Similar analysis of a cervical carcinoma (HeLa), fibrosarcoma (HT1080), and an Epstein-Barr virus (EBV)-transformed lymphoblastoid line (EBV-L) revealed that all three ANT isoforms were also expressed in these cells. Hence, changes in the expression of OXPHOS genes may be a common feature of transformed cells.
Did he not recognize the significance of the energy-dependent transformation of adenine (in the context of the adenine nucleotide translocator) and oxidative phosphorylation (OXPHOS) genes?
Did Douglas C. Wallace introduce the world to the pervasive nature of the first biologically-based Sokalian hoax, which was subsequently used to bastardize everything known to serious scientists about molecular epigenetics?
Is that how you become a corporate “Champion of Science?”
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)
Why isn’t Bruce McEwen a corporate “Champion of Science” in the context of his claims about the food energy-dependent creation of RNA via a type of “oxidative phosphorylation?”
When will so-called science journalists realize the difference between a serious scientist like Bruce McEwen and a pseudoscientist like Douglas C. Wallace?
Simply put, the difference is in their approach to explaining how biophysically constrained energy-dependent changes in base pairs are linked from fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types. In all living genera, fixation of RNA-mediated amino acid substitutions occurs in the context of the physiology of pheromone-controlled reproduction, which links feedback loops to all biodiversity.
People like Douglas C. Wallace claim that “evolution did it.” Serious scientists put his ridiculous claim into the context of experimental evidence of biophysically constrained energy storage.
See: Long-range coherence and energy storage in biological systems (1968)
Energy storage begins with the creation of energy and ends with the virus-driven degradation of messenger RNA that links mutations to all pathology. How many more victims of Sokalian hoaxes will there be? Who will help to prevent the next viral apocalypse? Will it be the “Trump Administration?”
I think that fact is obvious.
See: Double-layered protein nanoparticles induce broad protection against divergent influenza A viruses
The amino acid sequence of influenza matrix protein 2 ectodomain (M2e) is highly conserved among human seasonal influenza A viruses20.
“Vaccination is the most effective way to prevent deaths from influenza virus, but the virus changes very fast and you have to receive a new vaccination each year,”
Exosomes regulate cell-cell communication by transferring functional proteins and RNAs between cells. Here, to clarify the function of exosomes during influenza virus infection, we characterized lung-derived exosomal microRNAs (miRNAs).
MicroRNAs (miRNAs), as a major player in post-transcriptional regulation of gene expression, have been reported to regulate a broad variety of key biological processes, including growth, development and stress responses in both plants and animals. While the biogenesis and regulatory abilities of miRNAs have been extensively studied, the evolutionary history of miRNAs still needs more exploration. So far, several models explain the origination of plant and animal MIRNA (MIR) genes. Both inter-species and intra-species conservation and divergence of miRNAs exhibits functional adaptation to changing environments in evolution. Here we summarize recent progress in how these similarities and differences contribute to the characteristic features of miRNA evolution in the two kingdoms.
To understand why organisms look the way they do we need models that involve physical forces as well as biological variables, organised to produce organisms with specific morphologies, as described in my book, How the Leopard Changed its Spots.
In a critical review, biologist Catherine S. C. Price noted that although he had succeeded in providing an alternative to mutation as the only source of variation, he failed to provide an alternative to natural selection as a mechanism of adaptation.[7]
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).
…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.
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)
…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…
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.
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].
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
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.
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:
“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.
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?
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.
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.
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.
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.
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.
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 SweeneyI 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).
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.
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-208Wednesday, 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
Summary: Epigenetic mechanisms did not evolve. DNA methylation is food energy-dependent and RNA-directed. Phenotypes are not fixed by genetics. The food energy-dependent RNA-directed DNA methylation of all organized genomes is biophysically constrained by the metabolism of food to pheromones, which control the physiology of food-dependent reproduction.
