Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

How to biophysically constrain the flu virus (1)

Excerpt: John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
What the flu does to your body, and why it makes you feel awful

…when you have an influenza infection, you can rest assured that it is because your body is fighting hard. It’s combating the spread of the virus in your lungs and killing infected cells.

Why suffer needlessly or die prematurely. See: Cytosis: A Cell Biology Board Game 

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses! (2 to 5 Players, Ages 10 & up, Plays in 50 to 75 mins)

Download the “Science Behind the Game” to learn how food energy-dependent alternative splicings of pre-mRNA protect all cell types, or see Alternative splicing and the evolution of phenotypic novelty.
Link the alternative splicings to species-specific behaviors via the physiology of reproduction in From Fertilization to Adult Sexual Behavior and anything else I have published or presented during the past two decades.
All behavior is energy-dependent. The energy comes from sunlight. Quantized energy as information from sunlight is linked to healthy longevity via its anti-entropic virucidal effect.
For example: Special UV light safely kills airborne flu virus, finds study

Scientists have known for decades that broad-spectrum UVC light, which has a wavelength of between 200 to 400 nanometers, or nm), is highly effective at killing bacteria and viruses by destroying the molecular bonds that hold their DNA together.

For comparison to vaccinations:
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

A key advantage of the UVC based approach, which is in clear contrast to vaccination approaches, is that UVC light is likely to be effective against all airborne microbes. For example, while there will almost certainly be variations in UVC inactivation efficiency as different influenza strains appear, they are unlikely to be large7,10. Likewise, as multi-drug-resistant variants of bacteria emerge, their UVC inactivation efficiencies are also unlikely to change greatly9.

In the context of vaccinations:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Clearly, vaccinations may not protect you and prevention via use of UV light is desirable.
When you learn how UV light protects you at the level of particle physics, you will understand the horrors of neo-Darwinian theory and big bang cosmology .
See Subatomic
The link from quantum physics to quantum chemistry was reported last month. Modern diversification of the amino acid repertoire driven by oxygen.
Schrödinger at 75, The Future of Biology is scheduled for September 2018
John E Walker (Factor-dependent archaeal transcription termination) will probably explain the molecular mechanism of how ATP is made, which may be important to know for those who have learned how important ATP is by playing “Cytosis.” The creation of ATP can be linked to the creation of RNA and the prevention of messenger RNA degradation in the context of the Virus-mediated archaeal hecatomb in the deep seafloor.
People who have played “Cytosis” can predict what will happen at the Schrödinger at 75 conference. They will jump ahead of most academics if they play “Subatomic” and link particle physics to all biophysically constrained biodiversity.
The fun factor is important to most people. They don’t care about supercoiled DNA or the virus-driven degradation of messenger RNA. But other scientists are having fun watching the creator of the genious games teach facts to theorists. We are especially pleased about his help in teaching the facts about energy-dependent cell biology to anyone who wants to have fun, prevent or survive the flu, or to become a serious scientist.
Alternatively, play the Mutation-driven evolution game (available only as an outdated 2013 textbook).
But remember:  Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
Simply put, you could be dead by the time pseudoscientists start to tell the truth. For example, this is the truth:

There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Lander just admitted that their assumptions may have made many serious scientists wrong about every aspect of energy-dependent life on Earth.
See also: Real Heroes Have the Guts to Admit They’re Wrong

…one reason we can’t admit we have the facts wrong is that it’s too painful to our self-conception as smart, right-thinking people—or to our political tribal identity.

In the past year alone, mathematicians have pulled papers when they’ve learned their proofs don’t hold and economists have retracted work after finding they’d misclassified their data. The Harvard stem-cell biologist Douglas Melton had a hit 2013 paper that got cited hundreds of times—but when colleagues couldn’t replicate the finding, he yanked it.

They discount the fact that any claims that have been placed into the context of neo-Darwinian theories have been invalidated first by Schrödinger in “What is Life? (1944) and since then by all serious scientists who have linked  the sun’s anti-entropic virucidal energy from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See also: Windowed Granger causal inference strategy improves discovery of gene regulatory networks


Discovery of gene regulatory networks (GRNs) is crucial for gaining insights into biological processes involved in development or disease. Although time-resolved, high-throughput data are increasingly available, many algorithms do not account for temporal delays underlying regulatory systems—such as protein synthesis and posttranslational modifications—leading to inaccurate network inference. To overcome this challenge, we introduce Sliding Window Inference for Network Generation (SWING), which uniquely accounts for temporal information. We validate SWING in both in silico and in vitro experimental systems, highlighting improved performance in identifying time-delayed edges and illuminating network structure. SWING performance is robust to user-defined parameters, enabling identification of regulatory mechanisms from time-series gene expression data.

