angstroms to ecosystems

Natural selection for adaptation (10)

September 7, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Human Pheromones, Light Energy, microRNA editing, Model Organisms, Neuronal Plasticity, Physics, replication timing, RNA Directed, RNA editing, RNA interference, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA–Mediated Epigenetic Heredity, Variations
One Comment

See: Ignoring light-activated microRNA biogenesis 10/16/18, and compare our section on pre-mRNAs and molecular epigenetics in: From Fertilization to Adult Sexual Behavior (1996) to MicroRNAs buffer genetic variation at specific temperatures during embryonic development 10/16/18, which was previously published sans mention of microRNAs as Temporal development of Drosophila embryos is highly robust across a wide temperature range 7/11/18 Changing the term from pre-mRNAs to microRNAs obfuscated food energy-dependent pheromone-regulated genetic processes of cause and effect, but see ~127,000 indexed publications…

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Natural selection for adaptation (9)

September 7, 2021
James Kohl
Adaptations, Diseases & Disorders, Ecology, microRNA editing, Physics, replication timing, RNA Directed, RNA editing, RNA interference, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA–Mediated Epigenetic Heredity
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“Mapping the dynamic transfer functions of eukaryotic gene regulation” 8/31/21 links energy-dependent changes from angstroms to ecosystems via “Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion“ For review see Lynn Zechiedrich‘s group: “Structural diversity of supercoiled DNA” and the representation of God’s Creation of energy-dependent microRNA-mediated biodiversity in: See also: Chemists Know (10/6/14) Remember to start with Feynman’s claims about food energy. Stop the killing spree! Protect yourself sans synthetic mRNA vaccine-induced pathology. See also: Getting Closer to…

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microRNA-mediated replication cycles (9)

July 6, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Light Energy, microRNA editing, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, replication timing, RNA Directed, RNA editing, RNA interference, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Subatomic
One Comment

See first: microRNA-mediated replication cycles (8) Rotavirus research: 2014-2020 7/2/21 A temperature sensitive mutant… in the triplet encoding amino acid 138 of VP1 (L138P)…was separately expressed as a… protein, shown to interact with viroplasm-like particles (VLPs) in uninfected cells and to synthesize RNA in vitro…” My summary: The rotavirus steals the energy required for the ATP-dependent synthesis of RNA, which typically biophysically constrains viral latency across kingdoms. Contextual constraints occur via light-activated carbon fixation, oxidative phosphorylation and RNA interference (RNAi).…

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microRNA-mediated replication cycles (7)

July 5, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Human Pheromones, Model Organisms, Physics, replication timing, RNA Directed, RNA interference, RNA-mediated gene silencing, RNA–Mediated Epigenetic Heredity
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Infectious Thoughts: Discovering Biology as a Social Science (2021 preprint) “Regarding the Kohl papers; odors are clearly crucial for social communication and food has been a part of this (as has I think RNA). This is a nice summary. But curiously, he does not mention that if an individual honey bee feeds outside that of its own communal hive feeding it then becomes recognized as foreign and is killed by the hive. Missing is the concept of group identity. And…

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microRNA-mediated replication timing (5)

July 2, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Light Energy, microRNA editing, Model Organisms, Physics, replication timing, RNA Directed, RNA editing, RNA interference, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
One Comment

Facts about energy-dependent microRNA-mediated biophysical constraints, which link protonated RNA interference (RNAi) to cell type differentiation across kingdoms via the physiology of reproduction and fixation of amino acid substitutions in organized genomes, are included in: pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally 6/29/21 Our results suggest a model in which transcription and splicing are largely independent, and the existence of a slow moving zone around the transcription site allows for the unification of co-transcriptional and post-transcriptional models of…

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Quantum Darwinism (3)

April 15, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, Cytosis, Diseases & Disorders, Ecology, Physics, RNA Directed, RNA interference
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“Quantum biology” is quantum Darwinism Starting from…discovery of quantum coherence in low-temperature photosynthetic microbes in 2007, quantum coherence is emerging as a general principle of biological systems. See: MicroRNAs organize intrinsic variation into stem cell states 3/5/20 …naturally arising cell-to-cell variation, sometimes described as stochastic fluctuation, is in fact coherently organized biology. Theorists chose neo-Darwinian pseudoscientific nonsense about beneficial mutations and evolution via natural selection across billions to millions of years instead of the explanatory power of quantum Darwinism. Their ignorance…

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Quantum Darwinism (1)

April 8, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Model Organisms, RNA Directed, RNA interference, RNA-directed DNA methylation, RNA–Mediated Epigenetic Heredity, Variations
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See first: Pheromones protect us from viruses parts 1-10 For a historical perspective on the development of healthy ecosystems, see: Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus musculus L.) (1994) and From Fertilization to Adult Sexual Behavior (1996) For links from quantum Darwinism to all energy-dependent biophysically constrained biodiversity, see also: Quantum Criticality at the Origin of Life 3/3/15 The number of proteins grows exponentially with the number n of amino acids… Peptide synthesis at the…

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Defeating disease and Communism (4)

March 16, 2021
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Cytosis, Diseases & Disorders, Ecology, Light Energy, microRNA editing, Physics, RNA Directed, RNA editing, RNA interference, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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On 3/16/21, Timothy Normand Miller, in his role as the stupid atheist, @theosib2 wrote: If there were any of the typical indications of a designer in DNA, then I would consider that there must have been a designer. However, none of those can be found. Peptide synthesis at the origin of life 11/13/20 and The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors 9/13/18 were linked to Properties and biological impact…

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Creationism, Communism and Corruption (1)

December 22, 2020
James Kohl
Adaptations, biophotonics, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, RNA interference, Subatomic
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The Chinese Communist Party (CCP) consistently failed to address facts that link the National Microbiome Initiative to the Precision Medicine Initiative via what people eat and what is known to all intelligent serious scientists about the microRNA-mediated pheromone-regulated genetic processes of reproduction. See for instance more than 113,000 indexed published works that mention “microRNA.” See for example: Multiple microRNAs regulate tacrolimus metabolism through CYP3A5 12/18/20 MicroRNAs are novel regulators of tacrolimus metabolism and the… …CYP3A5 gene polymorphism accounts for the…

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The microRNA-mediated fight against COVID-19 (1)

August 21, 2020
James Kohl
Adaptations, Alternative Splicings, Autophagy, base editing, biophotonics, Diseases & Disorders, Ecology, Human Pheromones, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA interference, What's in the News
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History (1) Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) …the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. History (2) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014 unpublished) This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino…

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