5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.


Amino acid modification FA_Epigenetics_Table1

Physicists: Desperate Acts (revisited)

Physicists: Desperate Acts
Light-induced endogenous RNA interference in bioluminescent microbes links Schrodinger’s claims in “What is LIfe?” (1944) from a light-to-chemical pathway of information exchange in all living genera via amino acid substitutions in supercoiled DNA.
All subsequent works on the evolutionary synthesis failed to link  the anti-entropic virucidal energy of sunlight to Darwin’s “conditions of life” from the claims of Schrodinger (1944) or the claims of any other serious scientist.

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

See also: A theoretical physicist approaches the complexity — and mystery — of quantum gravity head-on

We thought that matter was continuous, and it took quite some time to realize that matter is not continuous,” he explains. “It’s atomic, it’s made by atoms and molecules, by particles. This was only understood about the beginning of the 20th century, not before that. It’s one of those ideas that is very old. It was suggested in ancient times. But it was realized recently.”

“So matter is discrete, and light is discrete, it’s made by photons. A wave of light is actually a cloud of photons. And it’s not surprising, after all, that space itself is sort of a cloud of little teeny small things.
Serious scientists used what is known about subatomic particles to show that all the assumptions of pseudoscientists have always been wrong. The pseudoscientists now must deal with serious scientists who have linked the creation of energy as information to all biodiversity and others who linked virus-driven energy theft to all pathology.
Some of the best among the serious scientists scientists who did that are young earth creationists who have always been right. They somehow knew that gravity did not create itself and most of them began to realize that hydrogen-atom transfer in DNA base pairs in solution must be linked from energy-dependent changes in chirality to autophagy.
When pseudoscientist failed to link chirality from autophagy to endogenous RNA interference and supercoiled DNA, which prevents virus-driven energy theft and genomic entropy in all organized genomes of all living genera, the serious scientists started to ridicule the theorists in parodies.
For a historical perspective on the ridicule, see Was ribosome the first self-replicator?

Two years ago, I asked Matti Pitkanen if differences between biophotons were recognized by the photons at the quantum level of their interactions. His response was a classic example of evading the question with claims that theoretical physicists tout in their pseudoscientific nonsense.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

See for comparison: “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: Why metabolism and what happens in bio-catalysis? Matti Pitkanen (2 February 2017)

  1. The simplest and at the same time most difficult question that innocent student can make about biology class is simple: “Why we must eat?”
  2. …the energies of the hydrogen atom depend on hbareff=n× h in as hbareffm, m=-2<0. Hydrogen atoms in dimension D have Coulomb potential behaving as 1/rD-2 from Gauss law and the Schrödinger equation predicts for D≠ 4 that the energies satisfy En∝ (heff/h)m, m=2+4/(D-4). For D=4 the formula breaks since in this case the dependence on hbar is not given by power law. m is negative only for D=3 and one has m=-2. There D=3 would be unique dimension in allowing the hydrino-like states making possible bio-catalysis and life in the proposed scenario.
  3. The condition that the dark binding energy is above the thermal energy gives a condition on the value of heff/h=n as n≤ 32. The size scale of the dark largest allowed dark atom would be about 100 nm, 10 times the thickness of the cell membrane.

Pitkanen is unable to grasp the fact that the speed of light on contact with water is the source of all binding energy, which links hydrogen-atom transfer in DNA base pairs in solution from endogenous RNA interference to healthy longevity in all living genera via chromosomal inheritance. His attempts to place dark binding energy above the anti-entropic virucidal energy of sunlight is still one of the most foolish attempts I have seen anyone make to deny that the energy in a hydrogen atom has been there from the time God created the heavens and the earth — as detailed in Biblical Genesis.
Matti Pitkänen What new physics do you want to introduce to support your claims about dark energy and dark matter for comparison to the claims of Schrodinger about the anti-entropic energy of sunlight?

I call it adelic physics or number theoretic physics.

Does everyone who knows you except Ulla Mattfolk laugh at your pseudoscientific nonsense?

Matti Pitkänen …one must assume that space-time is what topologist calle n-fold covering space. n sheets of covering effectively multiply Planck constant by n to give h_eff. The quantum of action is n-fold since there are n sheets.

I told him that all the assumptions made by others have been wrong.

Matti Pitkänen  It took more than 10 years to deduce this from adelic physics which is fusion of real physics for matter and various p-adic physics for cognition, p = prime.

Matti Pitkänen I think very few laugh to my theory now. If they do so I can safely conclude that they are idiots.

Matti Pitkänen …your understanding of physics could be better. One must distinguish between continuity at space-time level and continuity of matter.

Matti Pitkänen  The cognitive representations defined by the intersections of real and p-adic space-time surfaces as intersection of reality and imagination/cognition are discrete: points have coordinates in extension of rationals. In this sense discreteness makes sense but is has nothing to do with the quantum mechanical discretization of quantum numbers.

Matti Pitkänen …the odor of nutrients is determined by pheromones. Is this true. This would be nice since pheromones could provide information about distribution of h_eff=n*h and thus about the number theoretic evolutionary level of food or potential mating partner. Good odors would correspond to large average n. Bad odors to low value of n and low negentropy.

Matti Pitkänen  TGD predicts both dark matter and energy naturally and this explanation leads to vision about quantum biology and cognition unlike other proposals.

The pre-publication reviews of this book came from people who I think George FR Ellis and others probably believe are serious scientists. I do not believe those people are anything more than theorists. When they include claims about viruses, serious scientists may discuss the reality of pattern recognition with them. But not until then. Energy vs virus-driven energy theft must be considered in the context of adaptive changes in the brain, June 12, 2016

See for comparison: Thomas Hunt Morgan

Morgan contributed to the neo-Darwinian synthesis, despite his criticism of Darwin at the beginning of his career. Much work on the Evolutionary Synthesis remained to be done.

See also: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking
Reported as: Gamma oscillations coordinate food seeking

 “Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

Coevolutionary dynamics of phenotypic diversity and contingent cooperation
Reported as: Study finds mutual reinforcement of phenotypic diversity and cooperation

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism’s observable traits, co-evolves with contingent cooperation when organisms with like traits work together to protect themselves from outsiders, according to a Dartmouth-led study published in PLOS Computational Biology. The study also finds that diversity helps prevent the collapse of cooperation.

Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Reported as: Catalyst mediates energy-efficient proton transport for reversibility

Scientists at Pacific Northwest National Laboratory built a catalyst that mimics nature’s hydrogen-splitting enzymes—working reversibly at room temperature and pressure without added energy. This was achieved by stabilizing the catalyst’s structure by attaching an amino acid…

Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection

Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.

‘Virus-Like Particle’ Method to Make new Polio Vaccines Proven Effective

The investigators have demonstrated that stabilized VLPs can be utilized effectively under controlled conditions. Additional research with model organisms like mice and rats will be necessary and is planned as an important part of crucial procedure of ensuring the safety and efficacy of these new VLPs for use in people.

All experimental evidence of biologically-based cause and effect has shown that controlled conditions are not exemplified in the context of how ecological variation must be linked from natural selection for energy-dependent codon optimality to the physiology of reproduction. Energy-dependent changes must be linked from chirality to autophagy by natural information processing. The control of information processing links energy-dependent endogenous RNA interference from amino acid substitutions in supercoiled DNA to all healthy longevity in all living genera. Negative supercoiling links virus-driven energy theft from mutations to all pathology.

