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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Walk towards the light

Cockroaches Accumulate Light to See in the Dark Excerpt: “Taking into account the size of the experiment’s stripes, the optical properties of the roaches’ eyes and the amount of photons available, the team concluded that the roach nervous system pools information from its thousands of photoreceptors over time—in effect, accumulating electrical neural signals and using the summation of those signals to see.” My comment: If there were no link from light-induced amino acid substitutions to nutrient-dependent cell type differentiation in…

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Epigenetics Skeptism

Thanks to Joost G. Wouters for the alert to this nonsense: 1) Michael White in Pacific Standard magazine flatly states that “Epigenetics Is Not Revolutionizing Biology.” 2) Adrian Bird points out in the journal Cell that many of the field’s assumptions and promises remain unproven and are perhaps excessive. 1) White’s article sketches the field’s promise and hype, from questionable ‪epigenetic‬ diets and wild claims about controlling genes with your thoughts. He follows with a summary of epigenetics, then runs…

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Is DNA-directed transcription RNA-mediated?

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Concluding sentence excerpt: “…rather than a rigid deterministic mechanism, transcription is not hardwired and able to select against potentially adverse changes in the DNA template. Such transcription avoidance may be yet another layer of protection against the detrimental consequences of mutations and provide further clues to understanding its possible consequences, including reduced penetrance and variable expressivity.” Reported as: Rather than being a one-way street, DNA-directed RNA transcription may have profound adaptability Excerpt:…

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Assembling yourself: Molecular self / other recognition

Chiral recognition and selection during the self-assembly process of protein-mimic macroanions Abstract excerpt: “We believe that delicate long-range electrostatic interactions could be responsible for such high-level chiral recognition and selection.” Article excerpt: “This self-assembly allows relatively simple building blocks to organize themselves into larger supramolecular structures, a phenomenon that has parallels with the formation of viral capsids (both in morphology and kinetics)37.” Reported as: Discovery demystifies origin of life chirality phenomenon Excerpt: “The origin of life is still a mystery…

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Virus-driven cell type differentiation

A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus Abstract excerpt: These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes Conclusion: Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence,…

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Let there be anti-entropic light (1)

Summary: Light-induced amino acid substitutions link cell type differentiation in plants to nutrient-dependent pheromone-controlled reproduction in animals via the biophysically constrained chemistry of protein folding. Protein folding is perturbed by mutations that limit the ability of organisms to adapt to ecological variation. Viruses contribute to mutations. The sun’s biological energy appears to supply the anti-entropic force that links entropic elasticity to the development of successful morphological and behavioral phenotypes that are exemplified in extant versus extinct biodiversity. The importance of…

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Physicists: Desperate Acts

Participation on the FB group Thinking Allowed Original led to an invite by Ulla Mattfolk to participate on her secret group  Quantum Biology, coherence and decoherence. On January 22 at 11:45pm, discussion led me to ask whether biophotonic energy differences could be recognized by the photons at the quantum level of their interactions/energies. I thought the answer might explain biodiversity via a link from quantum level self – other recognition to immune system recognition and to macromolecular self – other recognition. My focus has been on well-established…

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Biophysically constrained beginnings of RNA and DNA

Any anonymous participant in the discussion of: DNA may have had humble beginnings as nutrient carrier (Sep 01, 2014 by Adam Hadhazy) asks: “when are you going to keep quiet?” In a series of responses, I have explained the problem I have with honoring his request. The following excerpts from Wikipedia and other sources are loosely strung together because there is no point to providing more extensive details of biologically-based cause and effect until others accept the fact that mutations…

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  • Randomness and Divine Providence
    A Q&A on randomness and God’s providence …the main goal is to really put together a collection of scholarly studies of these issues: physicists, biologists, […]
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