
The link from bacteria to our visual perception of energy and mass via food odors and pheromones was established earlier this year by Wen Zhou’s group in China.
Olfaction Warps Visual Time Perception
They placed everything known to serious scientists into the context of the space-time continuum and refuted every aspect of neo-Darwinian pseudoscientific nonsense at the same time they refuted every aspect of “Big Bang” cosmology. Serious scientists start with claims about the creation of light.  They link top-down causation to:

 Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid

vibrational energy deposited in the system is also transferred via inter- and intramolecular hydrogen bonds

Luca Turin’s group inadvertently linked everything known about quantum physics to quantum souls with facts about vibrational energy that links intermolecular bonds to intramolecular bonds. He placed the facts into the context of what is known about food odors, pheromones, and hydrogen-atom transfer in DNA base pairs in solution, and RNA interference.
RNA interference has since been linked to our receptor-mediated structure and function of supercoiled DNA and to our behavior via inhalation.
Quark Pharmaceuticals, Inc. to Present Preclinical Efficacy Data on Inhaled siRNA Co-Developed with Biocon for Prevention of Primary Graft Dysfunction following Lung Transplantation at the 6th Annual RNAi China Conference

The presentation will summarize the preclinical efficacy data for inhaled small interfering RNA (siRNA) against an undisclosed target gene on preventing primary graft dysfunction and acute rejection in an animal model of lung transplantation.

For example, if you cannot inhale and exhale, your body will reject energy-dependent RNA-mediated life.

For God and Country

Life and death via chemical effects on photosynthesis

Summay: “…chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.”
Serious scientists linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)


For evidence of the link from the anti-entropic virucidal energy of sunlight to all biodiversity, see also: 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri

Sublethal atrazine concentrations induced a general inhibition on growth, photosynthesis, and dark respiration in the green alga Chlorella kessleri….. Progressive reduction in protein synthesis was associated with increasing herbicide concentration at all experimental periods. The herbicide had preferential effect on the associated fatty acid composition of total and phospholipids. After 24 and 48 hr the herbicide stimulated fatty acids synthesis at concentrations where photosynthesis was inhibited. Meanwhile, stearic and miristic acids disappeared at 15 μM after 24 hr and the total polyunsaturated fatty acids were not affected after 48 hr. Fatty acid synthesis was sensitive to treatment at 72 hr by 5 and 10 μM atrazine, whereas the total saturated fatty acids were completely inhibited.

Sublethal effects of  chemicals on protein biosynthesis and degradation have been linked to all pathology via the virus-driven degradation of messenger RNA, which links changes in the microRNA/messenger RNA balance to mutations and all pathology. For example, this is what must happen to link the sun’s anti-entropic virucidal energy from electrons to ecosystems via the chemistry and physiology of pheromone-controlled reproduction in all living genera.

A dietary difference in nematodes links their chemistry of metabolism from what they eat to the pheromone-controlled physiology of reproduction in C. elegans and the ecological adaptations manifested in P. pacificus, a predatory nematode with teeth.
See other information on biophysically constrained biologically based cause and effect in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

The epigenetic effects of nutrients on evolved differences in the diet and starch digestion of dogs and wolves (Axelsson et al., ) were detailed at the same time differences in the socialization of these subspecies were attributed to explorations involving only chemosensory input in 3 to 4-week-old wolf pups. For comparison, differences in starch digestion and exploration involving multisensory input in dogs begin a mere 2 weeks later (Lord, ). The differences in nutrient-dependent pheromone-controlled socialization, however, extend across a life-time of more aggressive behavior in wolves that have not been domesticated because less digested starch from their diet genetically predisposes infants to first respond to olfactory/pheromonal cues as they initially explore their postnatal environment.

See also: Dogs Recognize Themselves in Test Based on Smell, Not Sight

But, she said, her test and the mirror tests “all show that there’s this selective sensory investigation of something that comes from yourself, but is changed.”

The link from a light-induced change in an endogenous substrate — that comes from yourself — to the physiology of reproduction is changed by the pheromone-controlled physiology of reproduction, which is linked to all biodiversity.
That fact and facts about intelligence in different species started to become clear when Schrodinger (1944) 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.) (pp. 73 and 74)

Perfect clarity was achieved among all intelligent serious scientists when McEwen et al, (1964) wrote; 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.