If you would like to learn more about how virus-driven energy theft is linked to messenger RNA degradation and all pathology in species from microbes to humans, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection clearly links energy-dependent RNA-mediated amino acid substitutions to the functional structure that enables the search for nutrients, which are metabolized to pheromones that control the physiology of reproduction in species from microbes to humans.


Expunging the distinguished public

Royal Society Expunges Public From Evo Record

Many of the attendee-participants were, in fact, more distinguished than many of the actual speakers. So the audience came to be heard as well as to listen. But the official recording (now posted) has been wiped clean of public comment — the most robust part of the meeting — and what we are left with, with few exceptions, is a series of academic lectures and old science.

Thanks for continuing to make the Royal Society Meeting organizers look as foolish as they are. Life will go on without them, although the increasing number of virus-driven pathologies may wipe out billions the next time something like the Spanish Flu hits populations across the globe — as it did in 1918. Or maybe the transgenerational epigenetic inheritance of Zika virus-damaged DNA will do it, slowly.

Until then, intelligent scientists will want to keep track of works by Nobel Laureates like Ben Feringa (Chemistry) and Yoshinori Ohsumi (Physiology or Medicine) who have linked quantized energy as information from the sun to autophagy, which biophysically constrains all energy-dependent RNA-mediated protein folding chemistry.

Gunter Witzany seems to be so far ahead of the Nobel Laureates that they can’t see him. Thank you for mentioning the conference he is organizing in your book, since it will probably put an end to the pseudoscientific nonsense touted by all theorists. Others may want to see (and you may want to interview) the senior authors of these two recently published works:

(Ohsumi) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes


(Feringa) Dynamic control of chirality and self-assembly of double-stranded helicates with light

See for comparison:

See also: Why the Royal Society Meeting Mattered, in a Nutshell

He quoted paleontologist Graham Budd who has observed: “When the public thinks about evolution, they think about [things like] the origin of wings….But these are things that evolutionary theory has told us little about.”

Many fascinating talks at the Royal Society conference described a number of evolutionary mechanisms that have been given short shrift by the neo-Darwinian establishment. Unfortunately, however, the conference will be remembered, as Suzan Mazur intimated in her coverage, for its failure to offer anything new. In particular, in our judgment, it failed to offer anything new that could help remedy the main “explanatory deficit” of the neo-Darwinian synthesis — its inability to account for the origin of phenotypic novelty and especially, the genetic and epigenetic information necessary to produce it. These are still problems that evolutionary theory tells us little about.

See for comparison: Ancient Enzyme Morphed Shape to Carry Out New Functions in Humans

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

The claim that “Nature” causes new functions could have been addressed at the Royal Society Meeting. Instead, we will probably continue to see pseudoscientific nonsense touted about the reshaping of wings into tails.

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis

See also: Tasting light links energy from creation to adaptation

Developmentally defined forebrain circuits regulate appetitive and aversive olfactory learning

reported as: When neurons are ‘born’ impacts olfactory behavior in mice

My summary:

The de novo creation of different cell types is placed into the context of their energy-dependent birth and the transgenerational epigenetic inheritance of molecular mechanisms that link virus-driven energy theft to all pathology via olfaction, food odors, and human pheromones.

See for comparison: Metabolism and neurogenesis

…it seems quite obvious that cellular metabolism determining for example the cell’s energy status will be linked to NSPC activity and neuronal differentiation processes, as cell division and differentiation are associated with an increase in cell volume and biomass production and require substantial amounts of energy for DNA replication and organelle synthesis [7].

See also: Extensive variability in olfactory receptors influences human odor perception

…the underlying amino acid sequence can vary slightly for each of the 400 receptor proteins, resulting in one or more variants for each of the receptors.

See my comments:

1) The truth revealed in the context of amino acid substitutions is that the theory of mutation-driven evolution does not make sense and it never did.

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

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.”

One reason you may not know this yet is that you were taught to believe in a theory that was never supported by experimental evidence from any species.
See for review: An experimental test on the probability of extinction of new genetic variants.

2) For contrast, note the insistence by the moderator of the International Society for Human Ethology’s yahoo group. He thinks that random mutations are the substrates on which directional natural selection acts. This is what happened when I told him that natural selection is for food:


Jay R. Feierman, best known to me for his ridiculous question: “What about birds?” wrote:

“It is very sad for me to see that when several different people on this group, all with doctorate degrees, tell you that you are not correct, you don’t consider that they might be telling you something helpful. Instead, you respond with arrogance and ignorance. I’ll add my voice to the other people on this group who have told you that you are not correct in terms of your understanding of what “variation” means in Darwinian biological evolution and what is doing the selecting. Variation is not nutrient availability…”

All experimental evidence of biologically-based energy-dependent cause and effect has proved that Jay R. Feierman and others like him are biologically uninformed and that they choose to remain that way. This evidence from December 2012 shows that nutrient availability is the only variant that can be directly linked from the energy-dependent physiology of reproduction in bacteria to neurogenesis in the human brain!

See also: No two people smell the same

A difference at the smallest level of DNA—one amino acid on one gene—can determine whether you find a given smell pleasant.

See also: Human-specific genomic signatures of neocortical expansion

 My unedited comment:

The genomic signatures are energy-dependent and biophysically constrained by the availability of nutrients. Supercoiled DNA links what is known about nutritional epigenetics to all cell type differentiation in all living genera.

See: Metabolism and neurogenesis

  “…it seems quite obvious that cellular metabolism determining for example the cell’s energy status will be linked to NSPC activity and neuronal differentiation processes, as cell division and differentiation are associated with an increase in cell volume and biomass production and require substantial amounts of energy for DNA replication and organelle synthesis [7].”

I have access to this excellent review on the subject.

See for comparison: [MODERATOR NOTE: Edited for publishing. jrf]


Now that Clarence Williams is back and jrf is again editing the responses he allows me to post, I hope everyone will see more than 800 examples of what they have missed.

The examples link energy-dependent epigenetically effected alternative RNA splicing from amino acid substitutions such as BDNF Val66Met and COMT Val158Met to cell type differentiation in all cell types of all living genera via what is known about biophysically constrained biologically-based cause and effect.

In the context of what is known about animal models, Samir et al (2016) published: MicroRNAs in the Host Response to Viral Infections of Veterinary Importance MicroRNAs in the Host Response to Viral Infections of Veterinary Importance

 Many people are now aware of the role that virus-driven energy theft plays in all pathology . . ..

Feierman’s passive/aggressive ignorance and his editing of my comments has reached peak efficiency. I do not expect any attempt to contribute to discussion to appear without his editorial omissions of my content.

He exemplifies academic suppression at its finest, and has done that for more than a decade. His legacy of ignorance may be historically significant. His question “What about birds?” was answered by researchers who linked epigenetic effects of nutrients and pheromones to chromosomal rearrangements in white-throated sparrows, which led others to look for, and to find, evidence of chromosomal rearrangement and biodiversity in other species.

See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Their results were perfectly predictable, and so were the Nobel Prize winning results of these two researchers.

