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.

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.

Autophagy in health and disease (1)

Novel Treatment Strategies for the Nervous System: Circadian Clock Genes, Non-coding RNAs, and Forkhead Transcription Factors

Each of these pathways have an intimate relationship with the programmed death pathways of autophagy and apoptosis and share a common link to the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) and the mechanistic target of rapamycin (mTOR). Circadian clock genes are necessary to modulate autophagy, limit cognitive loss, and prevent neuronal injury. Non-coding RNAs can control neuronal stem cell development and neuronal differentiation and offer protection against vascular disease…

The author includes what is known about the links from biophysically constrained RNA-mediated energy-dependent pheromone-controlled reproduction in yeasts to mammals.
See also this comment by Frank Xavier on Eat Yourself to Live: Autophagy’s Role in Health and Disease

Amino acids are not all the same, EAA and NEAA messages epigenetically control sometimes univocal responses, but more often they rule opposing effects.

I wrote:

Thanks for mentioning that. In a recent interview about his forthcoming book, Carl Zimmer claimed

…we need to be much more skeptical about other forms of heredity, like epigenetics.

(edited) Food energy-dependent biophysically constrained viral latency has been linked to healthy longevity in all living genera via autophagy, in the context of fixation of RNA-mediated amino acid substitutions and game play in Cytosis, for ages 10+.

In that context, we included a section on molecular epigenetics in this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Our claims have since been supported at every level of examination that now links the sun’s anti-entropic virucidal energy from electrons to ecosystems via cryo-EM technology and the creation of microRNAs.

See: Regulation of Luteinizing Hormone Receptor mRNA Expression in the Ovary: The Role of miR-122 and Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells and Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells
The microRNA-mediated link from Vitamin C to ecological adaptations in a modern human population in China established the facts about alternative splicings of pre-mRNA that we included in our 1996 review. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See also:  Reproductive role of miRNA in the hypothalamic-pituitary axis
See also: Chemistry at the nexus of water and energy

Our ability to harness reactions that absorb or release energy is often contingent on water as a mediator. We can appreciate this simply by considering the steam that drives our electricity-generating turbines, the rivers that flow through our hydroelectric plants, and the freshwater–saltwater interface from which we can harvest blue energy. Whether we split water (as plants do), make it (as a product of combustion) or just drink it, this compound is inexorably tied to energy. Chemistry is at the heart of these topics and this collection brings together content from across Nature Research that focuses on the chemistry of energy production and water treatment.

Philip C. Ball and Carl Zimmer continue to display their overwhelming ignorance of cell biology in two books:
Beyond Weird

We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information…

See for comparison: Life is physics and chemistry and communication and What is life when it is not protected from virus driven entropy
See also: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

Both so-called science journalists have ignored everything known to serious scientists about biophysically constrained viral latency. They reach a very large target audience of others who are biologically uninformed.
In the context of those who are equally uninformed, so-called science journalists have the power to contribute to increasing amounts of  unnecessary suffering and premature deaths. Only the emergence of Timothy J. Cunningham as director of the CDC is likely to stop them. May God help us all if Timothy J. Cunningham has somehow vanished without a trace and fails to return to put pseudoscientists and their idiot minions into their proper place.

An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 2017)

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.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

Alternative splicing of pre-mRNA

Trashing the 2nd Law

Summary: Autophagy is the antiphage defense strategy. (December 8, 2016) Other definitions no longer apply.
See: Experiment shows that arrow of time is a relative concept, not an absolute one
Everything that theorists were taught to believe about entropy was probably based on the ridiculous assumption that “…there are no correlations between particles.”
Everything known to serious scientists about energy-dependent autophagy shows that the creation of energy must be linked from the biophysically constrained physiology of pheromone-controlled reproduction via feedback loops that protect life from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
See:
1) Olfaction Warps Visual Time Perception
2) Molecular recognition in olfaction
3) QuEBS 2018: Workshop on Quantum Effects in Biological Systems
Research in the intersection of physics, chemistry and biology has been developed for more than 20 years based on what is known about the creation of quantized energy as information and details of the quantum effects in biological light-harvesting systems, which have been linked from the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See for comparison: Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes
Reported on December 6, 2017 as: Separated Since the Dinosaurs, Bamboo-Eating Lemurs, Pandas Share Common Gut Microbes

“This really underscores the role that diet plays in determining what lives in our guts – and, in turn, how these microbial ecosystems can shape the way animals live,” McKenney says.

