substitutions

Pattern recognition: biogeochemical structure and function

Microbes Effect on the Brain Excerpt: Recent research shows dramatic effects of microbe products from the gut on mental function—depression, stress, autism, and degenerative illness. In humans, many studies show microbes affect anxiety, mood, depression and social behavior. Direct effects are through secreted products, stimulation of the enteric nervous system and travel of microbes into the brain, while indirect factors are microbes’ influence on immune function affecting behavior. Microbes produce molecules that transform into hormones and neurotransmitters or they produce…

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Ignoring systems complexity (it’s too complicated)

Host, heal thyself: Immune system self-organizes to minimize biological cost of pathogenic infections Excerpt 1) This approach allowed the scientists to create a new framework that makes it unnecessary to explicitly model intracellular communication, cell differentiation, activation of cofactors, coordination of different cell types, the interaction with the innate immune system, and the full complexity of the recognition process. My comment: Population geneticists took that approach when they invented neo-Darwinian evolution. They eliminated all aspects of nutrient-dependent cell type differentiation…

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Retinoic acid + one receptor regulate the genome

See also: Epigenetics: microRNAs effect an integrative pathway for my additional comments on Master orchestrator of the genome is discovered, stem cell scientists report) Retinoic acid is a metabolite of vitamin A (retinol) that mediates the functions of vitamin A required for growth and development. The fibroblast growth factor receptor 1 “…gene provides instructions for making a protein called fibroblast growth factor receptor 1. This protein is one of four fibroblast growth factor receptors, which are related proteins that are…

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DNA Methylation and organized genomes (2)

The Darwin Code by Greg Bear Excerpt (from 2005): “The picture we see now in genetics is complex. Variation can occur in a number of ways. DNA sequence is not fate; far from it. The same sequence can yield many different products. Complexes of genes lie behind most discernible traits. Genes can be turned on and off at need. Non-coding DNA is becoming extremely important to understanding how genes do their work. Non-coding RNA, sugars, and lipids–including many cellular components…

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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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Epigenetic effects of soil bacteria on plants

Soil Bacteria Live on Wine Grapes The earthiness of Merlot may have to do with grapevine-dwelling microbiota. By Kerry Grens | March 25, 2015 Excerpt: “…our next step is to figure out how those bacteria are affecting the chemistry of the plant.” My comment: Progress may then lead others to learn how the balance of viral microRNAs and nutrient-dependent microRNAs is linked to cell type differentiation in plants and animals via RNA-directed DNA methylation and RNA-mediated amino acid substitutions linked…

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Mimicking claims and ignoring facts

Summary: Last week, researchers reported they had caught up to “Nature” despite their inability to link viral microRNAs and nutrient-dependent microRNAs from the nature of non-living viruses to the nature of cellular life and to cell type differentiation via RNA-mediated amino acid substitutions, metabolic networks, and genetic networks. Today, we see the “billions of years” claim, with no mention of the over-the-weekend re-evolution of the bacterial flagellum or 1.8 billion years of epistasis in bacteria at the bottom of the…

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Questions about life’s diversity

Questions about life can be answered in the context of what sustains it. 1) Answers must explain the diversity of life. 2) The diversity of life may help to explain the purpose of life. 3) Explaining the purpose of life may assist anyone who does not think they will live forever. 4) Answers to questions about life that explain life’s diversity must include what is known about the conserved molecular mechanisms that link differences in morphological and behavioral phenotypes in…

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UV-light mutations and gene loss (not gain)

The Neanderthals live on in us March 13, 2015 Excerpt: “He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus.” My comment: If he had done what he was supposed to be doing, he might have learned how viral microRNAs and nutrient-dependent microRNAs contribute to cell type differentiation in all cells of all individuals of all species. If he had done…

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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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