  1. Ben Feringa (2016 Chemistry)
  2. Yoshinori Ohsumi (2016 Physiology or Medicine)

1) Dynamic control of chirality and self-assembly of double-stranded helicates with light Feringa with co-authors (2016)

2) Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates Ohsumi with co-authors (2016)

The works, cited above, predictably linked the works of these two 1933 Nobel Prize-winner to everything currently known about biophysically constrained energy-dependent RNA-mediated protein folding chemistry

  1. Thomas Hunt Morgan (Physiology or Medicine 1933)
  2. Erwin Schrodinger (Physics 1933)

1) Thomas Hunt Morgan (September 25, 1866 – December 4, 1945)[1] was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.[2]

2) Schrodinger monograph (1944) What is Life?

Thermodynamic cycles of protein biosynthesis and degradation link Schrodinger’s claims about higher temperatures from autophagy to nutrient energy-dependent fixation of RNA-mediated amino acid substitutions and all cell type differentiation in humans via transgenerational epigenetic inheritance.  Everything known to all serious scientists about all cell type differentiation suggests that our immune system typically functions at it best when the supply of nutrients is linked from natural selection for codon optimality to ecological adaptation via the nutrient energy-dependent pheromone-controlled physiology of reproduction.

See also: When neurons are ‘born’ impacts olfactory behavior in mice
My summary: The de novo creation of different cell types is placed into the context of their energy-dependent birth and transgenerational epigenetic inheritance of the molecular mechanisms that link virus-driven energy theft to all pathology via olfaction, food odors, and human pheromones.
See also: TET proteins drive early neurogenesis
All neurogenesis is energy-dependent and biophysically constrained by RNA-mediated protein folding chemistry. Energy drives neurogenesis.
Proteins do not evolve. If they did, biologically uniformed theorists could claim that virus-driven energy theft linked mutated proteins to the evolution of the human brain without linking the physiology of reproduction to behavior. Simply put, as others have learned sex is a biological variable.

Addressing sex as a biological variable

Each new misrepresentation of biophysically constrained cell type differentiation outside the context of energy-dependent differences or sex as a biological variable must be viewed in the context of how theorists must continue to try to deceive those who might otherwise become serious scientists.
In this case, the journal article about the TET proteins, Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling, claims: “…Wnt3 was shown to activate Nodal expression directly through its proximal epiblast enhancer at the gastrulation stage (58, 59).
58. Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martinez, J. A., Goyal, P., Mahapatra, S., et al. (2013). Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature, 500(7461), 222-226.
59. Hashimoto, H., Pais, J. E., Zhang, X., Saleh, L., Fu, Z.-Q., Dai, N., et al. (2013). Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. [Letter]. Nature.
If you are not told that the epiblast enhancers must first link nutrient energy-dependent changes in base pairs to cell type differentiation via RNA-mediated amino acid substitutions before the structure of functional proteins can be linked to anything else, you are less likely to learn that fixation of the substitutions in organized genomes only occurs via the physiology of reproduction. The pheromone-controlled physiology of reproduction links the metabolism of nutrients to all morphological and behavioral diversity in species from microbes to humans via the conserved molecular mechanisms of transgenerational epigenetic inheritance.
There is no question that transgenerational epigenetic inheritance is nutrient-dependent and pheromone-controlled is species from microbes to humans. That fact is now appearing in articles co-authored by the guest editors of a special issue of “Nutrients” who invited me to submit this review of nutritional epigenetics.

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

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

My invited review was returned without review. Since then, one of the guest editors incorporated my claims into this: Insights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes Published: 10 December 2014

The other guest editor incorporated my claims into this: The Interaction between Epigenetics, Nutrition and the Development of Cancer  Published: 30 January 2015

Many academics clearly cannot be trusted with accurate representations of biophysically constrained biologically-based cause and effect. Unless they have a record of accurate representations they are forced to try to establish a record after-the-fact. For example, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. This is the 2013 published review that led Justin O’Sullivan and Lynnette Ferguson to request the invited review of nutritional epigenetics, which they returned without review.

My model was cited in Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

It was also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis (see #10)

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

If others had not cited my model, which is a refutation of neo-Darwinian pseudoscientific nonsense, there would be no record of experimentally established facts that link energy-dependent changes in the microRNA/messenger RNA balance to all cell type differentiation via RNA-mediated amino acid substitutions in all invertebrates and vertebrates.

Filtering light through a prism to identify tissue type

Hydrogen-atom energy in DNA base pairs

See also: Consciousness is simply food rearranged
Role of Double Hydrogen Atom Transfer Reactions in Atmospheric Chemistry
Abstract excerpt: 

Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry.

My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain about the energy-dependent links from angstroms to ecosystems via hydrogen-atom energy in all living genera.
See also: For first time, researchers see individual atoms keep away from each other or bunch up as pairs

Different configurations of electrons give rise to specific elements, making carbon atoms, for instance, distinct from hydrogen atoms.

My comment: Without the different configurations of electrons,  energy-dependent changes in angstroms could not be linked from hydrogen-atom transfer (HAT) in DNA base pairs in solution to all biodiversity in all ecosystems. Simply put, the sun’s biological energy must be linked from atmospheric chemistry to biophysically constrained protein folding chemistry on Earth.
When these interactions are seen for the first time the experimental evidence must confirm theories. Otherwise physicists will try to come up with new untestable theories to stall scientific progress.  Serious scientists make progress when experimental evidence is accepted. Chemists typically know what to accept. So do molecular biologists.
What do evolutionary theorists or other social scientists know about physics, chemistry, or molecular epigenetics? How do pseudoscientists known what to accept when they already have accepted only theories?
For comparison, serious scientists know that angstroms measure distance, and every angstrom is dynamic in the context of energy-dependent RNA-mediated cell type differentiation. How can any serious scientist understand the claims of theorists made in the context of articles like this:
Humans and Neanderthals had sex. But was it for love? An investigation

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

My comment:  Elizabeth Kolbert lied and used Svante Pääbo’s works to support her ridiculous claim:

We know for sure humans and Neanderthals had sex…

Serious scientists know that Svante Pääbo is the senior author of two articles. The two articles linked Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
Natural selection for the de novo creation of olfactory receptor genes and the loss of genes is not an indicator that humans and Neanderthals had sex. It is an indicator that natural selection for energy-dependent codon optimality occurred in the context of the physiology of reproduction in all primates. For contrast, all serious scientists know that members of two different species do not have sex. Chromatin remodeling and chromosomal rearrangements limit fertility among species via their nutrient-dependent pheromone-controlled physiology of reproduction and their behavior. The behavior is linked to energy-dependent codon optimality via the physiology of reproduction, not by sex between consenting humans and Neanderthals.
Is is silly to ask questions about sex for love without consideration of fertility, since the sexual interactions must be linked to survival of the species via biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction. The biophysical constraints are energy-dependent, but the theorists’ and journalists’ preference for fiction is clear.

