DNA

Riding the wrong direction

July 17, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Light Energy, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, Variations
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Riding the Evolution Paradigm Shift With Eugene Koonin Excerpt: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… Excerpt: [T]he entire ideology of personalized medicine should be taken with many grains of salt. My comment: Personalized medicine links the conserved molecular mechanisms of biologically-based cause and effect from nutrient-dependent RNA-mediated gene duplication to RNA-mediated amino acid substitutions, which differentiate…

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RNA-mediated gene duplication, fixation, and ecological adaptation

July 11, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed
One Comment

Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication Excerpt: The simplicity of this coordination mechanism suggests that it may be widely applicable in a variety of gene regulatory and stress-response settings. Reported as: Bacteria use DNA replication to time key decision Excerpt: “Successful sporulation requires two complete copies of the bacterial chromosome, so coordination between the sporulation decision and the completion of DNA replication is very important,” Narula said. “A good analogy might be a semester-long course in…

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“New” epigenetic mechanism for lifelong learning?

July 2, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, Variations
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Critical Role of Histone Turnover in Neuronal Transcription and Plasticity Reported as: Lifelong learning is made possible by recycling of histones, study says Also reported as: New epigenetic mechanism revealed in brain cells Excerpt: In humans, researchers used a technique called 14C/12C bomb pulse dating to measure turnover. The technique is based on the fact that high levels of radioactive carbon (14C) were released into the atmosphere during the 1950s and 1960s, when open-air nuclear bomb testing occurred following the…

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Ignoring systems complexity (it’s too complicated)

May 15, 2015
James Kohl
Adaptations, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed
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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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Nutrient-dependent RNA interference (2)

April 15, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, RNA Directed
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Cell type differentiation in all genera begins with the recognition of self vs non-self differences such as those we attributed to RNA-mediated pheromone-controlled sex differences in the cell types of species from yeasts to mammals. See: From Fertilization to Adult Sexual Behavior Excerpt: “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and…

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The Darwin Code by Greg Bear

April 14, 2015
James Kohl
Adaptations, Alternative Splicings, Autophagy, Ecology, Human Pheromones, Model Organisms, RNA Directed, RNA interference
53 Comments

“The Darwin Code: Intelligent Design without God” by Greg Bear, who wrote on April 14, 2015: “Happy to have this version of the talk posted. It’s a variation on the talk I gave at the American Philosophical Society in 2004, and a few times after that.  This one was delivered in Seattle at the Primate Genome Conference in the late 2000s.” —————————————— “Sometimes we hear explorers saying that the adventure is over, the territory has been mapped, there’s nothing more…

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Nutrient-dependent RNA interference

April 14, 2015
James Kohl
RNA Directed
One Comment

This David Sloan Wilson interview of Eva Jablonka reflects the desperation of evolutionary theorists. Jablonka claims there is no need to re-define “evolution.” She also places all prior claims about evolution into the context of “symbolic evolution.” She attests to the fact that “evolution” (e.g., change over time) will probably be re-defined to fit whatever anyone was taught to believe it might be. See: Beyond Genetic Evolution. A Conversation With Eva Jablonka Excerpt: “This is a good opportunity to move…

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Correctly modeling ecological adaptation

March 22, 2015
James Kohl
Adaptations, Ecology, Model Organisms, Physics, RNA Directed
One Comment

Statistics requantitates the central dogma Excerpt: “Mammalian proteins are expressed at ∼103 to 108 molecules per cell (1). Differences between cell types, between normal and disease states, and between individuals are largely defined by changes in the abundance of proteins, which are in turn determined by rates of transcription, messenger RNA (mRNA) degradation, translation, and protein degradation. If the rates for one of these steps differ much more than the rates of the other three, that step would be dominant…

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Behavior (4): All responses are RNA-mediated in birds

March 20, 2015
James Kohl
Adaptations, Ecology, Model Organisms
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Bird Genomes Abound Scientists complete the largest-ever comparative genomic study of birds. By Ruth Williams | December 11, 2014 Excerpt: “The results of this effort provide not only the most precise genetic history of birds to date, but also reveal why avian genomes tend to be small compared to those of other vertebrates: because they have lost a lot of genes and have far fewer repeat sequences. Furthermore, the data show that, compared with mammals, both the nucleotide sequences and…

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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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