DNA methylation

Human pheromone deniers: What’s next?

Adapted from Human pheromones: What should these idiots do next? RNA-directed DNA methylation and RNA-mediated gene duplication and RNA-mediated amino acid substitutions link the nutrient-dependent physiology of pheromone-controlled reproduction to morphological and behavioral phenotypes in species from microbes to humans. Why would any serious scientist claim that there is a need to find human pheromones? Does any serious scientist not realize that the molecular mechanisms that link ecological variation to ecological adaptation must be the same in all living genera?…

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700 million years of evolution?

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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RNA-mediated retrotransposon-mediated biodiversity

Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. See also: A Single Amino Acid Change in the Yeast Retrotransposon Ty5 Abolishes Targeting to Silent Chromatin Excerpt: Target site biases observed among retroviruses and retrotransposons are thought to be the consequence of interactions between the retroelement integration complex and chromosome-localized proteins. My comment: Clearly, the way to make scientific progress is…

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Preventing genomic entropy

Tethering Transposons Excerpt: Transposons—thought to be related to viruses—can copy themselves and insert randomly around the genome. A paper published today (October 15) in Science provides a greater understanding of how cells shut down these rogue jumping genes. My comment: Shouldn’t someone else be claiming that nutrient-dependent microRNAs prevent the accumulation of viral microRNAs that leads to perturbed protein folding, which links mutations to all pathology in the context of an atoms to ecosystems model? Nutrient-dependent pheromone-controlled ecological adaptations: from atoms…

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Let there be anti-entropic light (2)

Predicted Inactivation of Viruses of Relevance to Biodefense by Solar Radiation (2005)Excerpt: Sunlight or, more specifically, solar UV radiation (UV) acts as the principal natural virucide in the environment. UV radiation kills viruses by chemically modifying their genetic material, DNA and RNA. See also: Let there be anti-entropic light (1) Excerpt: Nutrient-stress and social stress contribute to the accumulation of viral miRNAs that would typically be prevented by nutrient-dependent pheromone-controlled feeback loops that link food odors and social odors to…

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Foundamentals of theory

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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“New” quantum biology. Pirating the old

Jim Al-Khalili is a nuclear physicist. Luca Turin is a biologist. Both presenters link Schrödinger’s claims in What is Life? Which one knows most about it? Jim Al-Khalili  frames his presentation in the context of evolutionary theory. See the text or the 20-minute Video presentation: Jim Al-Khalili: How quantum biology might explain life’s biggest questions Luca Turin frames his presentation in the context of what is known to serious scientists about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding. See also: …

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Cell types, SNVs, CNVs, and chromosomes

See also: A “new” code enables ecological adaptation For comparison, see: Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell Excerpt: Single-molecule and single-cell studies reveal behaviors that are hidden in bulk measurements (1, 2). In a human cell, the genetic information is encoded in 46 chromosomes. The variations occurring in these chromosomes, such as single-nucleotide variations (SNVs) and copy-number variations (CNVs) (3), are the driving forces in biological processes such as evolution and cancer. Such dynamic…

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Anti-entropic containment of energy: symbiosis 1.0

Scientists explore the origins of energy in chemical reactions using experimental quantum chemistry Excerpt: One thing that all chemical reactions have in common—whether they are the reactions that take place inside a battery, the metabolic reactions inside a living organism, or the combustion reactions that cause an explosion—is that they all involve some kind of change in energy. My comment: Therein lies the problem with attempts by pseudosceintists to link nutrient energy from ecological variation to epigenetically-effected ecological adaptation, which…

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Information and communication (2)

Leaving an Imprint Among the first to discover epigenetic reprogramming during mammalian development, Wolf Reik has been studying the dynamics of the epigenome for 30 years. By Anna Azvolinsky | August 1, 2015 Excerpt: In the mammalian field, the imprinting field, together with the X-inactivation field, was the birthplace of epigenetics. My comment: Researchers like Wolf Reik never mentioned the role viruses play in preventing cell type differentiation. The birthplace of epigenetics became associated with a “still-birth.” The still-birth continued to…

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