biodiversity

Epigenetics and autophagy vs mutations and evolution (5)

Two-Photon Microscopy’s Historic Influence on Neuroscience Excerpt: Yuste says he’s proud of what he and Denk accomplished. “But now I go to meetings where everyone is presenting two-photon calcium imaging, and no one knows, or remembers, or cites our work,” he says, laughing. My comment: What else can be done but laugh? Most researchers still have not linked the anti-entropic energy of virucidal ultraviolet light from the biophysically constrained RNA-mediated chemistry of protein folding to all biodiversity in all genera…

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Polycombic ecological adaptation as a science, not a theory (2)

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation Conclusion: … the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate…

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Polycombic ecological adaptation as a science, not a theory

Multi-omic data integration enables discovery of hidden biological regularities   Excerpt: Tracing the central dogma of biology (left column), we can link specific data types (middle column) to explain each of these biological processes. In this work, novel biological regularities that relate these processes are discovered through: (i) primary omics data (top box, right column) and (ii) integration with GEMs (bottom box, right column).   Excerpt: The approach directly addresses the BD2K grand challenge and is made conceptually accessible by…

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Attacking Young Earth Creationists

‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data Abstract excerpt: Evolutionary dynamics such as speciation are inherently a phylogenetic process, and only an explicitly phylogenetic approach will correctly model this process. Reported as: Flawed analysis casts doubt on years of evolutionary research The method assumes that variations in the number of different fossils at any given time are a reflection of how much rock was available. It has been used in more than 150 published research…

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Did evolution autophosphorylate your kinases? (3)

Did evolution autophosphorylate your kinases? (1) Did evolution autophosphorylate your kinases? (2) See also: N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection Reported as: Chemical tags affect ability of RNA viruses to infect cells Dynamics of Human and Viral RNA Methylation during Zika Virus Infection Reported as:  Zika virus infection alters human and viral RNA My comment: Virus-driven hecatombic evolution of all pathology is linked from the failure of energy-dependent phosphorylation to biophysically constrain the RNA-mediated damage to DNA via…

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Predictable idiosyncratic evolved convergence

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings Excerpt: …predictable changes in biochemical phenotype do not have a predictable molecular basis. My comment: Biochemical phenotypes are predicted at every level of examination that starts with hydrogen-atom energy transfer in DNA base pairs in solution, and at least two of these authors know that. See: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin June 14, 2013 Excerpt: Fig. 2 Difference in the network of hydrogen bonds between high- and low-altitude…

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The natural success of RNAi and failed treatment

see my other blog posts on m6A Dynamics of Human and Viral RNA Methylation during Zika Virus Infection Excerpt: …ZIKV infection alters m6A location in mRNAs, methylation motifs, and target genes modified by methyltransferases. Our results identify a mechanism by which ZIKV interacts with and alters host cell functions. Reported as: Zika virus infection alters human and viral RNA Excerpt: When Zika virus infects a human cell, Rana’s team found, the cell modifies viral RNA with m6A as a means…

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Nutrient-dependent pheromone-controlled autophagy (2)

See also: Nutrient-dependent pheromone-controlled autophagy Autophagy: cellular and molecular mechanisms (2010) Conclusion: … autophagy has emerged as a new and potent modulator of disease progression that is both scientifically intriguing and clinically relevant. My comment: Autophagy is energy-dependent and linked to supercoiled DNA by epigenetic effects on the innate immune system, which are linked to the physiology of energy-dependent reproduction. If you think that the innate immune system automagically “emerged,” you might also think that autophagy has automagically emerged as the…

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Nutrient-dependent pheromone-controlled autophagy

See also: Nutrient-dependent pheromone-controlled autophagy (2) The Excitable Mitochondria links 4 neurons from a nutrient energy-dependent pheromone-controlled network in a marine invertebrate to human brain development via the conserved molecular mechanisms that link the speed of light on contact with water to the de novo creation of G protein-coupled receptors (GPCRs).  Receptor-mediated species -specific chromatin remodeling links chromosomal rearrangements to all biodiversity via energy-dependent chemotaxis and phototaxis. See: The central pattern generator underlying swimming in Dendronotus iris: a simple half-center…

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Life is energy-dependent task management

See also: Life is energy-dependent task management (2) Press Release: The Nobel Prize in Chemistry 2016  for the design and synthesis of molecular machines Excerpt: They have developed molecules with controllable movements, which can perform a task when energy is added. My comment: When energy is added is the key to understanding healthy longevity in the context of popular information Popular information (link opens pdf) Excerpt: All chemical systems strive for equilibrium – a lower energy state – but this…

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