Reported as: New machine learning algorithm uncovers time-delayed interactions in cells

SWING puts together a more complete picture of the cause-and-effect interactions happening among genes by incorporating time delays and sliding windows. Rather than only looking at the individual perturbations and responses, SWING uses time-resolved, high-throughput data to integrate the time it takes for those responses to occur.

Researchers will continue to scramble in attempts to put their findings into the context of what has already been presented in: Olfaction Warps Visual Time Perception
and in:



Alternative splicing of pre-mRNA

Agilent technology and energy-dependent autophagy

The first step towards understanding the link from the creation of energy to metabolism-related cellular function is called energy phenotyping. It requires the  technology to measure energy-dependent changes in RNA-mediated metabolic switches via the RNA interference (RNAi) screening strategy. Endogenous RNAi must then be linked  to the prevention of the virus-driven degradation of messenger RNA that causes all pathology.
Scientists discover possible master switch for programming cancer immunotherapy

…they employed an RNA interference screening strategy which can test the actual function of thousands of factors simultaneously.

See also: Energy as information and constrained endogenous RNA interference (video 6:46 minutes)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: Measuring the Metabolic Switch in Cancer Cells – Agilent (pdf)

Yoshida used TRAP1-null cells and transient TRAP1 mutants on an Agilent Seahorse XF96 Analyzer to show that TRAP1 regulates a metabolic switch between oxidative phosphorylation and aerobic glycolysis in immortalized mouse fibroblasts and in human tumor cells. TRAP1 deficiency promotes increased mitochondrial respiration, fatty acid oxidation, accumulation of TCA intermediates, ATP, and ROS, while suppressing glucose metabolism.

The virus-driven degradation of messenger RNA is the only perfectly obvious reason for changes in oxidative phosphorylation and aerobic glycolysis that prevent the metabolism of glucose. Natural selection for energy-dependent codon optimality links the creation of energy to the metabolism of glucose via the creation of enzymes that metabolize food energy. Energy-dependent RNA-mediated error-free DNA repair and fixation of amino acid substitutions is required to link the creation of enzymes and the species-specific production of pheromones from the physiology of reproduction to biophysically constrained viral latency and all morphological and behavioral phenotypes in all living genera.
In that context, energy-dependent natural selection for codon optimality links biologically-based cause and effect from hydrogen-atom transfer in DNA base pairs in solution to the transgenerational epigenetic inheritance of healthy longevity. For contrast, the virus-driven theft of quantized energy links changes in non-coding RNAs to all pathology.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
The link from the virus-driven theft of quantized energy to glioblastoma may be the best example of how viruses are readily linked to the cell death gene in all cell types of all individuals of all living genera. That fact is more obvious with further examination of details provided for free in book chapters from Codon Publishing.
See: Noncoding RNAs in Glioblastoma  Free book chapter from Codon Publishing

The vast majority of the human genome is transcribed into noncoding RNAs. Among these, microRNAs (miRNA) and long noncoding RNAs (lncRNA) are frequently deregulated in cancer, where they regulate a wide variety of functions.

See also: Epigenetic Mechanisms of Glioblastoma Free book chapter from Codon Publishing

Aberrant DNA methylation is a common event in the genesis and progression of tumors. The application of next-generation sequencing enables the identification and mapping of DNA methylation and its derivatives, 5fC and 5hmC, to base-pair resolution. This chapter describes nine novel hypermethylation genes and six hypomethylation genes, identified by constructing a DNA methylation profile, in glioblastoma. Abnormal promoter methylation and histone modifications were associated with differential expression of miRNAs in glioblastoma: miR-185 reversed global DNA methylation and the methylation level of the hypermethylation genes by targeting DNMT; and miR-101 regulated histone methylation of hypomethylation genes by targeting EED, EZH2, and DNMT3A. The long noncoding RNA CASC2c directly bound to miR-101 via microRNA response elements, and there was a reciprocal repression between CASC2c and miR-101. Despite being competitors they both led to the overexpression of their target hypomethylation genes CPEB1, PRDM16, and LMO3. Taken together, glioblastoma is a complicated pathological process with deregulated methylation and histone modifications. Focal differentially methylated region and differentially methylated site studies will be helpful for the identification of regulatory elements of transcription. Studies of intragenic and distant intergenic alterations in DNA methylation will help elucidate the nature of epigenetic deregulation in glioblastoma.

