Hydrogen-Atom Transfer in DNA Base Pairs

By: James V. Kohl | Published on: December 4, 2015

I requested a reprint of this article from the senior author on 10/29/15 and received it on 12/18/15.  Scientific progress moves fast, and Hydrogen-Atom Transfer in DNA Base Pairs (2) appears before the continuation of this post is linked to Hydrogen-Atom Transfer in DNA Base Pairs (3) and others in this series.
Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution [subscription required]
It was reported as:

Researchers observe one of the world’s fastest chemical reactions for the first time

My comment: I will try to explain what they claim to have observed in the context of an atoms to ecosystems model of RNA-mediated cell type differentiation. The explanation will invite attacks by biologically uninformed science idiots, because it becomes obvious that RNA-mediated cell type differentiation is biophysically constrained by epigenetic effects on the structure and function of DNA that begin with epigenetically trapped light. I have not found anyplace else to discuss the links from UV light to energy-dependent base pair substitutions without the interference of those who cannot comprehend why physics and chemistry must be linked from top-down causation to the conserved molecular mechanisms of biologically-based cause and effect.
I encourage discussion of the claims in the news report in the context of the reports that follow:

New NASA study reveals origin of organic matter in Apollo lunar samples

Re: Amino acids from four sources.
1) contamination from terrestrial sources 2) rocket exhaust precursor molecules contamination 3) solar wind 4) chemical reactions inside asteroids
Sutherland’s group “…created nucleic acid precursors starting with just hydrogen cyanide (HCN), hydrogen sulfide (H2S), and ultraviolet (UV) light.”
The virucidal property of UV light links the sun’s biological energy to the de novo creation of RNA and the de novo creation of all cell types in all individuals of all species via the prevention of virus-driven genomic entropy.
Simply put, this links atoms to ecosystems via everything currently known to serious scientists about biophysically constrained protein folding chemistry and all biomass, which does not appear to have its origins in outer space — except perhaps when viewed from the perspective of biologically uninformed science idiots.

New Video: Quantum Annealing Explained

Quantum annealing appears to link assumptions about the evolution of quantum states to the evolution of biomass and the evolution of biodiversity outside the context of an atoms to ecosystems model. It could be an example of the one miracle that must be given to theorists so that they can place their ridiculous theories about evolution into the context of big bang cosmology and support for the evolution industry.
The immediate impression I got from the explanation of quantum annealing was that something must be happening at the sub-atomic level that links the anti-entropic energy of the sun from the virucidal effects of UV light to supercoiled DNA, which appears to protects the organized genomes of all living genera from virus-driven genomic entropy.
The alternative would be random optimization of quantum states that somehow became organized in the context of links from the epigenetic landscape to the physical landscape of DNA that appear to be nutrient-dependent and controlled by the physiology of reproduction.  In other words, if an energy source is a secondary consideration, quantum annealing might act as adaptive selection for an energy source. That could be the explanation for how all biodiversity on Earth evolved from nothing, including no source of energy. Indeed, neo-Darwinian theorists might still claim that de Vries 1904 definition of mutation is all that is required to link sudden energy jumps from no energy at all to all biodiversity with or without natural selection.
For example, without natural selection, evolution might “just happen.” See: The Surprising Origins of Evolutionary Complexity

Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

My comment to the Scientific American site on 7/21/13

Darwin’s ‘conditions of life’ are nutrient-dependent. Nutrients metabolize to species specific pheromones that control reproduction in species from microbes to man via the same molecular mechanisms.
The epigenetic effects of food odors associated with nutrition and pheromones associated with socialization and with sexual reproduction are clearly responsible for linking the sensory environment directly to adaptive evolution sans consideration of mutation-driven evolution.
See for details: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology 2013, 3: 20553 – https://dx.doi.org/10.3402/snp.v3i0.20553
The model includes examples of how a change in a single base pair results in an amino acid substitution that clearly links adaptive evolution, which has occurred during the past ~30,000 years in a human population in what is now central China, to the same molecular mechanisms in mice, other mammals, insects, nematodes, and microbes.

