For God and Country

Sci-Hub vs limits on the dissemination of information

The ideology of “Americanism” is not consistent with the tactics of academics and politicians that constrain release of accurate information about  biologically-based cause and effect.

Americanism is an ideology, or belief in devotion, loyalty, or allegiance to the United States of America, or to its flag, traditions, customs, culture, symbols, institutions, or form of government.[2] In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”[3]

Americanism has two different meanings. It can refer to the defining characteristics of the United States and can also signify loyalty to the United States and a defense of American political ideals. These ideals include, but are not limited to self-government, equal opportunity, freedom of speech, and a belief in progress.

Scientific progress has been hindered by publishing companies whose corporate purpose is financial gain for stockholders, not the dissemination of freecinformation that is required to make scientific progress by serious scientists who are Combating Evolution to Fight Disease.
Rarely do the efforts of serious scientists get noticed because there is too much pseudoscientific nonsense that gets published in peer-reviewed journals. The nonsense overwhelms the ability to discern between facts and story-telling. Evolutionary theorists, for example, are story-tellers.
For an attempt to resolve the problem with theorists, see: Publishers’ Legal Action Advances Against Sci-Hub

Based on data from Google Trends, researchers found that the suits against Sci-Hub led to brief spikes in visits to the site.

The publishers contribute to the theft of information because most people do not care how they acquire it. People want the information on biologically based cause and effect for free, and many of them will use it to make scientific advances such as those that have linked energy-dependent changes in microRNAs to all pathology.
A PubMed search for “microRNA” reveals that nearly 65,000 indexed published works have already established facts that link virus-driven energy theft to all pathology. Most the publications are behind “pay walls.”
That means most researchers will be unable to access all of them. Anyone outside the specific discipline that is the focus of the article will not be likely to integrate the information across disciplines and accurately represent what is known about biophysically constrained biologically-based cause and effect.
For an example of the level of integration that is required, request a copy from the corresponding author and wait to see the information in this “pay-walled” publication: Olfaction Warps Visual Time Perception.
By the time you get it, there will probably be several hundred more publications that link the food energy-dependent physiology of pheromone-controlled reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See also:

Alternatively, see: Energy as information and constrained endogenous RNA interference
Cited works:
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
2)  Evolutionary drivers of thermoadaptation in enzyme catalysis
3). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
6) Metabolic theory predicts whole-ecosystem properties
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
13)  Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
16) All about the base
17) Chemists know.
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
20) RNA-Guided Human Genome Engineering
21) What is Life?
22) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
23) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
24) A Big Bang in spliceosome structural biology
The works cited above have been placed into the context of the cell biology game “Cytosis.”

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See for comparison: 2017 Royal Society Insight Investment Science Book Prize

The perfect science book marries scientific breakthrough with elegant, engaging communication. Reading these books side-by-side, we were struck by how creative and unique each voice was, and the varied ways these writers tackle their subjects, using metaphors and personal stories as much as scientific facts.

The perfect science book marries what is known about the creation of energy as information with the biophysically constrained physiology of pheromone-controlled reproduction, which prevents the virus-driven degradation of messenger RNA.

Biophysically constrained viral latency prevents all pathology. This year’s Prize winner linked testosterone to “gender” differences in behavior.

For comparison, see: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences


…this model incorporates a logical pathway that directly links sensory input from the social environmental to the development of sexual preferences and to the development of sexual behavior.

The five-step logical pathway that directly links sensory input from the social environment to the development of sexual preferences and sexual behavior is gene→cell→tissue→organ→organ system. Failure to incorporate any of the steps in this pathway makes it impossible to directly connect to sexual preferences and sexual behavior, a logical sequence of events that must somehow and somewhere begin with the effect of sensory input from the social environment.

See also: Intelligent Design – Science & Philosophy: discussion thread

Antagonist, Timothy Kershner wrote:

I have a PhD in Psychology and a minor degree in Microbiology and personally funded many Bacterial Consciousness studies between 2008 and 2012 and mentored directly under James Shapiro from 2009 to 2011.

Shapiro already is laughing at you and others as he tries to recover from teaching you to become biologically uninformed science idiots who believe in evolution outside the context of energy-dependent ecological adaptations that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.

See: Biological action in Read-Write genome evolution

Coincidentally, ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Shapiro’s latest is part of a Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland.

See for comparison: How life changes itself: The Read-Write (RW) genome

Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA.

See also: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

and UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

All cell-mediated processes are energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Energy dependent life does not change itself. RNA-mediated events must be linked to the stability of organized genomes. The organized genomes cannot come first. The details of energy-dependent cell-mediated RNA-directed DNA methylation clearly link the virucidal energy of sunlight from microRNAs in plants to the microRNAome of all mammals. All humans are included.