The Seahorse XF Cell Energy Phenotype Test kit is a simple assay kit that simultaneously measures the two major energy producing pathways in live cells – mitochondrial respiration and glycolysis, allowing rapid determination of energy phenotypes of cells and investigation of metabolic switching.
The simultaneous measurement of two major energy-producing pathways in live cells allows serious scientists to report their findings in the context of what is known about mitochondrial respiration and glycolysis. Glycolysis is epigenetically effected and RNA-mediated. No magic of evolution or nonsense about natural selection for anything except food and reproduction is required to explain how rapid metabolic switching determines whether or not viral latency is biophysically constrained across the time-space continuum.
See: From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See: Epigenetic modifications poster (Abcam)
Also from Abcam: Mechanisms of Recombination conference
The bottom line is The secret to safe DNA repair  (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

Clearly, the creation of the enzyme is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction. Pseudoscientists seem to know nothing about that, and most serious scientists are not telling you the facts that link the virus-driven degradation of messenger RNA to the “death gene” via the mechanisms that fail during recombination.
But see: microRNA autophagy  and also see: See:  Agilent Seahorse XF Publications Alert for December 2017
Selected publications
Autophagy maintains the metabolism and function of young and old stem cells
Ho, T. T., Warr, M. R., Adelman, E. R., Lansinger, O. M., Flach, J., Verovskaya, E. V., Figueroa, M. E. and Passegue, E.
Nature. 2017 Mar 9, 543 (7644):205-210.
Involvement of autophagy in the outcome of mitotic catastrophe
Sorokina, I. V., Denisenko, T. V., Imreh, G., Tyurin-Kuzmin, P. A., Kaminskyy, V. O., Gogvadze, V. and Zhivotovsky, B.
Sci Rep. 2017 Nov 6, 7 (1):14571.
Sugar or Fat?-Metabolic Requirements for Immunity to Viral Infections
Shehata, H. M., Murphy, A. J., Lee, M. K. S., Gardiner, C. M., Crowe, S. M., Sanjabi, S., Finlay, D. K. and Palmer, C. S.
Front Immunol. 2017 Oct 16, 8:1311.
System-wide Benefits of Intermeal Fasting by Autophagy
Martinez-Lopez, N., Tarabra, E., Toledo, M., Garcia-Macia, M., Sahu, S., Coletto, L., Batista-Gonzalez, A., Barzilai, N., Pessin, J. E., Schwartz, G. J., Kersten, S. and Singh, R.
Cell Metab. 2017 Dec 5, 26 (6):856-871 e5.
Late-onset Alzheimer’s disease is associated with inherent changes in bioenergetics profiles
Sonntag, K. C., Ryu, W. I., Amirault, K. M., Healy, R. A., Siegel, A. J., McPhie, D. L., Forester, B. and Cohen, B. M.
Sci Rep. 2017 Oct 25, 7 (1):14038.

BAG3 directly stabilizes Hexokinase 2 mRNA and promotes aerobic glycolysis in pancreatic cancer cells
An, M. X., Li, S., Yao, H. B., Li, C., Wang, J. M., Sun, J., Li, X. Y., Meng, X. N. and Wang, H. Q.
J Cell Biol. 2017 Dec 4, 216 (12):4091-4105.
Drug resistance induces the upregulation of H2S-producing enzymes in HCT116 colon cancer cells
Untereiner, A. A., Pavlidou, A., Druzhyna, N., Papapetropoulos, A., Hellmich, M. R. and Szabo, C.
Biochem Pharmacol. 2017 Oct 20, [epub ahead of print]
ISG15 governs mitochondrial function in macrophages following vaccinia virus infection
Baldanta, S., Fernandez-Escobar, M., Acin-Perez, R., Albert, M., Camafeita, E., Jorge, I., Vazquez, J., Enriquez, J. A. and Guerra, S.
PLoS Pathog. 2017 Oct 27, 13 (10):e1006651.
High throughput measurement of metabolism in planarians reveals activation of glycolysis during regeneration
Osuma, E. A., Riggs, D. W., Gibb, A. A. and Hill, B. G.
Regeneration. 2017 Nov 02, [epub ahead of print]
Current technical approaches to brain energy metabolism
Barros, L. F., Bolanos, J. P., Bonvento, G., Bouzier-Sore, A. K., Brown, A., Hirrlinger, J., Kasparov, S., Kirchhoff, F., Murphy, A. N., Pellerin, L., Robinson, M. B. and Weber, B.
Glia. 2017 Nov 7, [epub ahead of print]
Glucose-regulated protein 75 determines ER–mitochondrial coupling and sensitivity to oxidative stress in neuronal cells
Honrath, B., Metz, I., Bendridi, N., Rieusset, J., Culmsee, C. and Dolga, A. M.
Cell Death Discovery. 2017 Nov 06, [epub ahead of print]

