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

Energy-dependent physical and biophysical constraints (3)

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

My comment to The Scientist:

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

The de novo creation of energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which has been linked from mutations to all pathology via the claims Schrodinger made in “What is Life?” (1944).

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

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

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

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

Amino acid modification FA_Epigenetics_Table1

Food energy-dependent cell type differentiation (2)

Summary: The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
See first: Food energy-dependent cell type differentiation
See also: Bacterial Communication And Relevance Of Quantum Theory
Thanks to antagonist Jay R. Feierman for calling this to my attention, See: Fwd: Bacterial Communication And Relevance Of Quantum Theory

The recent findings confirm that bacteria communicate each other through chemical and electrical signals. Bacteria use chemical signaling molecules which are called as quorum sensing molecules (QSMs) or autoinducers. Moreover, the ion channels in bacteria conduct a long-range electrical signaling within biofilm communities through propagated waves of potassium ions and biofilms attracts other bacterial species too. Both communication process are used by bacteria to make their own survival strategies. In this article, we model this bacterial communication mechanism by complex Ginzburg-Landau equation and discuss the formation of patterns depending on kinematic viscosity associated with internal noise. Again, the potassium wave propagation is described by the non-linear Schrodinger equation in a dissipative environment. By adding perturbation to non-linear Schrodinger equation one arrives at Complex Ginzburg-Landau equation. In this paper we emphasize that at the cellular level (bacteria) we use Complex Ginzburg-Landau equation as a perturbed Non-linear Schrodinger equation to understand the bacterial communication as well as pattern formation in biofilms for certain range of kinematic viscosity which can be tested in laboratory experiment. Here, the perturbation is due to the existence of nonthermal fluctuations associated to the finite size of the bacteria. It sheds new light on the relevance of quantum formalism in understanding the cell to cell communication.

For everyone who does not follow my posts on groups and in forums where they are not commonly edited or fail to appear because the moderators and administrators are biologically uninformed theorists, I reiterate:
Natural selection for energy-dependent codon optimality and nutrient energy-dependent quorum sensing have been linked from the pheromone-controlled physiology of reproduction in bacteria that naturally produce a uranium isotope to all morphological and behavioral biodiversity via an atoms to ecosystems model that refutes every aspect of neo-Darwinian theory and all theories linked to the claims of “Big Bang” cosmologists.
Clearly, Feedback loops link odor and pheromone signaling with reproduction (2005) in all living genera can be compared in the context of two claims, which were made by the moderator of the ISHE’s human ethology group, soon after I published Nutrient-dependent/pheromone-controlled adaptive evolution: a model (6/14/13)
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.
See for comparison: Quantum Souls

The sun’s energy flows to Earth as information that is absorbed by energy-dependent organisms. Along with nutrient-dependency and pheromones, it effects all living genera and ensures reproduction. God’s “conditions of life,” described in part by Darwin, come before natural selection.

For additional evidence that links the anti-entropic virucidal energy of sunlight to all biodiversity and the concept of quantum souls, I reiterate:
Figure 4: Conceptual model of uranium roll-front deposit formation. — from Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits (open access)

Precursors and conditions favouring the formation of uraninite, biogenic uraninite and non-crystalline U(IV) are illustrated.

The nutrient energy-dependent pheromone-controlled physiology of reproduction of bacteria that live underground was linked from thermodynamic cycles of RNA-mediated protein folding chemistry to the production of uranium isotopes. The obvious link from the quantized energy of sunlight to the de novo creation of all biodiversity also was reported in the context of 16S rRNA microbial community analysis in fish. Most authors report this in the context of a “DNA-based” analysis. That way, there is no need to differentiate between abiogeneis and biophysically constrained biogenesis. Start with genes and you do not need to explain how DNA was created.

See for comparison: Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

The nucleotide variation in both the 16S and 12S sequences was suitable for identifying the large majority of the examined fish specimens to at least the level of genus, but was found to be less useful for the explicit differentiation of certain congeneric fish species. It is recommended that one or more faster-evolving DNA regions be analysed to confirm the identities of closely-related fish species in South Africa.

The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
The amount of food energy, measured in calories, is linked to whether or not the organism starves to death before it reproduces. That’s how ecological variation in the supply of nutrients may lead to extinction of any species that fails to evolve into another species. So far, no experimental evidence of biologically-based cause and effect suggests that any species has ever evolved into another species.
Claims about the need for energy-dependent changes in supercoiled DNA to protect all organized genomes from the virus-driven degradation of messenger RNA, which is linked to mutations and all pathology may have have peaked with this publication:
Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs (5/25/17)

Over the last decade, it has become increasingly apparent that miRNAs have many important roles in the development of disease and cancer. Recently, however, their role in viral and bacterial gene regulation as well as host gene regulation during disease progression has become a field of interest.

