biodiversity

Epigenetics: microRNAs effect an integrative pathway

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1) Excerpt 1) The accumulation of hypoglycosylated nuclear FGFR1 (nFGFR1) is stimulated by a variety of developmental signals, including various growth factors, hormones, and neurotransmitters as well as a reduction in cell contact. This is the reason that this pathway is referred to as integrative [1, 15]. Reported as: Master orchestrator of the genome is discovered, stem cell scientists report Summary: New research shows how a single…

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Tissue type variation and expression of genes

Exploring the Impacts of Genetic Variation on Tissue-Specific Expression Preliminary results from the Genotype-Tissue Expression project reveal that gene expression varies more across tissues than across individuals. By Jenny Rood | May 7, 2015 Excerpt: “You’ve got the genetic variation, you’ve got the gene expression levels, you’ve got the different tissues…” My comment: What you don’t have is a model of RNA-directed DNA methylation and RNA-mediated amino acid substitutions that links the epigenetic landscape to the physical landscape of DNA…

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Chance mutations — not natural selection

A Surprise for Evolution in Giant Tree of Life Excerpt (with my emphasis): Each variant adapted to suit a different ecological niche. But Blair Hedges, a biologist at Temple University in Philadelphia, has proposed a provocative alternative: Adaptation had little to do with it. It was simply a matter of chance and time. See also: The Surprising Origins of Evolutionary Complexity July 16, 2013 Excerpt: Some argue that life has a built-in tendency to become more complex over time. Others…

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Physics, chemistry, light, and life

Making Sense of the Chemistry That Led to Life on Earth By NICHOLAS WADE,  May 4, 2015 Excerpt: He and colleagues have spent the last six years doing experiments to see how the ribonucleotide chemistry pathway can be linked back to hydrogen cyanide as its starting point, and how other significant prebiotic chemicals might have emerged from the cyanide-to-nucleotide pathway. My comment: The starting point was UV light. See: Origin-of-life puzzle cracked Excerpt: Sutherland’s team now reports that it created nucleic acid…

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An epigenetic mark links algae, worms, and flies

New Epigenetic Mark Found on Metazoan DNA Three studies identify roles for N6-methyladenosine in algae, worms, and flies. By Jenny Rood | April 30, 2015 Excerpt (with my emphasis): “In bacteria, 6mA marks the template strand during DNA replication, enabling a cell to spot errors and regulate the cell cycle. The modification also helps differentiate bacterial DNA from viral genomic material, which lacks methylation.” My comment: The ability of a cell or organism to recognize self vs other differences enables…

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Pathology constrains X-linked evolution

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome Excerpt: “Experimental methods are already able to indicate the interactions between enhancers and genes8, 13, 17, 18, 19 but they are strongly constrained by the tissue and time where and when the interaction takes place. In contrast, evolutionary linkage is independent of the tissue or time of expression of the gene, and is applicable to any sequenced vertebrate genome, as it was done here for human.” My comment: Experimental…

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MicroRNAs and invasive phenotypes

Variability helps mammals to become invasive Excerpt: The authors argue that species exposed to a novel environment will have higher chances of surviving if they are variable and can therefore adapt to many different environmental conditions. My comment: Nutrient-dependent pheromone-controlled morphological and behavioral phenotypes are linked by microRNAs to adaptive radiation and to all of extant biodiversity. For an example of the role of RNA-mediated events that link metabolic networks to genetic networks, see: “Large Numbers of Novel miRNAs Originate…

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Deeply ingrained thoughts

A universal trend of amino acid gain and loss in protein evolution Excerpt: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all…

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Luis P. Villarreal tells it like it is

Luis P. Villarreal has led the way towards discovery of the “origins of life.” He has helped to elucidate what is currently known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to humans. Kudos to Suzan Mazur for admitting that she missed learning about his works. Perhaps a few neo-Darwinian evolutionary theorists will also admit they have missed something very important about the role of viruses in cell type…

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RNA directed DNA methylation and cell types

Cell type differentiation is included in all topics in biology, which is why it is important to understand what is currently known about top-down causation in the context of physics and chemistry. Taken together, physics, chemistry, and the conserved molecular mechanisms of biology link Drosophila to Octopuses and all other species on this planet via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types. See for examples: Let there be anti-entropic light (1) An antagonist led me…

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