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users
Panee, J., Gerschenson, M. and Chang, L.
J Neuroimmune Pharmacol. 2017 Nov 4, [epub ahead of print]
RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity
Trixl, L., Amort, T., Wille, A., Zinni, M., Ebner, S., Hechenberger, C., Eichin, F., Gabriel, H., Schoberleitner, I., Huang, A., Piatti, P., Nat, R., Troppmair, J. and Lusser, A.
Cell Mol Life Sci. 2017 Nov 4, [epub ahead of print]
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
Samandi, S., Roy, A. V., Delcourt, V., Lucier, J. F., Gagnon, J., Beaudoin, M. C., Vanderperre, B., Breton, M. A., Motard, J., Jacques, J. F., Brunelle, M., Gagnon-Arsenault, I., Fournier, I., Ouangraoua, A., Hunting, D. J., Cohen, A. A., Landry, C. R., Scott, M. S. and Roucou, X.
Elife. 2017 Oct 30, 6.
The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
Shen, H., Campanello, G. C., Flicker, D., Grabarek, Z., Hu, J., Luo, C., Banerjee, R. and Mootha, V. K.
Cell. 2017 Nov 2, 171 (4):771-782 e11.

See also: Research areas for this month include:

See for comparison: Autophagy

Autophagy is a process by which cellular material is degraded by lysosomes or vacuoles and recycled. Several autophagy pathways operate within a cell, including macroautophagy, microautophagy and chaperone-mediated autophagy.

Latest Research and Reviews

For example:

Dual role of autophagy in hallmarks of cancer

Quantitative assessment of cell fate decision between autophagy and apoptosis

The Nature Publications Group has fallen far behind the data and technical expertise of all the serious scientists in the world. It seems likely that they will attempt to portray autophagy as something besides the innate phage defense system and fail miserably.

Autophagy is the antiphage defense strategy December 8, 2016

What would you do if your publisher arrived at the “Autophagy Party” more than a year late and you had to introduce them as a supporter of neo-Darwinian nonsense and “Big Bang” cosmology?
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Science vs Secularism: Molecular Mechanisms or Math?

Summary: An example from ancient knowledge of trigonometry links pattern recognition as the basis for the science of creationism, and pattern recognition also is the basis for molecular biology.
What form of virus-driven pathology would you most like to see eliminated from future consideration by serious scientists who know how energy-dependent RNA-mediated cell type differentiation occurs? In any case, a PubMed search for microRNA and your disease of choice will be enlightening. See for example: microRNA + Alzheimer’s or microRNA + fragile X syndrome; Parkinson’s disease; diabetes; cancer; malaria; and/or other human diseases
See:  Are scientists who speak out against religion hurting science? for discussion of Why religion is not going away and science will not destroy it

…science needs all the friends it can get. Its advocates would be well advised to stop fabricating an enemy out of religion, or insisting that the only path to a secure future lies in a marriage of science and secularism.

Serious scientists have met the enemies of science. One of them is the author of Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

More than 64,000 indexed publications on the PubMed site attest to the fact that the energy-dependent de novo creation of plant microRNAs is linked to all healthy longevity via the food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans. Experimentally established facts about the virus-driven degradation of messenger RNA are linked to all pathology via changes in the microRNA/messenger RNA balance.

See: Cytosis: A Cell Biology Board Game

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

What form of virus-driven pathology would you most like to see eliminated from future consideration by serious scientists who know how energy-dependent RNA-mediated cell type differentiation occurs? In any case, a PubMed search for microRNA and your disease of choice will be enlightening. See for example: microRNA + Alzheimer’s or microRNA + fragile X syndrome; Parkinson’s disease; diabetes; cancer; malaria; and/or other human diseases
Role of miRNAs in development and disease: Lessons learnt from small organisms

MicroRNAs (miRNAs) constitute a class of small (18-22 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation. The miRNAs associated with fragile X syndrome, Parkinson’s disease, Alzheimer’s disease, diabetes, cancer, malaria, infectious diseases and several other human diseases have been identified from small organisms. These organisms have been used as platforms in deciphering the functions of miRNAs in the pathogenesis of human diseases and to study miRNA biogenesis. Small organisms have also been used in the development of miRNA-based diagnostic, prognostic and therapeutic strategies. The molecular techniques such as genome sequencing, northern blot analysis, and quantitative RT-PCR, have been used in deciphering the functions of miRNAs in small organisms. How miRNAs from small organisms especially those from Drosophila and C. elegans regulate development and disease pathogenesis is the focus of this review. The outstanding questions raised by our current understanding are discussed.

See for comparison: Quantum Theory Rebuilt From Simple Physical Principles by Philip Ball

“What is needed is new mathematics that will render these notions scientific,” he said. Then, perhaps, we’ll understand what we’ve been arguing about for so long.”

I do not believe that new mathematics will end the arguments, and I do not believe anything Philip Ball claims. Does any intelligent person on Earth believe this claim? “We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking”

For a historical perspective on the nonsense touted by theorists and so-called science journalists, like Philip Ball, see:

Secularism: This ancient Babylonian tablet may contain the first evidence of trigonometry

He and Wildberger concluded that the Babylonians expressed trigonometry in terms of exact ratios of the lengths of the sides of right triangles, rather than by angles, using their base 60 form of mathematics, they report today in Historia Mathematica. “This is a whole different way of looking at trigonometry,” Mansfield says. “We prefer sines and cosines … but we have to really get outside our own culture to see from their perspective to be able to understand it.”