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

For comparison, see this presentation text about Greg Bear’s novels in which he detailed for his non-technical audience how the nutrient energy-dependent pheromone-controlled physiology of reproduction is linked from RNA-amino acid substitutions to all cell type differentiation in all individuals of all species. The Darwin Code
See also: Structural and Functional MRI Differences in Master Sommeliers: A Pilot Study on Expertise in the Brain

This study identified enhanced structural and functional patterns in the olfactory network of sommeliers. These findings are consistent with the learning they undergo in achieving the status of Master Sommelier. Furthermore, the volume of a region of the brain involved in olfactory memory was associated with experience, suggesting that the continued training results in morphological changes of the brain. These results speak to the plasticity of the adult brain in response to sensory expertise.

Reported as: Smelling Lots Of Wine Makes Your Brain Alzheimer’s Resistant

Overall, these differences suggest that specialized expertise and training might result in enhancements in the brain well into adulthood,” the study states. “This is particularly important given the regions involved, which are the first to be impacted by many neurodegenerative diseases.

See also:  What Sensory Receptors Do Outside of Sense Organs
My comment to the Scientist (I have posted: 361 comments so far)

20 years ago, we published: From Fertilization to Adult Sexual Behavior, which was a review of RNA-mediated cell type differentiation. We included a section on molecular epigenetic in the Hormones and Behavior review.

Unfortunately, few people realize that natural selection for energy-dependent codon optimality links the de novo creation of genes from the creation of G protein-coupled receptors to chemotaxis and to phototaxis before biophysically constrained energy-dependent biodiversity via RNA-mediated protein folding biochemistry can be linked to all biodiversity by amino acid substitutions.
When others report that mutations are linked to pathology, they seem to miss the fact that virus-driven energy theft causes the mutations. Nutrient-energy dependent viral latency has gone missing from explanations that would otherwise link what is known about biologically-based cause and effect from physics to chemistry and everything known about molecular epigenetics.
See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
My comment: Pseudoscientists could challenge representations like this if they had experimental evidence for comparison. They don’t. They have only their ridiculous theories, which they report in the story about sex between modern humans and Neanderthals. It is unadulterated pseudoscientific nonsense and nothing more than an unsubstantiated fictional account. It is not science fiction. The theorists claims are not scientifically based.
See for comparison: Role of olfaction in Octopus vulgaris reproduction and Two fatty acyl reductases involved in moth pheromone biosynthesis
Both articles cite Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See also: The Ancient Origins of Consciousness: How the Brain Created Experience

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution.  — p. 263

My comment: Chemical ecology is the main driver of energy-dependent ecological adaptations. It is not not the driver of mutation-driven evolution, and so far there is no other model for comparison to my model of chemical ecology. I deliberately used the term adaptive evolution to see if someone would take the bait and offer another model for comparison. No one did.
See also: How Psychiatrist Jon Lieff Turned an Interest in Cellular Intelligence into Award-Winning Blogging!
My comment: Lieff still presents cellular intelligence in the context of evolution. He ignores what is known about hydrogen-atom energy in DNA base pairs in solution. That shows how successful a blogger can be if they simply fail to address what is known about biophysically constrained RNA-mediated cell type differentiation. His focus is on evolution! That means he does not need to explain anything about how evolution occurs, or explain what he thinks cellular intelligence is or where it came from!
See for comparison: Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Tight DNA is supercoiled DNA and it protects the orgnaized genomes of all living genera from virus-driven energy theft and genomic entropy. Simply put, supercoiled DNA biophysically constrains virus-driven energy theft, which is the only way to establish a link from ecological variation to ecological adaptation without inventing another ridiculous theory.

… viral latency is responsible for life-long pathogenesis and mortality risk…

Nutrient energy-dependent microRNAs are the obvious link from olfaction to biophysically constrained RNA-mediated protein folding chemistry, plasticity, and prevention of all pathology.
See for example: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

See also, from the Neuroscience FB group “As simple as random can be”
See also:  Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: There is no experimental evidence of biologically-based cause and effect that links anything except energy or energy theft to the species-specific COMT Val158Met amino acid substitution during life history transitions and the development of morphological and behavioral phenotypes.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia

…the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999).

My comment: That fact makes the COMT val158met polymorphism a “smoking gun” in the context of energy-dependent de novo gene creation and virus-driven energy theft that links gene losses to loss of function via differences in G protein-coupled receptors.
Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques
G protein-coupled receptor kinases as regulators of dopamine receptor functions
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb
Programmable RNA-binding protein composed of repeats of a single modular unit
Excerpt from the conclusion:

… Pumby may present a simplified context in which to insert Pumilio modules to study how specific amino acids contribute to the emergent properties of modular RNA binding, independent of position-specific effects.

See also: Another gate-keeping attempt by Feierman


RNA methylation

This is a brief history of events that led me to found the domain RNA-mediated.com with some follow-up on the latest news about cell type differentiation
In 2012, I attended this minisymposium
006.Transcribing Memories: New Mechanisms of Activity-Regulated Gene Expression and Their Roles in Experience-Dependent Plasticity.

Activity-regulated gene transcription is essential for orchestrating the gene expression programs that drive experience-dependent plasticity of neural circuits. Recent studies have not only vastly expanded our understanding of the mechanisms that mediate activity-regulated transcription, but have also identified direct links between activity-dependent gene expression, synaptic plasticity and/or behavioral outputs. This minisymposium will highlight these exciting new developments.

6.06. Memories of non-coding RNA
T. Bredy;
Queensland Brain Institute, The University of Queensland, St Lucia, AUSTRALIA.

Tim Bredy gratiously answered my question about the role of microRNAs in learning and memory. Subsequently, I’ve found these publications by Tim Bredy’s group to be among the most helpful. They may also help others learn more about the importance of understanding how microRNAs are involved in cell type differentiation.
MicroRNA regulation of neural plasticity and memory (2011)
Dynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation (2013)
Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation (2014)
Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation (2014)
Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice (2015)
Tim Bredy’s group is poised to make the most significant scientific progress towards understanding how microRNA flanking sequences link hydrogen-atom transfer in DNA base pairs in solution to learning and memory in species from microbes to humans via the experience-dependent de novo creation of olfactory receptor genes. It will be interesting to see what happens next, and whether more than a few serious scientists understand why virus-driven energy theft leads to memory loss in neurodegenerative diseases and to all other pathology via the same molecular mechanisms.
See also my RNA-mediated FB group

Energy is quantized information. The information links physics, chemistry, and molecular epigenetics to learning and memory via RNA-mediated events such as the de novo creation of olfactory receptor genes.
Creation via top-down causation is exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link amino acid substitutions and the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven energy theft.
Most people seem unwilling to accept the fact that virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would leads others away from pseudoscientific nonsense about beneficial mutations and evolution to what is currently known by serious scientists about the biophysically constrained nutrient-dependent chemistry of RNA-methylation and RNA-mediated protein folding.
In the absence of discussion, this FB group has become nothing more than another newsgroup. I will now begin to limit my attempts to encourage discussion.
The RNA-mediated.com will remain a source for information and discussion of more than 700 blog posts until I sell or lease it to someone who knows how to use it to move scientific progress forward at the same time theorists try to stop it.


Alternative splicing of pre-mRNA

Modelling life scientifically: RNA-mediated events

Experiment: “An attempt to arrive at an accurate result.” — James V. Kohl (3/27/16) EFBC fellowship class response to Dr. Tom Jordan who asked me to define “experiment”

For comparison, see: Experiment:

An experiment is a procedure carried out to verify, refute, or validate a hypothesis. Experiments provide insight into cause-and-effect by demonstrating what outcome occurs when a particular factor is manipulated. Experiments vary greatly in goal and scale, but always rely on repeatable procedure and logical analysis of the results.

