5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

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.

An evolutionary theory killer

Subatomic: From thermophiles to humans (3)

Summary: RNA-mediated cell type differentiation in species from insects to primates can be linked from claims about the lower percentage of food energy-dependent DNA methylation in Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae) to the conclusion from “Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility.”
See also: Starfish reveal the origins of brain messenger molecules (February 9, 2016)

One of the neuropeptides found is similar to kisspeptin, a chemical that triggers the onset of puberty in humans.

The link from kisspeptin to GnRH helped to establish the link from food odors and pheromones to the RNA-mediated physiology of reproduction in all invertebrates and vertebrates.
Placing facts about neuropeptides into the context of human brain evolution thus seems to exemplify incredible ignorance of physics, chemistry, and molecular epigenetics.
See for comparison: The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution
Conclusion:

The increasing number and diversity of these small and long ncRNAS in relation to the complexity and adaptability of living beings, explains that they have been paramount in complex biological processes and are not an evolutionary paradox.

The fact that miRNAs can be mobilized by the fluids of plants and animals, allows them to act at different distances to where they were transcribed, much like hormones or pheromones do. In addition, they can respond to environmental stimuli, favoring the adaptation of organisms through the modification of epigenetic marks and also a transgenerational inheredity and the evolution of species as part of a Neo-Lamarckian model.

There has never been a neo-Lamarkian model for the evolution of species. Lamarck put his observations into the context of Darwin’s “conditions of life.” If the conditions of life are met, ecological variation can be linked to food energy-dependent ecological adaptations. Only the bastardization of Darwin’s claims put natural selection for mutations first — when biologically uninformed theorist invented neo-Darwinian pseudoscientific nonsense.
SARCASM ALERT: Please do not tell anyone about this 2013 refutation of neo-Dawinism. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See for comparison. Others are  making the same claims:
Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells

…identification of vitamin C-dependent microRNA regulation is important for understanding the basic mechanisms underlying BMSC differentiation and tissue engineering.

All cell type differentiation in all tissues of all species with tissues is energy-dependent and RNA-mediated. That fact is consistently thrown into the political ring of nonsense touted by theorists who attack the President of the United States.
See: Trump: Tell us about your flu shot

Why are so few Americans getting the flu vaccine? And why isn’t the CDC doing more to change that?

The CDC can do nothing. Intelligent people know that the flu virus adapts each season. The CDC will abandon their claims about mutations, which were linked to evolution. More people will be angry when they learn that only a single amino acid substitution can cause an adaption.
Trump-hating liberals may be forced to repurpose their anger and use it to rid the academic swamp of their idiot minions — the so-called science journalists who refused to join the serious scientists who are Combating Evolution to Fight Disease
Most of the anger will be directed toward biologically uninformed science journalists who have failed to present the facts about all virus-driven pathology. For example see: The Quest to End the Flu (2013)

New pandemics don’t come out of the blue. They evolve from viruses that infect animals—typically birds.

Pandemics “evolve” from viruses? What kind of so-called science journalist makes a claim like that?
Is Most of Our DNA Garbage? (March 5, 2015)

…junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

The triumph is not slow and slovenly. One base pair change and fixation of one amino acid substitution is all that is required to start the process of ecological adaptation.
See for comparison: It’s time to put America’s health first

While the CDC neglected its mission here, Obama committed billions to build labs and train health personnel in Africa during the Ebola scare. Billions for a disease that killed only one person in the United States — and even he got infected elsewhere.

The so-called science journalists who also are Trump-haters have contributed to more unnecessary suffering and premature death than most people can begin to imagine. They spread their ignorance and hatred across the country and across the world. It is the pathology of their ignorance that must be removed if ever we are to put America’s health first. The first thing we must do, is rid ourselves of the unethical so-called science journalists.
 

https://media.springernature.com/lw900/springer-static/image/art%3A10.1038%2Fs41467-017-02632-8/MediaObjects/41467_2017_2632_Fig6_HTML.jpg

The MicroRNAome Strikes Back: A Sokalian hoax (4)

In this Sokalian hoax series, all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera via the physiology of reproduction and autophagy, the innate phage defense mechanism.
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

I reiterate the most obvious facts by mentioning again:

 Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

See also: The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding, and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.

The John Templeton Foundation typically seems to be involved in funding research reported that obfuscates facts that link science to Biblical Genesis. The claims about understanding energy-dependent biomolecular recognition in biophysical systems, which must biophysically constrain viral latency, invite more criticism of the Templeton-funded biologically uninformed theorists.

Does the “Extended Synthesis” Replace or Not Replace Neo-Darwinism? — What Has Templeton Funded?

Many terms in science have a different meaning from the public usage, because they depend on particular definitions of the phenomena to which they apply.