When have serious scientists not gone outside our own culture to understand how the history of human behavioral development has been misrepresented by so-called experts.

See: Past 5,000 years prolific for changes to human genome

The findings confirm their earlier work suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years.

Simply put, the harmful variants probably contribute to our relative lack of intelligence compared to the intelligence of our ancestors, unless you think that a single-celled organism is one of your ancestors. Obviously, however, even if that is the case, you are somewhat more intelligent that pond scum. But, let me apologize in advance for referring to you as a “biologically uninformed science idiot” — in the context of the definition of “idiot” as someone with no professional expertise. Apologists might use the term “fool” in the context of this passage from the Holy Bible:

Thou fool, that which thou sowest is not quickened, except it die:”

Feynman used the term “human idiocy” in the context of representations made by theoretical physicists:

Prepare yourself to experience more insults from experts who have, during the past 5-10,000 years confirmed the links from energy to physics, chemistry, and molecular biology in the context of food energy and the biophysically constrained pheromone-controlled physiology of reproduction.

Apologetics:Indiana Banks and the Tablet of Trig

This story attracted my attention because it is yet more evidence against the Darwinian narrative of human history, which holds that we evolved from apes and have been steadily gaining in technology and science ever since. The reality is very different. The evidence often points to initial brilliance followed by decline, the pattern that creationists would expect. In this instance, extremely ancient people pioneered a form of trigonometry that is more exact than the form used by later Mesopotamian nations and by the Greeks, Romans, and later Western Civilization.

Pattern recognition is the basis for the science of creationism and pattern recognition is the basis for molecular biology.

See also: Olfaction Warps Visual Time Perception

In their concluding paragraph, the authors link irreverent representations of the space-time continuum (Hawking, 1988) to our visual perception of mass and energy. With no vague representations of untested theories, they suggest that neural energy represents multisensory input at subsecond scales.

If what they suggest is true, their published work is an unprecedented refutation of neo-Darwinian pseudoscientific nonsense and an unparalleled refutation of “Big Bang” cosmology. Simply put, they concurrently link the creation of energy to the energy-dependent creation of the sense of smell in bacteria. The sense of smell is linked to the pheromone-controlled physiology of reproduction in all living genera via representations that link neural energy from the epigenetic landscape to the physical landscape of supercoiled DNA.

For example, the sense of smell in bacteria is linked to the weekend resurrection of the bacterial flagellum.

See:Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

Natural selection for food energy-dependent codon optimality was linked to the ability of P. fluorescens to find food, which was linked to their pheromone-controlled physiology of reproduction by everything known about quorum sensing. But wait, that fact defies attempts to put the refutation of all theories into the context of something as simple-minded as this claim:

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

For more information on the mutation-driven “dumbing down” of you and your ancestors play the game “Cytosis” when it becomes available later this month and watch for more information on the game “Subatomic.” It is less difficult now than it ever has been to link energy-dependent changes from atoms to ecosystems by what is known to serious scientists. But first, you may need to dismiss the pseudoscientific nonsense touted by theorists.

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See also: Protecting 4 billion people from virus-driven entropy September 8, 2016
See also: Recurrence-Based Information Processing in Gene Regulatory Networks

We also show that the readout layer can learn to decode the information stored in the reservoir via standard evolutionary strategies. Our work thus suggests that recurrent dynamics is a key element for the processing of complex time-dependent information by cells.

What evolutionary strategies led to the recurrent dynamics of time-dependent information processing and the use of trigonometry ~5000 years ago?
Learning from Bacteria about Natural Information Processing

It seems that bacteria have some sort of collective memory by which they keep track of how they handled their previous encounters with antibiotics. They know how to collectively glean information from the environment, “talk” with each other, distribute tasks, generate collective memory, and turn their colony into a “cybernetic system”—a massive “brain” that can perform natural distributed information processing, learn from past experience, and possibly alter the genome organization or even create new genes to better cope with novel challenges.8–13,17,18

Physiology is rocking the foundations of evolutionary biology

Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.



Creating gravity, nucleic acids, receptors, and supercoiled DNA (2)

See also: Creating gravity, nucleic acids, receptors, and supercoiled DNA

Scientists make first direct detection of gravitational waves


Almost 100 years ago today, Albert Einstein predicted the existence of gravitational waves — ripples in the fabric of space-time that are set off by extremely violent, cosmic cataclysms in the early universe. With his knowledge of the universe and the technology available in 1916, Einstein assumed that such ripples would be “vanishingly small” and nearly impossible to detect.