My comment: Experimental evidence of biologically-based cause and effect can be compared in the context of theory.

See: Theory: 

Theory is a contemplative and rational type of abstract or generalizing thinking, or the results of such thinking. Depending on the context, the results might for example include generalized explanations of how nature works.

My comment:  Theories about evolution have no explanatory power. The theories cannot be placed into the context of experimental evidence, which is used to model the understanding of life.

See also: Scientific modelling

A scientific model seeks to represent empirical objects, phenomena, and physical processes in a logical and objective way. All models are in simulacra, that is, simplified reflections of reality that, despite being approximations, can be extremely useful.[4] Building and disputing models is fundamental to the scientific enterprise. Complete and true representation may be impossible, but scientific debate often concerns which is the better model…

My comment: Which do you think has more explanatory power, the ridiculous theory in 1), or the model in 2)?

1) “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” — Mutation-Driven Evolution

2) “…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’. — Nutrient-dependent/pheromone-controlled adaptive evolution: a model

My comment: The model can be placed into the context of everything currently known to serious scientists about the biophysically constrained chemistry of RNA-mediated protein folding.

See: Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics

See also: Biological mechanism passes on long-term epigenetic ‘memories’


“We previously showed that worms inherited small RNAs following the starvation and viral infections of their parents. These small RNAs helped prepare their offspring for similar hardships,” Dr. Rechavi said. “We also identified a mechanism that amplified heritable small RNAs across generations, so the response was not diluted. We found that enzymes called RdRPs are required for re-creating new small RNAs to keep the response going in subsequent generations.

See also: Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system


A recent experiment4 suggests that room-temperature superconductivity is reachable in other hydrogen-rich compounds. Our results show that in such hydrogen-rich materials with prospects for high-Tc superconductivity, the quantum motion of the proton induces non-trivial effects that strongly affect the thermodynamical stability, the hydrogen chemical bonding and the electron–phonon coupling strength.

Reported as: Quantum effects at work in the world’s smelliest superconductor


…quantum nature affects structural and physical properties of many hydrogen compounds.

My comment: On 3/13/16, I discussed virus-driven energy theft in the context of hydrogen-atom transfer in DNA base pairs in solution and pathology with a college student who is familiar with my model. He intuitively realized that the energy theft must occur at the level of quantum mechanics.
That suggests these researchers, or others will someday integrate what is known about molecular epigenetics and place everything from quantum physics and chemistry into the context of nutrient-dependent RNA-mediated amino acid substitutions that link supercoiled DNA to biologically-based cause and effect via the physiology of reproduction in the context of the innate immune system and links from olfaction to the structure and function of the mammalian brain.
Physicists now seem to realize that epigenetically-effected RNA-mediated cell type differentiation is biophysically constrained by ecological variation. Jeremy England’s group is one of the first to start with an energy source at the molecular level.
SARCASM ALERT: Next, they may prove that food is the underlying source of what is known about nutritional epigenetics and RNA-mediated protein folding chemistry.
Physicists prove energy input predicts molecular behavior
Excerpt 1)

This is a general proof that shows that how much energy you feed the system is related in a quantitative way to how reliable you’ve made it,” England says. “Having this constraint immediately gives you intuition, and a sort of road-ready yardstick to hold up to whatever it is you’re trying to design, to see if it’s feasible, and to direct it toward things that are feasible.”

Excerpt 2)

“We have in mind trying to make some sense of molecular systems,” Gingrich says. “What this proof tells us is, even without observing every single feature, by measuring the amount of energy lost from the system to the environment, it teaches us and limits the set of possibilities of what could be going on with the microscopic motions.”

Excerpt 3)

“One of the things that’s confusing about life is, it happens on a microscopic scale where there are a lot of processes that look pretty random,” Gingrich says. “We view this proof as a signpost: Here is one thing that at least must be true, even in those extreme, far-from-equilibrium situations where life is operating.”

My comment: It’s challenging for serious scientists to see claims like this and not laugh about how long it has taken theorists to recognize that an energy source must link atoms to ecosystems in all living genera. All serious scientists know that the link from atoms to ecosystems has been placed into the context of the nutrient-dependent RNA-mediated immune system.
See: Regulatory evolution of innate immunity through co-option of endogenous retroviruses

It would be ironic if viral molecular adaptations had been evolutionarily recycled to fuel innovation and turnover of the host immune repertoire.

My comment: It would not be ironic. It would again prove that mutations can only be linked to pathology. It would prove that ecological variation must be linked from physics and chemistry to the conserved molecular mechanisms of cell type differentiation by the feedback loops that link odors and pheromones to reproduction in species from microbes to man.
See: Feedback loops link odor and pheromone signaling with reproduction

Interacting physical systems not only exchange energy, but also exchange information as they learn about and influence each other. Harnessing this information how to do useful tasks is vital in a variety of disciplines: engineers exploit information through feedback to control a system’s dynamical evolution [1, 2], biological organisms need to sense their environment in order to adapt [3], and physicists have been fascinated by the conceptual problems posed by Maxwell’s demon for over 100 years [4, 5].

See also: Single-molecule fluorescence measurements reveal the reaction mechanisms of the core-RISC, composed of human Argonaute 2 and a guide RNA

…biogenesis pathways and biological functions of these small RNAs are distinct.

My comment: Biogenesis of microRNAs is nutrient-dependent and controlled by the physiology of reproduction.
See also: Can a Quirky Chromosome Create a Second Human Species?

“Sci-fi author Greg Bear came very close in his marvelous 1999 and 2003 novels Darwin’s Radio and Darwin’s Children. He imagines that a latent retrovirus awakened in the genomes of pregnant women in 1999 shuffled the genomes of a new generation in ways that created cells with 52 chromosomes instead of 46, thereby instantly establishing a group that can successfully mate only among themselves. You’ll have to read the books to learn how and why the “virus children” are superior. Forced into camps by the fearful majority, they establish their own culture, further separating the two types of people, a little bit reminiscent of a presidential election in the US. Bear’s alternate reality is a compelling depiction of reproductive isolation leading, presumably, to speciation, with an initial chromosomal upheaval as the impetus.
I spoke to Bear back in 2004, again for The Scientist (a mechanism for the rapid extinction of a dedicated freelance writer is a change in editor-in-chief). Greg Bear is a self-taught scientist with a soaring imagination. Said he, “My secrets are few. I love biology. I have been researching it in constant reading since the early 1980s. I saw very clearly that DNA must be computational, a self-organizing, self-repairing system. In the early 90s, it became clear to me that modern evolutionary theory was incomplete. I set out to find all the out-of-the-way papers that I could to prove that nature was a network, from top to bottom.” The Darwin series arose from those thoughts… “

See for contrast: Sociobiology, The Sequel: Conflict about cooperation

Wilson says it is time for the popular paradigm of ‘kin selection’ to be replaced by group selection when it comes to the evolution of cooperation. What boggles the mind is that kin selection was earlier welcomed as a breakthrough in evolutionary theory just because it was seen as replacing the then prevailing group selectionist “good for the species” thinking.. What is going on?

