Sunlight as information

Hydrogen-Atom Transfer in DNA Base Pairs (4)

Historical perspective:
Behold James Vaughn Kohl.

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

Read more: One crank dies, another rises to take his place
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.
See also: Teleophobes vs teleophiles: a recent history I concluded:
You may also want to stay informed on the issues that arise as Researchers attempt to uncover the origins of water’s unusual properties.
Excerpt:

…water’s anomalous properties are related to its hydrogen bonds, which cause liquid water to arrange itself in a highly ordered way because of the attraction between the hydrogen atoms in one water molecule and the oxygen atoms in adjacent molecules.

———————————————————————————————————————————————————————————————————————————————————
See also: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution.
When I first learned about this, I wrote 3 blog posts:

  1. Hydrogen-Atom Transfer in DNA Base Pairs;
  2. Hydrogen-Atom Transfer in DNA Base Pairs (2);
  3. Hydrogen-Atom Transfer in DNA Base Pairs (3)

Prefacing the titles with Ultraviolet Absorption Induces and ending the titles with in Solution has become more important in the context of water’s highly ordered hydrogen bonds.
For instance, reportedly, albeit without my confirmation, Darwin mentioned a “warm little pond” in the context of his theory.

It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present.— But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed. — Letter to J. D. Hooker, 1 Feb [1871]

I vaguely recall that some teleophobes also claim evolution started in water, and that some have claimed proteins evolve. If so, it will be easier for me to refute their claims about mutation-driven evolution. If the solution is water, my refutations could start with the claim that “Ultraviolet Absorption Induces Hydrogen-Atom Transfer in DNA Base Pairs in Solution.” Nevertheless, I am concerned that some teleophobes will not accept the claims of other teleophobes. Warring factions of teleophobes tend to claim whatever suits them to be a potential start for evolution.

  1. Giant ice-balls in the form of asteroids passing through our solar system with links to the chirality of amino acids.
  2. Aliens who seeded our planet with life.
  3. Everything arose from nothing.
  4. Simultaneous hen and egg emergence from dark matter.

Is it possible to start with the important properties of water, or not?

The Origin of Information: How to Solve It

Excerpt:

where did the information in DNA come from? This is one of the most important and valuable questions in the history of science. Currently, no one knows the answer.

My comment: What does Perry Marshall mean when he claims that “Currently, no one knows the answer.”
I framed the answer in an invited review of nutritional epigenetics.

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

My comment: I tried to make it clear that the sun’s biological energy is the source for the genesis of variation that links ecological variation to ecological adaptations. Others have since helped to make it clear that atoms and ecosystems are linked via nutrient-dependent microRNAs and adhesion proteins to supercoiled DNA, which appears to protect all living genera from virus-driven entropy. What more will it take to win Perry Marshall’s prize?
Again, see: The Origin of Information: How to Solve It

Both ASCII and DNA are formal communication systems according to Shannon’s model because they encode and decode messages using a system of symbols. DNA is not like a communication system, or analogous to a communication system; it is formally defined as a communication system.
“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey,  Information Theory, Evolution, and the Origin of Life,  Cambridge University Press, 2005).

My comment: Perry Marshall seems to be asking for an explanation of the origin of the information that links atoms to ecosystems via “…transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading.”
But, the guest editors of the journal “Nutrients” who invited my review of nutritional epigenetics, seemed to want the same thing. How can anyone not know that sunlight must be the source for the information that links atoms to ecosystems in all living genera? Does someone need to prove that Schrodinger was right, in What is Life? when he claimed that…

… 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)

My comment: Do I need to prove that sunlight is the anti-entropic force that links information to hydrogen-atom transfer in DNA base pairs and the code that links physics and chemistry to all biomass and biodiversity?  Is that what Perry Marshall wants someone, like me, to do… again?