Microbial ecosystems are food energy-dependent and the pheromone-controlled physiology of reproduction biophysically constrains viral latency. Without the pheromone-controlled physiology of food energy-dependent reproduction, bacteriophages and the virus-driven theft of quantized energy would link mutations to loss of functional structures that protect organized genomes from the degradation of messenger RNA. Everything known about cell type differentiation in all living genera has been placed into the context of links from physics and chemistry to molecular epigenetics via what is known about supercoiled DNA.
For comparison, see this claim:

“The bamboo lemur’s evolutionary tree diverged from that of both panda species 83 million years ago – that’s 18 million years before dinosaurs went extinct,” says Erin McKenney, a postdoctoral researcher at North Carolina State University and lead author of a paper on the study. “These species are also separated by thousands of miles and the Indian Ocean. Red pandas and giant pandas aren’t closely related either, with their most recent ancestor coming 47.5 million years ago. Lemurs are primates, red pandas are related to raccoons, and pandas are related to bears.

“Yet all three species share these 48 gut microbes – more than 12 percent of the microbial types found in each species’ gut,” McKenney says. “The only common feature is their diet: all three species live almost exclusively on bamboo.”

The common feature was presented in this 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of all neo-Darwinian pseudoscientific nonsense, and also a refutation of the ridiculous misrepresentations of “Big Bang” cosmologists. Those misereqpresentations led to two retractions of works published by Jack Szostak’s group in which false claims were made about non-enzymatic RNA replication.
See for comparison to what is known about the links from food energy to the pheromone-controlled physioloy of reproduction in species from microbes to humans: Altered responses to social chemosignals in autism spectrum disorder
reported as: Study: Autism Linked with Different Reactions to Chemical Signals
Conclusion:

“we speculate that social dysosmia may underlie part of the impaired reading of emotional cues in ASD.”

See for comparison: Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
Reported as: Problems with senses may predict older adults’ overall health, ability to function

Until now, no studies have examined how losing multiple senses affects older adults. To learn more, a team of researchers from the University of Chicago [including Martha McClintock] designed a study to focus on just that. Their study was published in the Journal of the American Geriatrics Society.

Problems with the senses are tractable to differences in the energy-dependent changes in base pairs that link changes in the microRNA/messenger RNA balance from RNA editing to the pheromone-controlled fixation of amino acid substitutions that stabilize the organized genomes of all living genera by protecting the organized genomes from the virus-driven degradation of messenger RNA.
See: Structural diversity of supercoiled DNA
The complexity of the interactions was again recently placed into the context of quantum correlations — with new insights.

Reversing the thermodynamic arrow of time using quantum correlations 

…standard thermodynamics presupposes the absence of initial correlations between interacting systems. We here experimentally demonstrate the reversal of the arrow of time for two initially quantum correlated spins-1/2, prepared in local thermal states at different temperatures, employing a Nuclear Magnetic Resonance setup. We observe a spontaneous heat flow from the cold to the hot system. This process is enabled by a trade off between correlations and entropy that we quantify with information-theoretical quantities.

They linked the creation of the sun’s anti-entropic virucidal energy from the physiology of food energy-dependent pheromone-controlled reproduction to biophysically constrained viral latency in all living genera. Constrained viral latency exemplifies the constrained entropy that Schrodinger placed into the context of What is Life? (1944). The updated version of his work was reported as: Experiment shows that arrow of time is a relative concept, not an absolute one

The idea of entangled particles has been in the news a lot lately as researchers around the world attempt to use it for various purposes—but there is another lesser-known property of particles that is similar in nature, but slightly different. It is when particles become correlated, which means they become linked in ways that do not happen in the larger world. Like entanglement, correlated particles share information, though it is not as strong of a bond. In this new experiment, the researchers used this property to change the direction of the arrow of time.

Everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated pheromone-controlled entropy (aka the “arrow of time”) is now referred to in the context of autophagy, which links the food energy-dependent fixation of amino acid substitutions to healthy longevity during species-specific developmental staging in species from microbes to humans.

See:Micro RNAs mir-184 and let-7 alter Drosophila metabolism and longevity

… adult-specific overexpression of let-7 in female nervous tissue increased median fly lifespan by ~22%. We provide evidence that this lifespan extension is not due to alterations in nutrient intake or to decreased insulin signaling.

That fact about biophysically constrained entropy (autophagy/the “arrow of time”)  replaces all theories about the emergence of life and evolution of biodiversity. Ridiculous theories were based on the 2nd Law of Thermodynamics, which assumes there are no correlations between subatomic particles. Darwin’s “conditions of life” and “Kohl’s Laws of Biology” show that the correlations are manifested at every level of examination.

See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels

The feedback controls energy-dependent differences in H2, which consists of two different hydrogens. Control begins at the level of subatomic particles. The controlled differences link the speed of light on contact with water (H20) to all biodiversity via the physiology of pheromone-controlled reproduction. That fact is exemplified in Drosophila and in the Amish population of Berne, Indiana. That modern human population manifests a nutrient energy-dependent pheromone-controlled 10-year increase in their  RNA-mediated lifespan.