My comment: Virus-driven energy theft has been linked from mutations to loss of function via genes that are eliminated after first becoming pseudogenes. Simply put, all serious scientists have learned that there is no such thing as a beneficial mutation. That’s what’s going on. Pseudoscientists refuse to believe that facts about cell type differentiation. 
See for comparison:  Cori Bargmann: Genes, the Brain and Behavior

By focusing on the genes for a family of proteins found in many organisms, the G protein-coupled receptors, Bargmann illustrates that mutations in a single gene can cause significant behavioral changes in organisms as diverse as nematodes, dogs and humans. In Part 2, Bargmann presents work from her own lab in which the olfactory system in C. elegans was used to dissect the role of genes on behavior. She shows us how it was possible to map the neuronal circuits that modulate worm behavior in response to different odors.

See also: McGovern Institute awards prize to neurogeneticist Cori Bargmann

Building on her olfaction work, Bargmann has also studied the neural basis of social behavior, which in worms is strongly regulated by chemical cues. In one set of papers, for example, she identified a single neuron that integrates information from multiple chemical cues including food, oxygen and pheromones, to control the expression of social behavior.

My comment: On March 30, 2016 at 4.00 pm,  Dr. Bargmann at 4.00 pm will deliver a lecture entitled “Genes, neurons, circuits and behavior: an integrated approach in a compact brain”
It is hard for me to imagine anything that she might present that has not already been linked from RNA-mediated events to brain development and behavior.

See: Soma-to-Germline Transmission of RNA in Mice Xenografted with Human Tumour Cells: Possible Transport by Exosomes


Work from our and other laboratories indicates that spermatozoa act as vectors not only of their own genome, but also of foreign genetic information, based on their spontaneous ability to take up exogenous DNA and RNA molecules that are then delivered to oocytes at fertilization with the ensuing generation of phenotypically modified animals [35] – [37]. In cases in which this has been thoroughly investigated, the sperm-delivered sequences have been seen to remain extrachromosomal and to be sexually transmitted to the next generation in a non-Mendelian fashion [38]. The modes of genetic information delivery in this process are closely reminiscent of those operating in RNA-mediated paramutation inheritance, whereby RNA is the determinant of inheritable epigenetic variations [16], [17]. In conclusion, this work reveals that a flow of information can be transferred from the soma to the germline, escaping the principle of the Weismann barrier[39] which postulates that somatically acquired genetic variations cannot be transferred to the germline.

My comment: This ability is not spontaneous and their conclusion was reported on July 3, 2014. The delayed reporting can be attributed to the fact that RNA-mediated events link physics to chemistry and the conserved molecular mechanisms of cell type differentiation in all living genera via transgenerational epigenetic non-Mendelian inheritance. That fact links what Darwin knew about Mendel’s works to his claims about “conditions of life” and the need to put those conditions before any claims about natural selection. (Darwin knew nothing about Mendel’s works, but he obviously suspected that evolution via natural selection did not automagically happen outside the context of his “conditions of life.” Perhaps the real reason he waited so long to publish was that he could predict what pseudoscientists would do to his theory and make ridiculous claims about the fossil record was somehow linked to the evolution of new species from older extinct species.

In any case, Soma-to-Germline Transmission of RNA was reported on January 14, 2016 by Sayer Ji as: Previously thought impossible: Body cells transfer genetic information directly into sperm cells


…exosomes are the carriers of a flow of information from somatic cells to gametes,” and that their “results indicate that somatic RNA is transferred to sperm cells, which can therefore act as the final recipients of somatic cell-derived information.

Sayer Ji  also reported this on October 15, 2014

See: Body Cells Transfer Genetic Info Directly Into Sperm Cells, Amazing Study Finds 


…if foods that we eat are also capable of acting as vectors of gene-regulatory information, truly the old reductionist, mechanistic, unilinear models of genetics must be abandoned in favor of a view that accounts for the vital importance of all our decisions, nutritional factors, environmental exposures, etc., in determining the course, not only of our bodily health, but the health of countless future generations as well.

See also: 

  1. No Sex Required: Cells Transfer Genetic Info Directly Into Sperm Cells July 7th 2014
  2. Father’s Lifestyle Affects Future Offspring July 31, 2014

How many more times can we expect to see the same report raise questions about nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation that have been answered in all literature published by serious scientists since 1996? See: 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 comment: How else might sex differences or somatic differences arise? All cell type differences are nutrient-dependent and all cell type differentiation is RNA-mediated. If that fact were not true, teleophobes would have long ago offered an alternative model of how cell type differentiation occurs in the context of mutations and evolution. Compared to the claims of serious scientists who have linked atoms to ecosystems the claims of theorists are simple-minded and foolish.

See for example: Reversal of axonal growth defects in an extraocular fibrosis model by engineering the kinesin-microtubule interface

In the D279R KIF5B-β-R262H MT mutant pairs, neither the motility nor the ATPase was rescued (Table 1). This result is not surprising considering the high histidine activity in molecular interactions30. Because histidine is capable of interacting with various amino acids, the mutation R262H might have modulated the MTs by hydrogen bonding(s), which cannot be compensated by D279R KIF5B11.

My comment: They link the flow of energy as information from physics to a mutation that disrupts the flow and claim that an amino acid substitution restores the information flow. But they claim the amino acid substitution is a mutation. This is what Taylor et al., (2015) did with two amino acid substitutions in Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

See for comparison: Targeting NF-κB in glioblastoma: A therapeutic approach

(A) Diagram of the NBDwt and NBDmut peptides. The W amino acids in the NBDwt peptide were substituted by A in the NBDmut (highlighted in red).

My comment: They are treating mutations linked to cancer with amino acid substitutions. There must be a reason for accurately reporting their claims in the context of what is known about the nutrient-dependent stability of organized genomes. If they did not know how to link atoms to ecosystems in all living genera via metabolic and genetic networks, they could not be considered serious scientists by their peers. All serious scientists know the difference between a mutation and an amino acid substitution. Only teleophobes and pseudoscientists are confused. Serious scientists link top-down causation to cell type differentiation in the context of hydrogen-atom transfer in DNA base pairs.
My comment: They link a mutation/deletion to the need for DNA repair. That is what serious scientists have been doing for several decades. They start with E. Coli and link the conserved molecular mechanisms to the stability of all organized genomes in all living genera
See, for example: CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

…improving the resolution of our cryoET data to better than 8Å using the novel lipid-monolayer system described above would allow generation of an atomic homology model of the E. coli chemosensory array…