On the day after he posted content on the refutation of Karl Popper’s nonsense and the pseudoscientific nonsense touted in every aspect of neo-Darwinian theory, antagonist Jay Feierman posted this to the Human Ethology group:
DNA methylation is involved in gene regulation, silencing of transposons, imprinting, polyphenism, and consolidation of speciation. It may even act as a driver of evolution via stochastic developmental and environmentally induced epigenotype diversification, transgenerational inheritance of epigenetic patterns with phenotypic effects, and differential selection and genetic fixation of these phenotypes.
Epigenetic mechanisms did not evolve. DNA methylation is food energy-dependent and RNA-directed. Phenotypes are not fixed by genetics. The food energy-dependent RNA-directed DNA methylation of all organized genomes is biophysically constrained by the metabolism of food to pheromones, which control the physiology of food-dependent reproduction. Food and pheromones typically biophysically constrain all virus-driven pathology. That allows ecological variation to be linked to ecological adaptation via transgenerational epigenetic inheritance in species from microbes to humans. See: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
Simply put, increasing complexity does not automagically evolve. It is biophysically constrained by what organisms eat (i.e., food energy.)See also: RNA-mediated epigenetic regulation of gene expression
Jay Feierman‘s efforts to prevent the dissemination of accurate information about biophysically constrained biologically-based food energy-dependent RNA-mediated cause and effect have led to the unnecessary suffering and premature death of millions during the past 2 decades since I personally presented to him (at a conference) the model that has since been linked to all healthy longevity in all species. (His only question was “What about birds?”)
Rarely have I seen anyone display the lack of regard for biodiversity and for human life that Jay Feierman has included in his examples of “human idiocy.” His posts about the “Evolution of Epigenetic Mechanisms” and posts about the evolution of anything else should long ago have been the “last straw” for all serious scientists. And yet, it seems that no one can stop people like Jay Feierman.
For comparison, the late Charles Manson supposedly claimed: “I am the devil.” If true, in my opinion, another devil is alive and well and his name is Jay Feierman.
Search this domain for: RNA-directed DNA methylation or for RNA-mediated DNA methylation to find hundreds of blog posts that appear to attest to the devilish treachery of people like Jay R. Feierman. If you find one blog post that does not attest to his human idiocy and his treachery, please let me know. I may owe him an apology.
See also, this Google search: RNA mediated, which attests to the facts about why this is currently the top-ranked domain.
Feierman’s other posts to the Human Ethology Group on 11/20/17 include:
Formal Epistemology and Cartesian Skepticism: In Defense of Belief in the Natural World Eleven Telomere, Epigenetic Clock, and Biomarker-Composite Quantifications of Biological Aging: Do They Measure the Same Thing? Give one species the task to come up with a theory that spans them all: what good can come out of that? A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee Variability in Fitness Effects Can Preclude Selection of the Fittest Does it always pay to defend one’s nest? A case study in African penguin
Throughout the animal kingdom, individual variation in reproductive success is commonly observed, even under similar environmental conditions. However, the mechanisms behind such differences remain unclear.
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.
For comparison, see the comment by Jay R. Feierman on my model:
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.
No one has ever attempted to refute Darwinian evolution. Darwin reasserted the claim that others must start with his “conditions of life.” They are nutrient-dependent and pheromone-controlled. Anyone who has ever started with natural selection is as foolish as Darwin knew they would be.
In “Advancing Techniques Reveal the Brain’s Impressive Diversity,” Rusty Gage and two of his postdocs, Sara Linker and Tracy Bedrosian, describe nonvisual methods for delving ever deeper into neurons—analyzing not just what you see, but what you get by performing genome sequencing and transcriptional, posttranscriptional, posttranslational, and epigenetic analyses on single cells.
My comment:
The virus-driven degradation of messenger RNA has been linked to the destruction of all food energy-dependent pheromone-controlled biophysically constrained ecosystems in species from microbes to humans.
