Hydrogen-atom transfer in DNA base pairs (5)

By: James V. Kohl | Published on: January 21, 2016

(click to enlarge)

Can Anybody Actually Win The Evolution 2.0 Prize?

January 18, 2016 at 9:44 pm

In an invited review of nutritional epigenetics, I linked atoms to ecosystems without the pseudoscientific nonsense touted by neo-Darwinists.
Kohl, James V. (2014): Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
The invited submission was returned without review.
When I provide all the details for the origin of the DNA code, what prevents the submission from being rejected without comment?

January 18, 2016 at 11:13 pm

Can Anybody Actually Win The Evolution 2.0 Prize?

Thanks. I agree that the atoms to ecosystems model did not answer the questions. But your approach seems to limit any attempt to link the source of the code from information to hydrogen-atom transfer in DNA base pairs.

I’m not sure what “values of both encoding table and decoding table” have to do with linking the origin of the code to cell type differentiation via the code or via what is currently known about biophysically constrained protein folding chemistry.
You seem to be asking for someone to address the problem from the perspective of an engineer instead of from the perspective of a biophysicist who can link biologically-based cause and effect from the origin of the code to chromosomal rearrangements and biodiversity with examples from testing already performed in every hospital medical laboratory.

January 20, 2016 at 4:12 pm

Intelligent Design’s Blind Spot

Are you clarifying the fact that the de novo creation of the code is not to be considered in the context of the prize? Is that what you mean by the statement: “…the prize excludes any life form or any code introduced at the outset of the experiment.”

Are you attempting to limit an explanation of how the origin of the code links atoms to ecosystems via DNA repair?I’m somewhat confused about the purpose of your book. Did you intend to exclude any explanations of biologically-based cause and effect that would come from creationists or anyone who could link Sheldrake’s works from morphic resonance to Lipton’s works via Stuart Kauffman’s claims about the need for an anti-entropic force?

January 20, 2016 at 4:17 pm

Intelligent Design’s Blind Spot

Thanks. I start with the de novo creation of nucleic acids. Are you able to answer questions about the links from quantum physics to chemistry and the conserved molecular mechanisms that link atoms to ecosystems in all living genera?

James V. Kohl says:

January 23, 2016 at 6:45 pm

Thanks. I have demonstrated the well-known need for an anti-entropic force, which must be linked from Schrodinger’s claims to Stuart Kauffman’s claims. I have detailed the links from the anti-entropic force to RNA-mediated DNA repair at a time when Kauffman and Sheldrake are not discussing Lipton’s works and you are not discussing the works that refute Shapiro’s theories.
You have led many others to a point where they can dismiss “Evolution 2.0” as nothing more than another opinion. That’s what folks like PZ Myers want them to do, and that’s why he attacked me for my accurate representation of chromosomal rearrangements.
Others have linked the anti-entropic force from microbes in the guts of octopuses to chromosomal rearrangements and to human cognition via the conserved molecular mechanisms I have helped to detail during the past 20 years.
Simply put, you’re still trying to address the ridiculous claims of people like PZ Myers when it’s time to dismiss their nonsense and move forward using experimental evidence of biologically- based cause and effect.
For example: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit https://www.cell.com/cell/abstract/S0092-8674%2815%2900184-1 and Feedback loops link odor and pheromone signaling with reproduction https://www.ncbi.nlm.nih.gov/pubmed/16290036 are ‘cut from the same cloth.’
The metaphorical cloth emerged in the context of Dobzhansky’s “light of evolution,” which turned out to be the light that linked ecological variation to ecological adaptation in all living genera via nutrient-dependent RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living genera.

Perry Marshall says:

January 24, 2016 at 6:36 pm

I agree you have demonstrated the well-known need for an anti-entropic force. One comes to the same conclusion from many different approaches. But my priority is getting from chemicals to code, empirically.
Finally, Perry Marshall and I agree on the first part of what I wanted to include in two part prize submission.

