Witzhany2018

Ecological adaptation: A new definition of heredity (2)

The 1902 definition of mutation by Hugo de vries can again be placed into the context of facts about energy-dependent RNA-mediated cell type differentiation and healthy longevity before anyone else attempts to redefine heredity. Hopefully, that will be done before anyone else from the CDC goes missing. The threat to thos who understands how top-down causation is linked to the transgenerational epigenetic inheritance by cell survival is severe because they have linked virus-driven energy theft from mutations to the death gene. For comparison, mathematical models link mutations to evolution.
Historical perspective:

De Vries’s theory was one of the chief contenders for the explanation of how evolution worked, leading, for example, Thomas Hunt Morgan to study mutations in the fruit fly, until the modern evolutionary synthesis became the dominant model in the 1930s. Somewhat ironically, the large-scale primrose variations turned out to be the result of chromosomal duplications (polyploidy), while the term mutation now generally is restricted to discrete changes in the DNA sequence.

Thomas Hunt Morgan won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.[2]
See also: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990), which was co-authored by Michael Rosbash who shared the 2017 Nobel Prize in Medicine for development of the cryo-EM technology. Cryo-EM links energy-dependent changes in electrons to ecosystems via the physiology of reproduction and chromosomal rearrangements that biophysically constrain viral latency in all living genera.
See for comparison, this attack on my scientific credibility by P.Z. Myers: One crank dies, another rises to take his place
I wrote:

The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

Since December 25, 2017 I have been using my twitter account to reach a larger target audience at a pace of about 100,000 impressions each month.  For example, my top tweet in February got 12,500 impressions. I wrote:

I think the problem is why theorists placed their claims into the context of the emergence of energy and mutation-driven evolution. Sure that exemplifies idiocy, but it’s easy to understand without the metaphors. Complexity “just happens” — scientificamerican.com/article/the-su

See also:


See also: Ecological adaptation: A new definition of heredity (3)

Alternative splicing of pre-mRNA

The essence of precision medicine

…Trump’s labeling of the media as the enemy of the state was unfortunate and dangerous.

It was an accurate label that has been supported by Bill Gates and the Allen Institute in the context of the forthcoming viral apocalypse.
See for comparison this enemy of the state-issued media representation:
 

“We are all proud of professor Filipp’s accomplishments,” Vice Chancellor for Research Samuel Traina said. “He exemplifies the attributes of a great UC professor.”

 This biased representation was framed in the context of: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

Filipp misrepresented everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation and supercoiled DNA when he made this claim:
 
 

The Precision Medicine Initiative and National Microbiome Initiative link food energy to biophysically constrained RNA-mediated protein folding chemistry and viral latency. Virus-driven energy theft has been linked to all pathology in all living genera via the molecular mechanisms of chromosomal inheritance.

Evidence of chromosomal inheritance led to the 1933 Nobel Prize in Physiology or Medicine, which was awarded to Thomas Hunt Morgan.

The essence of precision medicine involves an understanding of how atomic energy-dependent RNA-mediated fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction, which has been linked to chromosomal inheritance by all serious scientists since Schrodinger (1944) in What is Life?.
 
For example, Horton et al (2014) put the facts about chromosomal inheritance into the context of epigenetic effects of food and pheromones on estrogen receptors and biodiversity of behavior in a single species.
 
 

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

Filipp and others like him probably do not want the details of chromosomal rearrangements to be linked from energy-dependent changes in estrogen receptor polymorphism to virus-driven energy theft and androgen receptor polymorphism in prostate cancer. 
For an example of threat to pseudoscientists posed by facts about sex differences in androgen and/or estrogen receptor polymorphism and healthy longevity compared to virus-drive pathology, see: A third of Americans don’t believe in evolution
My comment to Phys.org:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

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

There is no other model or model organism that so clearly integrates what is known to all serious scientists about energy-dependent endogenous RNA interference at a time when Church et al (2015) are waiting to cash in on this patent application. RNA-Guided Human Genome Engineering

Anyone who claims to be proud of professor Filipp’s accomplishments should be asked how he thinks the essence of precision medicine will link drug targets from each person’s unique genetic and epigenetic makeup to what others have claimed is a “billion dollar baby.”

Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

See also: Obituary: Robert L. Moss

 Most recently, his efforts were directed towards establishing the role of pheromonal signals in activating GnRH neurons.

The nutrient energy-dependent pheromone-controlled activation of GnRH neurons links the androgen and/or estrogen receptor context of different tissues to healthy longevity or to virus-driven pathology in all vertebrates via substitution of achiral glycine in position 6 of the GnRH decapeptide.

Other energy-dependent RNA–mediated amino acid substitutions also link morphological and behavioral phenotypes to all biodiversity via conserved molecular mechanisms in the context of the physiology of reproduction.

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Alternative splicing of pre-mRNA

Emily Witkin refutes theistic evolution

February 21, 2017
The SOS Response in Bacteria
Her professor/advisor was Theodosius Dobzhansky. She watched as Barbara McClintock indirectly linked the tobacco mosaic virus from Thomas Hunt Morgan’s work on chromosomal inheritance, and she helped link virus-driven energy theft to all biodiversity via experimental evidence of DNA repair.
Now that the structure and function of supercoiled DNA has linked the effects of sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from bacteria to humans, why does she fail to explicitly claim that sunlight is the common source of anti-entropic virucidal energy?
I think it is because her works were done in the absence of competition, which has since led unethical researchers to bastardize Darwin’s theory and fail to link natural selection from sunlight to energy-dependent codon optimality and Darwin’s “conditions of life.”
Listen for her claim that UV light activates 43 genes when DNA is damaged.

See for comparison: March 30, 2016

See also: Measurements of translation initiation from all 64 codons in E. coli

Translation initiation from non-canonical start codons may contribute to the synthesis of peptides in both natural and synthetic biological systems.

The peptides are the link from the de novo creation of G protein-coupled receptors to the RNA-mediated amino acid substitutions that differentiate all cell types in all living genera via the physiology of reproduction.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

See for comparison: 7/25/13
Jay R. Feierman: “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.”
See also: 7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

Alternative splicing of pre-mRNA

George Church refutes theistic evolution

Wednesday Afternoon Lecture Series (WALS) – The future of genetic codes and BRAIN codes

The NIH Director’s Wednesday Afternoon Lecture Series, colloquially known as WALS, is the highest-profile lecture program at the NIH.

The future of genetic codes and BRAIN codes (video)
My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.
Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.
Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
They showed that a single set of light-activated reactions gave rise to most of life’s building blocks simultaneously. Simply put, that fact refutes every aspect of neo-Darwinian nonsense. It also eliminates consideration of any theories proposed by “big bang” cosmologists.
The irony of this is that not one of the young earth creationists I know would fail to link the hydrogen-atom energy-dependent de novo creation of nucleic acid precursors to all biodiversity on Earth via the physiology of biophysically constrained cell type differentiation.
For example, see: Multipurpose Plant Sensors Startle Scientists
Even if a young earth creationist knew nothing about energy-dependent cell type differentiation, he or she would not be likely to link minimal mutational differences, called mutations to the mutation-driven evolution of all biodiversity.
As you can see in the video, George Church has been forced to abide by the rules of serious scientists.
Here is an unavoidable rule: 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.