The claim that “A null mutation in SERPINE1 protects against biological aging in humans” can be viewed in the context of what Richard Feynman claimed about human idiocy. Mathematical models of energy-dependent biophysically constrained entropy link autophagy to healthy longevity. They link the virus-driven degradation of messenger RNA from mutations to all pathology. Only biologically uninformed science idiots publish research that supports ideas about mutation-driven evolution.


Few intelligent people would argue against the fact that life is food energy-dependent. But see: 7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

My understanding is based on an understanding shared by many scientists and non-scientists, but no pseudoscientists.
Whether or not non-scientists know the facts about RNA-mediated cell type differentiation, they are not likely to believe that the selection of what to eat by the organisms that eat it is the most critical factor in species survival. That helps to explain why: A third of Americans don’t believe in evolution
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

See also the attack on my scientific credibility by PZ Myers and his idiot minions: One crank dies, another rises to take his place (2014)

Is alternative splicing the only mechanism to create variants in cells? No, of course not. External signals cause changes in the phosphorylation state of proteins in the cytoplasm, for example, that can affect metabolic activity; no alternative splicing involved. Signals can also switch on and switch off specific genes, again, no alternative splicing needed.

Most of the serious scientists I know laugh at people like PZ Myers. Some of them use sarcasm to address the ignorance of pseudoscientists. For example, see: A not entirely serious future history of neuroscience (2017)
Sarcasm alert. Thanks to Luca Turin for calling attention to this.
Excerpt 1)

Author’s note: resting for a moment in a dark corner of the Society for Neuroscience conference’s poster hall, on the quiet solitude of the Wednesday afternoon in the History of Neuroscience aisle, a shambling figure, bent with age, appeared with a speed that belied his years. Suddenly lunging for me, he shoved a sheaf of papers into my hand, hissing in my ear “it gets worse — so much worse”. Startled, I glanced at the front page, and the date written at the top: 6th October 2106. “What is…” I began, but he’d already whirled away — “A warning!” he spat back over his shoulder. Then he stopped, growled “I hate this bit”, squeezed his conference badge — and vanished.
What follows is the text I have been able to reconstruct from those crumpled, torn, faded pages.

Excerpt 2)

2037: Janelia Farm announces its Drosophila model of schizophrenia. HHMI instructs it to diversify its range of species.

My addendum: Electron spin changes during general anesthesia in Drosophila (2014)

Back to the future: The insect-to-elephant model of pheromone-controlled biophysically constrained viral latency is abandoned, again. Insect pheromone in elephants

The insect-to-elephant model of the food energy-dependent pheromone-controlled physiology of reproduction links alternative splicing of pre-mRNA, which now are called microRNAs by all serious scientists, to survival of all individuals in all species. The virus-driven degradation of messenger RNA links mutations to all pathology.

When should you unfriend someone on Facebook?

What we need to remember is that the devil is in the details.

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)
See for comparison: An Evolving Approach: The Public Response to Darwinism at Abilene Christian University, 1935-1989 (Stone-Campbell Journal 20:2, 2017)
Only by ignoring everything that has been learned about energy-dependent RNA-mediated biophysically constrained viral latency can historians and other pseudoscientists  continue to tout their ridiculous theories.
 

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (3)

See first: Energy-dependent physical and biophysical constraints (2)
Emily Balskus Pins Down the Chemistry and Metabolism of Human Microbiomes
Summary: The chemistry and metabolism of all microbiomes is food energy-dependent and pheromone-controlled via the physiology of reproduction.
See: Feedback loops link odor and pheromone signaling with reproduction

My comment to The Scientist:

…trans-4-hydroxy-L-proline (Hyp) dehydratase, a newly discovered member of an abundant family of proteins, produced by gut bacteria, known as the glycyl radical enzymes, helps in metabolizing trans-Hyp, an amino acid that is rare in bacteria but is common in eukaryotes.

The de novo creation of energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which has been linked from mutations to all pathology via the claims Schrodinger made 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.) (pp. 73 and 74)

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

Natural selection for food energy-dependent codon optimality links the sense of smell in bacteria to the biophysically constrained viral latency that links ecological variation to ecological adaptations in species from microbes to humans via the conserved molecular mechanisms of RNA-mediated cell type differentiation.

Sunlight has since been placed into the context of quantized energy as information, which links our visual perception of mass and energy from the space-time continuum to the concept of the energy-dependent creation of quantum souls.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016) and From Fertilization to Adult Sexual Behavior (1996)
 

Alternative splicing of pre-mRNA

Re-inventing mutation-driven evolution (2)

… we suspected that splicing efficiency, as defined by the fraction of pre-mRNA converted into mature mRNA, must have contributed to temperature-dependent Cirbp mRNA accumulation

Splicing efficiency is energy-dependent in the context of temperature-dependent oscillations that link the sun’s anti-entropic virucidal energy to all biodiversity via Turing’s claims and my model.