Nothing in life happens outside the context of the ATP-dependent creation of RNA.
Decades later, Roger Penrose wrote:

“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: Olfaction Warps Visual Time Perception
The authors linked the sense of smell in bacteria from the physiology of pheromone-controlled reproduction in all living genera to our visual perception of energy and mass in the context of the space time continuum.
The fact that food odors and pheromones biophysically constrain cell type differentiation in mammals was first placed into the context of [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994) in Russian
Abstract excerpt (in English)

The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: [Cytogenetic effect of volatile components of urine of sexually mature animals on bone marrow cells of young female house mice Mus musculus L] (1996) in Russian

Effects of volatile components of the urine (VCU) of mature male and female CBA/LacStoRap mice on proliferating bone marrow cells in young females of the same line were analyzed.

In 2005,  a 2004 Nobel Laureate and her co-authors caught up to what researchers in Russia had already been claiming for 20 years. See: Feedback loops link odor and pheromone signaling with reproduction
See also: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain (2014) with my emphasis

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system. Various psychoemotional states of the human nervous system can, in turn, disrupt the integrity of the chromosomal apparatus of target cells, for instance lymphocytes [41, 42]. Therefore, studies on the oppositely directional modulation of the mutagenic consequences of stress in rodents with the use of specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems (2015)

Genetic monitoring of the environment is an important component in the analysis of the status of the biosystems. Its efficiency depends on the correct choice of (a) natural bioindicator species; (b) appropriate signs reflecting the state of the environment; and (c) appropriate statistical analysis. The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

The nutrient energy-dependent pheromone-controlled ecological adaptations in all invertebrates and vertebrates were reviewed in the context of: 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

See for comparison 1): Riding the Evolution Paradigm Shift With Eugene Koonin

“[T]he entire ideology of personalized medicine should be taken with many grains of salt. It’s not useless, it’s useful to sequence thousands of genomes. It’s useful to sequence everyone’s genome. It’s useful and desirable — yet, it’s wrong and to some degree dangerous to think that, by peering into the sequence of the A, G, T, and Cs in your genome, your family doctor is going to tell you how to treat all your conditions and what conditions you are going to develop, and which ones you are not going to develop, and so on.” — Eugene Koonin

See also for comparison 2): 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…” — Eugene Koonin

The entire ideology of personalized medicine is based on what is known about how the anti-entropic virucidal energy of sunlight must be linked from endogenous RNA interference and foraging behavior to the physiology of biophysically constrained pheromone-controlled reproduction in species from microbes to humans. See this 7 minute representation from my Precision Medicine virtual conference presentation. Energy as information and constrained endogenous RNA interference (2017)
Do not be surprised if you cannot track the historical record of scientific advances in nutritional epigenetics from 1994 Effect of atrazine herbicide on growth, photosynthesis, protein synthesis, and fatty acid composition in the unicellular green alga Chlorella kessleri to the current representations of top-down causation and energy-dependent biophysically constrained biologically-based cause and effect. There are many pseudoscientists who will do everything possible to prevent you from learning that their ridiculous theories have never been supported by experimental evidence.
See for example: 7/25/13
Jay R. Feierman: “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.”
See also: One crank dies, another rises to take his place by PZ Myers

I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn’t get it the first time, just say the same thing again, twice. A kind of sneering anger that people don’t understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.
Behold James Vaughn Kohl.

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

Ecological adaptations are food energy-dependent and biophysically constrained in the context of biologically based chromosomal inheritance via the pheromone-controlled physiology of reproduction. There is only one model for that.
It’s my model:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See for comparison: Interactome analysis reveals ZNF804A, a schizophrenia risk gene, as a novel component of protein translational machinery critical for embryonic neurodevelopment
Reported as: Gene associated with schizophrenia risk regulates neurodevelopment

A gene associated with the risk of schizophrenia regulates critical components of early brain development, according to a new study led by researchers from Penn State University. The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.

Gene regulation is energy-dependent and RNA-mediated. That fact is twisted into this misrepresentation: “The gene is involved in the translation of proteins from RNA and in the proliferation and migration of neurons in the brain.”

What they claim, in the most twisted way possible, is that the energy-dependent RNA-mediated translation of proteins must be linked to ecological adaptations via the proliferation and migration of neurons in the brain.