George Church has, until yesterday, focused his efforts on exogenous RNA interference rather than what is known about endogenous RNA interference, which links supercoiled DNA to the prevention of all virus-driven pathology in all living genera. Most people will not recognize what President Trump has forced the NIH to do before the theistic evolutionist, Francis Collins is replaced. They may read this, but not understand what it means.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The likelihood that NIH funding will be used for any studies that do not link prevention from the National Microbiome Initiative to the Precision Medicine Initiative via the microRNAome and energy-dependent microRNA expression can be placed into the context of failed mathematical models, which have not addressed any aspect of energy-dependent biologically-based cause and effect.
Let me help others decipher the content of George Church’s claims in: The future of genetic codes and BRAIN codes
The question (at 54:22) about teratomas is answered with a classic attempt to obfuscate what is known about virus-driven energy theft and all pathology.
How organs assemble in the context of virus-driven energy theft has been placed into the context of energy-dependent viral latency since the time that Sinclair Lewis published “Arrowsmith” in 1925 and Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance.
At 59.00 the question about natural selection for energy-dependent codon optimality leads to another attempt to obfuscate what is known about top-down causation.
At 1:00 he begins to talks about adding a built-in sequencer in your phone.  At this point, you may need some comic relief, which Jon Stewart provided with his question about whether the new technology would be integrated with a camera. See: Jon Stewart interviews Greg Bear.
At 1:04, the question and answer about Alzheimer’s vs cognitive enhancement can be placed into the context of Greg Bear’s works, which were published in 1999 and 2003. They were reviewed by Michael A. Goldman in “Nature.”
Evolution rising from the grave
Living with the Neanderthals
See also: Newly found mechanism for protecting neurons could underlie brain disease

The neurons expel large (4- micron diameter) membrane-bound vesicles (dubbed “exophers”) that are filled with clumped protein and damaged cellular organelles including mitochondria.

The only mention of exopher in the extant literature indexed on PubMed is in the article published yesterday, C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress.  The authors seem to be trying to make everything known to all serious scientists appear to be new information about the biophysically constrained RNA-mediated transgenerational epigenetic inheritance of morphological and behavioral phenotypes.
This is roughly the equivalent of inventing de Vries 1902 term “mutation,” which was used by theorists to dismiss Darwin’s “conditions of life.”
For comparison, there are now 58,887 indexed articles on PubMed that mention microRNA.  For example, see: MCMDA: Matrix Completion for MiRNA-Disease Association prediction
If you do not object to the level of obfuscation that is required for pseudoscientists to continue touting their ridiculous theories, you may not be allowed to join those who are Combating Evolution to Fight Disease.
What career goals will you pursue after the Trump administration ensures that pseudoscientific nonsense is no longer funded?
Activity-dependent spatially-localized miRNA maturation in neuronal dendrites
Reported as: Bright Spots in Brain Cells

Thanks to Anna Di Cosmo for calling attention to more detailed facts about cell type differentiation that link energy-dependent changes in fluorescence from the weekend resurrection of the bacterial flagellum to endogenous RNA interference and the maturation of brain cells in rats.
Everything known appears to link the conserved molecular mechanisms of nutrient-dependent pheromone-controlled physiology of reproduction in species from archaea to humans.
In any case, no one is challenging the perspective that serious scientists like Anna Di Cosmo have added to what is known about everything that links quantum physics to quantum consciousness via energy-dependent “bright spots in brain cells.”
And there is still no other model for comparison to this model of biologically-based cause and effect. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
A good model predicts, and people who understand the need for a good model of biologically-based cause and effect predictably make the most scientific progress.
In 2013 I wrote:

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

In 2015, Role of olfaction in Octopus vulgaris reproduction, Anna Di Cosmo’s group concluded:

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). The knowledge of the nature of the factor released by the optic gland could shed light on the role played by this gland in the reproduction: is it a gonadotropin or a trophic factor? Intriguingly, even though the mechanisms and molecules regulating reproduction are the same in both male and female, O’Dor and Wells (1978) observed mature sperms in young O. vulgaris males independently from optic gland hypertrophy.

 

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.

rp_levels-of-organization.jpg

Dietary lutein and pheromone-controlled brain development

Parahippocampal Cortex Mediates the Relationship between Lutein and Crystallized Intelligence in Healthy, Older Adults
Reported as: How Leafy Greens May Protect The Brain From Aging

“As a neuroprotective nutrient, lutein may support structure and function in neural membranes, and ultimately may support the cognitive functions that rely upon these neural membranes,” Marta Zamroziewicz, a graduate student in neuroscience and the study’s lead author, told The Huffington Post.