But Researchers reveal new details on aged brain, Alzheimer’s and dementia
only recently
…revealed a surprising relationship between dementia and decreased quality of RNA—a key player in gene expression—in the more aged brain.
Obviously, something has gone horribly wrong. Serious scientists can now simply recommend that everyone older than 10 play the game Cytosis.
A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Anyone older than 10 can then dismiss the claims of people like Rusty Gage about ecology and simply link what organisms eat from ecological variation to ecological adaptation via the physiology of pheromone-controlled reproduction, or link the virus-driven degradation of messenger RNA from mutations to all pathology.
The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour. More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay.
They don’t understand the question that Schrodinger answered. He linked the anti-entropic virucidal energy of sunlight to the physiology of pheromone-controlled reproduction via what organisms eat. What they eat protects them from the virus-driven degradation of their messenger RNA. What they eat links food energy-dependent changes in base pairs from microRNA editing to RNA editing and fixation of RNA-mediated amino acid substitutions in organized genomes of all individuals of all living genera.
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.
Life that is not protected from the virus-driven degradation of messenger RNA links the reduced number of food energy-dependent microRNAs to activation of the death gene. See for example:
The natural contribution of food energy is linked to the endogenous level of microRNA expression seen in neuronal cells in the context of limited cell death compared control glioblastoma cells. That fact was linked to the treatment of brain cancers.
For a review of how food energy-dependent microRNAs protect the organized genomes of all living genera from the virus-driven degradation of messenger RNA that links mutations to all pathology, see:
One factor that is not always taken into account when studying gene expression in the aged brain is the quality of the genetic material itself,” says Miller. “This variable is not necessarily related to any specific pathology or disease, but these results highlight the importance of properly controlling for RNA quality when studying the aged brain and indicate that degradation of genetic material may be an underappreciated feature of neurodegeneration or dementia.
Re: degradation of genetic material may be an underappreciated feature of neurodegeneration or dementia.
….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’.
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. 7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
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.
Review article: Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley, Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja
Phil. Trans. R. Soc. B December 19, 2017 372 20160455; doi:10.1098/rstb.2016.0455
http://rstb.royalsocietypublishing.org/content/372/1736/20160455
Review article: The impact of recombination on human mutation load and disease
Isabel Alves, Armande Ang Houle, Julie G. Hussin and Philip Awadalla
Phil. Trans. R. Soc. B December 19, 2017 372 20160465; doi:10.1098/rstb.2016.0465
http://rstb.royalsocietypublishing.org/content/372/1736/20160465
Opinion piece: Connecting theory and data to understand recombination rate evolution
Amy L. Dapper and Bret A. Payseur
Phil. Trans. R. Soc. B December 19, 2017 372 20160469; doi:10.1098/rstb.2016.0469
http://rstb.royalsocietypublishing.org/content/372/1736/20160469
Review article: Coevolution between transposable elements and recombination
Tyler V. Kent, Jasmina Uzunović and Stephen I. Wright
Phil. Trans. R. Soc. B December 19, 2017 372 20160458; doi:10.1098/rstb.2016.0458
http://rstb.royalsocietypublishing.org/content/372/1736/20160458
Review article: Evolution of recombination rates between sex chromosomes
Deborah Charlesworth
Phil. Trans. R. Soc. B December 19, 2017 372 20160456; doi:10.1098/rstb.2016.0456
http://rstb.royalsocietypublishing.org/content/372/1736/20160456
Research article: Low recombination rates in sexual species and sex–asex transitions
Christoph R. Haag, Loukas Theodosiou, Roula Zahab and Thomas Lenormand
Phil. Trans. R. Soc. B December 19, 2017 372 20160461; doi:10.1098/rstb.2016.0461
http://rstb.royalsocietypublishing.org/content/372/1736/20160461
(openaccess) Review article: The consequences of sequence erosion in the evolution of recombination hotspots
Irene Tiemann-Boege, Theresa Schwarz, Yasmin Striedner and Angelika Heissl
Phil. Trans. R. Soc. B December 19, 2017 372 20160462; doi:10.1098/rstb.2016.0462
http://rstb.royalsocietypublishing.org/content/372/1736/20160462
(openaccess) Research article: The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Thibault Latrille, Laurent Duret and Nicolas Lartillot
Phil. Trans. R. Soc. B December 19, 2017 372 20160463; doi:10.1098/rstb.2016.0463
http://rstb.royalsocietypublishing.org/content/372/1736/20160463
(openaccess) Research article: Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Josep M. Comeron
Phil. Trans. R. Soc. B December 19, 2017 372 20160471; doi:10.1098/rstb.2016.0471
http://rstb.royalsocietypublishing.org/content/372/1736/20160471
(openaccess) Review article: Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison, Stephen Sefick, Chase Rushton and Rita M. Graze
Phil. Trans. R. Soc. B December 19, 2017 372 20160459; doi:10.1098/rstb.2016.0459
http://rstb.royalsocietypublishing.org/content/372/1736/20160459
(openaccess) Review article: Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?