In 1951, the brilliant British scientist Alan Turing published a paper proposing a theory in chemistry called morphogenesis, which explains how cells are grouped together within an organism.

According to Turing, oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.

Could Turing’s claim be linked to Peter Berean‘s claims about differences between “bio-functional information” and energy as information?

See also: Cellular Clocks and Metabolism

..each tissue and organ appears to have unique 24 hour cycles related to the specific functions of the organ and the unique metabolic functions. Also, cycles of available material and cellular activity appears to ubiquitous.

The cellular clock mechanisms are nutrient energy-dependent and linked RNA-mediated amino acid substitutions in supercoiled DNA to the differentiation of all tissues in all organs in all living genera via biophysically constrained protein-folding chemistry in the context of the physiology of reproduction.

See also: Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal

Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora.

There are no deep evolutionary traits because all traits are energy-dependent. All traits must link RNA-mediated autophagy from the innate immune system to supercoiled DNA in the context of the physiology of reproduction. That fact links everything known to serious scientists about nutritional epigenetics from autophagy to the biophysically constrained protein folding chemistry of all genera.

For example, nutrient energy-dependent supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy. Phylogenetic trees may be established by patterns of viral latency.

Viral latency recapitulates the past effects of virus-driven energy theft on gene activation via what is known about energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution that link angstroms to ecosystems in all living genera. Nutrient energy-dependent gene activation links the mitochondria to effects that viruses had on hydrogen-atom transfer before the anti-entropic virucidal effects of ultraviolet light linked ecological variation to ecological adaptation of organized genomes in species from bacteria to archaea.

Placing bacteria and archaea into different domains of life was a mistake made by Carl Woese who did not link the nutrient energy-dependent physiology of reproduction from autophagy to supercoiled DNA because he failed to consider the role of virus-driven energy theft in all pathology. That pathology is exhibited in the number of viruses in archaea compared to the number of viruses in ecologically adapted bacteria  and in ecologically adapted humans.

See also: Stanford manufactures gene-engineered cells to cure the incurable

1) To fix this, Stanford researchers use a virus to deliver a correct version of the gene onto batches of skin cells, then coax them to form sheets of healthy skin.

2) Cells are nurtured in a broth of sugars, carbohydrates, fats, growth factors and hormones, warmed at body temperature: 98.6 degrees Fahrenheit.

The virus links the natural information processing of all cell types from the innate immune system to autophagy and the nurturing helps to ensure that the pluripotent state leads to energy-dependent biophysically constrained protein folding chemistry that typically links the pheromone-controlled physiology of reproduction to all biodiversity via RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genome from virus-driven entropy.
See also: Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

In addition, over the past 15 years, a myriad of non-coding, but functional RNAs have been discovered, including microRNAs and long non-coding RNAs that can regulate transcription [42] but more commonly translation [43] of protein coding genes. Mutations affecting non-coding genes can thus lead to changes in the repertoire of proteins that determines cell behaviour in developmental programmes, resulting in phenotypic evolution. Long non-coding RNAs have been associated with development and evolution but they are less well studied than shorter microRNAs and small RNAs [44].

During the past 15 years nutrient energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated protein folding chemistry to all biophysically constrained biodiversity via autophagy and supercoiled DNA in the context of the physiology of reproduction. There are now more than 56,000 published works that link energy as information from changes in hydrogen-atom transfer in DNA base pairs in solution to all extant biodiversity via the physiology of reproduction.
See: microRNA (56,324 citations)
See also: Long noncoding RNAs in the p53 network

p53 regulates the expression of a repertoire of lncRNAs, and some of these lncRNAs are critical regulators of cell cycle arrest, DNA damage repair, chromosomal stability and apoptosis, altogether contributing to tumor-suppressor function of p53. LncRNAs are dysregulated in a variety of cancers and therefore can be utilized as biomarkers for disease progression and as therapeutic targets.98

Energy-dependent changes in the microRNA/messenger RNA balance are linked from every aspect of biophysically constrained protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans. The sun’s anti-entropic virucidal energy has been linked to DNA damage repair, chromosomal rearrangements and chromosomal stability. Rather than continue to ignore the facts about energy-dependent healthy longevity for comparison to virus-driven energy theft and all pathology, some people may still be interested in seeing this:
What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

 

fruit-dove

Theories vs facts about polycombic adaptation

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

Important aspects will be highlighted as a take-home message (THM) at the end of each paragraph.

THM: Extracellular vesicles transport miRNA in a paracrine and endocrine manner. Questions regarding the cellular options of producing either microvesicles or exosomes and their difference in miRNA composition and number are still unknown.

