The tipping point (revisited): 84,000 publications (1)

MicroRNA  Items: 1 to 20 of 83977

See for comparison: The tipping point (revisited): 83,000 publications (1) 2/9/19

See: Evolutionary Divergence of Brain-specific Precursor miRNAs Drives Efficient Processing and Production of Mature miRNAs in Human (11/10/18)

The higher processing efficiency of human Brain-specific miRNAs was reflected as an elevated production of corresponding mature miRNAs in the human brain.

This showed up in my alerts on 3/7/19. Delayed indexing allows biologically uninformed theorists to keep sneaking around touting their ridiculous theories.

No experimental evidence of biophysically constrained biodiversity suggests that microRNAs evolve. That means there is no such thing as the evolutionary divergence of Brain-specific Precursor miRNAs.

In this example of pseudoscientific nonsense, the authors linked the automagical emergence of higher nucleotide substitution rates from the expression pattern of brain-specific miRNAs to transcriptome divergence.

Emergence is the “magic trait” of neo-Darwinian evolution.

See also: Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks

…variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs).

… significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.

For comparison, the creation of nucleotides and nucleic acids is energy-dependent. The creation of energy links the microRNA-ribonucleic acid (RNA)-peptide nanocomplex to amino acid substitutions. Serious scientists do not link emergence to significant expression QTL (eQTL) x hQTL interactions and they do not link the interactions from gene expression to anything known about energy-dependent top-down causation.

For instance in the context of top-down causaton, glycine in position 6 of the gonadotropin releasing hormone decapeptide exemplifies a proteogenic amino acid with a single hydrogen atom as its side chain. It is the simplest amino acid and glycine is noteworthy because it is the only proteogenic amino acid that is achiral. That fact cannot be put back into the context of significant expression QTL (eQTL) x hQTL interactions.

Glycine is created/encoded in the context of natural selection for energy-dependent codon optimality by all the codons that start with GG (GGU, GGC, GGA, GGG).

Glycine can fit into hydrophilic or hydrophobic environments.

Supercoiled DNA is hydrophobic. Due to its minimal side chain of only one hydrogen atom glycine is referred to as an “alpha helix breaker.” Given that designation, there must be an “alpha helix fixer.”

Everything known about light-activated carbon fixation links light-activated energy-dependent RNA-mediated DNA repair from light activated microRNA biogenesis in plants to the microRNA-RNA-peptide nanocomplex and fixation of amino acid substitutions that differentiate all the cell types of all individuals of all living genera. That makes light a powerful alpha helix fixer. It also makes serious scientists laugh when theorists or biologically uninformed science journalists mention significant expression QTL (eQTL) x hQTL interactions.

Everything known to serious scientists about energy-dependent cell type differentiation links the power of the light-activated alpha helix fixer from microRNA biogenesis to the genesis of all diversity via the light-activated assembly of the microRNA-RNA-peptide nanocomplex.  Light-activated biophysically constrained viral latency, and the physiology of reproduction, are included in the context of natural selection for energy-dependent codon optimality and information processing that links the alpha helix fixer in bacteria to fixation of RNA-mediated amino acid substitutions in all living genera.

Serious scientists tend to think the facts about the creation of energy as information and information processing in species from bacteria to humans are awesome. Theorists are not sure they can trust the serious scientists. Some so-called science journalists seem to trust the theorists, which suggests the journalists are not capable of independent thought.

Among journalists,  Does awe lead to greater interest in science?

“Clearly awe makes us realize what we don’t know about the natural world. We come to know how much we do not know, which is a privilege because most people don’t know what they don’t know,” says McPhetres, referring to what psychologists call the Dunning-Kruger effect. This kind of experience makes people ask questions about nature and, his research suggests, seek answers to those questions in a methodological and systematic way.

There is no sense of awe when theorists and journalists link ecologically relevant magic traits to evolution. But, as you can see, that’s what theorists do. Similarly, there is no sense of awe when pseudoscientists or science journalists mention significant expression QTL (eQTL) x hQTL interactions.

See: Genetic dissection of assortative mating behavior (2019)

Ecologically relevant mating cues (sometimes known as “magic traits” [2,6]) are now predicted to be widespread in nature…

Are significant expression QTL (eQTL) x hQTL interactions also widespread in nature?

See: Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics (with my emphasis)

We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships.

For more inferences, see: Mutation-Driven Evolution

You can link the conservation of genes from inferences about constraint-breaking mutations to the source of all biodiversity in this world. Alternatively, you can stop to consider the awe-inspiring teleological elements that link the creation of anti-entropic virucidal light from microRNA biogenesis to the genesis of all biodiversity.

You can believe serious scientists have linked the light-activated assembly of the microRNA-RNA-peptide nanocomplex and amino acid substitutions to the differentiation of all cell types in all living genera via the physiology of reproduction. Alternatively, you can take everything known to serious scientists and place it back into the context of genome wide association studies (GWAS) and inferences.

“Genome-wide association studies” Items: 1 to 20 of 14211

Although the energy-dependent creation of microRNAs continues to be linked to all biophysically constrained biodiversity on Earth by ~1000 more published/indexed works each month, theorists still like to discuss theoretical nonsense.

See for example: The 2019 International Workshop on Statistical Genetic Methods for Human Complex Traits March 4th–March 8th, 2019

…with John Hewitt and Matt Keller as Local Hosts…

This advanced course is intended for those who are already familiar with the statistical and genetic principles for studying human complex traits and have some familiarity with programming in R. The course will focus on statistical methods for analyzing genome-wide association studies (GWAS) and genome sequence data.

See: Matthew Keller et al., (2018) Complete genome direct RNA sequencing of influenza A virus

Reported as: Flu virus finally sequenced in its native form

“The real excitement here is about RNA modifications,” says Ewan Birney, a bioinformatician and co-director of the European Bioinformatics Institute in Hinxton, UK. Birney says that the approach is “transformative”.

That approach looked at transcripts of messenger RNA, the family of RNA molecules that conveys information from DNA to build proteins. How could it be placed back into the context of GWAS and evolution?

Here’s how: In the context of the influenza virus, Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions, but the title of the 2013 journal article in Science was “Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution.

Each scientific advance made by serious scientists, such as the forthcoming cure for cancer, seems destined to be delayed by those who are still touting mutations and evolution or using the nonsensical language about significant expression QTL (eQTL) x hQTL interactions to ecologically relevant magic traits to species-specific changes in morphological and behavioral phenotypes outside the context of feedback loops that link what orgnaisms eat to the pheromone-controlled physiology of reproduction.

See: The tipping point (revisited): 84,000 publications (2)