Christopher H. Morgan, Huakun Zhang and Kirsten Bomblies
Phil. Trans. R. Soc. B December 19, 2017 372 20160470; doi:10.1098/rstb.2016.0470
http://rstb.royalsocietypublishing.org/content/372/1736/20160470
Research article: What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling
Sviatoslav R. Rybnikov, Zeev M. Frenkel and Abraham B. Korol
Phil. Trans. R. Soc. B December 19, 2017 372 20160460; doi:10.1098/rstb.2016.0460
http://rstb.royalsocietypublishing.org/content/372/1736/20160460
Summary: All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.
See for comparison: 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.”
…indole, a molecule produced by commensal bacteria, extends “healthspan” not only in mice but in the nematode worm Caenorhabditis elegans and in fruit flies as well. Taking away the bacterial production of the molecule ablated these anti-aging gains.
Does anyone need to repeatedly be reminded that food energy is required for the production of any molecule associated with nutrient-dependent pheromone-controlled anti-aging gains? The epigenetically effected gains are consistently manifested in the survival of species via the physiology of reproduction.
The food energy-dependent production of indole is the obvious link from nutrient-dependent pheromone-controlled feedback loops to biophysically constrained viral latency and ecological adaptation in all living genera. Testing for indole is used to determine the ability of an organism to split (deaminate) the amino acid tryptophan. Indole contributes to fecal odor and it is a chemical messenger that has been indirectly or directly included in detailed representations of biologically-based pheromone-controlled energy-dependent cause and effect like these.
See: Feedback loops link odor and pheromone signaling with reproduction (2005)
There is a model for that! See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans biophysically constrains the virus-driven degradation of messenger RNA. That fact links constraint-breaking mutations to all pathology in all living genera. A test protocol established that fact in the context of this book chapter, which links the test for indole to differences in the microRNA/messenger RNA balance in humans.
For example, the test protocol links the creation of energy as information to all biodiversity via the physiology of reproduction and links the virus-driven degradation of messenger RNA to all pathology. The complexity of the testing can be reduced via the focus on the energy-dependent creation of microRNAs.
See the abstract:
Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety…
MicroRNAs are identified and monitored through the use of locked nucleic acid (LNA)™-based detection probes. The LNA™ technology enhances the sensitivity and specificity of target binding for short, highly similar, microRNA sequences, which help to differentiate cell types in the context of everything known to serious scientists about how to link physics and chemistry from molecular epigenetics to all biodiversity via fixation of RNA-mediated amino acid substitutions.
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.
There is no such thing as transgenerational epigenetic inheritance of morphological or behavioral phenotypes outside the context of feedback loops that link food odors from the metabolism to pheromones and biophysically constrained viral latency. The consumption of choline by bacteria links food energy to protection from viral latency via the test for indole. The virus-driven theft of quantized energy can be linked from reduced amount of choline that link viruses in the bacteria to their ability to overwhelm the immune system. The effects of virus-driven energy theft link the CRISPR-Cas9 technology of gene-editing to DNA repair via exogenous RNA-interference because energy-dependent endogenous RNA-interference protects all organized genomes from virus-driven entropy.