See for comparison: Do Human Pheromones Exist? January 23, 2018

The people interviewed are not Nobel Laureates. For comparison, LInda Buck, co-author of Feedback loops link odor and pheromone signaling with reproduction is a 2004 Nobel Laureate.
I suspect that all serious scientists have since learned that pheromones biophysically constrain food energy-dependent viral latency in species from insects to mammals via the conserved molecular mechanisms of microRNA-mediated cause and effect. Serious scientists tend to be more likely than theorists or other pseudoscientists to recognize patterns.
For instance: Insect pheromone in elephants

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

That claim links what insects eat to the pheromone-controlled physiology of reproduction of s via the food energy-dependent creation of microRNAs in species from microbes to mammals.

See: Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, Signaling, and role of MicroRNA (with my emphasis)

Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

insects, arachnids, and crustaceans are arthropods. No experimental evidence of biologically-based cause and effect suggest that complex mechanisms evolved in any species. For contrast, the link from microRNAs to juvenile hormone crosses species via the molecular mechanisms that link the food energy-dependent creation of microRNAs from what is known about gonadotropin releasing hormone (GnRH) pulsatility to luteinizing horrmone secretion via the food energy-dependent GnRH-directed physiology of pheromone-controlled feedback loops in all mammals.

That fact has been placed into the context of ecological variation and biophysically constrained ecological adaptations.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes 

…lack of genome information hinders the understanding of the adaptation

See for comparison: Differential expression of microRNAs in luteinising hormone-treated mouse TM3 Leydig cells

Results showed that miRNAs might be involved in the regulation of LH to Leydig cells.

One way to understand the adaptations revealed in the context of mussel genomes involves ignoring all claims about how complex mechanisms “evolved to regulate” anything. The overwhelming systems complexity of biophysically constraints demand that all ecological adaptations be examined from the intelligent perspective of serious scientists.

The well-detailed understanding of how the light energy-dependent creation of microRNAs is linked to all nutrient-dependent pheromone-controlled ecological adaptations. But the facts were again placed back into the context of complex mechanisms that automagically evolved in  Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

…pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4.

The established biodiversity is obviously pH-dependent and oxidative phosphorylation was linked to the stability of organized genomes in 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Other serious scientists moved forward in the context of the energy-dependent hydrophobicity of supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Outside the context of the epigenetic effect of anti-entropic virucidal energy from sunlight on supercoiled DNA, or perhaps in the context of minimal exposure to ultraviolet light, the metagenomic diversity of bacteria in caves with sulfur water springs led  Bautista et. al., (2018) to conclude:

…20,901 reads of bacterial 16S rRNA gene sequences spanning V1–V3 hypervariable regions corresponded to seven phyla: Proteobacteria, Firmicutes, Chloroflexi, Chlorobi, Bacteroidetes, Actinobacteria and Acidobacteria. Proteobacteria phylum dominance could be due to the increased presence of organic matter, not only of bat guano but also that caused by man and animals, directly or through infiltrations. For the UJAT5 sample, we generated 6,691 reads, which, due to the
physicochemical characteristics (Table 1) and relative frequency obtained (Figure 4), could confirm the presence of acidophilic Proteobacteria in VL caves. All the bacterial communities identified are characteristic of caves, while Acidobacteria, Proteobacteria, and Actinobacteria are typical of volcanic surface terrain.

Simply put, they seem to assume that the increased presence of organic matter is the food energy that supports the pheromone-controlled physiology of reproduction in the different species. But they do not link the creation of sunlight to differences in the food the organisms eat.
By skipping the link from the creation of sunlight — as did Nonomura (2018) in his Sokalian hoax, evolutionists have tried to convince others who are biologically uninformed that the eyes of blind cave fish exemplify evolution in the process of the fish becoming blind.
See: Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
See (pun intended) Blind Cavefish Can Produce Sighted Offspring  (2008)

It’s a miracle! Blind cavefish, despite having adapted to their lightless environment for more than a million years, can produce sighted offspring in just a single generation, a new study reveals.

This means that even though the fish are blind, they basically have functional visual systems that have been deactivated by a few key mutations, said Jeffery, who was unaffiliated with the study.

See also: The fish evolved from surface-dwelling ancestors during the past million years. (2003)
Everything biologically uninformed theorists report must be linked toi evolution and back by mutations. They refuse to differentiate between mutations and food energy-dependent ecological adaptations because they cannot accept the fact that all biophysically constrained biodiversity is food energy-dependent and constrained by energy-dependent viral latency.
For comparison, what serious scientists see happening in the blind cave fish is the regression of food energy-dependent visual acuity in organisms that can find food without  the energy-dependent creation of G protein-coupled photoreceptors. Only the energy-dependent creation of chemoreceptors is required to link pH-taxis to survival of the microbes and the blind cave fish via what is known about oxidative phosphorylation in other species that display receptor-mediated behaviors.
What science journalists see happen is causing them to back away from their pseudoscintific claims from the past. See for example:

Hydration as a design element in biomaterials  Philip Ball January 24, 2018

John Hewitt January 24, 2018 N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications 
Will water link RNA modifications to stem cell self-renewal, or will light-activated endogenous substrates and biophysically constrained RNA-mediated amino acid substitutions be tossed into the brickyard for the win?

Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (4)

Excerpt: During the past 21 months, others have either learned nothing about microRNAs or they have ignored the fact that virus-driven energy theft is not the same as energy dissipation in the context of food energy (the quantized energy as information that is used by viruses to create the amino acid substitutions that stabilize their RNA and DNA).

The dark side of the new popularity of cryo-electron microscopy

…we need to stand together as a field, and support our colleagues by accepting to review their papers and grant applications in order to ensure a fair evaluation. In my opinion, we need to collaborate, support and acknowledge each other as best as we can so we can successfully move forward together into a bright future in cryoEM.

This invited review of nutritional epigenetics was returned without review.  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Food energy-dependent changes in base pairs were linked to ecological adaptation in species from microbes to humans via methylation and the fixation of RNA-mediated amino acid substitutions. There is no dark side to cryo-electron microscopy (cryoEM), and Ariane Briegel knows that. See: Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling (2014)

  1. …methylations confer adaptation on the system, modulating its response based on recent environmental conditions (Kleene et al., 1979; Toews et al., 1979; Lupas and Stock, 1989). The architecture of these membrane-bound chemoreceptor arrays is not specific to E. coli, indeed it is universal among bacteria (Briegel et al., 2009). The architecture of these arrays is likely key to the high sensitivity, wide dynamic range, cooperativity, and feedback control of this system…
  2. Interestingly, while transmembrane arrays remain intact upon cell lysis, presumably due to the stabilizing effect of the membrane, cytoplasmic arrays fall apart unless molecular crowding agents are added. This suggests that cellular crowding contributes to the stability of the array and may be an important factor in assembly of these, and likely other, cellular structures (Ellis, 2001; Zhou et al., 2008; Zhou, 2013). We observe the same requirement for molecular crowding (mimicking the cellular environment) in our in vitro preparation from E. coli. This supports the idea that chemoreceptor interactions can be enhanced by membrane binding (Shrout et al., 2003), but in the absence of a membrane, this can be achieved by molecular crowding and sandwiching (Fowler et al., 2010).

Briegel et  al., (2014) reestablished the facts from our 1996 review of biophysically constrained RNA-mediated cell type differentiation. See the molecular epigenetics section of From Fertilization to Adult Sexual Behavior.
Life on Earth exists within the confines of the energy that is required to maintain the functional structure of the cell membrane. The crowding of food energy-dependent microRNAs in the cell membrane is reduced by virus-driven energy theft. 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.

Bacteria become archaea and archaea become L-forms (with no cell wall).
See: L-form bacteria cohabitants in human blood: significance for health and diseases
That significance of L-forms was not placed into the context of this representation of how serious scientists will prevent or begin to effectively treat all virus-driven pathology in the context of what has been revealed by the cryoEM technology.
See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels
The circadian cycling of energy-dependent microRNA-mediated protein biosynthesis and degradation has been linked to healthy longevity via what is known about quantum physics and the link from quantized energy as information to quantum souls via hydrogen-atom transfer in DNA base pairs in solution that link microRNA flanking sequences in exosomes to RNA-mediated DNA repair.
See: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function (Jan 1, 2018)

It has been shown that exosomes contain large amounts of miRNAs and can serve as vehicles to transfer miRNAs to recipient cells, where the exogenous miRNAs can alter the gene expression and bioactivity of recipient cells [28].

28. Au Yeung CL, Co NN, Tsuruga T, Yeung TL, Kwan SY, Leung CS. et al. Exosomal transfer of stroma-derived miR21 confers paclitaxel resistance in ovarian cancer cells through targeting APAF1. Nat Commun. 2016;7:11150

These data suggest that the malignant phenotype of metastatic ovarian cancer cells can be altered by miR21 delivered by exosomes derived from neighbouring stromal cells in the omental tumour microenvironment, and that inhibiting the transfer of stromal-derived miR21 is an alternative modality in the treatment of metastatic and recurrent ovarian cancer.

All experimental evidence of biophysically constrained viral latency links the food energy-dependent creation of microRNAs from the bioreactivity of recipient cells to healthy longevity via  protection from the virus-driven degradation of messenger RNA, which all serious scientists have linked from mutations to all pathology.

