5th-6th Sept 2018 Dublin, Ireland

MicroRNA-mediated denuclearization (2)

Summary:
The virus-driven theft of quantized energy creates a cellular environment that promotes the survival and self-proliferation of viruses by encoding viral miRNAs or miRNA-like molecules. The viral miRNAs or miRNA-like molecules target different types of host cells.
The sun’s anti-entropic virucidal energy biophysically constrains viral latency in the context of global control of human ES cell differentiation via circRNAs derived from lncRNAs. That fact refutes all neo-Darwinian gene-centric pseudoscientific nonsense. That fact also attests to the link from Chinese philosophy to scientific creationism in South Korea.
Scientific creationism appears to have defeated communism in the context of the electron cloud superimposed over the yin yang symbol of constrained energy.
For scientific support of the claims that appear to have defeated communism, see:
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes.

CONCLUSIONS:

Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled.

Global control of human ES cell differentiation via circRNAs derived from lncRNAs refutes neo-Darwinian gene-centric pseudoscientific nonsense. The level of control comes as no surprise to serious scientists who start with the energy-dependent creation of microRNAs and link the energy to the RNA-mediated creation from genome assembly to the creation of all cell types.

The global control-based refutation is merely one more example of pattern recognition.

See: Three invariant Hi-C interaction patterns: applications to genome assembly

We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.

Schrödinger suggested that genome assembly was energy-dependent in What is Life? (1944)

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.)

See also: What is life when it is not protected from virus driven entropy (video)

See also: Rotavirus-encoded virus-like small RNA triggers autophagy by targeting IGF1R via the PI3K/Akt/mTOR pathway

Examining virus-host cell interaction is important for elucidating mechanisms of virus proliferation in host cells. Viruses can create an environment that promotes their survival and self-proliferation by encoding miRNAs or miRNA-like molecules that target various host cell.

See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

…fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

See also: Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

See also: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses. When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets.

The energy-dependent fine-tuning of the base-pair stability in plants prevents the emergence of rotaviruses via multiple interspecies re-assortment events linked to healthy longevity in post-vaccination era South Korea.

See for comparison: Engineered virus has artificial amino acid allowing it to serve as a vaccine

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus. In their paper published in the journal Science, the team outlines the means by which they modified an influenza virus causing it to incite an immune response without a risk of infection.

Scientific creationists in South Korea have showed that the Chinese cannot protect themselves from a viral apocalypse via vaccinations. The viruses adapt too quickly.

Knowing that also allows the scientific creationists to create a virus that damages the DNA of specific human populations who are less well-adapted to their food energy-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niches.

Would you threaten nuclear war after you learn that the population of your country could be decimated by a genetically engineered virus produced in a neighboring country. Or, would you denuclearize and de-escalate the tensions as soon as you learned that all niche construction is food energy-dependent and that the pheromone-controlled physiology of reproduction biophysically constrains viral latency.

That fact cannot be placed back into the context of atheism or communism. It is a neo-Darwinian theory killer and is the most likely reason for denuclearization in a reasonable world.

The facts about biophysically constrained viral latency and energy-dependent life will be discussed during Schrödinger at 75 – The Future of Biology – September 2018

See for comparison: Organ-specific metastases obtained by culturing colorectal cancer cells on tissue-specific decellularized scaffolds

…lung and liver decellularized scaffolds retained their tissue-specific tropism when injected in mice.

Reported as: Scientists create better laboratory tools to study cancer’s spread

The hypothesis is this is caused by both ‘seed and soil’ – that the cancer cells have something in them that drive them to a particular organ, and the soil has to be right for them to grow. Most of the focus has been on studying the cancer cell, or the seed, and not as closely looking at the soil, which is the organs that they go to. Our models will help us understand to better understand the conditions of the soil that help promote cancer metastasis.

The use of Schrödinger’s sunlight-to-soil metaphor of degraded organic matter and biophysically constrained viral latency is not likely to be a coincidence. It also appears in the context of the energy-dependent weekend resurrection of the bacterial flagellum and in the context of the weekend Resurrection of Christ.

See also:  Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

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

See also: Science, state, and spirituality: Stories of four creationists in South Korea

Scientific creationism in South Korea supposedly began with the support of the US government in their attempt to fight against communism and atheism. Pseudoscientists have not linked energy-dependent RNA-mediated biophysically constrained viral latency to all healthy longevity in the context of Communism and atheism.

