Code Biology vs Predatory Publishing (1)

There is a video (with English subtitles) devoted to open access scientific literature. It was released in October 2016 and has already collected more than half a million views.

There is no fake news or sensational hype in the video. The details may be “boring,” but they help to explain why I published my recent review of nutritional epigenetics in an open access publication. See: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

Others complain about the lack of free access to articles of interest, but they are forced to “publish or perish” so they publish wherever they can.

That is why the profitability of publishing in most journals is higher than the profitability most people could achieve on any Stock Exchange.

See: Sci.hub.org

“[W]elcome to the world of scientific publishing houses. The authors tell us how the cost of subscriptions to scientific journals has grown for the last 20 years. At the same time, the cost of issue of magazines fell due to the development of digital technologies. As a result, the profit of such a scientific publishing house as Elsevier grew 4 times. But the budgets of universities and libraries are completely exhausted: for example, the University of Montreal refused to subscribe to almost all Springer journals in 2016 due to lack of funds.”

Predatory publishing and the lack of funds may prevent researchers from learning about the coding coenzyme handle hypothesis (CCH). The so-called hypothesis suggests that amino acids attached to RNA handles enhance the catalytic activities of ribozymes. The amino acid substitutions have been linked to cell type differentiation and cell type stability at every level of biological organization.

See for review: Poly(A)-specific ribonuclease sculpts the 3′ ends of microRNAs

For comparison to everything known about how conserved energy-dependent mechanisms link the 3′ end formation of vertebrate miRNAs from light-activated changes in angstroms to ecosystems, see the hypothesis-free suggestions in The PsychENCODE Consortium Science. Vol. 362, December 14, 2018.

I think it has become clear that “Science” is a predatory publisher.

See for comparison, this 2012 report from another top-tier publication: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

This was reported as: Past 5,000 years prolific for changes to human genome

For the most recent and most relevant reports on energy-dependent top-down causation, microRNA-mediated biophysically constrained viral latency,  and the epigenetically-effected changes in hormones that have been linked to affects on the development of behavior during the past 5,000 years see:

S.L. Rhie et al. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Science Advances. Published online December 13, 2018. doi:10.1126/sciadv.aav8550.

C. Chen et al. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. Science Translational Medicine. Vol. 10, December 19, 2018. doi:10.1126/scitranslmed.aat8178.

Q. Meng et al. The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes. Science Translational Medicine. Vol. 10, December 19, 2018.

See also:  Code Biology: Special issue

What is code biology? Marcello Barbieri Pages 1-10

Overall summary of the Special Issue

The first Special Issue on code biology – A bird’s-eye view Jan-Hendrik S. Hofmeyr Pages 11-15

PART  1  –  Experimental Code Biology

On universal coding events in protein biogenesis Vladimir Kubyshkin, Carlos G. Acevedo-Rocha, Nediljko Budisa Pages 16-25

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow Pedro C. Marijuán, Jorge Navarro, Raquel del Moral Pages 26-38

The splicing code Marco Baralle, Francisco Ernesto Baralle Pages 39-48

Evidence for the implication of the histone code in building the genome structure Kirti Prakash, David Fournier Pages 49-59

Aggregating, polarizing, networking – The evolution of cell adhesion codes Marcella Faria Pages 60-67

The lamin code Nadir M. Maraldi Pages 68-75

The bioelectric code: An ancient computational medium for dynamic control of growth and form Michael Levin, Christopher J. Martyniuk Pages 76-93

Fundamental principles of the olfactory code Veit Grabe, Silke Sachse Pages 94-101

The sugar code: Why glycans are so important Hans-Joachim Gabius Pages 102-111

The evolution of the Glycomic Codes of extracellular matrices Marcos S. Buckeridge Pages 112-120

PART 2 – Theoretical Code Biology

Causation, constructors and codes Jan-Hendrik S. Hofmeyr Pages 121-127

The evolutionary dynamics of language Luc Steels, Eörs Szathmáry Pages 128-137

The search image as link between sensation, perception and action Morten Tønnessen Pages 138-146

Ecoacoustic codes and ecological complexity Almo Farina Pages 147-154

Insuperable problems of the genetic code initially emerging in an RNA world Peter R. Wills, Charles W. Carter Pages 155-166

Carrying pieces of information in organocatalytic bytes: Semiopoiesis—A new theory of life and its origins Wanderley Dantas dos Santos Pages 167-176

Towards measuring the semantic capacity of a physical medium demonstrated with elementary cellular automata Peter Dittrich Pages 177-185

Mathematical fundamentals for the noise immunity of the genetic code Elena Fimmel, Lutz Strüngmann Pages 186-198

Genetic coding algorithm for sense and antisense peptide interactions Nikola Štambuk, Paško Konjevoda, Petra Turčić, Katalin Kövér, … Mario Gabričević Pages 199-216

The evolution of the genetic code: Impasses and challenges Ádám Kun, Ádám Radványi Pages 217-225

… a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes.

For more examples of Predatory Publishing that can be placed into the context of claims about The evolution of the genetic code: Impasses and challenges Ádám Kun, Ádám Radványi Pages 217-225 , see these reports from: The PsychENCODE Consortium in Science. Vol. 362, December 14, 2018.

M. Li et al. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. Vol. 362, December 14, 2018, p. 1264. doi: 10.1126/science.aat7615.

M.J. Gandal et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia and bipolar disorder. Science. Vol. 362, December 14, 2018, p. 1265. doi:10.1126/science.aat8127.

D. Wang et al. Comprehensive functional genomic resource and integrative model for the human brain. Science. Vol. 362, December 14, 2018, p. 1266. doi:10.1126/science.aat8464.

Y. Zhu et al. Spatiotemporal transcriptomic divergence across human and macaque brain development. Science. Vol. 362, December 14, 2018, p. 1267. doi:10.1126/science.aat8077.

A. Amiri et al. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science. Vol. 362, December 14, 2018, p. 1268. doi:10.1126/science.aat6720.

P. Rajarajan et al. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science. Vol. 362, December 14, 2018, p. 1269. doi:10.1126/science.aat4311.

J.-Y. An et al. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science. Vol. 362, December 14, 2018, p. 1270. doi:10.1126/science.aat6576.

Keep this in mind: ASCO Poll Finds ‘Frightening’ Views on Alternative Cancer Tx: Many believe cancer can be cured without standard therapies 

The survey defined alternative therapies as enzyme and oxygen therapy, certain diets, and vitamins and minerals.

The energy-dependent creation of enzymes links oxygen therapy, certain diets, and vitamins and minerals from the creation of microRNAs to naturally occurring RNA interference, which typically prevents the virus-driven degradation of messenger RNA that all serious scientists have linked to all diseases.

That fact frightens many so-called medical practitioners. They currently treat people as if people had evolved from single-celled organisms.

For more than 50 years, the neo-Darwinian pseudoscientific nonsense of claims linked (above) to genome-wide de novo risk scores via promoter variation instead of microRNAs has been the biggest money-making scam that the world has ever known, because most people do not recognize it as a scam.

See for comparison: Discovery and resupply of pharmacologically active plant-derived natural products: A review.

Also, watch for part 2 of Code Biology vs Predatory Publishing

Author: James Kohl

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