gene regulation

A Mathematical Model Links Quantum Physics to Quantum Souls (2)

See for review: A Mathematical Model Links Quantum Physics to Quantum Souls (1) See for comparison: Zaugg Lab We are applying and developing computational biology tools for integrating large-scale biological ‘omics data to address questions in personalised genomics. The Zaugg Lab ignores everything known to serious scientists about energy-dependent top-down causation, which is the only way to link quantum physics to biophysically constrained biologically-based biodiversity. Watch them try to do that with a mathematical model, instead. Loops in DNA affect which proteins are coded …

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Who created your virus-driven death gene? (2)

Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity. The difference between an energy-dependent RNA-mediated amino acid substitution and a mutation has been largely ignored as pseudoscientists linked accidents…

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Denying Creation via RNA-directed DNA methylation

Summary: Epigenetic mechanisms did not evolve.  DNA methylation is food energy-dependent and RNA-directed. Phenotypes are not fixed by genetics. The food energy-dependent RNA-directed DNA methylation of all organized genomes is biophysically constrained by the metabolism of food to pheromones, which control the physiology of food-dependent reproduction. On the day after he posted content on the refutation of Karl Popper’s nonsense and the pseudoscientific nonsense touted in every aspect of neo-Darwinian theory, antagonist Jay Feierman posted this to the Human Ethology…

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What energy source do proteins prefer?

Quantized energy as information is the anti-entropic virucidal source of healthy longevity. All pathology is caused by virus-driven energy theft. Impact of cytosine methylation on DNA binding specificities of human transcription factors …many developmentally important proteins display preference for mCpG-containing sequences.   How do proteins display a preference for anything except food and codon optimality? Natural selection for quantized food energy-dependent codon optimality links the structure and function of supercoiled DNA to protection from virus-driven energy theft. That fact was…

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Theorists sell hidden energy (2)

Theorists sell hidden energy (Jan 5, 2017) January 6, 2017 Giant atoms could help unveil ‘dark matter’ and other cosmic secrets The universe is an astonishingly secretive place. Mysterious substances known as dark matter and dark energy account for some 95% of it. Despite huge effort to find out what they are, we simply don’t know. Our model is based on the fact that weakly interacting particles must bounce from the nucleus of the atom it collides with and exchange…

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Light energy-dependent active motifs

Active Motif claims that Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. See how the role of light is portrayed in LightSwitch™ Luciferase Assay System (with my emphasis) Excerpt 1) Combined with our large collection of miRNA Mimics and Inhibitors, you have everything needed to study miRNA-3´UTR interactions, validate miRNA targets, measure RNA stability, translation efficiency and the functional impact of miRNAs on a gene-by-gene basis. Excerpt 2) The…

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GC-rich neo-Darwinian train wreck

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells Excerpt: In this study, we demonstrate direct cellular reprogramming to induced neuronal cells through targeted activation of endogenous genes. Excerpt: Moreover, a recent study demonstrated that reprogramming efficiency can be limited by divergence to a competing cell identity (Treutlein et al., 2016). The molecular mechanisms and practical consequences of these limitations are largely unknown. My comment: They demonstrate what naturally must occur to link…

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Biophysically constrained cell type differentiation

Intrinsic limits to gene regulation by global crosstalk Excerpt: A paradigmatic example is that of the aminoacyl transfer RNA synthetase1, which uses kinetic proofreading2 to load appropriate amino acids onto matching tRNAs. This and other examples—including DNA replication, ligand sensing3, protein–protein interactions4,5,6,7,8,9, recognition events in the immune system10,11 and molecular self-assembly12—indicate that biology places a large premium on the reduction of unintended ‘crosstalk’, a generic term that encompasses all potentially disruptive processes due to reactions between non-cognate substrates. Reported as:…

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A million dollar paradox?

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…

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Neo-Darwinism vs the neocortex

From Fertilization to Adult Sexual Behavior Excerpt: (with my emphasis) Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to c in at least two species, Drosophila melanogaster and Caenorhabditis elegans…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes. Alternative splicing as a switch to enhance neuroprotection under stress Excerpt: Alternative splicing is an important post-transcriptional…

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