In my 2014 invited review, the four F’s, Formation–Function–Future and Copulation were included in details about how the nutrient energy-dependent de novo creation of microRNAs must be linked to nutritional epigenetics. My invited review was returned without review by the guest editors of a special issue of “Nutrients.”
I realized the guest editors had “baited me” into providing them with all the available current information and published my submission to Figshare. That’s how I show the level of deception that biologically uninformed theorists still use to obfuscate what is known to serious scientists about biologically-based cause and effect.

See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (April 10, 2014)

Abstract: “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. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.”

Lynnette Ferguson, was one of two guest editors that invited my review.
 
She is the co-author of The Interaction between Epigenetics, Nutrition and the Development of Cancer This article belongs to the Special Issue NutritionalEpigenetics
 

Conclusion:

…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.

There would be no future generations if diet could not be epigenetically linked from metabolism to the pheromones that control the physiology of reproduction in species from microbes to human via energy-dependent changes in the microRNA/messenger RNA balance. The microRNA/messenger RNA balance biophysically contrains RNA-mediated protein folding chemistry.

Protein folding chemistry links energy-dependent changes from angstroms to ecosystems in all living genera via the innate immune system and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. Supercoiled DNA exemplifies natural section for energy-dependent codon optimality, but theorists will not accept that fact. They would rather believe that the mutations in DNA are naturally selected and that mutation-driven evolution automagically occurs outside the context of energy or the virus-driven energy theft that causes all mutations and all pathology.

See also: The developmental basis for the recurrent evolution of deuterostomy and protostomy

This scenario challenges the assumed value of extant blastoporal behaviours for explaining the evolutionary origin and diversification of Bilateria that has been presumed for over 100 years4,5,6,7,9,10,11. Freeing the constraint that the mouth and anus have a necessary association with the embryonic blastopore will help in understanding the developmental events underlying the evolution of an alimentary canal5,20,21,50, and ultimately the appearance and diversification of bilaterian body plans.

All scenarios that failed to link energy-dependent behavior to the physiology of reproduction and also failed to link virus-driven energy theft to all pathology have always been based on questionable assumptions. The assumptions fall outside the context of Darwin’s “conditions of life,” which require links from what organisms eat to signaling and sensing and the behavior of other organisms.

For example, Schrodinger (1944) linked excretion from mammals to sunlight as the source of anti-entropic virucidal energy used to support all ecosystems. All serious scientists have done that since Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking chromosomes to transgenerational epigenetic inheritance long before most people understood what the term autophagy means.

Biology to a Physicist

Hypothesis free pseudoscience vs facts (1)

Old Earth Creationist (OEC) Peter Berean, thinks I should change the claims in my model of energy-dependent biophysically constrained RNA-mediate protein folding chemistry. He does not like the fact that my model explains all pathology in the context of virus-driven energy theft.
If viral latency is not nutrient energy-dependent and controlled by the physiology of reproduction in species from bacteria to humans, I will change my claims. If someone explains what is wrong with my model, I will try to correct what is wrong. Until someone explains what is wrong with my model, here is the latest experimental evidence that validates my model, and an example of an attempt to discuss the model in the context of the evidence.
See the evidence: Opposing Effects of Fasting Metabolism on Tissue Tolerance in Bacterial and Viral Inflammation
Reported as: What you eat when you’re sick may determine if you’ll get better
My comment: I think it is obvious that energy-dependent healthy longevity is nutrient-dependent because nutrient-dependent RNA-mediated amino acid substitutions are linked to supercoiled DNA, which protects all organized genomes from virus-driven entropy (i.e., all pathology).
For discussion, see: James Kohl… if you would like to state your scientific hypothesis (re virus driven energy theft leading to pathologies etc) and its implications … please do so here.

Peter Berean From the article you linked above. … quote:giving mice with flu glucose saved their lives, but it killed those that were infected with bacteria. See: 2 hrs

Peter Berean This suggests that bacteria can cause disease that is different from viral disease… 2 hrs

James Kohl From the author’s comment on this article: http://comments.sciencemag.org/content/10.1126/science.1244730 “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.” 2 hrs

Peter Berean The article does not make the case that ALL disease is caused by viruses… I think you should modify your model to state that Many di[s]eases are caused by viruses (but [not] necessarily all)…. you would have greater credibility with your readers if you were to do so…2 hrs
Peter Berean No problem with your latest article link (major antigenic…) It does not establish your original ALL model. But it is consistent with my recommended change to you[r] model… 2 hrs
James Kohl Plagiarist Tomi Aalto, has already taken the information I provided to him to make the claims I have been making for 20 years without mention of the model. I suspect you will do the same thing. You want me to modify the only model that explains biologically-based cause and effect in all living genera to gain the credibility that God has via His claims — as recorded across the history of life and death on Earth.
Is there some reason you think I would be willing to do that based on your opinions and recommendations? 2 hrs