For comparison, all serious scientists who understand the role that the creation of energy plays in the creation of supercoiled DNA have won the war against communism by combating evolution to fight disease.

All disease has been linked to the virus-driven energy theft that causes the degradation of messenger RNA, which has been linked to all pathology.

The energy-dependent creation of microRNAs has been linked from the creation of the innate immune system to all biophysically constrained behaviors via what is known about how the physiology of pheromone-controlled reproduction must be linked from soil bacteria to the growth of seeds and all food energy-dependent life on Earth.

5th-6th Sept 2018 Dublin, Ireland

Complexity: Routes and Patterns (4)

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors (2015)

…the current models are both consistent with available and new experimental data and offer a number of predictions – notably, through revelation of highly constrained residues (Supplementary Data 910) – to guide and visualise structure-function analyses of these unusual sensory receptors.

No experimental evidence of top-down causation links anything except the quantized energy-dependent creation of enzymes, hormones, and receptors to biophysically constrained viral latency and ecological adaptations.

See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

See for comparison: Tuning Insect Odorant Receptors (2018)

Analyzing the variation of insect OR protein amino acids during evolution revealed a model for transmembrane domain arrangement that is unrelated to GPCRs (Hopf et al., 2015).

Try to refute my model with the latest pseudoscientific nonsense about coevolved amino acids.

SARCASM ALERT:Alternatively, evolve and fly away.

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.

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

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

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (1973)

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

See also: 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.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

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…

See also: Cytosis: A Cell Biology Board Game for ages 10+

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

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

An evolutionary theory killer

Conceptual critique: Innateness vs the death gene (2)

Excerpt: Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See also: Conceptual critique: Innateness vs the death gene (1)
Re: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

See for comparison: Subatomic

…is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic…

See also: Cytosis: A Cell Biology Board Game

Players start out with a number of workers and on their turn, they will place one of their workers on any available location within that cell. Some of the locations provide players with resources (e.g., mRNA, ATP); some with actions (e.g., convert resources, collect cards). Resources are used to build enzymes, hormones, and/or receptors, which score Health Points.

Science Concepts: cell biology, nucleus, free ribosomes, smooth ER, rough ER, golgi apparatus, plasma membrane, mitochondria, enzymes, hormones, receptors, cell detoxification, antibodies and viruses
Alternatively, theorists may continue to ignore the Science Concepts: in the context of  The Hidden Intelligence of Hormones — How They Drive Desire, Shape Relationships, Influence Our Choices, and Make Us Wiser (Feb 13, 2018) for comparison to From Fertilization to Adult Sexual Behavior (1996)

Martie Haselton notes

“…there’s a hidden adaptive intelligence that has been shaped over eons. Martie Haselton places that ecological adaptation into the context of the claim that “…our bodies are designed to fight off invaders, whether they take the form of a cold virus… (p 73.) and she mentions the link from the designer to one theory about menstruation: “female bleeding serves to flush out “bad” sperm that may carry bacteria, viruses and other pathogens.” (p. 84)

See for comparison: Conditional expression of women’s desires and men’s mate guarding across the ovulatory cycle (2006)In 2006, it became clear to most serious scientists that Martie Haselton knew nothing about biophysically constrained RNA-mediated viral latency. Now, she places everything known back into the context of neo-Darwinian pseudoscientific nonsense and eons of evolution. Fortunately,  you can read and discuss her book in the context of what other pseudoscientists have been doing for the past two decades. Simply copy and paste from Wikipedia in attempts to promote ridiculous theories.

See for comparison: Evolution: Genetic Novelty/Genomic Variations by RNA-Networks and Viruses 2018 >

Preliminary List of Confirmed Speakers (41)
Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >

Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >

Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >

Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA
Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria

Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

For comparison to Martie Haselton’s February 13, 2018 publication of her pseudoscientific nonsense about hormonal women, see: Energy as information and constrained endogenous RNA interference from my February 15, 2017 virtual conference presentation on Precision Medicine.

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

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

Significance

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:

 

 

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.

BiondVax Universal Flu Vaccine Patent

Summary: …the dream to create an effective universal flu vaccine to ultimately eradicate the flu is placed into the context of claims about changes to the virus. The changes are energy-dependent ecological adaptations. No one claims that the virus mutates or that it evolves. Only biologically uninformed theorists make such ridiculous claims.
BiondVax Universal Flu Vaccine Patent Granted in India

The patent describes influenza vaccines comprised of multiple copies of several epitopes, such as M-001 which contains nine common and conserved influenza virus epitopes.