More than 61,000 works published peer-reviewed works show why differences in the types of microRNAs are the most important consideration to energy-dependent healthy longevity or to virus-driven pathology.
MicroRNA Items: 1 to 20 of 61426
See for comparison: It’s Time to Start Calling Evangelicals What They Are: The American Taliban

Atheistic hate-mongers like Magnus S. Magnusson continue to disseminate this nonsense and encourage attacks on any views that link Creationism to Americanism. The hate-mongers don’t know who created energy or how energy-dependent ecological adaptation is linked from changes in base pairs to all biodiversity, but they will claim that American evangelicals are like the Taliban.

See for comparison:  The in vivo structure of biological membranes and evidence for lipid domains

The structure and organization of the cell membrane are central to many biological functions, and although they have been extensively studied, there is still much that we don’t understand. A wealth of detailed information has been obtained from studies of model lipid membranes. However, these systems are often highly simplified in composition and always lack the active processes found in cells. The major obstacle to studying membranes in vivo in living cells has been that high-resolution physical methods used to investigate membrane structure are not compatible with living organisms. To overcome this obstacle, we employed a new in vivo approach that allows membrane structure to be observed directly in the gram-positive bacterium B. subtilis. This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å). We were also able to observe nanoscopic lateral membrane structures, consistent with the notion of lipid rafts. This experimental approach will allow for a wide range of future structural studies of the cell membrane (and possibly other classes of biomolecules) without the need for extrinsic probes or labels. In this way, it fundamentally changes the scope of nanoscale structural questions that can be addressed in vivo.

Reported as: This Is The First Ever Nanoscale Image of a Living Cell Membrane 

They link the energy-dependent de novo creation of the cell wall in Bacillus subtilus, a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans, to all biodiversity on Earth via differences in hydrogen ions, hydrogen atom transfer in DNA base pairs in solution, and the pheromone-controlled physiology of reproduction.

Hydrogen ions are made by the removal of one electron from atomic hydrogen. That fact supports the the claims of those who have linked energy-dependent changes from atoms to ecosystems in all living genera via what occurs at the level of changes in angstroms. The changes in angstroms are linked to the innate ability of all cell types to signal other cell types via changes in the membrane that biophysically constrains the contents of the cell.
Although it is important that these researchers showed how the role of quantized energy from the sun is linked to biophysically constrained hydrophobicity in supercoiled DNA, anyone who has ever performed a “catalase” test to distinguish between pathogenic and non-pathogenic strains of Staphlococcus and Streptococcus before testing for beta-lactamase and resistance to oxacillin/methicillin has observed the release of hydrogen caused by the breakdown of the cell membrane.

Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals). It catalyzes the decomposition of hydrogen peroxide to water and oxygen.[3]”

Beta-lactamase provides antibiotic resistance by breaking the antibiotics’ structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a β-lactam. Through hydrolysis, the lactamase enzyme breaks the β-lactam ring open, deactivating the molecule’s antibacterial properties.”

Congratulate the researchers who have just refuted every aspect of neo-Darwinian theory as was predicted by any intelligent microbiologist who has ever needed to identify and perform susceptibility testing on a pathogen to help a physician keep the pathogen from killing the patient.

And, remember the Hippocratic Oath. First, do no harm. If you are a physician who thinks that people evolved from bacteria, learn something about cell type differentiation via a visit to the microbiology lab at a local hospital. Most medical laboratory scientists will be happy to help you stop killing people with your ignorance.

Serious scientists have forced theorists to change their claims about the gene editing technology called CRISPR Cas9 to reflect the fact that the reason the technology failed miserably. The technology was based on naturally occurring endogenous RNA interference. It is now being reported as CRISPRi in the context of identifying new genes but outside the context of their energy-dependent de novo creation.

See: High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae

Genome‐wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn‐seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high‐content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi‐based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp‐proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP‐dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.

The de novo creation of essential genes has been placed into the context of a problem with antibiotic sensitivity testing.

 
The problem was introduced into susceptibility testing by biologically uninformed theorists who still may not know the difference between energy-dependent ecological adaptation and mutation-driven evolution.

Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch

The transient and conditional expression of our system using synthetic RNA could provide genome editing as a potentially ‘one-shot therapy’ to treat numerous genetic diseases. In conclusion, our miR-Cas9 switch combined with a RNA-delivery approach can selectively engineer genomes of target cells by detecting an endogenous miRNA signature, with potential benefits for synthetic biology, genome editing field and future therapeutic applications.

The conditional expression of genes is linked from food energy-dependent pheromone-controlled biophysically constrained viral latency to healthy longevity or from virus-driven energy theft to constraint breaking mutations and all pathology.

People like Jay R. Feierman and Magnus S. Magnusson tout the pseudoscienitific nonsense of theories in books such as this one. The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion
Their atheistic agenda is the antithesis of any factual representation of anything known to serious scientists about biophysically constrained energy-dependent biologically-based cause and effect.
See for comparison:  Mechanism of transmembrane signaling by sensor histidine kinases reported as:Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

See also: Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity
For a non-technical representation of everything currently known to serious scientists about the energy-dependent biophysically constrained physiology of pheromone-controlled biodiversity in all living genera see: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Could any serious scientist fail to link the novel transmembrane protein “Eros” from what organism eat to innate immunity via the non-technical representations in The Scent of Eros? If you know someone who you think is a serious scientist ask them about the representations made in The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion. If you learn that they think Faith and Religion “evolved,” I will add them to my growing list of pseudoscientists who continue to tout ridiculous theories.
 

fruit-dove

Food energy-dependent epigenetic adaptation (3)

Food energy-dependent epigenetic adaptation (2)

On 5/24/17 I attempted to post this to the ISHE’s human ethology group in response to the post on How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

For comparison, see the expanding role of anti-entropic virucidal energy that theorists claim automagically emerged to sustain all evolved biodiversity.