My comment: Kudos to Greg Bear for indirectly linking gravitational waves and the speed of light on contact with water to the nutrient-dependent pheromone-controlled structure of supercoiled DNA in species from microbes to humans, which prevents virus-driven genomic entropy in all living genera. He started to do that in 1985 and finished in less that 20 years.

See: The Darwin Code by Greg Bear
The gravitational waves can now be linked from energy-dependent hydrogen-atom transfer in DNA base pairs in solution to cell type differentiation in all genera via what is currently known about biophysically constrained RNA-mediated protein folding chemistry and supercoiled DNA. Olfaction links the gravitational waves to vibrations in supercoiled DNA. If no food odors are linked from the vibrations to the de novo creation of receptors that allow nutrients into the cells, the nutrient-dependent innate immune systems of cells and organisms is compromised.Viruses take advantage of compromised immune systems and they proliferate by stealing more energy from cells. Without the nutrient-dependent microRNAs that enable DNA repair, viruses proliferate and viral microRNAs prevent the nutrient energy-dependent supercoiling of DNA that prevents the virus-driven entropy, which is linked to all pathology.
See for instance: Molecular Vibration-Sensing Component in Human Olfaction
Excerpt: These results are consistent with a vibrational component in human olfaction.
Reported as:  ‘Quantum smell’ idea gains ground
See also: Terahertz underdamped vibrational motion governs protein-ligand binding in solution

It seems likely that proteins have evolved such underdamped vibrational motions by providing an interaction site which is pre-organized44 in order to arrive at the optimal degree of damping for efficient biochemical reactivity and function.

Reported as: Proteins ‘ring like bells’: Quantum mechanics and biochemical reactions

…quantum mechanics and coherent ringing might be at the basis of all biochemical reactions

My comment: The gravitational waves were not linked from quantum mechanics to classical physics, which means the physicists missed a link to the basis for all biochemical reactions via the de novo creation of olfactory receptor genes. De novo gene creation is the holy grail of biologically-based cause and effect.  The failure to link the gravitational waves to the creation of genes exemplifies the failure of physicists to link meaningful discoveries from chemistry to the conserved molecular mechanisms of biologically-based cause and effect.The discovery of gravitational waves may be the physicists most meaningful event in the past 100 years, but it is meaningless to chemists or to biologists, or to anyone who is interested in Combating Evolution to Fight Disease. Physicists make only vague inferences about the “nature” of the universe. Today’s reports on the discovery of gravitational waves attest to the amount of nonsense that can be heralded as if simulations, “real” simulations, and inferences might lead to something that would benefit anyone or anything on Earth. Can you find any benefit in these reports?

‘We can hear the universe’: Scientists detect gravitational waves, predicted by Einstein (LA Times)

“…these waves are the soundtrack of the cosmos.””Some physicists said this is as big a deal as the 2012 discovery of the subatomic Higgs boson, sometimes called the “God particle.” Some said this is bigger.””Sensitivity is crucial because the stretching and squeezing of space-time by these gravitational waves is incredibly tiny. Essentially, LIGO detects waves that stretch and squeeze the entire Milky Way galaxy “by the width of your thumb,” Hanna said.”
In Milestone, Scientists Detect Gravitational Waves As Black Holes Collide (NPR) Teukolsky says the discovery shows just how extraordinary the natural world can be. “The universe is stranger than any kind of fiction we could imagine,” he says. “I mean, it’s preposterous.”
Observation of Gravitational Waves from a binary black hole merger How did LIGO make the first detection of gravitational waves from a binary black hole merger? What did we learn? Read the science summary of our paper…
My comment:I do not intend to make “light” of this discovery, which cost billions of dollars and theoretically helped to confirm theoretical predictions that were made more than 100 years ago.However, if you read the paper, I think you will see that it avoids any claims that might link their computer simulations and inferences to refutations of neo-Darwinian nonsense, which means that millions to billions more research dollars may be spent to develop ridiculous theories that support the big bang cosmology industry and the evolution industry.Those theories have already been placed into the context of the importance of understanding Dobzhansky’s “light of evolution.” It is the light (and gravity) on Earth that supports femtosecond chemical reactions. The chemical reactions link quantum physics to quantum consciousness via the RNA-mediated amino acid substitutions that stabilize organized genomes in the context of the nutrient-dependent physiology of reproduction in all living genera. For comparison, see this report.
Observation of Gravitational Waves from a binary black hole merger
Alongside this substantial progress in the indirect observation of black holes, there have been dramatic improvements in our theoretical understanding of these bizarre objects
My comment: This theoretical understanding can be placed into the context of Schodinger’s claims in “What is Life?” This link opens the pdf.