RNA interference occurs in plants, animals, and humans. It is of great importance for the regulation of gene expression, participates in defense against viral infections, and keeps jumping genes under control. RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future.

Naturally occurring endogenous RNA interference links what organisms eat from their physiology of pheromone-controlled reproduction to all energy-dependent biodiversity on Earth via biophysically constrained viral latency. For example, see:

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

See for comparison: Alnylam’s rare disease drug shines in trial, paving way for a brand-new class of medicines

RNA interference, or RNAi, a technology that uses snippets of genetic code to shut down disease-causing genes. The scientists who invented RNAi were awarded the Nobel Prize for Medicine in 2006. Many years and more than $1 billion in research later, Alnylam is finally on the cusp of proving that RNAi can be transformed into a medicine that helps patients.

Scientists did not invent RNAi. They discovered that it links what organisms eat to their biophysically constrained pheromone-controlled physiology of reproduction. That fact links RNAi to all biodiversity without the pseudoscientific nonsense touted by evolutionary theorists. The cost of any RNAi drug that is approved will almost assuredly bankrupt the person who needs the drug and the cost will probably destroy the economy of the United States of America via the impact on the costs of Medicare and/or other insurance.
This is not Amercanism: Alnylam Data Puts a Nobel Discovery One Step Closer to Approved Drug

Shares of Alnylam soared more than 51 percent and closed at $113.84 apiece on Wednesday.


Bio-functional information

Peter Berean‘s attack on my model of energy as information led him to invent or re-introduce the term “Bio-Functional Information.” The comment from Greg Thurston (below) can be placed into the context of Schrodinger’s claims from “What is Life?”
For instance, Schrodinger challenged de Vries definition of the term mutation with this entry:

“Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)”

Watch as Greg launches another personal attack against me because I refuse to allow Peter Berean‘s comments on my representations of energy as information to go unchallenged. In my model, for comparison,  the anti-entropic energy of sunlight is linked to all biodiversity,
See: What is life when it is not protected from virus driven entropy?
Greg makes it appear that I am the only person who knows Peter Berean is trying to introduce a term that must be defined before others realize it is synonymous with de Vries 1902 definition of mutation. Peter Berean’s treachery could conceivably delay scientific progress for at least one more generation if students are taught that “Bio-Functional Information” is different that energy as information.
The success of all threats to scientific progress depends on the misrepresentations of theorists, and definitions are one way to eliminate energy as information from biologically-based cause and effect. De Vries definition of mutation did that and his definition has served biologically uninformed theorists very well during the past 114 years.
Sudden energy jumps were used to link the assumptions of theorists to claims about mutation-driven evolution, which supposedly occurred via natural selection. All serious scientists have since realized that natural selection for energy as information must be linked from codon usage to energy-dependent changes, which link the physiology of reproduction to supercoiled DNA in all living genera.
Theorists are not likely to ever accept that fact. The levels of complexity are too difficult for pseudoscientists to integrate, which helps to explain why many of them are also atheists or agnostics. When creationists tout the same pseudoscientific nonsense, it shows why we have come so close to the virus-driven apocalypse.
Greg Thurston wrote:
December 17 at 10:59am
James Kohl – it was nice to see your name in the comments on this thread when it first appeared. Then it was quite a surprise to see the nature of your comments. It’s been a while since we connected. I believe you are onto something, but somehow you are unable to convey it in a way that anyone (or at least most) can assimilate. As you may recall, I even thought for a while that I could help unpack it enough to make it clear (to me and then others), but the more I waded into it, the denser the thicket seemed to get, and I was overwhelmed. I don’t have the time. I am so disappointed to see the tone of your comment [to] Peter Berean. I thought you were above ad hominem et al. I hope you can take this as not an insult, but a caution from one who would like to be considered a friend, that it seems perhaps ego has clouded your ability to be gracious and have courteous discourse with others who see things differently. It is amazing to me how much ego commandeers intellect in so many instances. It is a threat to us all, of which we must be exceedingly diligent to resist.
See also: What is Life?
“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” — Roger Penrose (8 August 1991)
I get the impression that Greg Thurston might think Roger Penrose is an ego-maniacal threat to Peter Berean‘s intellect.
Perhaps, someone like Greg Thurston will first ask Peter Berean to tell others the difference between a “mutation” and “bio-functional information.” For contrast, in the context of my model, the fixation of energy-dependent RNA-mediated amino acid substitutions links biophysically constrained cell type differentiation to the physiology of reproduction in all living genera.
Theorists do not have a model for how that occurs in the context of biophysical constraints. They have theories, which helps to explain why Peter Berean is tweaking the theories via his usage of words. He knows nothing about natural selection for energy-dependent codon optimality. That requires the invention and/or reuse of the term “bio-functional information.” It is a great way for pseudoscientists to dismiss everything known to serious scientists via a vague term.