The use of the word epitope obfuscates cause and effect in the context of natural information processing, which is energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans. If they used the term conserved amino acid substitutions more people might understand the fact the fixation of amino acid substitutions biophysically constrains viral latency. Who knows what epitopes are or what they do or how they do it?
See for comparison: Learning from Bacteria about Natural Information Processing (Israel) and Generation of influenza A viruses as live but replication-incompetent virus vaccines, (China) which was reported as: Engineered virus has artificial amino acid allowing it to serve as a vaccine
Researchers in other countries, but not in the United States of America, have made scientific progress that helps to make sense of claims about energy-dependent natural information processing and RNA-mediated amino acid substitutions that biophysicaily constrain viral latency and typically prevent all pathology.
In this video, the dream to create an effective universal flu vaccine to ultimately eradicate the flu is placed into the context of claims about changes to the virus. The changes are energy-dependent ecological adaptations. No one claims that the virus mutates or that it evolves. Only biologically uninformed theorists make such ridiculous claims.

See for comparison: How to Build a Better Flu Shot (with my emphasis)
1) … the influenza virus has many rapidly mutating strains. And because the strains mutate so quickly
2) …the mushroom head of hemagglutinin mutates rapidly, so antibodies against one type of head won’t work against a mutant version.
3) To infect the cell, the stalk of the hemagglutinin mushroom becomes completely rearranged from its normal state. “It’s a machine,” Krammer explains. “It doesn’t tolerate mutations well. If you introduce mutations, you destroy the machine, so the virus doesn’t like to change it.”
4) Other teams are testing headless stalks made by anchoring the stalk to a ferritin protein nanoparticle or by creating genetic mutations at the top, as potential vaccines too.
5) In a study published January 19 in Science, University of California, Los Angeles, virologist Ren Sun and colleagues identified eight genetic mutations that make the flu virus sensitive to a host cell’s interferons.
6) “The team was able to mutate this virus for interferon sensitivity without changing the immune response, which is a challenge.”
7) Fauci says one essential piece of information scientists need to build a universal flu vaccine is to understand how serial exposure to the virus and vaccination affects the immune system.
8) “This is what we call immunological imprinting. It’s controversial, but we need to know what the influence is to create a broadly effective flu vaccine,” Fauci says.
9) Understanding the effect of pre-existing immunity on virus evolution is also important, given that vaccination itself could influence how flu strains evolve, Fauci and colleagues note in a paper published last summer in Immunity
10) The paper describes a path toward making a universal flu vaccine. “I see this work falling into three buckets,” Fauci says. “There’s the bucket on antibody development, the bucket on boosting the immune response to flu, and finally the bucket on prior exposure and how that affects the immune system,” he says.
Fauci wants others to believe that viruses mutate and evolve but that immunological imprinting is controversial. He has many others to help people in the United States accept the claims about mutations and evolution and put the claims of serious scientists who understand the facts about immunological imprinting into the context of controversy.
My comment to The Scientist:

In this report from the NIH: Flu infection study increases understanding of natural immunity the focus on the change in the influenza virus was properly placed into context of energy-dependent changes in the virus, which are called ecological adaptations when they occur in human populations.

For example, one energy-dependent amino acid substitution causes increased virulence in the influenza virus, as clearly stated here: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Simply put, all serious scientists know that viruses do not mutate and evolve. Viruses steal the energy that biophysically constrains viral latency and some humans in some human populations fail to ecologically adapt as quickly as others.

Is Fauci, or anyone else who made claims in the article from The Scientist, a serious scientist? Unfortunately, the answer is no. Serious scientists do not believe that mutations can be linked to evolution. That gives them an edge if they are working in other countries, but not the United States of America.
See how serious scientists in some countries will maintain their edge, and continue to put theorists from the United States of America to shame — along with all the so-called science journalists who report the nonsense about mutations and evolution.
Controversy over evolution in Israel (2010)

There are many people who don’t believe the evolutionary account is correct,” he was quoted as saying. “There are those for whom evolution is a religion and are unwilling to hear about anything else. Part of my responsibility, in light of my position with the Education Ministry, is to examine textbooks and curricula.”

See also: Israeli Middle Schools School to Include Theory of Evolution (2014)

 “…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.”