See this presentation from a Precision Medicine virtual conference for review

See also:

Mar 2, 2016  From hydrogen atom transfer in DNA base pairs to ecosystems
Mar 2, 2016  RNA mediated molecular epigenetics and virus driven entropy
Mar 30, 2016 What is life when it is not protected from virus driven entropy
May 3, 2016  RNA-mediated physics, chemistry, and molecular epigenetics

Not only did Telepresence robots let employees ‘beam’ into work (December 24, 2012), telecommuting established my ability to disseminate accurate information about biophysically constrained biologically-based cause and effect to those who want to inform themselves. After I learned about microRNAs during the 2012 Society for Neuroscience annual meeting, I did not waste anymore time or money attending scientific conferences. It became perfectly clear that biologically uninformed theorists ignored the facts that link the creation of energy-dependent microRNAs to healthy longevity — if only because I had never heard of them.

During the past 21 months, others have either learned nothing about microRNAs or they have ignored the fact that virus-driven energy theft is not the same as energy dissipation in the context of food energy (the quantized energy as information that is used by viruses to create the amino acid substitutions that stabilize their RNA and DNA.

See for comparison: Quantum secret sharing for a multipartite system under energy dissipation!

Only the virus-driven theft of quantized energy has been linked to all pathology in all living genera.

That fact makes this fact perfectly clear. Scientific progress toward the prevention or effective treatment of all pathology has been delayed at every level of examination by theorists. See for example:

 Complex Mutations can Help Drive Evolution

“This study is the first of its kind in complex organisms like the fruit fly. With this unique resource in hand, we have already characterized several candidate structural variation which show evidence for phenotypic adaptation, which can function to drive species evolution,” explained Emerson.

Species do not evolve. Natural selection for energy-dependent codon optimality links food energy from ecological variation to fixation of RNA-mediated amino acid substitutions in organized genomes via DNA repair. The RNA-mediated DNA repair is evidence of how organisms phenotypically adapt.
Food odors and pheromones biophysically constrain ecological adaptations in species from mice to humans. That fact was established via the works of people such as Eugene Daev, who used experimental evidence of biophysical constraints in their refutation of neo-Darwinian pseudoscientific nonsense.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See also: Size matters – the olfactory bulb as a marker for depression (2017)

We assume that reduced neural olfactory input to subsequent limbic and salience processing structures moderates this relation. However, the OB was in an inferior position compared to conventional questionnaires for diagnosis of depression.

Despite two decades of scientific progress, the authors assume that the link between olfaction and emotion processing structures may not be as strong in humans compared to mice. They are either biologically uninformed, or they are lying. In either case, serious scientists do not base their claims on ridiculous assumptions. There may be no serious scientists who have ever worked with Thomas Hummel.
See: Hummel T and microRNA
See for comparison: The tipping point (revisited): 68,000 publications
See also: Feedback loops link odor and pheromone signaling with reproduction (2005) and Olfaction Warps Visual Time Perception (2017)
Attacks on my scientific credibility by Nik Wilmore, who claims these credentials Chemist (Columbia/Harvard), can be linked to this Historical Perspective as the obvious basis for social media attacks by biologically uninformed chemists and other theorists:
A fear of pheromones (1971)

WHAT are we going to do if it turns out that we have pheromones? What on earth would we be doing with such things? With the richness of speech, and all our new devices for communication, why would we want to release odors into the air to convey information about anything? We can send notes, telephone, whisper cryptic invitations, announce the giving of parties, even bounce words off the moon and make them carom around the planets. Why a gas, or droplets of moisture made to be deposited on fenceposts?

Similarly, what are we going to do if it turns out that food odors are the link from quantum physics to quantum souls, and that only pheromones biophysically constrain the virus-driven entropy of organized genomes?
Let food be thy medicine and medicine be thy food.” ― Hippocrates
There are in fact two things, science and opinion; the former begets knowledge, the latter ignorance.” ― Hippocrates
Declare the past, diagnose the present, foretell the future.” ― Hippocrates
Wherever the art of Medicine is loved, there is also a love of Humanity. ” ― Hippocrates
Wherever Money is loved, it is loved more than the Art of Medicine and more than Humanity. ― James V. Kohl
See Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Reported as: Past 5,000 years prolific for changes to human genome

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

Only if you ignore everything that could be learned about cell biology by playing the game “Cytosis,” could you continue to believe in the ridiculous theories of “Big Bang” cosmologists and neo-Darwinian theorists.

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

Darwin’s “conditions of life” and Kohl’s Laws of Biology attest to the fact that food energy-dependent RNA-mediated DNA repair biophysically constrains viral latency. Changes in the diet lead to ecological variation or from virus-driven energy theft to mutation-driven pathology.
The only recommended use for the term evolution is in the context of the evolution of virus-driven pathology.
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.

See for comparison: Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

We provide a high-resolution cryo-EM structure of a virus-ICAM-1 complex, which revealed critical ICAM-1-binding residues. These data could help identify a possible conserved mode of receptor engagement among ICAM-1-binding enteroviruses and rhinoviruses. Moreover, we identify a single capsid substitution that has been adopted by all pandemic CV-A24v strains and we reveal that this adaptation enhances the capacity of CV-A24v to bind sialic acid. Our data elucidate the CV-A24v receptor repertoire and point to a role of enhanced receptor engagement in the adaptation to the eye, possibly enabling pandemic spread.