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

Sunlight, phytochemicals, microRNAs and cancer

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Summary: If the creation of the uranium isotopes was not biophysically constrained in the context of hydrogen-atom transfer in DNA base pairs in solution, the sun’s anti-entropic virucidal energy would be a less effective treatment for cancer than radiation therapy.
The link from the anti-entropic virucidal energy of sunlight to the de novo creation of microRNAs and prevention of all pathology will become clearer each day until the cell biology game “Cytosis” is available for play by anyone ten years old or older.
Jay R. Feierman continues his attempts to obfuscate that clarity. He failed to post three comments to the Human Ethology Yahoo Group and sent me three private messages: All three claim: “You can only post one message a day as you keep saying the same thing over and over again.”
This research was published yesterday.
Role of phytochemicals in the modulation of miRNA expression in cancer (published in Food & function)

…phytochemicals play an important role in the modulation of miRNA expression, which is related to changes in oncogenes, tumour suppressors, and cancer-related protein expression. Hence, phytonutrients can suppress tumour development, prevent metastasis, reverse the EMT, and improve drug sensitivity via the modulation of miRNA expression.

The research supports what I have been saying since the time I learned that Schrodinger (1944) stated it clearly:

“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.)”

People like Feierman must prevent others from learning facts about the anti-entropic virucidal energy of sunlight. The facts are neo-Darwinian evolutionary theory killers becasue Darwin’s claims began with food energy-dependent “conditions of life.”
See for comparison:
Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again. —In human-ethology@yahoogroups.com, he wrote :

Re: This claim is above my level of expertise to refute. — Jay R. Feierman

My response: It is unfortunate that the comment by James Gray about Jay’s understanding cannot be found in this series, and that no one seems interested in discussion of facts that attest to Jay’s claim.

Others who cannot refute the claim that “DNA Begins As a Quantum Wave” may continue to link the anti-entropic virucidal energy of sunlight to mutations, natural selection, and evolution despite my history of published works that led Jay to claim:

7/26/13
“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.” 

We may never know why others, like Jay, would make claims about random mutations without knowing the origin of DNA, which links energy as information to the biophysically constrained physiology of reproduction in my model of all biologically-based diversity.
Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again.

He blocked this comment:

Journal article abstract excerpt: “…isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis.”

Food energy-dependent RNA-mediated amino acid substitutions link ecological variation to ecological adaptations in species from microbes to humans in the context of the physiology of pheromone-controlled reproduction. That fact led to a counter-claim by Jay R. Feierman, and he has since limited all discussion of my model.

7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution. 

See for comparison:Nutrient-dependent/pheromone-controlled adaptive evolution: a model

MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.]

See for comparison: 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.”

My attempts to discuss
facts about food energy-dependent RNA-mediated cell type differentiation have consistently been placed into the context of attempts to discuss beliefs by a moderator who has consistently supported claims that link random mutations from natural selection to the evolution of biodiversity.

Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again.
He blocked this comment:

Genes Before DNA

How geneticists around the world struggled to bring the foundation of life’s building blocks to light.

Excerpt: “Information” was about to enter science, but had not done so when Schrödinger gave his lectures. Without that conception of the content of the code, Schrödinger’s insight was merely part of the zeitgeist, a hint of what was to come rather than a breakthrough that shaped all subsequent thinking.

My comment: In 1944, Schrödinger stated: Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

The fact that quantized energy is information seems to have escaped the grasp of many theorists, but virtually all the medical professionals I have encountered realize that organisms die if they do not find some form of quantized energy as information to eat.

Addendum: Arguably, Feierman is right. I do repeat myself. He forces me to repeatedly present my claims about energy as information by ignoring them. Instead, he makes ridiculous claims about mutations, natural selection, and evolution. That is what all pseudoscientists do.
USDA Emails: Don’t Use “Climate Change”

The news report suggested these were political moves to fall in line with the newly installed Trump administration.

The truth is that these moves are consistent with the claims that Schrodinger (1944) made in “What is Life” and the claims made in Role of phytochemicals in the modulation of miRNA expression in cancer.
Weather extremes link changes in the microRNA/messenger RNA balance in soil bacteria to healthy longevity or from the virus-driven degradation of messenger RNA to all pathology. Climate change is comparatively ambiguous, since it does not link the anti-entropic virucidal energy of sunlight to healthy longevity.
The biophysically constrained energy of sunlight also helps to reduce greenhouse gases and to sequester carbon, which links the de novo creation of energy as information to all life on Earth by building organic material in soil.  For example, sunlight has been linked from the metabolism of bacteria to the biophysically constrained creation of uranium isotopes.
See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits
If the creation of the isotopes was not biophysically constrained in the context of hydrogen-atom transfer in DNA base pairs in solution, the sun’s anti-entropic virucidal energy would be a less effective treatment for cancer than radiation therapy.