Darrell Mondeau James, serious scientists accept criticism of their models or hypotheses. It is important for the evaluation of the models or hypotheses. No scientific idea has ever moved forward without criticism and reevaluation. 2 hrs

Darrell Mondeau James, I think you would be willing to change your model so that it would fit more precisely with the evidence that not all disease is caused by viruses. i.e. fungal infections, man made toxins, natural toxins. The wording of “ALL” is too broad.  2 hrs
Peter Berean James, I promise that I will not steal your model or use it without attribution to you. Your model does appear to be true for some pathologies… however, as Darrell mentions above the use of the term ALL is too broad. Your model will gain more credibility if you modify it to say that SOME pathologies are caused by viruses … via these xyz mechanisms. … 1 hr
Peter Berean And your medical research can substantiate those pathologies (that are caused by viruses)… 1 hr
Peter Berean You do post a lot of interesting articles (which I enjoy skimming)…. but those do NOT make the case that ALL pathologies are caused by viruses. Yes, SOME pathologies, [but] not Not ALL pathologies. … 1 hr
Peter Berean The point I made with Neo Darwinism was not intended to be an insult. It was merely pointing out that Neo Darwinism makes the same mistake. ND is valid in a small portion of the biosphere (micro Evo and low level speciation etc)… but to extrapolate it to ALL creation of the biosphere (including the higher level taxa, phyla, new body plans etc) is an extreme unwarranted extrapolation…
And again, no offense meant. 1 hr
James Kohl Let’s continue discussion despite your offenses and lack of defense for any theory or for any other model.
Neo-Darwinian theory remains hypothesis free. The inventor’s claims were based on observations of change and statistics. They attributed the changes to “mutations” and natural selection. Darwin attributed the changes to “conditions of life.”
The fact that anyone would ask me to change a fully validated model of biologically-based cause and effect to something that was a better fit for ridiculous theories shows utter contempt for science and scripture. Darwin did not do that; neo-Darwinists always have.
Like the neo-Darwinists, you seem to hate the fact that experimental evidence of biophysically constrained energy-dependent RNA-mediated cell type differentiation supports claims that our ancestors chose to ignore the most basic of all constraints required for energy-dependent healthy longevity.
Is that a correct assessment of your current position on this debate? No offense meant. (September 28, 2016) Just now
Summary: Most theorists, atheists, and Old Earth Creationists (OEC) do not like my model of energy-dependent cause and effect. They have no alternative model and they seem to prefer theories. But they won’t tell me which theories they prefer, or why. They will not even cite a published work that they think supports their opinions.
See for example this description from a presentation by Kevin R. Foster: Social evolution in microbes: from model systems to the microbiome

Bacteria strains are often at war and we find that they can rapidly detect incoming attacks and respond in kind. Microbial interactions then follow the same evolutionary principles that were first understood through the study of animal behavior. However, one unusual and fascinating property of microbes is that an entire ecosystem can lie within another evolving organism: a host. This raises the possibility that hosts will act as ecosystem engineers that change the rules of microbial interaction for their own benefit.

See also: The evolution of cooperation within the gut microbiota, which was co-authored by Kevin R. Foster.
Abstract excerpt:

Cooperative phenotypes are considered central to the functioning of microbial communities in many contexts, including communication via quorum sensing, biofilm formation, antibiotic resistance, and pathogenesis.

My comment: Nutrient energy-dependent pheromone-controlled quorum sensing links angstroms to ecosystems in all living genera via RNA-amino acid substitutions in supercoiled DNA. Nothing evolves, not the organisms in the gut, and certainly not the host. No organism of any species has ever evolved. The biophysically constrained energy-dependent physiology of reproduction prevents evolution. Virus-driven energy theft causes genomic entropy when energy-dependent RNA-mediated DNA repair can no longer protect the organized genome from virus-driven energy theft.

See also: Hypothesis free pseudoscience vs facts (2)
 

poster-from-jesse

RNA-mediated theory killers (5)

Epigenetic regulation of puberty via Zinc finger protein-mediated transcriptional repression

Reported as:

Researchers elucidate network of genes that control when puberty begins

Excerpt:

…have identified for the first time members of an elaborate superfamily of genes that regulate the timing of puberty in highly evolved nonhuman primates.

My comment: Who do these researches and science journalists think they are fooling when they report the nutrient-dependent pheromone-controlled onset of puberty, which is obviously RNA-mediated, in the context of highly evolved organisms? No experimental evidence of biologically-based cause and effect links evolution and puberty.

