5th-6th Sept 2018 Dublin, Ireland

Less evolvable RNA-mediated ecological adaptations

No experimental evidence of biophysically constrained RNA-mediated cell type differentiation supports the claim about “…the evolutionary plasticity of the regulatory regions involved in transcriptional regulation…” The overwhelming systems complexity of energy-dependent RNA-mediated cause and effect can no longer be placed into the context of the pseudoscientific nonsense touted by theorists. Watch Andrea Wagner’s group try to escape from the claims made by losers.
But first see: Kalevi Kull: Censorship & Royal Society Evo Event

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

RNA-mediated gene regulation is less evolvable than transcriptional regulation

…nucleic acid binding sites of RNA-mediated gene regulation are less evolvable than those of transcriptional regulation. This observation is consistent with the high levels of mRNA target conservation for RBPs (10, 82, 83) and the evolutionary plasticity of the regulatory regions involved in transcriptional regulation (84⇓–86) as well as their role in the evolution of myriad adaptations and innovations (11, 87, 88).

It is obvious to anyone who has followed the works of Andreas Wagner that his group has reached an impasse.
See: Evolution of Viral Proteins Originated De Novo by Overprinting (2012)

We found that young de novo genes have a different codon usage from the rest of the genome.

There is no such thing as a de novo gene.
See: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

I collectively refer to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality links what organisms eat to their pheromone-controlled physiology of reproduction in species from microbes to humans. Ecological variation is linked to ecological adaptations only in the context of biophysically constrained viral latency. That fact is now perfectly clear in the context of more than 71,000 indexed published works that link the energy-dependent creation of ATP synthase to the creation of ATP and the creation of RNA in the context of McEwen et al., (1964) and Frohlich (1968).
People like Andreas Wagner are stuck with their ridiculous claims about evolution, when all serious scientists know that only the hecatombic evolution of virus-driven pathology is possible. Healthy longevity requires food energy-dependent biophysically constrained polycombic ecological adaptations. The metabolism of food to species-specific pheromones links RNA-mediated autophagy to all biodiversity. The virus-driven degradation of messenger RNA is linked to all pathology.
Andreas Wagner reversed every aspect of what is known in: Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014)

…he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

See for comparison: Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Andreas Wagner, and others like him, will probably continue to misrepresent what is known about how the creation of sunlight must be linked to food energy-dependent pheromone-controlled reproduction by natural selection for codon optimality. But the facts about how energy must be linked to increasing organismal complexity are not going to change.
See: Schrödinger at 75 – The Future of Biology – September 2018
and/or 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!

 
 
 

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.
5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry (2)

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

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).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

5th-6th Sept 2018 Dublin, Ireland

Light-controlled cell biology (revisited)

See Sci-Bay Scholar for citations and downloads of more than 3300 published works that link viruses to microRNAs
Summary: …either the organized genomes of all cell types use the energy source, or viruses use the biophysically constrained energy of the cell types. No extant species can be used as an example of how the virus-driven theft of quantized energy can be linked from natural selection to the evolution of a new species.
See also, with my emphasis:

Light Offers New Way to Control Cell Biology (3/16/17)

…the power of light-sensitive proteins is that they can be used to study the inner workings of any living cell.

Archaea:

Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both.

George Church At 15:10

…the cyanobacteria turn out that they fix light ah as well or better than land plants…

From the transcript:

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

The difference between the fixation of light and the fixation of carbon is that (see above)  no known species of archaea does both. That fact supports the claim that the ability to fix light is an ecological adaptation that links the quantized energy of sunlight to all biophysically constrained biodiversity in the context of energy-dependent viral latency.

Archaea that do not use sunlight as their energy source probably become L-forms in the context of the virus-driven degradation of their messenger RNA, which has been linked from mutations to all pathology in the context of one-carbon metabolism. Quantized energy is the obvious link from the fixation of light to the fixation of carbon in all carbon-based life forms on Earth.

Simply put, either the organized genomes of all cell types use the energy source that fixes carbon, or the viruses use the biophysically constrained energy of the cell types. For comparison, no extant species can be used as an example of how the virus-driven theft of quantized energy can be used in the context of natural selection and evolution.

See also:L-form bacteria

The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]
 
If the claim that L-forms are an early form of life was placed into the perspective of claims by Carl Woese about the different domains of life, theorists would need to explain how the cell wall “evolved” before all life on Earth evolved from archaea to bacteria and every other species.
 