The theft of quantized energy as information is linked to the adaptation of the virus. The creation of sunlight an its contract with water typically links the anti-entropic virucidal effects of the sun’s energy from food energy and the pheromone-controlled physiology of reproduction to fixation of amino acid substitutions in the organized genomes of all living genera. If Baggen et al., (2017) Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus was an accurate representation of how viral latency is biophysically constrained, the experimental evidence could help others to maintain their mental health.
See: Avoiding spiritual struggles and existential questions is linked with poorer mental health

Among the study’s findings:

  • An unwillingness to accept spiritual struggle could contribute to major social ills, leading to lost opportunities to engage with people of different faith beliefs and backgrounds and come to view them as threatening.

“This avoidance may lead to the rejection of whole groups of people based on their religious differences or perceived incongruence between, for example, their sexuality or gender-based identity and religious teachings,” Exline said.

  • Mental health providers may find it useful to help clients with spiritual struggles face their difficulties in a more proactive way.

“People seem to be more emotionally healthy if they’re able to accept troubling thoughts,” Exline said. “Looking at spiritual doubts in an objective way seems to help. You may or may not work through them, but at least you can tolerate having them.”

  • Avoidance itself is not a problem; rather, the behavior can become problematic when escaping becomes harmful or contrary to personal goals and sets a rigid pattern of experiencing and responding to the world.

“Regular spiritual avoidance can make it difficult to identify, work toward or experience the qualities that lend a sense of purpose to life,” she said.

  • Using emotional and cognitive energy to push thoughts away will not stop them from continuing to intrude over time.

“Continually being re-visited by these thoughts can create strains on emotional health, especially if a person sees this kind of questioning as morally unacceptable and dangerous,” Exline said.

See for comparison: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone

Dose of TRH is 200 μg and can be given once in a day. In the present study, an attempt has been made to prepare nasal spray of TRH by optimizing its pH, viscosity, osmolality and formulation parameters for use in crisis management.

The optimization of pH is essential in the context of prevention and all treatments that act on the potential of hydrogen. I don’t know of anything in life that does not act on the potential of hydrogen in the context of hydrogen-atom transfer in DNA base pairs in solutuon..
See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene

Together, these results provide an in-depth analysis of miRNA dysregulation in glioblastoma and demonstrate the potential utility of these data in the design of miRNA-regulated therapies for the treatment of brain cancers.

Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer’s disease

See also: Lack of sleep boosts levels of Alzheimer’s proteins December 28, 2017
In the study, people who took sleep medication had levels of amyloid beta no lower than people who had slept normally.
See for comparison: microRNA Alzheimer’s 
See also: Blind Loyalty – Why Civil Discourse is Dead October 14, 2017

The more we are tied to something, the stronger our reaction to it. I believe this is the problem with modern politics. We, both sides, have become so tied to our ideals that we cannot have a rational discussion about anything that goes against them.

The politicized practice of medicine prevents recognition of the facts established by serious scientists. For example, the innate antiphage defense system protects all organized genomes from virus-driven entropy via autophagy. That fact was placed into the context of the cell biology game Cytosis.
See also the discussion of Mitochondrial metabolite linked to regulation of neurotransmission

Pat Sweeney I am beginning to think that the genes in the mitochondria that direct the assembly of some of the necessary factors for nerve firing, are in cell types that have not had enough time to evolve or move the genes to the nucleus yet. Other cell types have had enough time to evolve or duplicate the mitochondrial genes into the cell genome and mutate them out of the mitochondrial genome.
Mitochondrial Genes Move to the Nucleus — but it’s not for the sex. The loss of endosymbiont genes can be complete, in which lost genes are absent from the host–endosymbiont complex, a substitution, in which a nuclear allele functions in place of the lost symbiont gene, or a functional transfer of an endosymbiont gene to the nucleus, followed by its loss (Adams and Palmer 2003). Such “functional transfer” involves the relocation of a mitochondrial gene to the nucleus, its acquisition of a promoter, successful targeting to the mitochondria for proper function, and the eventual loss of the gene from the mitochondrial genome altogether. Although this process is probably quite complex and requires numerous evolutionary modifications (Murcha et al. 2005), there is evidence that some mitochondrial genes are preadapted to functional transfer as they contain signals that target them to the mitochondria before functional transfer to the nucleus (Ueda et al. 2008a).
He cited: The Functional Transfer of Genes From the Mitochondria to the Nucleus: The Effects of Selection, Mutation, Population Size and Rate of Self-Fertilization (2009)
and Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade (2013)

My response:

I am beginning to think that some people still do not realize that cell types do not evolve. But now, Pat Sweeney makes claims that differentiate the terms “evolve or duplicate” from phrases such as “mutate them out of the mitochondrial genome” and “evidence that some mitochondrial genes are preadapted.”