My comment to the Scientific American site on 4/19/14
Ecological variation in nutrient availability and epigenetically-effected methylation is clearly the driver of ecological adaptations manifested in species diversity. If this had not already become clear to serious scientists, methylation would not be reported in the context of ‘Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan‘  (Instead, methylation is substituted for mutations and linked to epigenetic cause and effect.)
If nutrient-dependent pheromone-controlled ecological adaptations were not clearly responsible for species diversity, serious scientists might still claim that mutations somehow caused it, as they have claimed until recently. See: ‘A functional test of Neandertal and modern human mitochondrial targeting sequences. However, as serious scientists realized that there is no such thing as a fixed beneficial mutation, only evolutionary theorists continue to make claims based on the pseudoscience of population genetics.
It is unfortunate that pseudoscientists have influenced the ridiculous beliefs of so many people, because most of them can no longer grasp the scientific truth that life is nutrient-dependent and that the physiology of reproduction is controlled by pheromones in species from microbes to man. However, the fact that scientists like Svante Paabo have finally recognized the role of methylation is a sign that the next generation will be the one that dismisses mutation-initiated natural selection and/or mutation-driven evolution from any further consideration whatsoever.
Thus, there is still hope for scientific progress to be made by those who are not stuck with their opinions, while others examine the facts. See, for example, “Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.”
See also:

Entanglement at heart of ‘two-for-one’ fission in next-generation solar cells


…developed a model which showed that when the molecules are vibrating, they possess new quantum states that simultaneously have the properties of both the light-absorbing singlet exciton and the dark triplet pairs. These quantum ‘super positions’, which are the basis of Schrödinger’s famous thought experiment in which a cat is — according to quantum theory — in a state of being both alive and dead at the same time, not only make the triplet pairs visible, they also allow fission to occur directly from the moment light is absorbed.

My comment: The model also appears to link Schrödinger’s claims about the anti-entropic energy of sunlight to nutrient-dependent base pair changes in bioluminescent microbes and to RNA-mediated cell type differentiation in all individuals of all living genera via their physiology of reproduction and the supercoiled DNA that prevents virus-driven genomic entropy.
The viruses pirate the nutrient-dependent energy (e.g., light energy) that bacteria and plants need to reproduce. Their reproduction provides an ecological foundation for the food chain that links all life on Earth to the sun’s biological energy via top-down causation in the context of quantum physics, quantum chemistry, quantum smell, quantum biology, and quantum consciousness as demonstrated in works by Luca Turin’s group and by Anna Di Cosmo​’s group.

The Most Astounding Bioluminescent Wonders on Planet Earth


Through evolution, or at least the act of it, creatures in the animal kingdom have gained abilities that far exceed those of you and I. One of those characteristics is bioluminescence.

My comment: The attribution of bioluminescence to evolution fails to link it from the biological energy of the sun to the de novo creation of nucleic acids and fails to link the virucidal effect of UV light to the biophysically constrained RNA-mediated cell type differentiation of all living genera in the context of their physiology of reproduction.

Instead, like magic, the claim that bioluminescence “evolved’ is a way to direct your attention away from the fact that no experimental evidence of biologically-based cause and effect suggests that any morphological phenotype or behavioral phenotype has ever evolved because phenotypes must be linked to nutrient-dependent RNA-mediated amino acid substitutions and chromosomal rearrangements to the physiology of reproduction in species from microbes to humans.

Chemistry in evolution

First there was inorganic chemistry (the solar system, the elements and minerals – about 4 to 5 billion years ago, 4–5Ga). Then there was life, the crucial role of photochemistry, emergence of cells, of DNA, blue-green algae (circa 2Ga) and the production of oxygen, followed by animals (circa 1Ga).
My comment: First, there was nothing and there would never have been anything if not for the light-induced de novo creation of nucleic acids and RNA-mediated events that link the de novo creation of G protein-coupled receptors from nutrient uptake to the physiology of reproduction via the innate ability described as DNA sensing.
DNA sensing limits virus-driven DNA damage and typically ensures healthy longevity via nutrient-dependent RNA-mediated amino acid substitutions that enable the supercoiling of DNA.
Nothing has ever evolved outside the context of nutrient-dependent base pair substitutions and RNA-mediated DNA repair, which is why some evolutionary theorists have changed their claims to claims about co-evolution.
Co-evolution is ecological adaptation in the context of ecological variation and the physiology of reproduction in all living genera. Their knowledge of ecological speciation is why the 2015 Nobel Laureates in Chemistry were criticized for including too much biology — in the context of DNA repair. Many chemists ignored the fact that DNA repair is required for ecological speciation to occur because, like many theoretical physicists, they never learned to think about the requirement to link physics and chemistry to biology via conserved molecular mechanisms that link atoms to ecosystems.
See for example:

Photochemical genetics


We have developed ‘photochemical genetic’ methods to rapidly control the activity of proteins in living cells, providing insight into the dynamics of elementary steps in biological processes, as well as insight into the regulation of intracellular network connectivity in space and time; with these methods, we hope to understand molecular processes inside cells and organisms with the level of precision more commonly associated with in vitro biochemistry or biophysics.

See also:

Research offers new insight into light detection in vertebrates

“Some of the photopigments discovered were found to be UV-sensitive and have the potential to assist with functions such as cell DNA repair,” he said.
My comment: Unfortunately, he said nothing about the virucidal properties of UV light, which means we cannot link the sun’s biological energy to the de novo creation of nucleic acids. It also means we can’t link the anti-entropic energy from the sun from RNA-mediated DNA repair of damage to organized genomes that is caused by virus perturbed energy-dependent protein folding.  If any explanation of how UV light has the potential to assist with DNA repair were provided, we might link nutrient energy-dependent ecological adaptations to RNA-mediated gene duplication and RNA-mediated DNA repair via nutrient-dependent amino acid substitutions and what was learned about microRNAs and adhesion proteins via the sequencing of the octopus genome.
See also:

Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation

Deiters and co-workers controlled protein localization by incorporating a photoactive amino acid in a nuclear localization signal so that it could only interact with the nuclear import machinery when the chemical moiety was removed via irradiation with UV light [10, 11]. This approach is not reversible and requires the bioavailability of a non-natural amino acid.
My comment: They link light-activated control of what would typically occur in the context of a nutrient-dependent RNA-mediated amino acid substitutions to what is represented as “…a powerful and potentially general way of controlling multiple cellular functions.” In the context of the other reports in this post, UV light is linked from its virucidal property to RNA-mediated DNA repair via amino acid substitutions that must be fixed in the organized genomes of all living genera to protect them from virus-driven genomic entropy.
All serious scientists have learned that the speed of light must be linked from the sun’s biological energy to cell type differentiation in all living genera. Why is there no evidence that science journalists, like Carl Zimmer, are going to learn how to link atoms to ecosystems.
On 12/3/15, in A radically simple idea may open the door to a new world of antibiotics, Zimmer claimed: “Epstein is using ichips to understand the ecology of bacteria in the natural world.”
On 12/3/15, in Parents May Pass Down More Than Just Genes, Study Suggests Zimmer claimed that: “…pinning down the epigenetic effects that fathers pass to their children will take much more work.”
Zimmer’s claims represent the epic failure of all science journalists to learn about how epigenetically-effected RNA-mediated cell type differentiation occurs in all living genera. All reports by serious scientists have linked nutrient energy-dependent microRNAs and cell adhesion proteins to protection from virus-driven genomic entropy via the conserved molecular mechanisms of pheromone-controlled reproduction in species from microbes to humans. The only work that is still required to pin down the epigenetic effects of nutrient-dependent pheromone-controlled cell type differentiation, which is linked to morphological and behavioral diversity in all individuals of all species, is the work that will be required for science journalists to accurately portray what is known at the same time they quit touting the pseudoscientific nonsense about mutations and evolution.

Natural Selection Unfriends Darwin


Biological evolution exists only as a philosophical fact, not as a scientific fact.

Viral Genome Junk Is Bunk


Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

My comment: The time has come to ask neo-Darwinian theorists and theoretical physicists what they think they got right about the role of mutations and/or natural selection and how what they got right links atoms to ecosystems in the context of what is known to serious scientists about biologically-based cause and effect.

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