Physics

Plasma created by sunlight and RNA–mediated epigenetic heredity

Australian student confirms that giant plasma tubes are floating above Earth
Excerpt: The region of space around the Earth occupied by its magnetic field, called the magnetosphere, is filled with plasma created by the atmosphere being ionised by sunlight.
My comment: Scientists have believed in the creation of these structures for more than 60 years. Now visual evidence confirms structures exist that are created by sunlight on contact with the Earth’s atmosphere.
This reminds me of what someone who was born blind might claim if scientists claimed that rainbows exist. If scientists enabled sight in a congenitally blind person, would the sight of the rainbow confirm the belief that all life on Earth was created? If not, could the congenitally blind person still be considered to be blind to an obvious example of creation?
See also:
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

“…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry9”

See also:
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
reported as: Researchers identify ‘tipping point’ between quantum and classical worlds
See also:
RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2
My comment: Taken outside the context of everything currently known to serious scientists about the de novo creation of nucleic acids such as RNA and what is known about nutrient-dependent biophysically constrained RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living, these authors make the following claim:
Excerpt:

Our data show that at least two tRNAs are methylated in mouse sperm in a Dnmt2-dependent manner (Figure S4), which raises the possibility that methylation-dependent processing of tRNAs [17] could result in the generation of paramutation-inducing sncRNAs.

My comment: Their data can be interpreted in the context of neo-Darwinian claims about mutations that somehow link the creation of life on Earth to biodiversity via natural selection. This eliminates the need for sunlight as the anti-entropic force that enabled all aspects of creation whether or not any aspect of creation has yet been seen by blind or sighted researchers.
As is typical, anything interpreted in the light of neo-Darwinism appears to be a misrepresentation of facts that link the creation of the sun to the creation of all biomass and all biodiversity that ever existed or that may continue to exist.
See also: Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism, which was reported as: New evidence for quantum Darwinism found in quantum dots
and also reported as: Bridge to the quantum world: Darwinian concept of natural selection figures into theory about core of physical reality
Excerpt: 

It describes the transition from quantum to classical world as a “decoherence” process that involves a kind of evolutionary progression somewhat analogous to Charles Darwin’s concept of natural selection.

My comment: Darwin’s concept of natural selection was place after first consideration for “conditions of life.” Neo-Darwinian theorists are biologically uninformed science idiots who have failed to grasp the facts known to all serious scientists about the biophysically constrained creation of life and RNA-mediated cell type differentiation in all living genera. Life is all about that base and the sun’s biological energy is the biological basis of life’s diversity.

The sun’s biological energy effects the base pairs and the RNA-mediated events that link the sun to differences in morphological and behavioral phenotypes via the physiology of reproduction in all living genera.

rp_levels-of-organization.jpg

Positive feedback loops and epigenetic traps

Transcription factor trapping by RNA in gene regulatory elements

Conclusion:

…bidirectional transcription of active enhancers and promoters evolved, in part, to facilitate trapping of TFs at specific regulatory elements. The model also suggests that transcription of regulatory elements produces a positive-feedback loop that may contribute to the stability of gene expression programs in cells. The contribution of this TF trapping mechanism to cellular regulation has yet to be established but will be important to elucidate in future studies because much disease-associated sequence variation occurs in enhancers (20, 22) and may thus affect both DNA and RNA sequences that interact with gene regulators.

My comment: Bidirectional transcription did not evolve. It is nutrient-dependent and controlled by the physiology of reproduction. Feedback loops link odor and pheromone signaling with reproduction in species from microbes to humans. That fact links RNA-mediated gene duplication and RNA-mediated amino acid substitutions to the stability of organized genomes via what is known about supercoiled DNA. Supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy.
Researchers who consistently fail to recognize the fact that supercoiled DNA is an epigenetic trap also seem reluctant to acknowledge the epigenetic trap that Schrodinger claimed linked the anti-entropic effect of the sun’s biological energy life on Earth in What is Life?
Excerpt:

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)

My comment: By ignoring the epigenetic trap that links sunlight on contact with water to the energy spectrum manifested in the range from ultraviolet to infrared light, researchers become like theorists who must link the nutrient-dependent biophysically constrained chemistry of RNA-mediated protein folding in their ridiculous claims about mutations and evolution. For example: “…bidirectional transcription of active enhancers and promoters evolved…”
Stop the nonsense! Force all researchers to report their findings in terms of how ecological variation is linked to ecological adaptations via what is currently known about the stability of nutrient-dependent genome organization in all living genera.
See also: Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast and Stable recombination hotspots in birds
reported as: Putting the breaks on meiosis and predicted in Combating Evolution to Fight Disease
Conclusion:

“…an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.”

