Stuart Kauffman Archives

Richard P. Feynman refuted theistic evolution

July 14, 2017

Adaptations, base editing, Diseases & Disorders, Ecology, Human Pheromones, Light Energy, Model Organisms, Neuronal Plasticity, Nutrigenomics, 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

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Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution. The miR-23a~27a~24-2 microRNA cluster buffers transcription…

The Virus-Driven Suicide March for Science

April 24, 2017

James Kohl

Adaptations, biophotonics, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed, RNA-directed DNA methylation, Variations

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Genetic analysis of α-synuclein 3′ untranslated region and its corresponding microRNAs in relation to Parkinson’s compared to dementia with Lewy bodies My summary: Genetic predispositions and energy-dependent microRNA biogenesis link top-down causation to the biophysically constrained transgenerational epigenetic inheritance of neuronal type-specific expression. Energy-dependent variability in endogenous RNA interference and the SNCA gene contribute to synucleinopathies in the context of two different human pathologies. Virus-driven energy theft is linked to the regulation of the α-synuclein (SNCA) gene and the etiology…

Pseudoscientists fail to refute theistic evolution

February 17, 2017

James Kohl

Adaptations, Autophagy, biophotonics, Diseases & Disorders, Ecology, Human Pheromones, Light Energy, Model Organisms, Nutrigenomics, Physics, RNA Directed, 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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Darwinism for the Genomic Age: Connecting Mutation to Diversification …the chief cause of our natural unwillingness to admit that one species has given birth to other and distinct species, is that we are always slow in admitting any great change of which we do not see the intermediate steps. (Darwin, 1859) Darwin put energy-dependent “conditions of life” before what is now known about natural selection for codon optimality. That is the chief cause for ignoring anything that neo-Darwinists claim about…

Ecological law, cooperation, and DNA repair

January 10, 2016

James Kohl

Adaptations, biophotonics, Ecology, Light Energy, Model Organisms, Neuronal Plasticity, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations

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Ecological laws: what would they be and why would they matter? Abstract excerpt: … I argue, the existence of ecological laws would make ecological explanations irreducible to even the most complete possible physical explanations of the same phenomena. Ecological laws would make ecology genuinely autonomous from physics. My comment: This is a fool’s argument. Serious scientists know physics and chemistry must be linked to biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry. The links must be placed into the context of…

A million dollar paradox?

December 10, 2015

James Kohl

Adaptations, biophotonics, Ecology, Light Energy, Model Organisms, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations

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Paradox at the heart of mathematics makes physics problem unanswerable Excerpt 1) Cubitt and his collaborators focused on calculating the ‘spectral gap’: the gap between the lowest energy level that electrons can occupy in a material, and the next one up. My comment: I hesitate to suggest that the problem of the spectral [energy] gap must be placed into the context of what is known about the speed of light on contact with water and how the anti-entropic energy of…

The “great filter” is an epigenetic trap

August 19, 2015

James Kohl

Adaptations, Ecology, Light Energy, Physics, RNA Directed, Variations

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The great filter The silence of universe seems ominous. Was Earth lucky? Thanks to George Ellis for alerting others to this. Excerpt: Nick Lane in his magnificent new book The Vital Question thinks that a peculiar feature of all earthly life — that it traps energy in the form of protons pumped across membranes… Excerpt 2) Next, after a couple of billion years, creatures bigger than microbes emerged, once (Nick Lane argues) an energy-per-gene limit was breached by the invention…

Virus-driven origin of life

March 19, 2015

James Kohl

Light Energy, Physics, RNA Directed

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On the Origins of Life A new experimental system demonstrates that precursors of ribonucleotides, amino acids, and lipids may have simultaneously arisen from the same prebiotic chemistry. By Jef Akst | March 17, 2015 “This is a very important paper,” Jack Szostak, a molecular biologist and origin-of-life researcher… See also: Luis P. Villarreal: We Need a Nonlinear Language for Life Nobelist Jack Szostak has told me this about autocatalytic sets: the people who came up with the original idea, like…