James V. Kohl says:

January 26, 2016 at 3:50 pm

Thanks. Dobzhansky’s “light of evolution” (1973) is sunlight. See also, Dobzhansky (1964). Apparently, he had a bizarre sense of humor. He linked ecological variation to ecological adaptation in all living genera via the chemistry of RNA-mediated amino acid substitutions and nutrient-dependent protein folding.
At that point, the physiology of reproduction replaces ideas about random mutations and evolution. Experimental evidence of chromosomal rearrangements and ecological speciation trump neo-Darwinian theories (separately and collectively).
Anyone who excludes the epigenetic effects of sunlight cannot get from chemicals to code. Thus, if you keep me from submitting details that link top-down causation to all cell type differentiation in all individuals of all living genera, your prize money is safe.
No serious scientist will attempt to claim the prize money without first linking Schrodinger’s sunlight and Dobzhansky’s “light of evolution” to current representations, which must be placed into the light of what is known about supercoiled DNA.

James V. Kohl says:

January 28, 2016 at 6:53 pm

Thanks. You are speculatively interpreting my works when you have not accepted part 1 or part 2 of the submission. Why do you think I have not addressed the creation of the first cell?
Today, others reported everything I reported in what could have been part 1 of a 2 part submission.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
Now see: “Team uses internet network theory to decipher the first epigenetic communication network” January 28, 2016
In part 2 of my submission, I will detail the origin of the code and explain how information leads to the de novo creation of receptors and all cell types in all living genera.
If you want part 2, accept part 1. If not, others will keep reporting the details I want to report in the context of mutations and evolution.

Evolution 2.0’s blind spot

Perhaps the problem is that my model challenges Perry Marshall’s representations in Evolution 2.0. For comparison, some biophysicists and molecular biologists will link the following 4 published works:

1) Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder

2) The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

3) Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress and

4) Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

My comment: There is only one way to link transgenerational epigenetic inheritance from the nutrient-dependent pheromone-controlled physiology of reproduction in soil bacteria to ingestion of plants and toxicosis via the sperm microRNAome in a mammal. Serious scientists must start with nutrient energy-dependent Hydrogen-Atom Transfer in DNA Base Pairs. That is the way that’s exclude in Evolution 2.0. Sunlight is not a code, but I have already repeated linked it to the origin of the code and the biophysically constrained molecular mechanisms that link chemistry to all cell type differentiation.
The problem for neo-Darwinian evolutionary theorists and for Perry Marshall has since been succinctly reported in:
Researchers observe one of the world’s fastest chemical reactions for the first time
Excerpt:

Extremely fast reactions are often covered up by slower ones.

My comment: The fact that theorists have never before observed the world’s fastest chemical reactions explains why Perry Marshall claims the origin of the DNA code is unknown. Serious scientists know that, whether or not the reactions are observed, the origin of the DNA code must link atoms to ecosystems in all living genera.
No new labels are required, no new calculations. Nothing new under the sun is required. Others need only look further into Perry Marshall’s claims and link them to the claims of serious scientists who know how ecological variation leads to ecological adaptation in the context of the sun’s biological energy and hydrogen-atom transfer in DNA base pairs.
See also:

See also: Published on 25 Aug 2014 with my emphasis

Base pairs, which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs (G-C and A-U) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g., G-U or A-A) allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins.

My comment: In my model, hydrogen-atom transfer in DNA base pairs link the nutrient energy-dependent amino acid sequence to the the physiology of reproduction and to all biodiversity.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology.

My comment: I’ve since added the molecular mechanisms that link base-pairing to supercoiled DNA and chromosomal rearrangements that link the physiology of reproduction to ecological speciation. By starting with the sun’s anti-entropic biological virucidal energy, terms like mutations and evolution can be replaced with the terms used by ecologists.
See for example: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA, which was reported as Base-pairing protects DNA from UV damage.
Excerpt:

… the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy.

My comment: Protection from UV damage via the Watson-Crick base-pairing mechanisms also links the virucidal property of UV light to antibiotic resistance.
See: Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation
Excerpt:

Bacteria use these systems to sense and respond to their environment, which include stresses and nutrient conditions, but also include other bacteria and their antagonistic enzymes and specialized metabolites.

My comment: The systems are nutrient-dependent and they link ecological variation to ecological adaptation via specialized metabolites called pheromones. The pheromones control the nutrient-dependent physiology of reproduction in species from microbes to mammals. Again, please note the fact that there is no need to mention any theoretical links from mutations to evolution. The Antibiotic Resistance was reported as: Bacteria battle: How one changes appearance, moves away to resist the other

Excerpt:

Straight said the common understanding of the usefulness of antibiotics, however, sidestepped the ecological dynamics of the bacteria themselves in how they form communities, and interact with each other.

My comment: The ecological dynamics of social niche construction are nutrient-dependent and pheromone-controlled in species from microbes to mammals. In this example of that fact, biophysically constrained cell type differentiation was linked from UV light to the DNA base pairing protection mechanism. The facts about cell type differentiation were revealed in context of UV absorbances at 319, 333, and 351 nm. The differences in the UV absorbances link RNA-mediated amino acid substitutions to a conjugated pentaene moiety.
Every level of investigation that links UV light from energy dependent changes in base pairs to cell type differentiation becomes increasingly complex. None of de Vries “jump-like” changes are required, so there is no reason to mention his definition of “mutation.”
Definitions and assumptions about how long it might take one species to evolve into another are irrelevant. No experimental evidence of biologically-based cause and effect suggests that any species has ever mutated and evolved into any other species.

See also: [Antiviral action of carbonyl-conjugated pentaene macrolides]
Abstract excerpt:

Clear antiviral activity of carbonyl-conjugated pentaene macrolides, such as flavofungin, mycothicin, brunefungin and flavopentin was shown on models with infectious and oncogenic viruses.

See also the indexed articles in a search for: UV light toll-like receptor
For example with my emphasis: A Light-Controlled TLR4 Agonist and Selectable Activation of Cell Subpopulations; Ultraviolet radiation signaling through TLR4/MyD88 constrains DNA repair and plays a role in cutaneous immunosuppression; TLR3: a receptor that recognizes cell injury is essential for permeability barrier homeostasis following UV irradiation
My comment: There are now clear links to controlled and contrained DNA repair and homeostasis from UV light via the innate immune system and cell type differentiation. Differences in somatic cell types also have been linked from the germ lines of plants (like fescues) to the germlines of mammals (like bulls).
See: Soma-to-Germline Transmission of RNA in Mice Xenografted with Human Tumour Cells: Possible Transport by Exosomes reported again on January 14, 2016 as No Sex Required: Body Cells Transfer Genetic Info Directly Into Sperm Cells, Amazing Study Finds and Previously thought impossible: Body cells transfer genetic information directly into sperm cells
Again, see also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
My comment: Everything known to serious scientists about cell type differentiation links nutrient energy-dependent changes in base pairs from Darwin’s “conditions of life” and Schrodinger’s “What is Life?” to Dobzhansky’s “light of evolution.” Nothing in Biology Makes Any Sense Except in the Light of Evolution. However, nothing about evolution makes sense outside the context of nutrient energy-dependent changes in base pairs that Dobzhansky mentioned in this context:
Excerpt:

…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 also: Combating Evolution to Fight Disease
Excerpt:

The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.

My comment: The current molecular understanding of the genesis of variation links the availability of nutrients to ecological adaptation via hydrogen-atom transfer in DNA base pairs linked to RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
See also: 2003 Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
See also: 2009 Bacterial Quorum-Sensing Network Architectures
See also: 2014 Life is physics and chemistry and communication
See also: (unpublished) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
I suspect that by now all serious scientists understand that hydrogen-atom transfer in DNA base pairs must be linked to RNA-mediated amino acid substitutions in the context of biophysically constrained chemistry of protein folding. They should also understand why I have not re-submitted my invited review of nutritional epigenetics to another publisher.
Having arrived at the additional complexity that links quantum physics to cell type differentiation via hydrogen-atom transfer in DNA base pairs, I doubt that I will ever again publish in a peer-reviewed journal. My peers can, however, direct their comments and criticisms of my atoms to ecosystems model in the comments section here, or comment on my FB group.
Until then, I will keep reporting news, like this. CERN scientists ‘break the speed of light’
Whether or not this is confirmed makes no difference. The speed of light on contact with water has not yet been linked by anyone else from hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via the physiology of reproduction in all living genera.
Until others are willing to look at the anti-entropic epigenetic effects of the sun’s virucidal biological energy, learning about cell type differentiation in the context of pathology or healthy longevity will be more difficult. The obvious requirement is to start with the de novo creation of genes and link gene activation to biodiversity without the pseudoscientific nonsense of mutations and evolution.
See also: Cancer: Evolution 2.0’s Blind Spot