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)

My comment: Unless the claims about gravitational waves are placed into the context of “negative entropy,” serious scientists are left with an attempt to ensure more government funding for research that might also support theories, while failing to acknowledge Schrodinger’s facts or the facts that Darwin integrated into his claims about the “conditions of life.” For contrast, see this report:

The first measurement of a black hole merger and what it means” What Made the Gravitational Waves? Once we have identified a gravitational wave in the data (more details here and here) supercomputers around the world start buzzing to determine what created the signal that we detect. We do this by trying out millions of combinations of different numbers (parameters) that describe a gravitational wave signal. The parameters that describe you might be height, age, hair and eye color, etc. The gravitational wave signal from GW150914 came from two dense objects spiraling in to one another and merging.”

My question(s): Who made the two dense objects and when were they made? How are the parameters that describe us linked to the gravitational wave signal?Here is my summary of all the reports I have seen on gravitational waves.

Biology to a Physicist

Should I keep looking at more reports?

They did not link their finding from atoms to ecosystems. I had hoped that someone would ask a question to elicit an answer that links their finding to what is known about molecular epigenetics.

Gravitational waves detected 100 years after Einstein’s prediction (Science Daily)

My comment: A reporter for the Christian Science Monitor asked about the source of the information. The presenters answered in terms of simulations, “real simulations” and inferences — after some individual claims about “nature” and the billions of years that it took for the gravitational waves to reach earth.Is the billions of years an estimate based on simulations, “real simulations” and inferences?

Gravitational waves discovery ‘is monumental,’ physicist says These waves radiate from their sources at the speed of light, stretching and squeezing the very fabric of space-time with predictable cadences. The achievement “is monumental,” says Lawrence Krauss, a theoretical physicist and cosmologist at Arizona State University in Tempe. There are very few times in the history of astronomy where new windows open, and this is one of them, he says, adding, “This will be the astronomy of the 21st century.”Beyond expectations for astrophysical discoveries, gravitational waves may also hold the potential to reveal important clues about the nature of gravity itself.This has been a nagging thorn in the side of theoretical physicists working an another Big Idea – that the four basic forces of nature are low-energy remnants of what was a single force during the earliest fractions of a second after the big bang. These forces are gravity, electromagnetism, the strong force binding particles in the nuclei of atoms, and the weak force governing radioactive decay.Physicists have been able to show through quantum theory that three of the four forces have a common ancestor. Gravity remains the stubborn holdout.Through the direct study of gravitational waves, “we potentially can learn about the nature of gravity” in ways that might point to a quantum theory of gravity, speculates Dr. Krauss at Arizona State University.

My comment: During the live newscast, Dr. Weiss mentioned that “a miracle of sorts” links the equations from 1915 to their inferences. I’m not sure what he thinks is a miracle. I think it is a miracle that people like Lawrence Krauss and Neil de Grasse Tyson are willing to discuss how nothing became everything known to serious scientists about the links from atoms to ecosystems.

See: The Existence of Nothing 2013

My comment: The people who presented their findings on gravitational waves said good-bye to all newscast watchers at (11:41). They continued with questions off-line a few minutes after Dr. Weiss mentioned the “miracle of sorts” that links their discovery to the equations from 1915 based on computer simulations, “real” computer simulations and inferences.Hopefully, we will learn more about what the Russians and Japanese and perhaps even the Chinese think about this “miracle of sorts” and the presentation of the findings funded by the National Science Foundation.

Scientists glimpse Einstein’s gravitational waves (Update)
Wobbling like jelly“The waveform that we can calculate based on Einstein’s theory of 1916 matches exactly what we observed in 2015,” Shoemaker told AFP.
“We can now listen to the universe rather than just look at it,” said professor B S Sathyaprakash of Cardiff University. “This window turns on the soundtrack for the universe.”
Indirect proof of gravitational waves was found in 1974 through the study of a pulsar and a neutron star. Scientists Russell Hulse and Joseph Taylor won the Nobel Prize for physics for that work in 1993.

My comment: Somehow I knew someone would report the discovery of gravitational waves instead of just the ability to detect them. I did not think this would come from “Nature.”

Discovering gravitational waves

For comparison: Findings from the 2015 Nobel Prize winner in Physics, Chemistry, and Medicine link atoms to ecosystems via feedback loops and biologically-based cause and effect reported, with co-authors, by one of the two 2004 Nobel Laureates in Medicine.
See for example: A novel multigene family may encode odorant receptors: a molecular basis for odor recognition
See also: Feedback loops link odor and pheromone signaling with reproduction

My comment: Reproduction is important to the survival of all species on Earth. For comparison, see yet another report on the gravitational wave discovery.

