reproduction

Mystery machine vs model (2)

October 22, 2015
James Kohl
Adaptations, Ecology, Model Organisms, Physics, RNA Directed, Variations
No Comments

See: Mystery machine vs model Here are links to reports that attest to the accurate representation of links from nutrient energy-dependent base pair changes to RNA-mediated amino acid substitutions and protection of organized genomes from virus-driven genomic entropy. See also: Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria Re: direct interspecies electron transfer (DIET) Excerpt: HotSeep-1 comprises the genes for the biosynthesis and assembly of type IV pili, as well as large multi-haem cytochrome c proteins, both with…

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Energy and evolution: another opinion?

October 14, 2015
James Kohl
Adaptations, Ecology, Light Energy, Physics, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, Variations
No Comments

The Vital Question: Energy, Evolution, and the Origins of Complex Life Excerpt: Building on the pillars of evolutionary theory, Lane’s hypothesis draws on cutting-edge research into the link between energy and cell biology in order to deliver a compelling account of evolution from the very origins of life to the emergence of multicellular organisms while offering deep insights into our own lives and deaths.” My comment: The pillars of evolutionary theory have been toppled by facts that link the biological…

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Microbes to humans 2015 Nobel Prize

October 6, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, RNA Directed, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing
No Comments

3 Scientists Win Nobel Prize in Medicine for Parasite-Fighting Therapies Excerpt 1) Success in antimalarial therapy depends on how clever scientists are in using combinations of drugs. Excerpt 2) Dr. Omura played down his accomplishments, saying, “I merely borrowed the power of microbes.” My comment: These two excerpts appear within the context of three paragraphs that clearly link RNA-mediated cell type differentiation in species from microbes to humans. The context attests to what at first may appear to be a…

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Mechanisms of stress: from genes to cancer

October 2, 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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Biophysically constrained nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation link the epigenetic landscape to the physical landscape of DNA in all living genera. Genomic stability arises in the context of a fine-tuned balance of viral microRNAs and nutrient-dependent microRNAs.  RNA-mediated gene duplication and RNA-mediated amino acid substitutions stabilize organized genomes. Nutrient-dependent microRNAs are linked by RNA-mediated amino acid substitutions from ecological variation to protection from DNA damage caused by viral microRNAs. The microRNA/messenger RNA balance links ecological variation to…

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Viruses come alive: Tree of life pseudoscience

September 28, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed
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See also: The creation and activation of GPCRs ‘Tree of life’ for 2.3 million species released This comment was removed from a “tree of life” discussion site by the “site staff.” In the context of anonymous “peer” review, the comment was removed for the following reason: PSEUDOSCIENCE, with an added threat that my account might be suspended in case of regular violations of the guidelines that led the “site staff” to remove this comment. Young earth creationists addressed the “Tree…

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Theorists have not seen the light

September 24, 2015
James Kohl
Adaptations, Ecology, Light Energy, Model Organisms, Physics, RNA Directed, Variations
No Comments

2015 Physiologists uncover a new code at the heart of biology Excerpt: It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons. My comment: That fact underlies our representation of RNA-mediated cell type differentiation from our 1996 review From Fertilization to Adult Sexual BehaviorSee our section on molecular epigenetics. Our representation was subsequently linked to organization of genomes in insects…

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A Darwinian pediatrician and expected life span

September 21, 2015
James Kohl
Adaptations, Alternative Splicings, Ecology, Model Organisms, RNA Directed, Variations
No Comments

See also: A 5-10K comparison of design priciples to evolution CEM Thursday Seminar – Paul Turke Excerpt: The human immune system reboots every generation. It’s a lifelong process, but much of it is accomplished before birth. My comment: The world’s first Darwinian pediatrician appear to know nothing about nutrient-dependent RNA-mediated cell type differentiation. See for comparison: Regulating S-adenosine-methionine (SAM) levels to extend life span Excerpt: Limiting S-adenosyl-methionine (SAM) synthesis, the first metabolic reaction of dietary methionine, extends longevity in Caenorhabditis elegans…

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Exosomes and the RNA-mediated future of medicine

September 10, 2015
James Kohl
Adaptations, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed, Variations
One Comment

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins Reported as: The exosome regulates the processing, degradation, and surveillance of a plethora of RNA species. Excerpt: …the exosome employs a general mechanism of recruitment to defined substrates and that this process is regulated through adaptor proteins. Journal article excerpt: (subscription required) The nuclear exosome processes precursors of numerous stable RNA species (Allmang et al., 1999) (rRNA, snoRNA, and snRNA) and degrades by-products of RNA processing reactions. Additionally, it…

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Cell types, SNVs, CNVs, and chromosomes

August 26, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, Variations
One Comment

See also: A “new” code enables ecological adaptation For comparison, see: Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell Excerpt: Single-molecule and single-cell studies reveal behaviors that are hidden in bulk measurements (1, 2). In a human cell, the genetic information is encoded in 46 chromosomes. The variations occurring in these chromosomes, such as single-nucleotide variations (SNVs) and copy-number variations (CNVs) (3), are the driving forces in biological processes such as evolution and cancer. Such dynamic…

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A “new” code enables ecological adaptation

August 26, 2015
James Kohl
RNA Directed
One Comment

Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity Reported as: Discovery of new code makes reprogramming of cancer cells possible Excerpt: …an unexpected new biology that provides the code, the software for turning off cancer,” says the study’s senior investigator, Panos Anastasiadis, Ph.D., chair of the Department of Cancer Biology on Mayo Clinic’s Florida campus. That code was unraveled by the discovery that adhesion proteins — the glue that keeps cells together —…

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