Corporate America is not willing to tell the truth about that. You will probably suffer unnecessarily and die prematurely because the goal of every corporation is to make more money.
Absent a war or an epidemic, it’s unusual and alarming for life expectancies in developed countries to stop improving, let alone to worsen. “Mortality is sort of the tip of the iceberg,” says Laudan Aron, a demographer and senior fellow at the Urban Institute. “It really is a reflection of a lot of underlying conditions of life.”
Darwin’s “conditions of life” were food energy-dependent. Serious scientists have since learned that all “conditions of life” also are fixed in the organized genomes of all living genera via the physiology of reproduction. Without the link from ecological variation to ecological adaptation via fixation of amino acid substitutions in supercoiled DNA, natural selection for energy-dependent codon optimality would link mutations to evolution instead of linking mutations to all pathology.
Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.
The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).
Addendum: Fish odor syndrome is the link from the virus-driven theft of quantized energy. The odor links ecological variation to failed ecological adaptation and all pathology when there is insufficient food energy. Any scientist who does not already know that based on the facts known to every medical laboratory scientist is an example of “human idiocy” (Feynman) or a biologically uninformed science idiot (Kohl).
Serious scientists have begun to effectively use energy-dependent microRNAs to the prevention of all virus-driven pathology. That fact is being reported in the context of gene therapy using ‘junk DNA’ at a time when all serious scientists realize there is no such thing as ‘junk DNA.’
The LeXis gene belongs to a unique group of genes that until recently were considered “junk DNA” because scientists believed they served little purpose. However, evidence from the human genome project led to the discovery that genes like LeXis are actually active. The study of these genes, now referred to as long noncoding ribonucleic acids, or lncRNAs, is a rapidly evolving area in biology.
Long noncoding (lnc) RNAs form the vast majority of transcriptionally active regions and are arbitrary defined as transcripts >200 bps that biochemically resemble mRNA and yet do not template protein.2
Diet and drug-induced changes in LeXis link energy as information to liver X receptor activation of genes via the “promoter binding of RNA-binding proteins.” That fact supports the claim that a transcriptional coactivator for genetically predisposed cholesterol biosynthesis in the mouse liver links promoters, enhancers, quantitative trait loci, et al., to the transciptional coactivator referred to as “Rally” without mention of energy-dependent changes in the microRNA/messenger RNA balance.
If you believe that the long noncoding ribonucleic acids (RNAs) are genes, you may be convinced that mutations in RNA are the same as mutations in genes. But mutations are the cause of all pathology. Linking mutations in RNA to pathology outside the context of energy-dependent healthy longevity allows others with no expertise in laboratory testing to continue to believe that mutation-driven evolution is the link from natural selection to the origin of new species. That belief is probably common among others who believe that the Universe itself may be conscious.
Subatomic is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic enabling players to pay energy to shuffle through their deck quicker, or to offset the cost of more powerful deck building cards.
We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking
The question arises: “Who needs this kind of nonsense?” Does anyone at any level of examination believe that “the Universe is always looking” is the best representation of what we can expect from a “Conscious Universe?”
A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy was reported on the Exiqon FB page. Exiqon is a biotechnology company that specializes in RNA products and services. I recommend that they purchase this domain (RNA-mediated.com) in an attempt to promote their products, which obviously link energy-dependent healthy longevity to all biodiversity and also link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.
See also: ‘Chromatin modifiers and remodellers in DNA repair and signalling’ The fact that food energy as information must be linked from ecological variation to ecological adaptation via the pheromone-controlled physiology of reproduction in all living genera appears to be the focus of this Theme issue.