The link from the sun’s anti-entropic virucidal energy to lutein and cell type differentiation in all living genera was placed into the context of this review of human brain development.
The role of docosahexaenoic and the marine food web as determinants of evolution and hominid brain development: The challenge for human sustainability
The link from the sun’s anti-entropic virucidal energy to the de novo creation of olfactory receptor genes and to all biodiversity was placed into the context of this article: Feedback loops link odor and pheromone signaling with reproduction
“Evolutionary processes” fail to link docosahexanoic acid and lutein to luteinizing hormone and healthy longevity. The “processes” can be viewed in the context of what is known about energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, energy is linked to healthy longevity in all living genera and virus-driven energy theft is linked to all pathology.
In all vertebrates, the stability of of organized genomes has been linked from the substitution of achiral glycine in position 6 of the luteinizing hormone releasing hormone (LHRH) decapeptide. The LHRH decapeptide is also referred to as the gonadotropin releasing hormone (GnRH) decapeptide.
The LHRH / GnRH decapeptide links dietary lutein to the nutrient-dependent pheromone-controlled cell type differentiation of all cell types in all vertebrates via the substitution of the achiral amino acid, glycine, and via measurements of luteinizing hormone, which initially was referred to as the “yellow hormone.”
See our section on “Tracking the Yellow Hormone” in: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
See also: From hydrogen atom transfer in DNA base pairs to ecosystems (video representation)
Abstract:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.

See also: Understanding and accounting for relational context is critical for social neuroscience

9 Comments – James Vaughn Kohl and George F R Ellis.

James Vaughn Kohl “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc

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See for comparison, the recent attempt to replace what is known to all serious scientists about energy as information with the term “bio-functional information.”

The theorists are desperately seeking new terms that can be used to replace mutation in the context of their ridiculous theories about Mutation-driven evolution.

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.”

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

Energy-dependent changes in base pairs link differences in nucleotide substitutions from insertions and or deletions to gene duplication in the context of autophagy, which links the physiology of reproduction to supercoiled DNA and chromosomal rearrangements. The energy-dependent chromosomal rearrangements were first linked to transgenerational epigenetic inheritance of all morphological and behavioral diversity by Thomas Hunt Morgan who won the 1933 Nobel Prize in Physiology or Medicine.

rp_levels-of-organization.jpg

Happy biophysically constrained Thanksgiving (in the USA)

Is there any other holiday in the world that celebrates biophysically constrained cell type differentiation in all living genera?
The availability of amino acids and proteins in new genes is nutrient energy-dependent. The de novo creation of genes is biophysically constrained by the innate immune system and the physiology of reproduction. That fact was detailed for a general audience in Biblical Genesis.
Today, all of us can be thankful that the pseudoscientific nonsense of neo-Darwinian theory was replaced earlier in the month with experimental evidence of how new genes are created in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution, single nucleotide polymorphisms, microRNA flanking sequences and RNA-mediated amino acid substitutions that stabilize the naturally fluorescent supercoiled DNA in all organized genomes.
We had this: “…insight coming from re-analyses of translated transcripts in yeast that suggested that de novo gene evolution could even be more prevalent than gene duplication-divergence processes [13]
The energy-dependent de novo creation of genes in the context of duplication and divergence was accurately portrayed like this: “…the exact network of interactions between the nuclear lamina and the genome depends on the protein components of the nuclear envelope, the epigenetic state of the genome, and the availability of specific proteins that interpret these epigenetic signals and mediate interactions with the nuclear lamina.
Naturally occurring DNA fluorescence in bacteria and dinosaur osteocytes proves that the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution is the basis for the creation of all biodiversity on Earth.

Simply put, God started with the creation of energy contained in hydrogen atoms as information, which is exactly what the Holy Bible says about His Word and the Light (the quantized anti-entropic virucidal energy of sunlight).Schrodinger (1944) linked it to the works that led to the Nobel Prize in Physiology or Medicine (1933) awarded to Thomas Hunt Morgan for linking inheritance to chromosomal rearrangements. Schrodinger and Dirac shared the prize in Physics that year.

If you remember how your sheets smelled after they had been hung out to dry in the sun, you have already experienced an example of purifying selection for energy-dependent codon optimality, which can be placed into the context of the Nobel Prize-winning works from 1933, or not. You can tell atheists and agnostics about the energy-dependent purifying selection before asking them where they think the energy in a hydrogen atom came from, or not.

