Epigenetic

Modelling life scientifically: RNA-mediated events

June 10, 2016
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, RNA Directed, Variations
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Experiment: “An attempt to arrive at an accurate result.” — James V. Kohl (3/27/16) EFBC fellowship class response to Dr. Tom Jordan who asked me to define “experiment” For comparison, see: Experiment: An experiment is a procedure carried out to verify, refute, or validate a hypothesis. Experiments provide insight into cause-and-effect by demonstrating what outcome occurs when a particular factor is manipulated. Experiments vary greatly in goal and scale, but always rely on repeatable procedure and logical analysis of the…

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RNA-mediated physics, chemistry, and molecular epigenetics (4)

May 9, 2016
James Kohl
Adaptations, Alternative Splicings, biophotonics, Diseases & Disorders, Ecology, Light Energy, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, 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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Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein 5/6/16 Summary excerpt: Visualizing a response to light Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein Article excerpt: Ultrafast fluorescence and transient absorption spectroscopy of PYP have shown that excited state decay is multi-phasic (3, 5, 39). The fast…

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RNA-mediated physics, chemistry, and molecular epigenetics (3)

May 9, 2016
James Kohl
Adaptations, Alternative Splicings, biophotonics, Diseases & Disorders, Ecology, Light Energy, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, 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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Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism reported as: Using microRNAs to target cancer cells By Dawn Hayward Conclusion:  MicroRNAs stand out from conventional gene-therapy-based approaches and have a niche in lipid metabolism. They can be designed specifically to target a gene and serve as modulators rather than on/off switches. Increased lipid formation and breakdown in cancer cells creates vulnerability that might be taken advantage of by microRNAs. In addition, cancer as a whole involves a…

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Wasted Templeton Funding (2)

April 22, 2016
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, Physics, RNA Directed, 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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See also: Wasted Templeton Funding (1) Templeton grant funds evolution rethink Excerpt: The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology. My comment: That is an understatement! The problems with the so-called modern synthesis are perfectly…

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Confusing effects and affects of visual input

March 24, 2016
James Kohl
Adaptations, Alternative Splicings, biophotonics, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Light Energy, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, 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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Their report indicates that these researchers never learned to differentiate between epigenetic effects on RNA-mediated cell type differentiation compared to the experience-dependent affects on behavior of amino acid substitutions. Experience Affects Critical Period Plasticity in the Visual Cortex through an Epigenetic Regulation of Histone Post-Translational Modifications Excerpt: We show that the early exposure of rat pups to enriching environmental conditions accelerates the critical period for plasticity in the primary visual cortex, linking this effect to increased histone acetylation, specifically at…

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Theorists can’t understand biology

November 19, 2015
James Kohl
Adaptations, biophotonics, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Light Energy, Model Organisms, Neuronal Plasticity, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, Variations
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See also: Neuroplasticity Thanks to Teresa Binstock for calling my attention to this:   Thanks to Anna Di Cosmo for calling the attention of others to this: My comment: Attempts to explain the “binding problem” of integration in the context of ecoimmunology and disease ecology compared to emergence and evolution are examples of how much pseudoscientific nonsense has been accepted and touted in the context of the neo-Darwinian “Modern Synthesis.” For comparison, serious scientists have detailed a model of top-down…

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The virome, microbiome, replisome and supercoiled DNA

November 3, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, Variations
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First Complete Pictures of Cells’ DNA-Copying Machinery Excerpt: This architecture could also potentially play an important role in developmental biology by providing a pathway for treating the two daughter strands differently. Many modifications to DNA, including how it is packaged with other proteins, control which of the many genes in the sequence are eventually expressed in cells. An asymmetric replisome may result in asymmetric treatment of the two daughter strands during cell division—an essential step for making different tissues within…

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Skip the politics; embrace the facts

November 2, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Human Brain, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, RNA Directed, Variations
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It’s Not Brain Surgery, Ben Carson Excerpt: …“Heal Inspire Revive,” invokes an image of him pounding on the chest of a pulseless America. Whether or not he actually knows how to handle a crash cart of that size, many voters don’t seem to doubt that he can. And he doesn’t doubt it either. My comment: I do not expect anyone who understands what is currently known about how physics and chemistry are linked to the biophysically constrained conserved molecular mechanisms…

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700 million years of evolution?

October 29, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Human Pheromones, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, Variations
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Analysis of 5′ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals Conclusion: It is our hope that each and every one of these regions will make interesting candidates for experimental analysis, helping to increase our understanding of regulation of gene expression, and particularly our understanding of regulatory elements in RNA. My comment: In other words, they hope what has already been detailed in the context of how nutrient-dependent microRNAs link the epigenetic landscape…

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Foundamentals of theory

October 8, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Neuronal Plasticity, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing
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There are foundations of epigenetics and fundamentals of molecular mechanisms. They have been detailed in this atoms to ecosystems model of RNA-mediated cell type differentiation. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. I have never seen anyone mention the “foundamentals” of epigenetics. It appears the word has been invented. Similarly, the word “mutation” was invented in 1904 by de Vries. Inventing words and defining them to fit ridiculous theories about neo-Darwinian evolution is required to continue convincing theorists that…

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