Conserved molecular mechanisms of biophysically constrained cell type differentiation link protein folding chemistry from thermodynamic cycles of nutrient-dependent protein biosynthesis and degradation to the stability of all organized genomes via microRNAs, cell adhesion proteins, and supercoiled DNA. Networks of genes link metabolism to survival of cell types and species via the metabolic networks and genetic networks that control organism-level thermoregulation.
A single nutrient-dependent RNA-mediated amino acid substitution in a virus links energy theft from cells to perturbed protein folding and mutation-driven pathology. That explains why PKU was linked from nutritional epigenetics to pharmocogenomics several decades ago and why nutrient-dependent base pair substitutions and RNA-mediated cell type differentiation was linked to human life history transitions by the Val158Met substitution last year.

See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

There is no explanation for the ignorance of evolutionary theorists who claim that Zinc finger protein-mediated transcriptional repression can be placed into the context of the evolution of puberty. Nothing currently known about RNA-mediated cell type differentiation can be placed into the context of evolution. Everything  known to serious scientists has been placed into the context of ecological variation and ecological adaptation.

See: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

My comment: Everything  known to serious scientists also supports our claims about Zinc finger proteins from the “Genetic Considerations” section of our 1996 Hormones and Behavior review From Fertilization to Adult Sexual Behavior

Excerpt:

Another example of biological sex differences which are neither gonadal nor hormonal, however, is provided by the homologous but dimorphic zinc finger proteins ZFX and ZFY encoded on the X and Y chromosomes (North et al.,1991). An early study of human expression of ZFX and ZFY reported different transcript sizes from the two genes and this difference was even apparent in somatic tissues (Page, Disteche, Simpson, De La Chapelle, Andersson, Alitalo, Brown, Green, and Akots, 1990). ZFX and ZFY are described as “DNA-binding proteins” and via their binding of sexually dimorphic proteins, chromatin structure and transcription could be modulated in sexually dimorphic ways as a result of females having only ZFX binding events, whereas males would have a mixture of both ZFX and ZFY binding events (Fiddler, Abdel-Rahman, Rappolee, and Pergament, 1995; Lau and Chan, 1989; Zwingman, Erickson, Boyer, and Ao, 1995).

My comment: Any report that links sex differences in cell types to somatic differences in cell types and claims that the differences exemplify how evolution has altered life history transitions in highly evolved primates exemplifies the amount of pseudoscientific nonsense about hormone-organization and hormone-activation that has continued to be taught to researchers and science journalists.

terrarium-eco-system

Theorists can't understand biology

See also: Neuroplasticity
Thanks to Teresa Binstock for calling my attention to this:
 

Biology is imposssible

Optimizing neuroplasticity by linking atoms to ecosystems

Thanks to Anna Di Cosmo for calling the attention of others to this:

My comment: Attempts to explain the “binding problem” of integration in the context of ecoimmunology and disease ecology compared to emergence and evolution are examples of how much pseudoscientific nonsense has been accepted and touted in the context of the neo-Darwinian “Modern Synthesis.” For comparison, serious scientists have detailed a model of top-down causation that links the design of the brain from the bottom up in an atoms to ecosystems model of cell type differentiation. The model links our experiences from our first breath to our behavior during life history transitions via biophysically constrained protein folding.
Re: “Man is the measure of all things.” Intelligent scientists understand that their measurements from physics, chemistry, and the molecular mechanisms of biologically-based cause and effect must link all other scientific disciplines to biology.
See for example: Oxygen regulation of breathing through an olfactory receptor activated by lactate
Conclusion:

Although ORs [olfactory receptors] were first identified for their role in smell, they may be involved in myriad chemosensory pathways detecting endogenous and exogenous ligands throughout the body.

For comparison to what is known to serious scientists about receptor-mediated cause and effect in the context of chemosensory pathways, evolutionary theorists and theoretical physicists continue to misrepresent all measures of all things. For example, they refuse to explain how “re-evolution” of the bacterial flagellum occurred in four days but claim that an example of no evolution in ~2 billion years supports the claims included in the “Modern Synthesis.”
See: Scientists discover organism that hasn’t evolved in more than 2 billion years
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
My comment: Try to place the evolutionary resurrection of flagellar motility into the context of the binding problem that must link receptor-mediated events to chemosensory pathways after watching this video.