The preadaptations are quantized energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction. There is a model for that.

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

There is still no mathematical model of biologically-based cause and effect for comparison, which is why all serious scientists are laughing at the pseudoscientists who still tout “evolution” as an explanation for cell type differentiation in different species that must eat to reproduce.
See for comparison: Impaired mitochondrial β-oxidation in cardiomyocytes: role of the cardiac renin-angiotensin system and miR-208 Wednesday, January 24, 2018
In this webinar we will discuss [facts]:

  • Analysis of mitochondrial function in cardiomyocytes using Agilent Seahorse XF technology
  • Application of mito stress test, glycolysis stress test and palmitate oxidation assays in HL-1 cardiomyocytes
"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Science vs Secularism: Molecular Mechanisms or Math?

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

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

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

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

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

See: Cytosis: A Cell Biology Board Game

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Apologetics:Indiana Banks and the Tablet of Trig

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

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

See also: Olfaction Warps Visual Time Perception

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

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

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

See:Evolutionary Rewiring

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

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

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

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

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

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

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

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

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

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

Physiology is rocking the foundations of evolutionary biology

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

 
 
 

Biology to a Physicist

Measuring energy vs human idiocy (social science)

Summary:
The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the energy-dependent assembly of cell types with fixed amino acid substitutions that link natural selection for energy-dependent changes in base pairs from atoms to ecosystems in all living genera.

Richard Feynman complains about all the different units that are used to measure the single concept of Energy in this snippet  from one of his lectures in the series “The character of Physical Law.”

For an example of how the anti-entropic virucidal energy of sunlight can be measured and linked to the creation of microRNAs, see: Universal Ratiometric Photoelectrochemical Bioassay with Target-Nucleotide Transduction-Amplification and Electron-Transfer Tunneling Distance Regulation Strategies for Ultrasensitive Determination of microRNA in Cells

…using microRNA-141 (miRNA-141) as target model, the constructed biosensor demonstrated favorable accuracy and excellent sensitivity down to femtomolar level. Impressively, the proposed assay overcame the heavily dependence of target on photoactive materials in current ratiometric PEC assay, and demonstrated admirably universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins by merely two different photoactive materials

The “… universal applicability for determination of various targets such as metal ions, miRNAs, DNAs and proteins…” is the key to understanding the differences in the food energy-dependent assembly of cell types with fixed amino acid substitutions that link changes in base pairs from atoms to ecosystems in all living genera.
There is a model for that: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See for comparison: A step-by-step microRNA guide to cancer development and metastasis

We propose that the balance between oncogenic versus tumor suppressive miRNAs acting within transcription factor-miRNA regulatory networks, influences both the multistage process of neoplastic transformation, whereby normal cells become cancerous, and their stress responses.

See for comparison: Feynman on social science
See also: Quantum common sense

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

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All of "like kind" in the (bigger) family (2)

See first: All of “like kind” in the (bigger) family

Excerpt:

Researchers who want to understand why the changes occur should be among the first to examine how fixation of the amino acid substitutions occurs in the DNA of organized genomes. For example, fixation of amino acid substitutions appears to occurs via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man.

Instead SICB dictator Billie Swalla and her co-authors made a ridiculous claim. How could their data support the null hypothesis of evolution in ctenophores, when they seem to claim evolution somehow occurred outside the context of the biophysically constrained chemistry of protein folding?

See also: First living example of giant ancient mollusc found in the wild

The giant shipworm is the world’s longest bivalve and the only known extant species of its genus. Unlike other shipworm species that typically burrow into and eat driftwood, the giant shipworm inhabits organic rich, noxious mud and doesn’t seem to feed much at all. Instead it relies on symbiotic bacteria in its gills.

“Bacterial symbionts have been cropping up in various bivalve families,” says John Taylor at London’s Natural History Museum, who was not a member of the expedition. “It’s only since the early 1980s that we recognised that bivalves have bacterial symbionts at all.” Finding them in the family that K. polythalamia belong to as well expands this relationship.

The bacteria break down the mud’s hydrogen sulfide, which give the shipworm’s habitat a distinct rotten egg smell, and produce organic carbon, feeding their host. The shipworm is so reliant on the bacteria that many of its internal digestive organs have shrank from lack of use.

Experimental evidence of biologically-based cause and effect link bacterial symbionts from survival of virus-driven messenger RNA degradation to all biodiversity via the physiology of pheromone-controlled reproduction.
4/22/17 Billie J. Swalla April 22 at 10:25am

It’s Earth Day today, and I am joining the Seattle March for Science. This is to remind our leaders that science is an important way of understanding the world and should be funded and used to make good decisions about the future. I am marching for a better world for everyone, through informed decisions and policies that protect the Earth for future generations. I march for my family, my granddaughters, students and researchers around the globe. I march for the ocean and the mountains, and the prairies. I march for humanity and love for all the people on Planet Earth!