But wait: Here is one of the articles from the Theme issue:
Nucleosome remodelling (NR) regulates transcription in an ATP-dependent manner, and influences gene expression required for development and cellular functions, including those involved in anti-cancer and anti-ageing processes. ATP-utilizing chromatin assembly and remodelling factor (ACF) and Brahma-associated factor (BAF) complexes, belonging to the ISWI and SWI/SNF families, respectively, are involved in various types of DNA repair.
McEwen et al., knew that “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” That statement of fact was the beginning of the abstract from 1964. When he told me my model could not be validated unless I started with energy-dependent gene activation in gonadotropin releasing hormone (GnRH) neurons, I had no reason to doubt him. When I learned that Robert L. Moss had already linked pheromones to energy-dependent gene activation in GnRH neurons, I continued to pursue top-down causation as if it was energy-dependent — because it obviously is energy-dependent.
I never considered that my model of food energy-dependent pheromone-controlled biophysically constrained gene activation would not be accepted by theorists. See for comparison:
We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity…
All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.
See for comparison: 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.
See for comparison: Quantum Biology: An Introduction (video) by Philip Ball and Quantum common sense
To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.
See also these restricted and unrestricted articles: ARTICLES
…too many analyses focus on correlational evidence while advocating a single explanation to the exclusion of all others; as a result, they rarely make serious attempts to integrate the various explanations (for all of which there is convincing evidence) into a single unitary explanatory framework.
…when God forbids the man to eat from that particular tree, he says that if he does so, he is “doomed to die”.
I am fascinated by the facts that link the Biblical metaphors from eating a virus-infected “fruit” to the death of everyone who will ever live and die. That fact can be placed into this context: 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.
ISH of biopsy material has become routine pathology procedure for monitoring gene expression and sample characterization. This could be of microRNAs which prove excellent as biomarkers for disease diagnosis, patient stratification and treatment efficacy.
A fast and robust microRNA ISH protocol well-suited for clinical biomarker studies has just been published in Methods Mol Biol using DIG or FAM double-labeled microRNA-specific LNA™-enhanced detection probes in formalin-fixed, paraffin-embedded (FFPE) tissue sections.
Monitoring gene expression and sample characterization via natrurally occuring microRNA biomarkers is the key to developing biomarkers for use in “…disease diagnosis, patient stratification and treatment efficacy.”
The microRNAs need only be linked from flanking sequences to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution and the physiology of reproduction, which links energy-dependent changes in the microRNA/messenger RNA balance from the fixation of amino acid substitutions in supercoiled DNA to protection from the virus-driven degradation of messenger RNA.
See: Optical control of membrane tethering and interorganellar communication at nanoscales
All the observed interactions seem to require the presence of at least two consecutive positively charged residues (‘KK’ or ‘KR’). Replacement of a single lysine with alanine in such dyad motifs could lead to pronounced reduction in puncta formation; whereas KK-to-AA substitutions often abrogate the PB-lipid/PM associations (Fig. 4 and S4†). Further structural studies on the interaction between PB domains and PIs will likely provide a definitive answer by pinpointing the exact molecular determinants.
The temporal and spatial control that connects subcellular compartments to interorganellar communication, which links energy-dependent changes from angstroms to ecosystems in all living genera is RNA-mediated and biophysically constrained by the pheromone-controlled physiology of reproduction. The temporal and spacial control is linked to our visual perception of mass and energy via the sense of smell in bacteria and RNA-mediated amino acid substitutions in the organized genomes of all living genera.
See also: Mechanism of metabolic puncta formation and its functional significance
Many metabolic enzymes have recently been shown to assemble into multi-component puncta in cells, and this assembly is though to play some role in controlling metabolic flux. For example, substrate channeling within these structures could play an important role in metabolism, enabling intermediates to be directly fed from one enzyme to another without dilution. Therefore the assembly of enzymes into these puncta could be an important mechanism for cells to manipulate their metabolism in response to different signals. However, the mechanism of formation of these puncta is completely unknown.
