- Hydrogen-Atom Transfer in DNA Base Pairs (2);
- Hydrogen-Atom Transfer in DNA Base Pairs (3)
- Hydrogen-Atom Transfer in DNA Base Pairs (4)
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.
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.
… 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.
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
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.
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
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:
…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
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: 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