RNA-mediated epigenetic regulation of gene expression

From dust to genomic entropy?

Extreme eolian delivery of reactive iron to late Paleozoic icehouse seas Reported as: Dust, iron, life: How atmospheric dust prepped Earth for life Excerpt: The biogeochemical impacts of iron-rich dust to the oceans are known for Earth’s recent record but unexplored for deep time… My comment: The fact that this has been unexplored requires another untestable theory about dust-prepped Earth to explain the origin of what is happening in this video. My comment: The origins of how the dust-prepped Earth…

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Virus, transposon and plasmid evolution

A novel group of diverse Polinton-like viruses discovered by metagenome analysis Excerpt: This class of selfish elements is extremely widespread and might have been a hotbed of eukaryotic virus, transposon and plasmid evolution. New families of these elements are expected to be discovered. My comment: How much longer will Koonin’s group keep trying to convince biologically uninformed science idiots that selfish elements evolve or that species evolve? All serious scientists know that ecological variation leads to ecological adaptation via nutrient-dependent…

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Conserved molecular mechanisms

Functional Conservation of the Glide/Gcm Regulatory Network Controlling Glia, Hemocyte and Tendon Cell Differentiation in Drosophila Abstract excerpt: High throughput screens allow us to understand how transcription factors trigger developmental processes including cell specification. A major challenge is the identification of their binding sites because feedback loops and homeostatic interactions may mask the direct impact of those factors in transcriptome analyses. My comment: Evolutionary theorists must accept the fact that feedback loops and homeostatic interactions are conserved and stop making…

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Models are not theories (2)

MicroRNA-encoded behavior in Drosophila Editor’s summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene activity. They repress expression through complementary base pairing interactions with target messenger RNAs. MiRNAs are involved in regulating many cell and developmental processes. Picao-Osorio et al. find that miRNAs can also control behavior in the fruit fly Drosophila. My comment: Ridiculous claims from 1) We are all mutants and from 2) Mutation-Driven Evolution can now be placed into the context of what is known to…

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Models are not theories (1)

Cells or Animals: Which model is better? Excerpt: …animal models allow testing on intact physiological systems of many cell types simultaneously. Excerpt:  …it is important to note that human and rodent physiology is not identical, and even sophisticated animal models can have shortcomings. My comment: For comparison to neo-Darwinian theories, it is more important to note that the RNA-mediated cell type differentiation of all living genera is nutrient-dependent and controlled by the physiology of reproduction. Also note, in species from…

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Cyclic cosmology and the stability of organized genomes

Current observations with a decaying cosmological constant allow for chaotic cyclic cosmology Abstract excerpt: ‘We present only a proof of principle, with no definite claim on the physical mechanism required for the present dark energy to decay.” My comment: Unlike nearly all theorists, they do not claim to be certain about any of the physical mechanisms that link atoms to ecosystems in the context of supercoiled DNA in the organized genomes of all living genera on this planet. For comparison,…

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Unraveling the secrets of RNA-mediated events

Unraveling the Secrets of DNA Excerpt: Belmont’s team will “rewire” chromosome regions to different nuclear locations and then determine the functional consequences of this rewiring. My comment: The “rewiring” can be placed into the context of nutrient-dependent pheromone-controlled rewiring of the genome that led to a report of over-the-weekend” re-evolution of the bacterial flagellum. Two nutrient-dependent amino acid substitutions linked the metabolic networks to the genetic networks and the RNA-mediated substitutions led to a second-chance resurrection of a functional structure.…

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RNA central and RNA-mediated.com

What are lncRNAs? Excerpt:  There are many specialized lncRNA databases, which are organized and centralized through RNA central. lncRNAs can be transcribed as whole or partial natural antisense transcripts (NAT) to coding genes, or located between genes or within introns. Some lncRNAs originate from pseudogenes (Milligan & Lipovich, 2015). lncRNAs may be classified into different subtypes (Antisense, Intergenic, Overlapping, Intronic, Bidirectional, and Processed) according to the position and direction of transcription in relation to other genes (Peschansky & Wahlestedt, 2014,…

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Ecological speciation. Get it, theorists?

A Prkci gene keeps stem cells in check Excerpt: In the presence of Prkci, the Notch pathway remains silent, and stem cells differentiate into specific cell types. My comment: Several days of attempted discussion led to this question Do you get it now, jvk? My response: Everyone who is not a biologically uninformed science idiot gets it. The Zechiedrich lab‘s focus links energy-dependent base pair changes from atoms to ecosystems. The Rosenberg lab‘s focus on stress shows why others must…

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Designing, engineering, and protecting biodiversity

Engineering Life Flipped Course Introduction: How did life evolve? How can we understand the principles of biological systems to create new proteins, new chemicals, biological structures, cells and tissues? The course title led me to think they might include the required information on energy-dependent base pair flipping that links atoms to ecosystems. See, for example: Structural diversity of supercoiled DNA When I saw that the first presentations of the series featured Jack Szostak, I realized that no facts about biologically-based…

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  • What Darwin proved: there’s no such thing as a species
    GENETICS As Animals Mingle, a Baffling Genetic Barrier A short stretch of DNA is challenging what it means to be a species. By: Emily Singer August 5, 2014 Excerpt: “Scientists have dubbed such regions of the genome “islands of speciation.” The persistence of such islands is a phenomenon that has been observed in a variety of […]
  • 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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