If the energy-dependent formation of these puncta was not known to be linked from differences in the microRNA/messenger RNA balance to the pheromone-controlled physiology of reproduction in all living genera, I could not have found the obvious link from food energy to all biodiversity in this PubMed search. puncta formation microRNA
For example, food energy is the obvious link from changes in chirality to autophagy. Autophagy protects all organized genomes from the virus-driven degradation of messenger RNA. Simply put, biophysically contrained energy-dependent autophagy protects all living genera from the mutations that serious scientists have linked to all pathology. See also: MicroRNA-141 Targets Sirt1 and Inhibits Autophagy to Reduce HBV Replication.
For comparison, see: “For the past century some people have regarded natural selection as “that secular God.” Now, that title belongs to CRISPR. “— Jay R. Feierman
Feierman has not learned that natural selection for energy-dependent codon optimality links a light-activated endogenous substrate from the innate immune system in bacteria: CRISPR, to the biophysically constrained physiology of pheromone-controlled reproduction in all living genera. That fact is proof of God’s energy-dependent Creation. The claim that the title of “secular God” belongs to CRISPR is as ridiculous as this claim. 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.
See also: 7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
CRISPR is the only obvious link from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the theft of quantized information that links mutations to all pathology via the degradation of messenger RNA.
See also: Your indifference is killing you and others (4)
At the time that Zilantophis dwelled there, the site was a sinkhole surrounded by forest, attracting a variety of animals. The local fauna included ancient representatives of familiar North American creatures such as bears, beavers and salamanders. Others were more exotic, including unique species of rhinoceros, alligator and the site’s famous red panda.
“This is a time when the world was moving in the direction of a modern climate and modern fauna,” Jasinski said.
How can humans be so compassionate and altruistic — and also so brutal and violent? To understand why we do what we do, neuroscientist Robert Sapolsky looks at extreme context, examining actions on timescales from seconds to millions of years before they occurred. In this fascinating talk, he shares his cutting edge research into the biology that drives our worst and best behaviors.
I did not learn anything about cutting edge research from this TED talk. I learned that Robert Sapolsky believes in the evolution of human behavior. That surprised me because Robert Sapolsky is one of the most famous students of Bruce McEwen, who linked a single amino acid substitution (BDNF Val66Met) from nutrient energy-dependent biophysically constrained biologically-based top-down causation to behavior in the dramatically different pheromone-controlled ecosystems of mice and humans.
See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.
The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”
Until Robert Sapolsky helps others to make sense of how the energy-dependent pheromone-controlled de novo creation of olfactory receptor genes is linked to differences in epigenetic effects that link sensory stimuli from hormones to the affects of hormones on animal behavior, his lectures will be of little use to those who study the biology of behavior.
In all vertebrates, the study of behavior begins with the epigenetic effects of food odors and pheromones on gene activation that link changes in microRNAs from gonadotropin releasing hormone to the physiology of reproduction. In the early 90’s, Bruce McEwen told me that my model of biologically-based cause and effect could not be validated unless I found experimental evidence that could be linked to gene activation in gonadotropin releasing hormone (GnRH) neurosecretory neurons.
The late Robert L. Moss provided preprints from his group that now link everything known about energy-dependent RNA-mediated cell type differentiation in all vertebrates to the pheromone-controlled physiology of reproduction in mice and in humans via amino acid substitutions.
The early gene expression of cFos has since linked the Fos protein to proof of the concept that links food odors and pheromones to all receptor-mediated behavior in all living genera via what is known about vertebrate GnRH.
See: Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males
See: A hypothalamic circuit that controls body temperature
…we used cFos staining to identify neurons that are activated by a thermal challenge and found induced expression in subsets of neurons…
Over a decade in the making, this game-changing book is Robert Sapolsky’s genre-shattering attempt to answer that question as fully as perhaps only he could, looking at it from every angle. Sapolsky’s storytelling concept is delightful but it also has a powerful intrinsic logic: he starts by looking at the factors that bear on a person’s reaction in the precise moment a behavior occurs, and then hops back in time from there, in stages, ultimately ending up at the deep history of our species and its genetic inheritance.