Those who learn about ecology are less likely to make claims about mutations or evolution.
Turkish schools to stop teaching evolution, official says (2017)

The secular opposition has long argued that the government of Recep Tayyip Erdoğan is pursuing a covert Islamist agenda contrary to the republic’s founding values.

Does anyone in the United States think that the Trump administration is pursuing a covert Christian agenda?  If so, 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!

 

For God and Country

Diet-driven RNA interference and cancer prevention (4)

Excerpt: What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
“micrornas”[MeSH Terms] OR “micrornas”[All Fields] OR “microrna”[All Fields] Items: 1 to 20 of 68871
See:  The tipping point (revisited): 68,000 publications
69,000 published works on microRNAs will be the next “tipping point.” Predictably, it will be reached during the same 28 day period in which my tweets (@jvkohl have received more than 70,000 impressions.
On 1/18/18: Tweet impressions 71.2K 602.0%
The 602.0% increase has not been accompanied by a significant increase in followers or a significant increase in engagements.
What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
See: A curcumin-loaded polymeric micelle as a carrier of a microRNA-21 antisense-oligonucleotide for enhanced anti-tumor effects in a glioblastoma animal model

DP-Cur is an efficient carrier of miR21ASO and the combined delivery of miR21ASO and curcumin may be useful in the development of combination therapy for glioblastoma.

See also: Pharmacological blockade of ASCT2-dependent glutamine transport leads to antitumor efficacy in preclinical models

This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism.

Reported as: Researchers find a way to ‘starve’ cancer

Glutamine is an essential amino acid for many cell functions including biosynthesis, cell signaling and protection against oxidative damage. Because cancer cells divide more rapidly than do normal cells, they need more glutamine.

A protein called ACST2 is the primary transporter of glutamine into cancer cells. Elevated ASCT2 levels have been linked to poor survival in many human cancers, including those of the lung, breast and colon. Genetic studies that silence the ACST2 gene in cancer cells have produced dramatic anti-tumor effects.

See also: MicroRNA[s] and glutamine Items: 1 to 20 of 65
The facts about food energy-dependent microRNA-mediated RNA-directed DNA methylation and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera were removed from this report. Use off the cryo-EM technology links energy-dependent changes in electrons to healthy longevity in all ecosystems. It is apparent that some researchers do not want more people to learn about that fact.
See: Structural basis of RNA polymerase III transcription initiation

The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.

The information that links the virus-driven theft of quantized energy from the negative supercoiling (unwinding) of supercoiled DNA was removed in this attempt to support the neo-Darwinian pseudoscientific nonsense about the three domains of life. The bastardization of the use of cryo-EM technology occurred in the following context(s).
1) There is no mention of the quantized anti-entropic virucidal energy as information that is required to create ATP and RNA.
2) The energy-dependent creation of ATP and the creation of RNA is not linked to healthy longevity in all living genera via the physiology of pheromone-controlled reproduction.
3) The fixation of RNA-mediated amino acid substitutions that stabilize the differentiated cell types of all living genera are viewed in the context of negative supercoiling that occurs in an ATP-independent manner.
4) A spontaneously formed transcription bubble links the energy-dependent stability of supercoiled DNA to cell type differentiation in species from bacteria to humans.
5) The claim that promoters can be opened without ATP hydrolysis is used to suggest that no energy-dependent supercoiling is required to link the three kingdoms of life — assuming that there are three kingdoms of life.
6) The fact that the virus-driven degradation of messenger RNA in humans causes them to become non-human primates and the fact that it also cause bacteria to archaea and L-forms is ignored.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

By deliberately removing virus-archaea interactions from the representations reported as: Scientists zoom in to watch DNA code being read, pseudoscientists have reverted to promotion of their ridiculous gene-centric theories.
See for comparison: “Cytosis

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

See also: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.

Accurate representations of how natural selection for food energy-dependent codon optimality links the physiology of pheromone-controlled reproduction to the transgenerational epigenetic inheritance of healthy longevity will continue to be attacked from all sides.
Biologically uninformed theorists and philosophers can do nothing else but attack after proclaiming the nonsense of mutation-driven evolution during the past decades. They have failed to link their nonsense to the prevention of all pathology or to effective treatments via optimization of autophagy: the innate antiphage defense mechanism of all living genera.

GPX4-Cys bypasses the requirement of selenoproteins for cell viability

Diet-driven RNA interference and cancer prevention (2)

See first: Diet-driven RNA interference and cancer prevention
A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer

Our data highlight the capability of RNA-seq to discover novel lncRNAs involved in human carcinogenesis, which may serve as alternative biomarkers and/or molecular treatment targets.