When a friend asked me about that, I was forced to learn more about subatomic particles, but what I learned does not matter as much now that the energy has been linked to the creation of new genes. The de novo creation of genes is referred to as the “holy grail” of biology.

However, the energy-dependent protection of the new genes from virus-driven energy theft is also important. If energy-dependent protein folding chemistry is not biophysically constrained and protected from energy theft, life on Earth could not exist.

Thank God, for the anti-entropic virucidal effects of ultraviolet (UV) light, which links femotosecond blasts of UV light to energy-dependent RNA-mediated DNA repair outside the context of claims about emergence and evolution. For comparison, see:

Evolution: Dynamics of De Novo Gene Emergence

Conclusion (with my emphasis):

It has been suggested that the seemingly finite amount of stable protein folds observed across all domains of life is indicative of an early origin of all folds [16–18], possibly under different conditions and functions than the ones today [17]. However, entirely new folds have been shown to arise de novo in viruses [19] and new domains are present in recently acquired regions of old genes, as well as in young genes [20]. Until now, de novo evolved genes are largely underrepresented in structural analyses, and it seems that resolving their structure is a challenge that will provide us precious information about the origin of stable folds, molecular functions and the interaction between genome and environment.

Resolving the issues of virus-driven energy theft, which have been underrepresented in claims about the structure of functional DNA requires all serious scientists to include the role of virus-driven energy theft in the context of protein folding chemistry. There has never been a suggestion made by any serious scientist that the de novo creation of genes could occur outside the context of biophysically constrained protein folding chemistry. That’s why all serious scientists have linked energy-dependent changes from angstroms to ecosystems via the creation of genes and the virus-driven energy theft that links mutations to loss of function manifested in all pathology.

See also: Although sequence-specific association of co-regulated genomic loci is appealing, random interactions between loci with shared chromatin properties might be an equally effective way of modulating transcription levels.

Pseudoscientists who make claims like this have never supported them with experimental evidence of biologically-based cause and effect. Why would anyone include such a claim in the same article that proved the de novo creation of genes was energy-dependent and biophysically constrained via supercoiled DNA, which protects all organized genomes from virus-driven energy theft?

Alternative splicing of pre-mRNA

Energy-dependent purifying selection / autophagy (4)

Energy-dependent purifying selection / autophagy (3)

My question: What is an abiotic environment?

See:

abiotic factors found in aquatic systems may be things like water depth, pH, sunlight, turbidity (amount of water cloudiness), salinity (salt concentration), available nutrients (nitrogen, phosphorous, etc.), and dissolved oxygen (amount of oxygen dissolved in the water). Abiotic variables found in terrestrial ecosystems can include things like rain, wind, temperature, altitude, soil, pollution, nutrients, pH, types of soil, and sunlight.

My question: When did Schrodinger’s negative entropy of sunlight become an abiotic factor/variable?

See: What is Life? (1944)

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

Erwin Schrödinger (1887–1961) is best known as a co-recipient of the 1933 Nobel Prize in Physics, which is the same year that Thomas Hunt Morgan won the Nobel Prize in Physiology or Medicine for discoveries elucidating the role that the chromosome plays in heredity. Simply put, between two 1933 Nobel Laureates from different disciplines, we learned why the concept of the environment must include everything from energy-dependent changes in angstroms to ecosystems in all living genera.

See for instance:

The concept of the environment used for our discussion is very broad; it incorporates considerations of both the molar and the molecular levels.(1996)

See also, the alternative:  One crank dies, another rises to take his place

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

The unprovoked attack on my accurate representation of biologically-based cause and effect can only be compared to the attacks of PZ Myers on the accurate representations of others. For comparison, Roger Penrose may become best known for leading the way with his support of Schrodinger’s claims in this concise statement:

“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)

I hope that PZ Myers will become well known for ignoring all the claims that have ever been made by serious scientists and for touting only the claims made by other pseudoscientists and their idiot minions.

See: Energy-dependent purifying selection / autophagy (5)