Billie J. Swalla, and others like her, marched in an attempt to support ridiculous theories about evolution that have been replaced with facts about energy-dependent biophysically constrained RNA-mediated cell type differentiation in all living genera.
See who else is living in the dark ages compared to what is known to serious scientists about energy-dependent protein folding chemistry and supercoiled DNA.
The ctenophore genome and the evolutionary origins of neural systems

…we were unable to experimentally detect microRNAs…

Absence of experimental evidence is not evidence of absence, and no experimental evidence links anything except microRNAs from ecological variation to ecological adaptation in all living genera. The failure to detect microRNAs is no excuse for continuing to tout ridiculous theories about evolution.
See for comparison: The phylogenetic utility and functional constraint of microRNA flanking sequences

Conclusion
Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes. Such alignments exhibit strong conservation across populations, which can add utility for inference of relationship above the species level, but limits the use of miRNA sequences for biogeographic inference. Despite historic issues regarding their use for phylogenetic inference [8], miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here. Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages. Such a method provides novel characters for assessing phylogenetic relationships that will be of use in a range of contexts for resolving branches across the tree of life.

Re: biogeographic inference
See also: Virus-mediated archaeal hecatomb in the deep seafloor

…viral infections can be one of the main drivers of chemoautotrophic production in deep-sea sediments…

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.

No biogeographic inference was made in the context of global biogeochemical cycles. Bacterial symbionts in shipworms were linked from their nutrient energy-dependent survival in ocean sediments, which clearly shows that all extant species are survivors of virus-driven messenger RNA degradation. Survival is biophysically constrained via the physiology of pheromone-controlled reproduction, which can readily be linked to all biodiversity on Earth in organisms that must find food to reproduce.

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Epigenetically-effected nucleosome repositioning sheds Dobzhansky's light on evolution

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

My summary: Nucleosomes are dynamic entities that are repositioned by energy-dependent links from sunlight to ATP and RNA biosynthesis that act on DNA during the chromatin remodeling, which is biophysically constrained by the pheromone-controlled physiology of reproduction during the transgenerational epigenetic inheritance of all morphological and behavioral phentoypes. processes.

Reported as: Unveiling how nucleosome repositioning occurs to shed light on genetic diseases

…an incomplete formation of overlapping dinucleosome may trigger abnormalities in the genetic switch, turning normal cells into tumor cells. Accordingly, understanding the atomic structure of the overlapping dinucleosome may provide valuable information for understanding how the abnormal dynamics of chromatin are related to cancer…

The atomic structure of the dinucleosome is energy-dependent. The atomic structure links the sun’s anti-entropic virucidal energy to all healthy longevity via endogenous RNA interference (RNAi). RNAi is is the nutrient energy-dependent link from atoms to ecosystems via what is known to all serious scientists about supercoiled DNA. Virus-driven energy theft causes the incomplete formation of the overlapping dinucleosome and all pathology in all living genera.
See for comparison my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

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.

See also: Structural diversity of supercoiled DNA and the parody from the Zechiedrich lab.

Nothing in Biology Makes Any Sense Except in the Light of Evolution

…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.

Combating Evolution to Fight Disease

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Feedback loops link odor and pheromone signaling with reproduction
Roles of differential expression of microRNA-21-3p and microRNA-433 in FSH regulation in rat anterior pituitary cells

Taken together, our results show that both miR-21-3p and miR-433 down-regulate FSHb expression and cause FSH secretion decreased. These findings provide insights into the effects of the regulatory mechanisms of miRNAs on the reproductive functions of the pituitary.

FSH secretion links the nutrient energy-dependent pheromone-controlled epigenetic effects on endogenous RNA interference to healthy longevity and biodiversity in all vertebrates via the substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
See also: Gonadotropin releasing hormone and human sexual behavior (1991)

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s   (2/21/17)

…mice with Alzheimer’s have a different gut bacterial profile than those that do not have the disease.


 

terrarium-eco-system

George Church refutes theistic evolution (3)

Fifty years of illumination about the natural levels of adaptation

… George C. Williams developed in his 1966 book Adaptation and Natural Selection the essentials of a unifying theory of adaptation that remains robust today and has inspired immense progress in understanding how natural selection works.

Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

See also: George Church refutes theistic evolution and George Church refutes theistic evolution (2)
Why did so many pseudoscientists fail to link ecological variation to ecological adaptation via natural selection for energy-dependent changes in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy? Why have they continued to tout ridiculous theories for comparison to what is being reported about adaptation by serious scientists. Almost every day there is something old reported as if it was new information to be considered before it is again ignored by theorists.
See for examples from this past week:
Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Interplay between miRNAs and Human Diseases: A Review
400 pilot whales stranded on New Zealand’s ‘whale trap’ beach

Other factors include whales’ incredibly tight social bonding, which is especially strong within groups of pilot whales.
 
