genomics

Ecological Adaptations vs the Randomness of Evolution (2)

Summary: See for comparison: Make ‘Em Resistant to Viruses In the new proposal — which Science says was released in advance of a meeting today — GP-write leaders say “ultrasafe” cells could be developed by making some 400,000 changes to the human genome. A Fast One–Step Digestion of DNA or RNA for Global Detection and Characterization of Nucleotide Modifications (link opens pdf) Product information: The Nucleoside Digestion Mix is an optimized mixture of enzymes that provides a convenient one-step method…

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Autophagy is the antiphage defense strategy (2)

2/15/17 Energy as information and constrained endogenous RNA interference (video) The 6.46 minute-long technical presentation (above) from the Precision Medicine Virtual Conference is difficult to understand.Thus, 10 months later, Nik Willmore asked: 12/24/17 What are your insights into CRISPR and mTOR, for a young audience? I’m not mocking you…yet, Humpty Dumpty. What is the basis of your unifying principle? Vibration? Bohmian morphogenetic fields? Modified Darwin? God? –Nik Willmore @nikwillmore 12/25/17 Replying to @nikwillmore @jhewitt123 God created the anti-entropic virucidal energy of sunlight and…

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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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From base editing to RNA editing

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine “Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist. The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories…

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Energy-dependent physical and biophysical constraints (3)

See first: Energy-dependent physical and biophysical constraints (2) Emily Balskus Pins Down the Chemistry and Metabolism of Human Microbiomes Summary: The chemistry and metabolism of all microbiomes is food energy-dependent and pheromone-controlled via the physiology of reproduction. See: Feedback loops link odor and pheromone signaling with reproduction My comment to The Scientist: …trans-4-hydroxy-L-proline (Hyp) dehydratase, a newly discovered member of an abundant family of proteins, produced by gut bacteria, known as the glycyl radical enzymes, helps in metabolizing trans-Hyp, an…

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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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Antithetical conclusions (7)

Streamlining the E.coli Genetic Code Once the E. coli genome is pared down to 57 codons, the seven blank codons can be reintegrated and used to introduce nonstandard amino acids, the researchers have proposed; this would open the door to creating a wider range of proteins for industrial applications. A recoded genome also imparts resistance to viral infection and can be used for biocontainment: the DNA incorporated from wild-type E. coli or viruses can’t be used to build proteins successfully…

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Energy-dependent creation and entropy

Theorists tend to use the term de novo when they don’t know. If they don’t know how energy-dependent structures and functions are created, functional structures are created de novo. See for example:  Lymphotoxin-Dependent B Cell-FRC Crosstalk Promotes De Novo Follicle Formation and Antibody Production following Intestinal Helminth Infection If theorists don’t know what causes mutations, the mutations are de novo mutations. See for example: Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures My comment: The…

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Ecological variation and niche construction: 1, 2, 3

Part 1 From its most basic expression in grazing and predatory nematodes with differences in morphological and behavioral phenotypes, neurogenic niche construction is nutrient-dependent and pheromone-controlled. One of these two worms has teeth. It also recognizes self vs other differences and eats other worms. “The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes. Evolutionary theorists concluded and continue to claim that “…without mutation, evolution would not…

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