My comment: The genesis of variation is nutrient-dependent and nothing evolves from anything else. All living genera exemplify links between ecological variation and ecological speciation that is nutrient-dependent and controlled by the physiology of reproduction.
See also: Long non-coding RNAs as a source of new peptides, but stop claiming that there is any such thing as de novo protein evolution. Claims that proteins or species evolve are made only by the biologically uninformed.

Biology to a Physicist

Is life the balance between quantum and classical physics?

If life hangs in the balance between quantum and classical physics, the anti-entropic effect of the sun’s biological energy is what keeps it hanging, albeit not indefinitely.
Until you consider the fact that viruses link entropic elasticity to genomic entropy in all genera, you may not realize that your life hangs in the balance between pseudoscientific nonsense about mutations and facts about the biophysically constrained nutrient-dependent RNA-mediated protein folding.
Protein folding links physics and chemistry to biology via everything know to serious scientists about molecular epigenetics and nutrient-dependent fixation of amino acids that stabilize the organized genomes of all genera. Viruses perturb protein folding, which links them from entropic elasticity to genomic entropy — not from mutations to evolution.

Good Vibrations

Does a delicately orchestrated balance between quantum and classical physics distinguish living from nonliving things?

By Johnjoe McFadden and Jim Al-Khalili | August 1, 2015

My comment to The Scientist:
Re: in his 1994 book, What is Life?, Schrödinger proposed that genes had an organized molecular structure, which he called an aperiodic crystal, and were therefore subject to quantum laws.

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) – Schrödinger (1943)

The anti-entropic force of light can be linked from the slowing of its speed on contact with water to all of life’s biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding by the amino acid substitutions that differentiate all cell types of all individuals of all genera.
Fixation of the amino acids is manifested in nutrient-dependent ecological adaptation in the context of the physiology of reproduction and chromosomal rearrangements. For example, see: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes.
The link from microbes to vertebrates, includes humans. The honeybee model organism may be the best “bridge” to understanding the similarities in the birds and the bees.
The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).
Luca Turin’s works began to link quantum smell to quantum consciousness in the mid 1990’s and the sequencing of the octopus geneome links his works via olfaction from octopuses to crustaceans insects to mammals via conserved molecular mechanisms and symbiosis.
Symbiosis is the ultimate across species example of the anti-entropic force of sunlight. Facts that link physics to chemistry and biology via molecular epigenetics have forced revision of the “Modern Synthesis.”
Theorists are scrambling to make it appear that they still may have some semblance of credibility despite their failure to link anything known about viruses and entropic elasticity to genomic entropy via the accumulation of viral microRNAs. The viral microRNAs perturb protein folding and leads to all pathology when nutrient-dependent microRNAs are not available to support DNA repair mechanisms. DNA repair was linked to a single transcription factor in Heterotypic Signals from Neural HSF-1 Separate Thermotolerance from Longevity
Excerpt:

…it was hypothesized that hsf-1 regulates the aging process by modulating chaperone network components to directly influence the folding state of the proteome ( Morimoto, 2008). Our data suggest an alternate method by which hsf-1 can regulate the aging process. In this model, hsf-1 activates the FOXO transcription factor, which initiates a pro-longevity stress response that is distinct from the heat shock response.

This atoms to ecosystems model links the aging process and anti-aging to a single transcription factor that coordinates different stress response pathways in all cell types that enables organism-level thermoregulation via thermodynamic cycles of protein biosynthesis and degradation that are nutrient-dependent and RNA-mediated via the physiology of nutrient-dependent reproduction.

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

poster-from-jesse

Informing the biologically uninformed

Please help those who are not biologically uninformed link the latest information from Science Magazine to RNA-mediated cell type differentiation in all genera. For example, see: 

Eukaryotic plankton diversity in the sunlit ocean

Introduction:

The sunlit surface layer of the world’s oceans functions as a giant biogeochemical membrane between the atmosphere and the ocean interior (1).