My comment: Improving the resolution is less important that finding a teleophobic theorist who will publicly admit that no neo-Darwinian theorist, since Dobzhansky (1973) has ever understood anything about how nutrient-dependent pheromone-controlled cell type differentiation occurs in the context of hydrogen-atom transfer in DNA base pairs linked to the amino acid substitutions that determine RNA-mediated cell type differences in all living genera.
The facts about hydrogen-atom transfer in DNA base pairs attest to the misrepresentations made in the context of ridiculous theories about mutations and evolution. For example, the Red Queen hypothesis arose in the context of claims that “Evolutionary change may be required to stay in the same place. Cessation of change may result in extinction.”
But ecological variation must lead to ecological adaptation via RNA-mediated amino acid substitutions, not by mutations and evolution. Simply put, organisms that cannot find food and reproduce become extinct, they do not change and become another species.
Summary: None of the factual representations of biologically-based cause and effect seem to be integrated in the latest report from Science, which could have a huge impact on the future of synthetic biology. The team created a new species of microorganism with a minimal genome. The bacterial cell has 473 synthetic genes. The function of 31.5% of these genes remains unknown, and very few reports make the obvious connection from the unknown function of 149 genes to the function of the innate immune system.
Synthetic microbe lives with fewer than 500 genes (Science news)
Craig Venter’s Synthetic Genome 3.0 Evokes Classic Experiments (DNA Science Blog)
‘Minimal’ cell raises stakes in race to harness synthetic life (Nature News)
The Mysterious Thing About a Marvelous New Synthetic Cell (the Atlantic)
After 20 Year Quest, Biologists Create Synthetic Bacteria With No Extra Genes (Forbes)

See also: Year of Darwin – RNA-Mediated Epigenetic Inheritance

It is a video review of what neo-Darwinists still believed about biophysically constrained energy-dependent RNA-mediated events only 7 years ago (April 2009)


Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics (4)

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein 5/6/16

Summary excerpt:

Visualizing a response to light

Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein

Article excerpt:

Ultrafast fluorescence and transient absorption spectroscopy of PYP have shown that excited state decay is multi-phasic (3, 5, 39). The fast (sub-picosecond) time constants are significantly more productive in creating the cis-like photoproduct than the slow (picosecond) time constants; the long-lived excited state population primarily decays back to the ground state (5, 36)

reported on 5/5/16 as

Scientists watch bacterial sensor respond to light in real time


The researchers had already studied light-induced structural changes in PYP at LCLS, revealing atomic motions as fast as 10 billionths of a second. By tweaking their experiment, they were now able to improve their speed limit 100,000 times and capture reactions in the protein that are 1,000 times faster than any seen in an X-ray experiment before.

My comment: Their results link femtosecond blasts of ultraviolet (UV) light from hydrogen-atom transfer in DNA base pairs in solution and microRNA flanking sequences to energy-dependent changes in the microRNA (miRNA)/messenger RNA (mRNA) balance. Changes in pH and changes in the miRNA/mRNA link the energy-dependent physiology of reproduction to healthy longevity via what is known about supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.

See also: Edward Snowden nominated for Nobel peace prize

Withholding information is usually a tactical measure. Promoting ignorance that fails to link the de novo creation of G protein-coupled receptors (GPCRs) to morphological and behavioral diversity contributes to belief in ridiculous theories and beliefs about other people that are based on those ridiculous theories.
If you can’t link energy-dependent changes to hydrogen-atom transfer in DNA base pairs in solution via the speed of light on contact with water, you may have missed everything known about how angstroms are linked to ecosystems via the creation of the sun and energy-dependent creation of GPCRs. The GPCRs link the epigenetic landscape to receptor-mediated behaviors via nutrient-dependent hormone organization and hormone activation in all vertebrates and invertebrates.
Information dissemination
4/6/16 Race/Ethnicity-Specific Association of Vitamin D and Global DNA Methylation: Cross-Sectional and Interventional Findings
reported on 5/2/16 in Engaging Epigenetics Experts:

This PLoS ONE study is the first to show that vitamin D regulates global DNA methylation in humans. This is important because decreased global DNA methylation is associated with higher disease risks, (cancer, cardiovascular, immune function). Our bodies need sunshine to be healthy!

See for comparison:

“…calcitriol is the active form of vitamin D. Its effects on the microRNA(miRNA)/messenger RNA (mRNA) balance appear to protect against perturbed protein folding, which is associated with colorectal cancer. MiRNA-627 targets the mRNA that encodes an enzyme linked to histone demethylation and amino acid substitutions that increase stability of hydrogen bonds in DNA, which are important to protein folding (Padi, Zhang, Rustum, Morrison, & Guo, 2013). Rarely does a week go by without yet another report that details cause and effect in the context of miRNAs (Follert, Cremer, & Beclin, 2014). For example, the potential for therapeutic use of miRNA-126-5p to treat atherosclerosis was reported in time for me to note the importance of miRNAs to cell type differentiation via the circulatory system (Schober et al., 2014).” — Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

My comment: My invited review of nutritional epigenetics was returned without review. It linked the conserved molecular mechanisms of Vitamin D regulation of global DNA methylation to energy-dependent healthy longevity and to energy-loss, which I have since linked from virus-driven energy theft to all pathology.
If you’re not interested in at least scanning the works I have already presented, published, or those that editors returned without review, you’re not likely to grasp the magnitude of the problem with reviewers. Most of what is being published as mainstream science attempts to continue to support the ridiculous theories invented by neo-Darwinists. If you believe in the ridiculous theories, you won’t look for accurate representations of biophysically constrained energy-dependent cause and effect. You will miss the link from nutrition to DNA methylation and the link from virus-driven energy theft to hypomethylation and cancer. Virus-driven energy theft will continue to be ignored and biologically uninformed theorists will help the viruses to kill us all.
For more examples of ignorance about cell type differentiation, see:
An inter‐species protein–protein interaction network across vast evolutionary distance 4/22/16
Altered primary chromatin structures and their implications in cancer development 3/23/16
Identification of a Novel RNA Virus Lethal to Tilapia 9/17/14
Structure and mechanism of the ATPase that powers viral genome packaging 7/8/15
Ancient Virus DNA Gives Stem Cells the Power to Transform  3/30/14
Virus-based piezoelectric energy generation 5/13/12 reported as: A virus that creates electricity 5/16/12
See also: Is Biodiversity Research Biased? 4/11/16
The report of a virus that “creates” electricity shows how reports that link viruses to pathology are placed into the context of a battle between neo-Darwinian theorists and serious scientists. Biodiversity research is biased by the neo-Darwinian theorists. Anyone who attests facts forces biologically uninformed theorists to add to their theories. None of their theories link energy-dependent biologically-based cause and effect, which means that none of their existing theories have any explanatory power.
For example, On day two of the Molecular Diagnostics event, Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity was reported as Virus fighter may have played a key role in human evolution.
Genetic and environmental influences interact with age and sex in shaping the human methylome was reported with no mention of how energy-dependent RNA-dircted DNA methylation must be linked to supercoiled DNA via the immune system so that all organized genomes are protected against virus-driven energy theft and entropy.
Thus, even after others admit that no experimental evidence links mutations to the biophysically constrained chemistry of energy-dependent RNA-mediated protein folding, they do not admit that Schrodinger’s claim about the anti-entropic energy of sunlight in “What is life?” (1944) was correct. Instead, one day after the Molecular Diagnostics event Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs was reported as Scientists say the ‘R’ in RNA may be abundant in space.
The ultraviolet irradiation was not linked to ultraviolet absorption on contact with water on Earth, which left serious scientists to ask for an explanation of what ultraviolet irradiation in deep space has to do with energy-dependent hydrogen-atom transfer in DNA base pairs in solution and the link from the RNA-mediated innate immune system to supercoiled DNA. Instead, on April 8, 2016, Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water was reported as A single ion impacts a million water molecules and  Viruses work together to attack their hosts was reported based on a published work from October 14, 2015.

