molecular mechanisms

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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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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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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Hydrogen-atom energy in DNA base pairs

See also: Consciousness is simply food rearranged Role of Double Hydrogen Atom Transfer Reactions in Atmospheric Chemistry Abstract excerpt:  Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry. My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain…

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Displays of ecological adaptation (2)

On 9/12/16 Philip Qua wrote I have not verified that all of his papers are peer review, but I do believe that some of them are. It is going to take some time and reading of James Kohl papers before I am even willing to venture whether they have merit or not. But on a first glance basis, what I think James is positing here is the causal-effect that drives evolution is more an energy based availability than a random…

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Antithetical conclusions (3)

Local modulation of chemoattractant concentrations by single cells: dissection using a bulk-surface computational model This is part of the Theme issue ‘Coupling geometric partial differential equations with physics for cell morphology, motility and pattern formation’ Excerpt: “The computed ligand concentration and receptor occupancy on the evolving cell membrane are shown in figure 5.” Conclusion: “…the detailed information gained through simulations of single cells or the interaction of a few cells could be used to better inform agent-based approaches and the…

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Thermotolerance and longevity (2)

See also: Thermotolerance and Longevity This article is part of the Research Topic Brain nutrient sensing in the control of energy balance: new insights and perspectives Excerpt: It is well established that nutrients act as signaling molecules in synergy with nervous and hormonal signals to inform the brain about the nutritional status of the body. The integration of these signals within the hypothalamus and other brain regions triggers behavioral and physiological responses through efferent autonomic nerves, hypothalamic-pituitary-Adrenal and thyroid axis…

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Teleophobes vs teleophiles: a recent history

  Teleology is a reason or explanation for something in function of its end, purpose, or goal. The teleological or physico-theological argument, also known as the argument from design, or intelligent design argument is an argument for the existence of God or, more generally, for an intelligent creator “based on perceived evidence of deliberate design in the natural or physical world” My comment: Teleophobes make weak arguments peppered with logical fallacies.  They do not make physico-theological arguments, which can be supported…

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Ecological genomics: teleophobes respond (too late)

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing Conclusion: Twenty years ago, an essay about sequencing genomes and remotely tracking animals across the globe in real time would have been the subject of science fiction. In 2015, there are over 50,000 animals being tracked [12], and single research groups now sequence dozens, up to hundreds, of individual genomes [17,82]. By embracing new technology and integrating these data streams into an ecological genomic framework (Fig 1), we are now poised…

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