Cell Type

Anti-entropic solar energy

March 24, 2015
James Kohl
Adaptations, Ecology, Light Energy, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed
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“We have a group trying to model the mitochondrion” — Ulla Mattfolk Trash pickup problem Excerpt: “The PGAM5 protein would be regulated by an allosteric mechanism, in which its biological function would switch from activation of the PINK1/PARKIN pathway for removal of damaged mitochondria to the FUNDC1 pathway for removal of damaged mitochondria,” according to Hannink. “Peptides behave like drug molecules; any time you can identify a biological process that is regulated by a peptide, that peptide becomes a leading…

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Questions about life’s diversity

March 20, 2015
James Kohl
Diseases & Disorders, Ecology, Model Organisms, Physics
No Comments

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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Epigenetics Skeptism

March 15, 2015
James Kohl
Adaptations, Ecology, Light Energy, Physics, RNA Directed
No Comments

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?

March 15, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Light Energy, RNA Directed
No Comments

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

March 15, 2015
James Kohl
Ecology, Light Energy, Physics
No Comments

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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RNA directed DNA methylation and cell types

March 12, 2015
James Kohl
Adaptations, Alternative Splicings, Ecology, Human Pheromones, Model Organisms, Nutrigenomics, RNA Directed
One Comment

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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Implicating microRNAs in cancer

March 9, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology
No Comments

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis Reported as: In vivo CRISPR-Cas9 screen sheds light on cancer metastasis and tumor evolution Excerpt: “Unexpectedly, the screen also implicated several microRNAs — small RNA segments that are functional in the cell. More experimental work remains to fully explore the genes and microRNAs uncovered in the screen.” It is the perturbed balance of viral microRNAs and nutrient-dependent microRNAs that obviously makes the difference between RNA-directed DNA methylation and…

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Let there be anti-entropic light (1)

February 23, 2015
James Kohl
Adaptations, Alternative Splicings, base editing, Diseases & Disorders, Ecology, Light Energy, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, RNA editing, Variations
4 Comments

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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An epigenetic trap (the prequel)

February 23, 2015
James Kohl
Ecology, Human Brain, Human Pheromones, Physics
No Comments

See also: An epigenetic trap (the sequel) Excerpt: “Support for the link from one epigenetic trap to cell type differentiation was included in the molecular epigenetics section of our 1996 review, which detailed how RNA-mediated chromatin remodeling occurs.” My comment: One epigenetic trap leads to the de novo creation of olfactory receptor genes and cell type differentiation. See also: Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons. The first epigenetic trap links the sun’s biological energy to cell type…

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