My comment: That fact links the anti-entropic epigenetic effects of the sun’s biological energy from the de novo creation of amino acids to RNA-mediated cell type differentiation that prevents viral microRNAs from causing entropic elasticity that leads to pathology. The anti-entropic epigenetic effects of the sun link photosynthesis and nutrient-dependent microRNAs, which are obviously the key to biodiversity.

The “giant biogeochemical membrane” biophysically constrains the chemistry of nutrient-dependent RNA-mediated protein folding that links RNA-mediated amino acid substitutions to cell type differentiation via fixation of the substitutions in the context of the nutrient-dependent physiology of reproduction.

The evolutionary theorists who invented neo-Darwinism got everything wrong. They started with de Vries definition of mutation and assumed that accumulated mutations could somehow lead to something besides perturbed protein folding and pathology.

terrarium-eco-system

Epigenetics Skeptism

Thanks to Joost G. Wouters for the alert to this nonsense:
1) Michael White in Pacific Standard magazine flatly states that “Epigenetics Is Not Revolutionizing Biology.”
2) Adrian Bird points out in the journal Cell that many of the field’s assumptions and promises remain unproven and are perhaps excessive.
1) White’s article sketches the field’s promise and hype, from questionable epigenetic‬ diets and wild claims about controlling genes with your thoughts. He follows with a summary of epigenetics, then runs through a list of his ridiculous qualms about the field. White paraphrases, “the hype has outrun the science” at a time when serious scientists are Combating Evolution to Fight Disease by integrating everything known about epigenetic links between metabolic networks and genetic networks.
“…scientists have long been aware that our genes aren’t chiseled in stone—they are in a constant dialogue with our environment,” White says. Obviously, he means “gene expression” is not chiseled in stone because the epigenetic landscape is linked to the physical landscape of DNA in all organized genomes by RNA-mediated events. But that point gets glossed over in his excited attack on everything he thinks is not supported by what is currently known about physics, chemistry, and molecular epigenetics.
He doesn’t like the fact that many of the field’s supposed findings for humans — say, that you can inherit specific fears — are based entirely on animal studies, although that is the basis for nearly everything incorporated into today’s medical practice. And of course, pseudoscientists make an issue of whether epigenetic marks are truly a cause or an effect of changes wrought on gene expression by other factors. They have no concept of how the epigenetic landscape is linked via sensory input to the physical landscape of DNA.
White says, “There is no reason to believe that drugs, treatments, or health advice that target these DNA markings will be unusually effective compared to therapies that aren’t specifically epigenetic.” He concludes that it’s overall a good development, but perhaps we need to mind the hype. But see: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing. It links what is also known about nutritional epigenetics to biologically-based cause and effect in species from microbes to man.
2) Edinburgh University’s Adrian Bird writes in the journal Cell about the overblown idea that biology is undergoing some sort of revolutionary turmoil, only part of which is due to epigenetics.
“So that’s not *junk* DNA?”, “What’s the definition of a gene?”, and “What how much effect does long, non-coding RNA actually have?” These issues consume the article’s first half, but he really gets rolling later. We have good evidence of transgenerational epigenetic inheritance in precious few places, which include C. elegans inheritance of RNA-based viral resistance. That Swedish “hunger winter” stuff is interesting, but hardly rigorous just yet.
And anyway, says Bird, why would passing along diabetes or obesity — as with the hunger winter — be some sort of adaptive mechanism? After all, perhaps the apparently inherited traits just result from malfunctions in the slate-wiping that every animal seems to do early in development.’
My comment: Viral resistance is nutrient-dependent and in animals it is controlled by the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction. Thanks to Joost for permission to use pars of his original introduction, with alterations. He wrote: “No permission required on my part…”
Most links are in the PSMAG article itself. Check out those articles here! See also: Serving epigenetics before its time and Scrutinizing the epigenetics revolution

Epigenetics Is Not Revolutionizing Biology

[if you are a social scientist]