For comparison, I claim that quantized energy as information carried by light is the link from the creation of the cell wall to all epigenetically-effected biophysically constrained food energy-dependent pheromone-controlled biodiversity. However, Carl Zimmer seems to want someone to redefine “heredity” to make the definition fit back into the context of evolution outside the context of Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution

(quotes)

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

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

See also: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing

…different SNPs may be present and confer risk for inefficacy or toxicity among AAs, as well as Asians, Hispanics, or other populations.

The light energy-dependent differences in the SNPs confer the diversity of morphological and behavioral phenotypes in all living genera. The SNPs also are linked to healthy longevity or pathology via the fixation of RNA-mediated amino acid substitutions. That fact must be placed into the context of pheromone-controlled reproduction and transgenerational epigenetic inheritance. That is why Carl Zimmer wants people to think that we need a new definition of heredity.
See the book description for: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

See for comparison: 6 Bacteria with Awesome Superpowers (Excerpt)

Chemolithoautotrophic, which means they get their energy from inorganic compounds in their environment

SARCASM ALERT: If neo-Darwinian evolutionary theorists make claims about chemolithoautotrophic heredity, will you still believe them?

See also: March for Science: How Democracy Kills Expertise (3/20/17)

“People don’t care how much you know until they know how much you care.”

Until the public is convinced that scientists and journalists care about truth and society, then I fear all of our labors will be in vain.

Serious scientists care about the truth and about society. Many so-called science journalists want the efforts of people who care to be viewed in the context of their pseudoscientific nonsense about heredity via evolution.
See: Changes in the vascular system may trigger Alzheimer’s disease (3/21/17)

The plasma protein, called Factor XII, is part of a cascade of enzymes that induces blood coagulation and inflammation.

If Alzheimer’s disease evolved, you do not need to know about the energy-dependent cascade of enzymes that starts with the creation of ATP synthase. What if you had become a so-called science journalist who did not know that proteins do not create themselves? For example, that’s how energy-dependent changes in the microRNA/messenger RNA balance can be linked to all healthy longevity. You wouldn’t know that.
Virus-driven energy theft causes Alzheimer’s and all other pathology. All serious scientists know that. All pseudoscientists, atheists, and theorists do not want you to know it. For example, viruses cause antibiotic resistance.

This antibiotic will ruin you (3/18/17)

It gets worse. There is no cure. No treatment. No relief. No specialist even.

2011 Researchers to study positive genetic contributions of viruses (3/18/11)

  1. The two-year, $550,000 grant has been awarded to K. Eric Wommack…
  2. These discoveries come from the study of marine ecosystems but allow researchers to learn more about the predominant biological features of viruses overall, which can affect how human conditions – such as cancer – are diagnosed and treated. “Within some of the samples we’ve collected, we found genes critical to protein folding,” says Polson. “In many cases, protein has to be directed to fold in the proper way. Protein misfolding is a component in the cause of some diseases, so this knowledge can be very important in our understanding of viral infection processes.”

Reported as: Social selection: genetic contribution of viruses to life on earth

… science fiction author Greg Bear successfully predicted the involvement of specific viruses in speciation (read Darwin’s Radio and Darwin’s Children). This new report attests to the likelihood that the mechanisms may someday be found. Bear’s concept of viral induction of species evolution — with further consideration given after reading this article — also sheds light on differences between what most people call “natural” selection and what some people are beginning to call “social” selection. There may be no evidence of transitionary species in the fossil record because viruses elicited comparatively sudden and dramatic changes in the genotype and phenotype of extant organisms as other organisms became extinct. One of the mechanisms involved in speciation, as indicated by Bear, is likely to be pheromones that signal similarities and differences in species that occupy similar social niches. I’m now suggesting that transfer of genetic material between species — not just single genes, but large segments of genetic code – could rather suddenly result in what might at first appear to be a newly evolved organism. If ever a newly evolved organism is found, it might be a good idea to look around its neighborhood for genetic clues that provide evidence of parenthood, or of Creation.

Virus-mediated archaeal hecatomb in the deep seafloor (2015)

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 updates: Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory (2017)

While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.

Re-examination of the relationship between marine virus and microbial cell abundances (2017)

…viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales.