Cosmic breakthrough: Physicists detect gravitational waves from violent black-hole merger (Washington Post: February 11 at 6:41 PM)

Until now, astronomy has been almost exclusively a visual enterprise: Scientists have relied on light, visible and otherwise, to observe the cosmos. But now gravitational waves can be used as well.Since they pass through matter without interacting with it, gravitational waves would come to Earth carrying undistorted information about their origin. They could also improve methods for estimating the distances to other galaxies.A black-hole collision sounds like a dramatic event, but it’s not really the big news for the physicists. The headline is that LIGO finally worked. Success in detecting gravitational waves is a win for Big Science and for the institutions that backed the project.
My comment: The “Big Science” of biophysically constrained RNA-mediated protein folding chemistry and the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans has lost another round to the theorists.
See for example, the report by Rachel Feltman: What Do We Actually Know About Pheromones?
What qualifies a science journalist to report on biologically-based cause and effect and dismiss what is known to serious scientist before moving on to tout the pseudoscientific nonsense of theoretical physics as if it was more important? Feltman interviewed me and two human pheromone-deniers, who appear to know nothing about the nutrient-dependent pheromone-controlled physiology of reproduction in any species.
See my comments on her science journalism.
Now this: En’Cas’ing The Stress: Engineering a Human Cell Line Knockout of Heat Shock Response Genes


The Heat Shock Response (HSR) is an evolutionarily conserved response to high temperatures and other stresses that controls adaptive proteostasis, and is primarily regulated by the factor, Heat shock transcription factor 1 (HSF1).

See also: From Toxins to Culture: How Environment Shapes the Infant Brain

Description: Prenatal and perinatal environmental factors, from toxins to maternal care and culture, profoundly influence the brains of infants, sometimes resulting in lifelong pathologies. The effects of these factors have only recently been rigorously assessed in humans, and the mechanisms by which they affect the brain are only beginning to be understood. This symposium discusses recently established links between autism and vehicular air pollution in both the developed and developing world; and how the microbiome, a target for infections and nutrition-related pathologies, directly affects the developing brain and can contribute to development of autism. The session also discusses how maternal inputs and cultures modify the impact of the physical environment on the brain, and how epigenetic mechanisms mediate the long-term impacts of prenatal and perinatal factors. These findings have broad implications for policies to preserve the health of children and adults around the world.

Beate Ritz, UCLA
Air Pollution Impacts Fetal Development and Increases Autism RiskElaine Y. Hsiao, University of California, Los Angeles (UCLA)
The Role of Gut Microbiomes in Neurodevelopmental DisordersBruce McEwen, Rockefeller University
Mother-Infant Interactions Influence Both Cognitive and Physical DevelopmentMoshe Szyf, McGill University


Dr Szyf will present evidence that the “social environment” early in life can alter DNA methylation, the basis for the emerging field of “social epigenetics”. By highlighting the impact that external factors and the social environment can have on gene expression, he will provide a mechanistic basis for the long term effects of early childhood experience.

My comment:  All big wins for biomedical science link metabolic networks to genetic networks in the context of model organisms that link atoms to ecosystems in all living genera by what is already known to serious scientists about supercoiled DNA.Energy-dependent changes in base pairs link atoms to ecosystems via hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA. The supercoiled DNA links RNA-mediated amino acid substitutions to what is known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding chemistry. The chemistry is linked to supercoiled DNA during thermodynamic cycles of protein biosynthesis and degradation, which is perturbed by viruses. Virus-driven energy theft is linked to all pathology on Earth.If you were a researcher whose work was supported by the big bang cosmology industry or by the evolution industry, would you reveal the fact that all theories about biologically-based cause and effect are missing the most important link from atoms to ecosystems if they do not include what is known to serious scientists about virus-perturbed protein folding?


ASCP MLS certification

The American Society for Clinical Pathology (ASCP) is a professional association based in Chicago, Illinois encompassing 130,000 pathologists and laboratory professionals.
(MLS is the acronym for Medical Laboratory Scientist)
I received this notice today from the American Society for Clinical Pathology:

Dear James V Kohl, MLS(ASCP)CM,
Congratulations on successful completion of the ASCP Board of Certification (BOC) Certification Maintenance Program. Your MLS certification is now valid through August 31, 2018.
You will receive a new CMP wall certificate within 3-5 weeks with your new valid certification dates.
Board of Certification

Other scientists who are required to successfully complete continuing education credits that cross the disciplines that are integrated into what is known about Medical Genetics might also have updated their knowledge base. It may include what is known about the role of viruses and the role of nutrient-dependent RNA-mediated amino acid substitutions in cell type differentiation via the physiology of reproduction in all living genera.
Unfortunately, no one can be forced to learn anything knew, which is why some people do not — unless their certification status is threatened by their failure to do so. What have you learned about anti-entropic epigenetic traps and color perception? Is the epigenetic effect on hormones that affect behavior linked from big bang cosmology and creation to biophysically constrained virus-driven genomic entropy?

  • Color perception