The bacteria that “re-evolved” their flagella over a weekend exemplify how the nutrient-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation in all living genera via receptor-mediated events that link food odors and pheromones to the physiology of reproduction in all living genera.
For comparison, Simon LeVay challenged my model of ecological adaptation, which resolved issues of the “binding problem” that links receptor-mediated behaviors in the context of sex differences in cell types and differences in sexual orientation.
See: Gay, Straight, and the Reason Why: The Science of Sexual Orientation
Excerpts:

That the odor of gay men is recognizably different from the odor of other people is believable, although the claim hasn’t been independently verified and its chemical basis hasn’t been studied. (p. 209)
It seems unlikely to me, though, that gay men have an innate preference for the odor of gay men over that of straight men because many gay men are attracted to straight men and, given the opportunity, will have sex with them even in preference to gay partners. Thus this finding, if replicable, is more likely to represent a learned association resulting from gay men’s prior history of intimacy with other gay men. (p. 210)
James Kohl, an independent researcher who also markets “human pheromones” to the general public, believes that pheromones may have a primary influence in setting up a person’s basic sexual orientation. Other, more consciously perceived aspects of attractiveness, such as facial appearance, are attached to a person’s basic orientation through a process of association during early postnatal life, according to Kohl. 35 (p. 210)
This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions. (p. 210)
Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (p. 210 – 211)

The chapter 8 notes entry number 36 attempts to show there is “…no compelling evidence for the primacy of one sense over another.” LeVay tries to support that ridiculous claim by citing Spieth (1974) “Courtship behavior in Drosophilia” and Stockinger et al (2005) “Neural circuitry that governs Drosophilia male courtship
Excerpt:

Anatomical differences in this circuit that might account for the dramatic differences in male and female sexual behavior are not apparent.

My comment: In our 1996 Hormones and Beahavior review, From Fertilization to Adult Sexual Behavior, we placed anatomical differences and sex differences in behavior into the context of RNA-mediated cell type differention. The conserved molecular mechanisms we detailed in our section on molecular epigenetics extend across species, regardless of whether LeVay or anyone else can find sex differences in neuroanatomy that correlate with differences in the behaviors of flies and humans.
See for comparison: Courtship behavior in Drosophila melanogaster: towards a ‘courtship connectome’

Excerpt: 

The construction of a comprehensive structural, and importantly functional map of the network of elements and connections forming the brain represents the Holy Grail for research groups working in disparate disciplines.

My comment: None of my former colleagues from the Society for the Scientific Study of Sexuality has since made any attempt to challenge LeVay’s claims about my model. However, LeVay’s claims can be compared in the context of two recent reports from serious scientists:
1) Feedback loops link odor and pheromone signaling with reproduction
Excerpt:

Compelling evidence that links the feedback loops from microbes to humans

2) MicroRNA-encoded behavior in Drosophila
Conclusion:

The results of this study contribute to the understanding of how complex innate behaviors are represented in the genetic program. Our data lead us to propose that other miRNAs might also be involved in the control of behavior in Drosophila and other species.

See also: The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling, which was reported as: Receptor methylation controls behavior 
Excerpt:

Likhite et al. found putative arginine methylation motifs in some human G protein–coupled receptors (GPCRs), including the D2 dopamine receptor, and in homologs in the worm Caenorhabditis elegans.

My comment: Nutrient-dependent RNA-directed DNA methylation of GPCRs in nematodes and humans, links the pheromone-controlled physiology of reproduction to the nutrient-dependent pheromone-controlled physiology of reproduction in yeasts and other microbes via the conserved molecular mechanisms of cell type differentiation we detailed in our 1996 review. Serious scientists have linked the facts from our review from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all living genera.
See: DNA twist as a transcriptional sensor for environmental changes (1992) and DNA supercoiling and bacterial gene expression (2006) and Flagellar and global gene regulation in Helicobacter pylori modulated by changes in DNA supercoiling (2007).
Addendum: Only pseudoscientists and other who are among the biologically uninformed have failed to accept the scientific progress that led to publication of Structural diversity of supercoiled DNA (2015).
This parody links what is known to serious scientists about biologically-based cause and effect to the ridiculous claims of theorists in an amusing musical rendition of insults to the theorists that is unlike any other collection of polite insults that you may ever see.

See also: Combating Evolution to Fight Disease
My comment: Help serious scientists to force pseudoscientists to learn about biologically-based cause and effect. Join the fight to stop the pseudoscience and preventable diseases!

Compare what is known to serious scientist to the claims of these pseudoscientists in the context of the most recent attempt to convince others that evolution is true.

Evolution website sets out to tackle great scientific unknowns

Excerpt: 

The site was created by a team led by Simon Conway Morris, Professor of Evolutionary Palaeobiology and a Fellow of St John’s College at the University of Cambridge. “Evolution is true, and if it didn’t happen, we wouldn’t be here,” he said.

My comment: Are you willing to accept that circular logic rather than examine life in the context of Schrodinger’s claims from “What is Life?
Excerpt:

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: The anti-entropic epigenetic effect of the sun’s virucidal energy on DNA repair links ecological variation to nutrient-dependent ecological adaptation via the physiology of reproduction or to virus-driven pathology in all living genera. That is not circular logic, and molecular mechanisms linked to the physiology of nutrient-dependent reproduction exemplify how the differences between life and death arose.
See also: Consciousness Mechanics: The Movie for more philosophical nonsense than most people have seen integrated into something to entertain the masses.