Like all other data, their data refutes the pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists. The energy-dependent creation of the novel biomarkers is the link from quantized energy as information to healthy longevity via the physiology of pheromone-controlled reproduction in all living genera.
Conclusion:

Functional relevance of CRCAL-3 and CRCAL-4 related to cell cycle was suggested by in vitro experiments as well as by GO term enrichment analysis in the TCGA dataset. Our data highlight the capability of RNA-seq technology to discover novel lncRNAs involved in human carcinogenesis, which may serve as alternative biomarkers and/or molecular treatment targets for human cancers.

The functional relevance of anything that has consistently been linked from energy-dependent RNA-mediated cycles of protein biosynthesis and degradation is that all the evidence links supercoiled DNA to protection of organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
No matter how many attempts are made in the future to claim that the facts have not been known to all serious scientists, the obfuscations will fail.
See: Cytosis

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

Serious scientists know that enzymes, hormones and receptors do not automagically create themselves and that the virus-driven degradation of messenger RNA prevents the creation of the enzymes, hormones and receptors that serious scientists have linked to healthy longevity and interethnic similarities and differences in all human populations.

For God and Country

The "walking fish" walks straight from quantum physics to quantum souls

Happy New Year! In 2018, serious scientists are prepared to help you prevent or effectively treat all pathology. We have nearly stopped the pseudoscientific nonsense touted by theorists — although some of them didn’t get the memo from 1968, which is when Frohlich published: Long-range coherence and energy storage in biological systems.
He linked certain processes in living systems from the creation of energy to hydrogen bonds in cell membranes and to dipolar oscillations that link the creation of the sense of smell in bacteria from the physiology of pheromone-controlled reproduction to all biodiversity via the creation of ATP; the creation of RNA, and fixation of energy-dependent RNA-mediated amino acid substitutions.
See: The vibrational theory of olfaction for the win
Historical perspective, based on Frohlich’s “speculation.”
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

The sexual differentiation of cell types protects them from the virus-driven theft of quantized energy, which Frohlich linked to the degradation of the cell wall and what is now known about how unicellular bacteria become archaea before they become L-forms.
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!

Food energy-dependent pheromone-controlled biophysically constrained viral latency keeps egg cells fresh in the context of autophagy and sexual differentiation. Biophysical constraints prevent the transgenerational epigenetic inheritance of virus-driven pathology, which is caused by the virus-driven theft of quantized energy that links the degradation of messenger RNA to all pathology.
See for comparison: Keeping egg cells fresh with epigenetics (2017)
As soon as the Medical Xpress news source realized that they had destroyed neo-Darwinian pseudoscientific nonsense with their report on epigenetics, the post went missing.

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The page might have been removed, had its name changed, or become temporarily unavailable.

They cited: Courtney W. Hanna et al, MLL2 conveys transcription-independent H3K4 trimethylation in oocytes, Nature Structural & Molecular Biology (2017). DOI: 10.1038/s41594-017-0013-5
The cited work is not yet available at the DOI: I attempted to add this comment:
The speed of light on contact with water links food energy to the physiology of pheromone-controlled reproduction and all biophysically constrained biodiversity. Now, there is a mathematical model that refutes neo-Darwinism and “Big Bang” cosmology. Use it to make all biologically uninformed theorists recognize their foolishness. Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules
The human idiocy exposed by Courtney W. Hanna et al (2017?) was also exposed at least twice in September. See: Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells Published online 2017 Sep 25

Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) (,). Retrotransposons shape host genome landscape and evolution through introducing, deleting or modifying cis-regulatory elements or genes (,). However, they can also induce detrimental genome instability and numerous human diseases (,).

The claim that retrotransposons shape host genome landscape and evolution is a ridiculous claim. Food energy links ecological variation to ecological adaptations via the pheromone-controlled physiology of reproduction in all living genera. Nothing links retrotransposons to evolution because viral latency must be biophysically constrained in the context of increasing organismal complexity.
See also: Genomic imprinting beyond DNA methylation: a role for maternal histones 2017 Sep 19

Sperm and oocytes exhibit different patterns of chromatin organisation: the sperm DNA is highly methylated and tightly packaged, with protamines replacing most canonical histones, while the oocyte genome has a bimodal methylation pattern, an extensively open chromatin conformation and atypical patterns of histone modifications [].Methylation and chromatin organization are food energy-dependent and biophysically constrained in the context of the physiology of pheromone-controlled reproduction and the space-time continuum.

See why Feynman was forced to comment on the facts about food energy, years before this information became generally known: Trinucleotide Repeats: Fragile X Syndrome

DNA (deoxyribonucleic acid)… contains a “code” of 3-letter words known as “codons” or “trinucleotides.” Many genes normally contain trinucleotide sequences that can be repetitive. These are called “trinucleotide repeats.” But when the number of trinucleotide repeats increases to a larger than normal number of copies, the DNA is changed. The gene may not function as it should, or may not work at all.

…extra trinucleotide repeats cause the DNA to become unstable, the repeats within that gene expand even more. The result is that the child has a gene that is not functioning properly (if at all), and the child is said to have the “full mutation.” An example of a trinucleotide repeat disorder is Fragile X syndrome.

See also: Researchers discover how cells remember infections decades later

On the surface and through the actions of their genes, they look like cells that have never been exposed to an infection, but on their DNA the researchers found a fingerprint, called a methylation pattern, that identifies them as having been through battle as an infection-fighting cell, which are called effector cells.

Thanks to passive-aggressive antagonist Jon Lieff for repeatedly bringing the difference between pseudoscientists and serious scientists to my attention. Pseudoscientists refer to “effector cells” so that the obvious link from food energy to autophagy to healthy longevity is obfuscated.
See for instance: Ancient Mutation may Help Explain Origin of Human Organs

1) Researchers have reported that a neutral mutation having no real purpose and occurring randomly over 700 million years ago may help to explain the origins of complex structures like organs in humans and other vertebrates.

The pseudoscientific nonsense reported by Labroots may have reached its peak.

2) The same gene can give rise to different proteins that can act in entirely different ways by editing those genes a little differently, in a phenomenon called alternative splicing…

A link to a video about alternative splicing is included; See: Alternative Splicing
Conclusion: 

“The new discovery confirms how versatile biological evolution is: the same foundation and gene tools can be used to build a wood cabin or a skyscraper,” concluded Garcia-Fernàndez.

There is no such thing as versatile biological evolution. It is long past time for serious scientists to stop the pseudoscientific nonsense touted by theorists.
For a reminder of how long serious scientists have known the facts about alternative splicing, see again:
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

Alternative splicing is food energy-dependent and RNA-mediated in the context of the physiology of pheromone-controlled biophysically constrained viral latency.
All niche construction is food energy-dependent and controlled by the physiology of reproduction.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction.

This model organism exemplifies how ecological variation must be linked to ecological adaptation in species from microbes to humans. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway. Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ, which begins to commandeer control of the fleQ regulon at the cost of disrupting nitrogen uptake and assimilation. Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator. Our results demonstrate that natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps.

This was reported in the context of the classic phrase from the Jurrasic Park series of movies: Life finds a way (video)
The claim that life finds a way to resurrect the bacterial flagellum over the weekend via mutations can be compared in the context of this model organism. See: The Axolotl Limb Regeneration Model as a Discovery Tool for Engineering the Stem Cell Niche

…this model has identified a number of proregenerative signals, including growth factor signaling associated with nerves, and signals associated with the extracellular matrix (ECM) that induce pattern formation.

Educational video: Meet the creature that can regenerate its brain and resist cancer.
At the end of the video, the yin yang symbol from Chinese philosophy is superimposed over the electron cloud, which links the anti-entropic virucidal energy of sunlight to the physiology of pheromone-controlled reproduction and the viral latency that protects all organized genomes from the degradation of messenger RNA.
The virus-driven degradation of messenger RNA is clearly the link from mutations to all pathology, and all pathology can be examined in the context of the axolotyl model organism (aka: The “walking fish.”)
The portrayals of the “walking fish” as an example of neo-Darwinian evolution is a ridiculous example of what Feynman called human idiocy. Darwin place his “conditions of life” before natural selection because he knew that organisms must eat and reproduce. Neo-Darwinists assumed that the 2nd Law of Thermodynamics did not need to include any aspect of quantum entanglement.
Energy-dependent changes have since been linked from electrons to ecosystems by autophagy — the innate antiphage defense mechanism.
The defense mechanism protects the cell types of axolotyl and all other living genera from the virus-driven energy theft that links the destruction of the cell wall from bacteria to archaea and to L-forms, the last example on Earth of virus-driven energy theft and failed autophagy.