Excerpt:
“…in most cases, the RNA is an mRNA, carrying a protein coding sequence which is translated by the ribosomal machinery into a covalently attached series of amino acids—a protein—which by nature of the varied side chain chemistries and their electrostatic, hydrogen bond, and hydrophobic interactions folds up to a thermodynamic energy minima state to create a functional enzyme or structural protein.”
Thermodynamic cycles of the energy-dependent “minima state” can be explained in this context:
Highlighting the hematology in immunohematology
As research elucidates function, opportunities will be revealed for therapeutic and perhaps pharmacologic intervention into the pathologies that affect the red cell membrane composition and cytoskeleton. The “hematology” of the human red blood cell may be likened to a molecular Rubik’s cube with an intricate array of antigens that literally affect the quality of life and even survival itself.
Simply put, the construction of functional cell membranes is food energy-dependent in all cell types of all living genera.
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations
Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.
Molecular defects are biophysically constrained via microRNA biogenesis and RNA-mediated fixation of amino acid substitutions in the context of the physiology of reproduction.
Dobzhansky’s 1973 joke about the so-called light of evolution has since been placed into the context of jokes made by theorists about
Enhancers, repressors, and promoters
Let’s go back to some very basic molecular biology. The genome contains genes, which are regions of DNA which get transcribed to RNA; in some cases this RNA is itself directly functional (things like tRNAs or the 18S component of the ribosome, for instance) but in most cases, the RNA is an mRNA, carrying a protein coding sequence which is translated by the ribosomal machinery into a covalently attached series of amino acids—a protein—which by nature of the varied side chain chemistries and their electrostatic, hydrogen bond, and hydrophobic interactions folds up to a thermodynamic energy minima state to create a functional enzyme or structural protein. Mutations—changes to the underlying DNA sequence—within any of this coding region are statistically likely to cause unwanted changes of function…
James V. Kohl detailedl how quantized energy-dependent microRNA biogenesis links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency and healthy longevity. Links from what organisms eat to the enzyme-dependent metabolism of food also link metabolic networks to microRNA-mediated genetic networks in the context of RNA interference. Drug therapies alter RNA interference by altering cell type differentiation in all cells of all individuals of all species. For comparison, during the past 26 years, Kohl has detailed how the chemistry of protein folding is biophysically constrained at every level of biological organization by conserved molecular mechanisms.
My comment:
Thank you for making sense of 1) light-activated microRNA biogenesis, 2) naturally occurring RNA interference, and 3) biophysically constrained viral latency. They collectively link the fixation of food energy-dependent RNA-mediated amino acid substitutions to cell type differentiation via the physiology of reproduction and transgenerational epigenetic inheritance in species from microbes to humans.
Please comment soon on the fact that the USAF is actively involved in placing the patent on naturally occurring RNA interference into the context of the prevention or effective treatment of all diseases. The level of obfuscation is increasing at the same time serious scientists, like you, elaborate on the differences between mutations and amino acids.
This claim was added to the accepted claims of serious scientists:
…mutations can be silent (meaning not causing a protein sequence change), or not harmful (causing a change which doesn’t have significant impact), or even possibly advantageous, yielding a biologically more fit product.
No experimental evidence of top-down causation has ever linked any mutation to a “…biologically more fit product.”
See for comparison: Inside the drive to collect DNA from 1 million veterans and revolutionize medicine (2015) and US Air Force Studying Impact of Exome Sequencing in Routine Care (2017-subscription required). Reported also in the context of: Next Generation DNA Sequencing (March 18, 2016)
…Dr. Charla Marshall, Chief, Emerging Technologies Section, Kim Andreaggi, Research Scientist and I worked tirelessly to turn that idea into a forensic protocol, validate and then implement it.”
The massive parallel sequencer used to create the new NGS protocol was originally created to sequence small fragments of DNA with fewer than 350 base pairs, but AFDIL took it even further when they began work on sequencing mtDNA that could be smaller than 120 base pairs.
Anecdote: Dr. Charla Marshall is the daughter of a friend from high school who became a physician. Charla’s mother, Diane, sat behind me in a chemistry class of ~20 people. I was amazed to learn that her works with the forensics of death paralleled my works with ecological adaptations required for life.
See also: The R/evolutionary Divide (2018)
Think of revolutionaries such as Nikola Tesla, Albert Einstein, and Steve Jobs, and of evolutionaries including … well, you probably can’t think of any famous counterparts. They just don’t make it to the pinnacles of science or business stardom.
In 1975, I learned that the future of biology would rely on direct imaging of viruses and the ability to count every single base pair in the DNA of any organism. I was trained to operate and maintain one of the first “laser hematology analyzers.
The cost of the analyzer was ~$50,000 in the context of a bulk purchase agreement with the USAF. People who still make claims about mutations and evolution were already 120 years behind the claims from 1855 that linked nutrition to cell type differentiation via what is now known. For example, laser beams link single-digit percent differences to DNA content via what is known about links from femotosecond blasts of UV light to RNA-mediated DNA repair.
How many more years behind the serious scientists will you and your group fall if you fail to examine the experimental evidence that links energy-dependent changes from angstroms to ecosystems in the context of light-activated microRNA biogenesis and biophysically constrained viral latency?
See for example: Exosomes ‘swarm’ to protect against bacteria inhaled through the nose
Along with this new understanding of the innate immune system, the authors on the JACI paper suggest that their findings may have implications for new methods of delivering drugs through the airway to be developed. More specifically, as natural transporters, exosomes could be used to transfer inhaled packets of therapeutics to cells along the upper airway — and possibly even into the lower airways and lungs.
Exosomes protect all organized genomes from the viruses in bacteria that are inhaled or those that are ingested with food.
The protection of organized genomes by exosomes is the only obvious link to my most recently published review of nutritional epigenetics:
Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems