protein-folding

Is mainstream science in “Science” pseudoscience?

See: Single neuron may carry over 1,000 mutations (with my comments),  A natural history of neurons: Diverse mutations reveal lineage of brain cells (with my comments), and Study examines scale of gene mutations in human neurons, All three of the links above are to reports on the study results published as: Somatic mutation in single human neurons tracks developmental and transcriptional history Excerpt 1) We also observed a signature of methylated cytosine (meC) to thymine (T) transitions (fig. S8), which…

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Viruses come alive: Tree of life pseudoscience

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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Gene creation (revisited)

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation Abstract: The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces,…

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Theorists have not seen the light

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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Alternative pre-mRNA splicing and ecological adaptation

This startup thinks it can speed up a cure for cancer by bringing scientific research into the YouTube era Excerpt: The current scholarly publishing model did not allow me to present the research I was doing. I created [Figshare] initially out of purely selfish reasons and I spent my evenings and weekends creating a platform that allowed me show, in a super simple way, data sets, and videos to put me ahead of the rest of my peers. I’ve used…

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Exosomes and the RNA-mediated future of medicine (3)

September 11, 2015 Case Western Reserve scientists discover long-sought genetic mechanism for cancer progression Excerpt: Action of a key lncRNA different in colon cancer versus normal colon tissue My comment: In yet another ridiculous misrepresentation of all that is currently known about how the epigenetic landscape is linked to the physical landscape of DNA in all cell types of all individuals of all living genera, these researchers are reporting epigenetic links between metabolic networks and genetic networks as if the…

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Multi-omic analysis features (SNPs, miRNA)

See also: Viral and Cellular Genomes Activate Distinct DNA Damage Responses Excerpt: Central to life is the faithful replication, inheritance, and maintenance of genomic DNA. The MRE11/RAD50/NBS1 (MRN) complex andATMplay a critical role in this biological mandate (Ciccia and Elledge, 2010). Cellular double-strand breaks (DSBs) are sensed by MRN and trigger the assembly of DNA damage response (DDR) foci that amplify global ATM signaling to induce cell-cycle arrest and DNA repair (Polo and Jackson, 2011). DNA viruses are an ancient…

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Natural selection: an anti-entropic force?

The second law of thermodynamics is the first law of psychology: evolutionary developmental psychology and the theory of tandem, coordinated inheritances: comment on Lickliter and Honeycutt (2003). This link opens the pdf Excerpt 1) Over the individual life span, what causes organisms to start out as single cells and then anti-entropically climb to dizzyingly greater heights of order (in the case of humans, to cell populations in the trillions built into intricate intercellular structures such as the eye, vasculature, and…

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Genome sequencing, cadherins, and quantum consciousness

Brave new epigenomes: the dawn of epigenetic engineering Reported as: Opinion: Engineering the Epigenome Excerpt: . ..until recently, we were not able to assess the influence of individual marks on gene activity because it was only possible to alter chromatin marks globally through mutational approaches or pharmacological inhibition. My comment: Mutational approaches led to assumptions about cell type differentiation that failed to include the role of viruses, viral microRNAs,  and the nutrient-dependent microRNAs that prevent the accumulation of viral microRNAs…

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“New” quantum biology. Pirating the old

Jim Al-Khalili is a nuclear physicist. Luca Turin is a biologist. Both presenters link Schrödinger’s claims in What is Life? Which one knows most about it? Jim Al-Khalili  frames his presentation in the context of evolutionary theory. See the text or the 20-minute Video presentation: Jim Al-Khalili: How quantum biology might explain life’s biggest questions Luca Turin frames his presentation in the context of what is known to serious scientists about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding. See also: …

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