See also: Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes 4/26/16

Reported on 4/20/16 as Scientists sharpen view of gene transfer between pathogenic bacteria

Excerpt 1)

Bacteria possess the ability to take up DNA from their environment, a skill that enables them to acquire new genes for antibiotic resistance or to escape the immune response.

Excerpt 2)

Our findings — that two-thirds of the core activated genes in streptococcus have transformation functions — suggest that this is an ancient response, maintained because of its value in promoting ready access to external DNA.

My comment: Femtosecond changes in time constants link fast or slow changes in energy-dependent hydrogen-atom transfer in DNA base pairs in solution from the speed of light on contact with water to thermodynamic cycles of protein biosynthesis and degradation.  Virus-driven energy theft perturbs those cycles. That is how viruses are linked from the accumulation of mutations to all pathology. Watch closely as each day goes by and more news reports try to misrepresent what is known about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.  Theorists are scared, and they will do anything they can to help science journalists continue to misrepresent the facts known to serious scientists who are Combating Evolution to Fight Disease.

Filtering light through a prism to identify tissue type

RNA-mediated physics, chemistry, and molecular epigenetics (3)

Summary of the metabolic pathways altered in cancer that are described in this review

Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism

My comment: Metabolic networks are linked to genetic networks by the normal metabolic landscape, which is linked to healthy longevity. Virus-driven energy theft links changes in the metabolic landscape to changes in the physical landscape of supercoiled DNA, which typically maintains healthy longevity across the lifespan by preventing virus-driven entropy. When no consideration is given to facts about virus-driven entropy, you are stuck with theories about brain evolution.
See for example: Metabolic acceleration and the evolution of human brain size and life history 5/4/16 reported as: Humans have faster metabolism than closely related primates, enabling larger brains

My comment: Place that claim into this regression.

Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum 1/15/16
My comment: Copy number variation is nutrient energy dependent
Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants 2/28/16
My comment: MicroRNA flanking sequences link hydrogen atom transfer in DNA base pairs in solution to nutrient energy-dependent copy number variation.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers 4/1/16
reported 4/14/16 as: Scientists document rare DNA transfer between animals and plants
My comment: “Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).” — Kohl (2012)
My comment: Place all claims (above) that link nutrient-dependent ecological adaptations into the context of healthy longevity. Place all claims (below) into the context of  virus-driven energy theft and all pathology.
Wolbachia Blocks Currently Circulating Zika Virus Isolates in Brazilian Aedes aegypti Mosquitoes 5/4/16

reported 5/4/16 as: Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing 5/3/16

reported 5/1/16 Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers

My comment: Place all claims about nutrient energy-dependent cell type differentiation and all claims that link virus-driven energy theft into the context of physics and chemistry linked to the conserved molecular mechanisms of cell type differentiation in twin studies. For example,  NASA’s Twins Study Explores Space Through You: Videos Highlight Omics  4/20/16

What does it take to detect entanglement with the human eye?
reported 5/3/16 as  An experiment seeks to make quantum physics visible to the naked eye

RNA splicing is a primary link between genetic variation and disease 4/29/16

3/31/16 Carl Zimmer Episode 5: Everything you thought you knew about the shape of DNA is wrong

4/24/16 Sea Slug Senses 1/15/13 The sea slug that eats the sun (video)

Saturation of recognition elements blocks evolution of new tRNA identities 4/29/16

reported 5/2/16 Discovery of a fundamental limit to the evolution of the genetic code

Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity and Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPRmt

reported 5/2/16  Genetic switch could be key to increased health and lifespan

The Role of Correlation and Solvation in Ion Interactions with B-DNA 1/19/16

delayed reporting till 5/3/16 A new model for simulating DNA’s ‘atmosphere’ of ions

5/3/16 Part I: Epigenetics: Why Your DNA Isn’t Enough C. David Allis

5/3/16 Part II: Epigenetics in Development and Disease C. David Allis

Genomic instantiation of consciousness in neurons through a biophoton field theory 6/13/14
4/18/16 Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb and 5/1/16 Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy 
collectively reported 5/2/16 as Unraveling complex neuronal networks
My comment: The de novo creation of G-protein coupled receptors (GPCRs) links the epigenetic landscape to the physical landscape of supercoiled DNA via olfaction and the innate immune system.

Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons. Delgado-Peraza F, Nogueras-Ortiz C, Acevedo Canabal AM, Roman-Vendrell C, Yudowski GA. Methods Cell Biol. 2016;132:25-33.
Chapter 1 – Localization and signaling of GPCRs in lipid rafts

Chapter 2 – Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons
Chapter 4 – Single-molecule resolution of G protein-coupled receptor (GPCR) complexes
Chapter 13 – Resonance Energy Transfer-Based Approaches to Study GPCRs
My comment: Place everything known about nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation into the context of virus-driven energy theft and cancer.

Deletion of Amino Acid Transporter ASCT2 (SLC1A5) Reveals an Essential Role for Transporters SNAT1 (SLC38A1) and SNAT2 (SLC38A2) to Sustain Glutaminolysis in Cancer Cells (4/26/16)
reported on 5/5/16 Starving cancer the key to new treatments

The research team blocked gateways through which the cancer cell was obtaining the amino acid glutamine and found the cells almost completely stopped growing.

My comment: They prevented the viruses in the cancer cell from adapting. Otherwise, energy theft enables amino acid substitutions in the virus that would link ecological variation to healthy longevity when nutrient-stress or social stress is biophysically constrained. Links from the epigenetic landscape to the physical landscape of supercoiled DNA biophysically constrains energy-dependent RNA-mediated cell type differentiation. They have been placed into the context of mutation-driven evolution by theorists who have killed millions with their ridiculous theories.

See for comparison:

reported 5/2/16 We are pleased to announce that today marks the formal release of our latest title: Amber Palaeobiology by Dr David Penney.


Wasted Templeton Funding (2)

See also: Wasted Templeton Funding (1)

Templeton grant funds evolution rethink


The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology.

My comment: That is an understatement! The problems with the so-called modern synthesis are perfectly clear:
1) [W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.
2) 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…
3) …evolutionary science has now “moved on to such an extent” that she and Peter Saunders don’t really care anymore about “trying to convince the neo-Darwinists.”
All serious scientists have since linked angstroms to ecosystems via what is known about the biophysically constrained chemistry of energy-dependent protein folding and links from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and entropy in the context of the physiology of reproduction.
See for example:

See also: Precision Medicine Program to Get $9.3M in NHLBI Funding for Omics Research
One of the things they are asking for is:

“Causal modeling using whole genome sequences and functional genomics data to enhance discovery of influential genetic and epigenetic variants that influence [heart, lung, blood, and sleep] HLBS disorders;”

My comment: They are asking for what has already been included in every model of biologically-based cell type differentiation that has ever been detailed by serious scientists.  Now, the  Templeton Foundation has awarded $8.7M to fund research that can only benefit humanity by answering Schrodinger’s question “What is Life?” in the context of what is known about how the energy-dependent RNA-mediated innate immune system and supercoiled DNA protect life from virus-driven energy theft.”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