If you let them, researchers like these will spend millions of dollars and never learn that viral latency is biophysically constrained in the context of the sun’s anti-entropic energy and the physiology of food energy-dependent pheromone-controlled feedback loops.
See for comparison: 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.)

What is life when it is not protected from virus driven entropy (2016)

See also: MicroRNA and autophagy

Witzhany2018

Polymaths and paradigm shifts: From Asimov to Bear (5)

Summary: Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.

Renowned Physicist Stephen Hawking Dies

The comments by Neil deGrasse Tyson and Lawrence Krauss can be linked to this discussion: 2013 Isaac Asimov Memorial Debate: The Existence of Nothing and to the 2017 representation of biomolecules in On the Difference between Physics and Biology: Logical Branching and Biomolecules.
The food energy-dependent pheromone-controlled creation of the biomolecules will be discussed during Schrödinger at 75 – The Future of Biology – September 2018 after the virus-driven degradation of messenger RNA and all pathology is discussed during Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
For comparison, Stephen Hawking gained fame by collaborating with Roger Penrose and with George FR Ellis, who co-authored The Large Scale Structure of Space-Time.
In the forward to the reprint edition of What is Life?, 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? (8 August 1991)

In the cell biology game Cytosis, anyone age 10+ can learn that the creation of energy as ATP protects all organized genomes from the virus-driven degradation of messenger RNA, which all serious scientists since Schrödinger have linked from mutations to all pathology.That’s all you need to know about Roger Penrose.
George FR Ellis is the co-author of On the Difference between Physics and Biology: Logical Branching and Biomolecules. He helped to link the food energy-dependent creation of microRNAs to biophysically constrained viral latency, but is determined to undermine the works of other serious scientists with his use of the ambiguous term biomolecules.
Taken together, Stephen Hawking, Roger Penrose, and George FR Ellis have done more than most to bastardize Darwin’s claims about the need to start with food energy-dependent  “conditions of life.” Their unproven ideas from physics should never have been substituted for experimental evidence.
The evidence links the premise of the game “Subatomic” from what is known about particle physics to biophysically constrained viral latency and healthy longevity via this claim, which was made by Schrödinger.

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.)

Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.
See: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis
Reported as: Here’s How Viruses Inactivate the Immune System, Causing Cancer

“Ultimately viruses are causing these tumors to form and are further manipulating the immune system to allow tumors to keep growing,” Kuss-Duerkop says. “But these same mechanisms may be key in combating tumors with immune-based therapies or in keeping cancer from developing in the first place.”

If not for the bastardization of Darwin’s claims by theorists, Kuss-Duerkop and others like her probably would have learned that sunlight is the source of energy for the growth of food that links food energy to the pheromone-controlled physiology of reproduction in species from microbes to humans. The energy links changes in the microRNA/messenger RNA balance from virus-driven energy theft to all unnecessary suffering and premature death.The fact that Stephen Hawking suffered throughout his life with a neurodegenerative disease may be fitting in the context of his ignorance.
The 4 Scientific Lessons Stephen Hawking Never Learned

  1. We have a tendency, when we turn people into heroes, to lionize their achievements and ignore their failings, but to do so cheats humanity out of recognizing all the facets of a complicated character.
  2. May we memorialize him in the best way possible: by increasing our own knowledge and curiosity to live better lives.

Until then, see: Prominent Neuroscientist Fired by Columbia, HHMI
This is the first clear indicator of how the Trump administration will drain the academic swamp.
Jessell is the serior author of: Activity Regulates the Incidence of Heteronymous Sensory-Motor Connections

The positioning of newly born neurons is a tightly regulated process that is critical for the assembly of the nervous system. In the spinal cord, nuclear organization of motor neurons into pools is an elaborated morphogenetic feature at the basis of the wiring of spinal sensory motor circuits (Sürmeli et al., 2011, Hinckley et al., 2015, Bikoff et al., 2016). The events controlling motor neuron positioning during development have yet to be clearly defined.