And so the first category of explanation is the neurobiological one. What goes on in a person’s brain a second before the behavior happens? Then he pulls out to a slightly larger field of vision, a little earlier in time: What sight, sound, or smell triggers the nervous system to produce that behavior? And then, what hormones act hours to days earlier to change how responsive that individual is to the stimuli which trigger the nervous system? By now, he has increased our field of vision so that we are thinking about neurobiology and the sensory world of our environment and endocrinology in trying to explain what happened.
Sapolsky keeps going–next to what features of the environment affected that person’s brain, and then back to the childhood of the individual, and then to their genetic makeup. Finally, he expands the view to encompass factors larger than that one individual. How culture has shaped that individual’s group, what ecological factors helped shape that culture, and on and on, back to evolutionary factors thousands and even millions of years old.
The result is one of the most dazzling tours de horizon of the science of human behavior ever attempted, a majestic synthesis that harvests cutting-edge research across a range of disciplines to provide a subtle and nuanced perspective on why we ultimately do the things we do…for good and for ill. Sapolsky builds on this understanding to wrestle with some of our deepest and thorniest questions relating to tribalism and xenophobia, hierarchy and competition, morality and free will, and war and peace. Wise, humane, often very funny, Behave is a towering achievement, powerfully humanizing, and downright heroic in its own right.
Researchers paired proteins with a process that amplifies RNA which could be used to detect cancer cells
One of the most fascinating things that I have repeatedly encountered is the failure to link CRISPR from the nutrient-dependent pheromone-controlled physiology of reproduction to the biophysically constrained viral latency that links ecological variation to ecological adaptation via natural selection for energy-dependent codon optimality in all living genera.
It’s as if the gene-editing technology could not be understood in the context of femtosecond blasts of virucidal UV light and RNA-mediated DNA repair, which has been linked to the prevention of all pathology until stress overwhelms the immune system.
Summary: It seems likely that Schrodinger’s anti-entropic virucidal effect of sunlight will be linked to the RNA-mediated de novo creation of all organized genomes and the maintenance of the “spotless epigenome” in this presentation later today. If so, even theorists and other pseudoscientists who planned to “March for Science” will finally be seen in the context of Dobzhansky’s claims about the “…light of evolution.”
The variety of epigenetic modifications and their influence on gene expression
How editing or erasing epigenetic marks might be used in a therapeutic manner
Topics already covered elsewhere: IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography was reported as: Atomic structure reveals how cells translate environmental signals The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions. Case for the genetic code as a triplet of triplets was reported as: Reading the genetic code depends on context University of Utah biologists now suggest that connecting amino acids to make proteins in ribosomes, the cell’s protein factories, may in fact be influenced by sets of three triplets – a “triplet of triplets” that provide crucial context for the ribosome.
Placing the atomic structure of any functional protein into the context of energy-dependent changes in RNA-mediated amino acid substitutions links natural selection for energy-dependent codon optimality to all biodiversity. That fact about natural selection refutes neo-Darwinian theories by making the link from virus-driven energy theft to the degradation of messenger RNA the obvious link from mutations to all pathology.
It seems likely that the virucidal anti-entropic effect of sunlight will be linked to the creation and maintenance of the spotless epigenome in this presentation later today. Hopefully, they will mention that femtosecond blasts of UV light appear to biophysically constrain energy-dependent protein folding chemistry. For instance, see also: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)
Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!
If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!
1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].
In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality
This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher
The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.
…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).
…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.
Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.
This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution? Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.
Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.
It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).
Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.
…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.
Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.
The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.
Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.
I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.
Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:
— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking
“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”(Roger Penrose 8 August 1991)
See also:
James Vaughn Kohl “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).
Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.
