RNA-mediated.com (topic descriptions)

The life cycle of an mRNA in a eukaryotic cell RNA is transcribed in the nucleus processing, it is transported to the cytoplasm and translated by the ribosome. Finally the mRNA is degraded
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Another companion domain has been added to the ScentofEros.com; Pheromones.com, PerfumingtheMind.com collection

Intro to topics/catagories at RNA-mediated.com

RNA-Mediated

Information that links physics, chemistry, and molecular epigenetics from ecological variation to ecological adaptations via RNA-mediated events, such as the de novo creation of olfactory receptor genes, will be posted here to encourage discussion of a paradigm shift. When viewed in the context of RNA-mediated ecological adaptation:

Evolution is all about competition and cooperation–and communication.

Traditional theories of evolution emphasize the competitive aspect and de-emphasize or ignore the cooperative aspect. But developments in genetics and molecular biology render this emphasis implausible.”

— Greg Bear “THE DARWIN CODE” Mar 22 2005

The paradigm shift leads away from pseudoscientific nonsense about mutations and evolution to what is currently known by serious scientists about communication and about biophysically constrained nutrient-dependent RNA-mediated nutrient-dependent protein folding. The nutrient-dependent chemistry of protein folding links ecological variation to ecological adaptations in species from microbes to man via conserved molecular mechanisms during life history transitions.

Nearly everything known about cell type differences in species from microbes to man has been learned since the turn of this century. We predicted most of what has been learned about the molecular epigenetics of cell type differentiation in our 1996 review: From Fertilization to Adult Sexual Behavior. My other published works, presentations, and blog posts continue to explore that paradigm-shifting work and show how ecological variation leads to ecological adaptations.

Already, more than 200 blog posts about RNA-mediated cause and effect have integrated scientific discoveries as they have appeared. It is time to separate RNA-mediated cause from the epigenetic effects of food odors and pheromones. At PerfumingtheMind.com, I will continue to explain how new scientific discoveries link food odors and pheromones to differences in the development of behavior via conserved molecular mechanisms in species from microbes to man. Intelligent discussion among self-identified participants will be encouraged.

RNA-mediated.com details aspects of physics, chemistry, and conserved molecular mechanisms that link communication between metabolic networks and genetic networks to what is known about differences in morphological phenotypes (bodies) and behavioral phenotypes (brains). It is resource for technical information about the molecular neuroscience of the mind that helps to ensure you will learn more learn more about similarities and differences than any social scientist could ever tell you. Some content is directed towards a general audience, but most people will find they are in ‘over their head’ unless they have an interest in learning about accurate representations of why there are similarities across species and how RNA-mediated differences develop. If you would rather continue to believe that mutations in genes cause differences to evolve, this is not a source of information for you. It is a source of embarrassment for all theorists.

“Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene.” See: Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer

RNA-directed DNA methylation links RNA-mediated alternative splicings to nutrient-dependent cell type differentiation. See: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

Nutrient-dependent alternative splicings link what is currently known about nutrigenomics to metabolic networks and genetic networks. See: Nutrigenomics: A controversy

Metabolic networks and genetic networks are linked from the metabolism of therapeutic drugs to epigenetically effected amino acid substitutions and RNA-mediated outcomes. See: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing

Amino acid substitutions are linked from metabolic networks and genetic networks to human behavior during life history transitions. See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Model organisms link top-down causation to epigenetically-effected differences in morphology and behavior. For example, the honeybee is 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. See: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.

The epigenetic effect of human pheromones on the development of RNA-mediated changes in morphology and behavior parallel the effects on morphology and affects on behavior in the honeybee. See our award-winning review: Human pheromones: integrating neuroendocrinology and ethology

Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind won the same award in 2002. Excerpt: “Evolutionary psychologists often overlook a wealth of information existing between the proximate genotypic level and the ultimate phenotypic level. This commonly ignored level of biological organization is the ongoing activity of neurobiological systems.”

In 2014, Israeli middle schools began to teach the theory of evolution. “…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.” Serious scientists throughout the world have been learning the difference between theory and biologically-based facts during the past decade. Some think it is time to teach facts before students begin to believe in ridiculous theories.

Claims that “…mutations supply the raw material from which new life forms evolve…” continue to be replaces as experimental evidence shows that “Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

Physics
“The absorption of quanta of light (photons) is important for many biological processes such as vision, photosynthesis, and animal magnetoreception…” Photoactivated biological processes as quantum measurements. “Analyzing photosynthesis, vision, and magnetoreception, they concluded that only the latter requires quantum coherence. For the other two, the ensuing chemical reactions may still occur without it, albeit with reduced efficiency.” Synopsis: When is Biology Quantum? The fact that biophysical constraints prevent mutations from leading to increasing organismal complexity has been virtually ignored by population geneticists. An extreme example of this ignorance is manifested in the conclusion from Mutation-Driven Evolution (p. 199). “… genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” Population geneticist ignore the need for anti-entropic epigenetic traps that link entropic elasticity to epistasis.

Light-induced amino acid substitutions link the biophysically constrained chemistry of RNA-mediated protein folding from the biological energy of the sun to cell type differentiation in plants and animals. Unfortunately, some researchers do not know the difference between a mutation and an amino acid substitution.

Ecological variation is linked to ecological adaptations by differences in viral microRNAs and nutrient-dependent microRNAs. The nutrient-dependent microRNA/messenger RNA balance links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via the physiology of their pheromone-controlled reproduction and fixation of amino acid substitutions.

The development of the central nervous system is nutrient-dependent and pheromone-controlled. It can be viewed in the context of differences in nutrient-dependent microRNAs MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains. It can also be viewed in the context of differences in amino acid substitutions in primates. 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. — Dobzhansky (1973, p. 127)

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