The activity is food energy-dependent and RNA-mediated in the context of sensory input and the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency in species from microbes to humans.
See for example: Meet the creature that can regenerate its brain and resist cancer.(video) The superimposed electron cloud over the yin yang symbol of Chinese philosophy and medicine is a clear representation of the complexity. If neuroscientists cannot link energy-dependent changes in electrons to ecosystems in all living genera, they will be dismissed and replaced with serious scientists.
For example, the facts about regenerating the brain and resisting cancer suggests Jessell’s termination occurred due to his ongoing failure to link the virus-driven degradation of messenger RNA to loss of motor control in all neurodegenerative diseases.
See for comparison: “Blood Music” (1985) by Greg Bear, who presciently linked energy-dependent changes in the microRNA/messenger RNA balance to the creation of an advanced human species via naturally occurring biophysically constrained viral latency.
See also: Actor Steven Kearney reads excerpts from Greg Bear’s 1985 novel Blood Music.

Bear was one of the first sci-fi authors to delve deep into the possibilities of synthetic biology. In this section, a biologist named Michael Bernard is infected with a killer virus that has wiped out most of North America. The virus is made up of tiny biological computers called “noocytes,” where were intended to improve the human body — giving it routine maintenance and maximizing human potential. Instead, it wiped out most of North America.

Remember, without the food energy-dependent pheromone-controlled RNA-mediated DNA repair that biophysically constrains viral latency:
Image may contain: text

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 (2)

Polymaths and paradigm shifts: from Asimov to Bear (1)
See also: Search results for virus-driven energy theft
Summary: The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
Modifying Other’s Originality without Quote is an Act of Piracy

A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.

See for comparison: Here’s how viruses inactivate the immune system, causing cancer

It’s no new news that viruses cause cancer.

The full text of the article is free: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…

RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:

  1. 12 Sep 2010

What do proton motive force driven multidrug resistance transporters have in common?

2. 19 Jun 2010

The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids

The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.

 Philip Ball @philipcball Mar 2

This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)

See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.

See also: The legacy of Frankenstein: A series of events celebrating 200 years of Frankenstein

The origin of life

Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.

Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight  from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

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: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Abstract:

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. 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 ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to 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 for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an 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. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See for comparison: On the Difference between Physics and Biology: Logical Branching and Biomolecules

In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.

Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.

An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 2017)

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.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. 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. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

APS 2018

From photons to the proton motive force (2)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5th-6th Sept 2018 Dublin, Ireland

From photons to the proton motive force (1)

Conclusion: If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.
Fly’s Blood-Brain Barrier Has Circadian Rhythms

“the anatomic characteristics of insect and vertebrate BBB structures are quite distinct.”

The molecular mechanisms are conserved.
My comment to The Scientist:

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

The levels of complexity have since been placed into the context of how energy-dependent changes in the microRNA/messenger RNA balance link atoms to ecosystems in all living genera via feedback loops.

For instance, see: Feedback loops link odor and pheromone signaling with reproduction

When theorists fail to start with energy-dependent changes they are forced to use de Vries 1902 definition of mutation in attempts to link the virus-driven theft of quantized energy to evolution. Two forthcoming conferences will place that pseudoscientific nonsense into its proper perspective.

Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses

Schrödinger at 75 – The Future of Biology – September 2018

See also:  Here Comes Single-Cell Optogenetics

.. two-photon excitation with computer-generated holography (a way to precisely sculpt light in 3D) allow light to be focused tightly enough  to hit one cell.

OLYMPUS experiment sheds light on structure of protons

…most of the time, only one of the photons has high energy….

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

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).

Researchers who have not linked differences in the energy of photons to the proton motive force are not likely to be among those who are presenting in September: Schrödinger at 75 – The Future of Biology
See for comparison: Subatomic

Subatomic is a deck building game where players are competing to build a number of available Elements, which score them points. Each player starts with the same small deck of cards that consist of Proton, Neutron, and Electron Cards. They use these cards to build upon their current Atom (by playing these cards face-up as Subatomic Particles) in an attempt to construct one of the available Element Cards. Or players may use their hand of cards to purchase more powerful cards for later use (by playing them in combinations of face-down as energy and face-up as Subatomic Particles!) Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

If you would like to learn how to link quantized energy-dependent changes in atoms to ecosystems in all living genera via the physiology of reproduction, join others age 10+ who will be playing this game in September 2018.

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.

Ecological adaptation: a new definition of heredity (4)

Experimentally Induced Metamorphosis in Axolotl (Ambystoma mexicanum) Under Constant Diet Restructures Microbiota Accompanied by Reduced Limb Regenerative Capacity (2018)

Our results show that distinct bacterial communities inhabit individual organs of Axolotl and undergo substantial restructuring through metamorphosis.

The restructuring during metamorphosis is biophysically constrained by feedback loops that link olfaction from food odors and pheromones to the creation of enzymes in bacteria and the secretion of the vertebrate decapeptide hormone GnRH (gonadotropin releasing hormone).
See: Gonadotropin-releasing hormone agonist binding in tiger salamander nasal cavity (1993)
The authors presciently linked food odors and pheromones from epigenetic effects on feedback loops to gonadotropin-releasing hormone (GnRH) and microRNA-mediated morphological and behavioral diversity, and also to differences in the behavior of monogamous and polygamous prairie voles.
See: The prairie vole vomeronasal organ is a target for gonadotropin-releasing hormone (2001)
For comparison, Larry Young claimed that the evolution of viruses caused the differences in prairie vole behavior. He linked the virus-driven differences from three other hormones to the evolution of heterosexual love. See: Virus Evolution Amazing Documentary Full HD National Geographic Documentary 2015
Others, who are like Larry Young, have failed to link anything known to serious scientists from sensory input to energy-dependent changes in the creation of enzymes, receptors and hormones. The anti-entropic energy-dependent creation of enzymes by bacteria links the creation of receptors and hormones in vertebrates to protection of organized genomes from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
See for comparison: 2013 Isaac Asimov Memorial Debate: The Existence of Nothing

Isaac Asimov, “…perhaps, the last polymath of our civilization.”

Originally a zoology major, Asimov switched to chemistry and earned a Doctor of Philosophy degree in biochemistry in 1948. In 1977, he contracted HIV from a blood transfusion. He was president of the American Humanist Association, which suggests that his atheism led to his death via his ignorance.
For example, in 1964, Dobzhansky wrote:

“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.”

If Isaac Asimov was the last polymath of our civilization, we are doomed. Clearly his ridiculous beliefs have led to the teaching of pseudoscientific nonsense about evolution despite the claims of Schrödinger (1944) and those who will link the anti-entopic virucidal energy of sunlight from the physiology of reproduction to biophysically constrained viral latency and all biodiversity during Schrödinger at 75 – The Future of Biology – September 2018
See for comparison: How One Child’s Sickle Cell Mutation Helped Protect the World From Malaria
Once again, so-called science journalist Carl Zimmer shows that he does not know the difference between a mutation and an RNA-mediated amino acid substitution.
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

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

Hemoglobin variants alter the oxygen carrying capacity of red blood cells. They are clear indicators of how ecological variation must be linked to ecological adaptation via food energy-dependent changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
There are more than 1700 human variants. Anyone who claims that the variants are mutations should be required to link them from the transgenerational epigenetic inheritance of morphological and behavioral phenotypes in all living genera to ecologically adapted human populations.
The alternative is sexist and racist. Much more is needed than a new definition of heredity. All intelligent people must dismiss the neo-Darwinian pseudoscientific nonsense about mutation-driven evolution. Then, we can start over with accurate representations of top-down causation and biophysically constrained viral latency.
But first see: EPA’s Scott Pruitt Doesn’t Buy Evolution

Andrew Rosenberg, director of the Center for Science and Democracy at the Union of Concerned Scientists, counters that Pruitt should not act as “the nation’s pastor.”

Andrew Rosenberg should become familiar with the extant literature or play the cell biology game “Cytosis” for ages 10+. There is no excuse for his level of ignorance.
Cytosis is a board game that details what takes place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses! In the context of everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation, a new tool is now available to help theorists link cause and effect via a mathematical model.
See: VarQ: a tool for the structural analysis of Human Protein Variants. The mathematical model has replaced neo-Darwinian theories with facts about how the energy-dependent structure of functional supercoiled DNA biophysically constrains viral latency.
See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy (2013)
and Role of bacterial efflux pumps in biofilm formation
Only a few people I know would link antibiotic resistance from Escherichia coli to Acinetobacter baumannii via the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens. Until they are willing to do it in a public forum, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.
Pseudoscientists and most other theorists are still focused on mutation-driven evolution. Isaac Asimov’s “humanist” influence has prevailed across more than one generation of students who learned how to link nothing to everything from people like Neil deGrasse Tyson, Lawrence Krauss, and Carl Zimmer.