Social bonding is nutrient energy-dependent and controlled by the physiology of reproduction. In species from microbes to humans, the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones.
 

Rather than tout theories about solar storms and geographical traps, serious scientists investigate the facts that link the sun’s anti-entropic virucidal energy to endogenous RNA interference via olfaction and the innate immune system. Serious scientists link food odors and pheromones to behavior in all living genera.

2005 Feedback loops link odor and pheromone signaling with reproduction

2015 Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Ecological variation that is not manifested in ecological adaptation links virus-driven energy theft to the stranded whales. The energy theft prevents nutrient energy-dependent ecological adaptation. Unfortunately, theorists do not understand any aspect of natural selection for energy-dependent codon optimality.The prefer to use definitions and assumptions for comparison to the experimental evidence of biologically-based cause and effect that serious scientists must use in the context of their religion.

Pseudoscientists claim that atheism is not a religion. Atheism is a religion by definition.

See: atheism

  1. 1a :  a lack of belief or a strong disbelief in the existence of a god or any godsb :  a philosophical or religious position characterized by disbelief in the existence of a god or any gods

See for comparison:  How an obscure oriental cult in a corner of Roman Palestine grew to become the dominant religion of the Western world
Even historians know that the history of a religion can influence the faith of believers today. For example, atheism today arose in the context of de Vries 1902 definition of “mutation” and acceptance of assumptions that accumulated mutations could lead from natural selection to the evolution of one species from another species.

Christianity can clearly be linked from events that start from the creation of energy as information in Biblical Genesis to the weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces with exposure to UV light.

Atheism as a religion cannot stand up to the overwhelming amount of experimental evidence that supports claims in the Old Testament, which were linked to claims in the New Testament. There is nothing that appears to link the emergence of everything from nothing or the evolution of one species from another. That fact links three more definitions to all biodiversity on Earth.

The emergence of atheism as a world religion can now be placed into the context of definitions that recently were added to the Merriam-Webster dictionary.

Phytoremediation

the treatment of pollutants or waste (as in contaminated soil or groundwater) by the use of green plants that remove, degrade, or stabilize the undesirable substances (such as toxic metals)

CRISPR

The CRISPR segment encodes, via transcription, short RNA sequences that pair with complementary sequences of viral DNA. The pairing is used to guide an enzyme to cleave the viral DNA and prevent further infection.

 Microbiome

  1. 1 :  a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body <Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. — Carl Zimmer> < … what’s arguably become the hottest area of medicine: microbiome research, an emerging field that’s investigating how the bacteria that live in and on our bodies affect our health. — Sunny Sea Gold>
    1. 2 :  the collective genomes of microorganisms inhabiting a particular environment and especially the human body <They form one community among the many that make up the human microbiome: the full genetic complement of bacteria and other organisms at home on your skin, gums, and teeth, in your genital tract, and especially in your gut. — Nathan Wolfe>

The definitions that were recently added to the Merriam-Webster dictionary link the energy-dependent pheromone-controlled physiology of reproduction in bacteria from the National Microbiome Initiative to the Precision Medicine Initiative via endogenous RNA interference, which prevents the virus-driven energy theft that links mutations to all pathology.

For comparison, see: How algorithms (secretly) run the world

“Algorithms are not inherently fair, because the person who builds the model defines success,” she said.
See also: Digital Star Chamber

Following the advice of Jeff Jarvis’s What Would Google Do, they are collecting data from both workers and customers, using algorithmic tools to make decisions, to sort the desirable from the disposable.

What would Jesus do about the use of algorithms to predict outcomes?

Algorithms can be made more accountable, respecting rights of fairness and dignity for which generations have fought. The challenge is not technical, but political, and the first step is law that empowers people to see and challenge what the algorithms are saying about us.

Did Jesus know the creation of energy and virus-driven energy theft are predictable links to outcomes that pseudoscientists think can be linked via algorithms? Did He ever mention the fact that pseudoscientists might be called theorists by serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about the physiology of reproduction and the functional structure of supercoiled DNA.

See for example: Structural diversity of supercoiled DNA
The functional structure of supercoiled DNA links what organisms eat to endogenous RNA interference and the physiology of reproduction, which links chromosomal inheritance from chirality to autophagy and all biodiversity on Earth. That cannot be done with definitions and/or algorithms.

See also: microRNA
How will you continue to avoid discussing the energy-dependent link from nutrient-dependent changes in the microRNA/messenger RNA balance to all healthy longevity, as everything known about virus-driven energy theft continues to be linked to all pathology?