horizontal gene transfer

Cytosis: Biology Content

  Help Me Write Some Biology Content Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games) Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This…

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Virus-driven mutation or amino acid substitution

A computer program just ranked the most influential brain scientists of the modern era Excerpt: “My first thought was, ‘Who could I tell without appearing immodest?’” he said. “I then realized the only people who would want to hear about this are my children!” My comment: Oxytocin-related peptides are 9-13 amino acids long, but they can be recognized in genomic sequences. That allows them to be placed into the context of claims that link the nutrient energy-dependent de novo creation…

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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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Biophotonics, glycobiology, quantized biodiversity (2)

From Fertilization to Adult Sexual Behavior (1996) In our section on Molecular epigenetics, we wrote: Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility…

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Energy-dependent RNA methylation (8)

Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach Mutation Monte Carlo method (MMC): Excerpt: The mutation moves change the bp sequence but keep the DNA configuration fixed. Both moves change the energy, Eq (1), of the two bp steps involved. My comment: Moves that change energy cost energy. Attributing energy-dependent changes in base pairs to mutations without linking them to the source of the energy change is a neo-Darwinian trick. Nucleosome-amino acid correlation analysis: Excerpt: This produces occurrence probabilities…

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Rivals cast doubt on facts about HGT

See first: Creating nothing but a theory (3) Rival Scientists Cast Doubt Upon Recent Discovery About Invincible Animals Excerpt: A recent claim that tardigrades got a sixth of their DNA from microbes is starting to unravel. My comment: No, it is not. Ed Yong has already admitted that the problem with such claims is that evolutionary theorists refuse to accept facts that link atoms to ecosystems in the context of biologically-based cause and effect. He even accepted the blame for…

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The Sherlock lab: Beneficial mutations

After he challenged me in a discussion of two works on tardigrades, Gavin Sherlock‘s comments were removed from the facebook page of Serafim Batzoglou. In the context of The genome of the tardigrade Hypsibius dujardini and Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade, it quickly became clear that Gavin Sherlock knows nothing about how cell type differentiation occurs. Sherlock is the senior author of Quantitative evolutionary dynamics using high-resolution lineage tracking Excerpt: Our results…

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Organization of biological sequences

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps Excerpt: Biological evolution is characterized by the inheritance, mutation and translation of biological information. My comment: Genome organization is nutrient-dependent and controlled by the physiology of reproduction in all living genera. Nutrient-dependent RNA mediated gene duplication and RNA-mediated amino acid substitutions link RNA-mediated protein folding  chemistry from supercoiled DNA to protection against virus driven genomic entropy via the physiology of reproduction. Virus-driven genomic entropy…

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Thermotolerance and Longevity

Heterotypic Signals from Neural HSF-1 Separate Thermotolerance from Longevity Excerpt: …it was hypothesized that hsf-1 regulates the aging process by modulating chaperone network components to directly influence the folding state of the proteome ( Morimoto, 2008). Our data suggest an alternate method by which hsf-1 can regulate the aging process. In this model, hsf-1 activates the FOXO transcription factor, which initiates a pro-longevity stress response that is distinct from the heat shock response. My comment: The separation of the nutrient…

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RNA-mediated permanent symbioses

See also: Ecological validity vs evolutionary theory Symbiosis becoming permanent: Survival of the luckiest Published in: Proceedings of the National Academy of Sciences (PNAS) f the United States of America Excerpt: …since the 1980s, the idea that the mitochondria and plastids (chloroplasts) of eukaryotic cells arose through endosymbiosis has been about as universally accepted as such things ever are (1). However, enormous gaps remain in our knowledge about just how this happened. My comment: Symbiosis becomes permanent via RNA-mediated biologically-based…

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