I included a link to:


I also included a link to:

The moderator of the group responded quickly: Jay R. Feierman wrote:

What you are posting has nothing to do with the thread article.

See also: 7/25/13
Jay R. Feierman:

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

My summary of past interactions with Jay R. Feierman:

He refuses to accept the fact that conditions of life are energy-dependent. He refuses to accept the fact that other biologically uninformed science idiots and many anonymous fools have consistently removed Darwin’s ‘conditions of life’ and replaced them with ridiculous theories about mutations and evolution.

At a conference we both attended in 1995, Jay R. Feierman was the first to challenge the entirety of the model I presented with the question “What about birds?”

He has continued to prevent dissemination of accurate representations of energy-dependent biologically-based cause and effect since then. He exemplifies the impact that one biologically uninformed science idiot can have across an entire generation of unsuspecting anonymous fools who are likely to believe that the creation of energy has nothing to do with the claims in: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

See also: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, the authors attest to the fact that every aspect that has ever been included in mathematical models of natural selection cannot link natural selection to anything that could not be predicted by what is known about how food energy must be linked from ecological variation to ecological adaptation by the sense of smell in all living genera. The sense of smell predictably links what is known about natural selection for energy-dependent codon optimality to biophysically constrained viral latency via publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.

There has never been any experimental evidence of biologically based cause and effect that link anything but olfaction, food odor, and pheromones directly to the survival of all species. Yet Feierman’s claim continues to be echoed in the claims of all others who are biologically uninformed:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. — Jay R. Feierman

See for comparison: Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

 

Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.
 

Dispensing with all pseudoscientific nonsense about evolution (1)

No experimental evidence of biophysically constrained biologically-based cause and effect supports claims that the mammalian placenta “evolved.”
All experimental evidence of biophysically constrained biologically-based cause and effect supports claims that the mammalian placenta is an energy-dependent pheromone-controlled ecological adaptation.
See also: Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory
Chemoautotrophic symbiosis is nutrient energy-dependent and pheromone-controlled. Nothing about life involves autotrophy. Everything known to serious scientists links chirality to autophagy, which protects the supercoiled DNA of all organized genomes from virus-driven energy theft and genomic entropy that links extinction to the fossil record. Claims about the last known common ancestor of shipworms are the clearest indicator that pseudoscientists do not realize no last known common ancestor has ever been found for any form of energy-dependent RNA-mediated life.
See “March for Science: Dispatches from Washington, DC

“We made history!” marchers chanted at the terminus of a mile-and-a-half walk from the Washington Monument to Capitol Hill in Washington, DC.

See “March for Science: Dispatches from Berlin

“We just watched a documentary on Charles Darwin the other night, and my older daughter, when I told her that in some countries—Turkey, Russia, and parts of the United States—evolutionary theory is taken out of the school curricula, she said, ‘We have to make a sign!’ And we [created] these ones.” —Percy Rohde

See “March for Science: Dispatches from Chicago

The science march in Chicago was was a blend of scientists and nonscientists alike. Peggy Mikros, a caterer, came up from the south side of the city because she said she cares about the environment and “science is everything.” The event has inspired her to continue to advocate for science.KERRY GRENS

“I’ve never done this and I am so excited to be here.” —Peggy Mikros, caterer from Chicago

See “Science March Sights and Signs

Here’s a sampling of sights and signs from the Marches for Science in Berlin, Chicago, and Washington, DC.

Here is the scientific support for what my sign would have said;
See: A novel strategy to dissect endogenous gene transcriptional regulation in live cells (2017)

The ARID1A gene, encoding a subunit of the ATP-dependent chromatin remodeling complex SNF/SWI, has recently been identified as a tumor suppressor in multiple cancers. Despite studies that elucidate the mechanism of ARID1A’s tumor suppressor function, little is known of the genes/events that regulate ARID1A expression. Using the HEK293 cells as a model, we discovered novel aspects of ARID1A transcription regulation in response to cell cycle progression, DNA damage, and microRNAs, exemplifying the potential of our strategy in providing new insight to the mechanism of gene transcription regulation.

I don’t know any serious scientist who has ever started with a claim about evolution, mutation, or natural selection. All serious scientists know they must start with the energy-dependent de novo creation of ATP, and link it to cell type differentiation in all living genera via the physiology of pheromone-controlled reproduction.
See for a historical perspective: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Connecting energy as information to ATP-dependent synthesis of RNA and healthy longevity is not difficult unless you do not know where the energy comes from. If you do not know or fail to acknowledge the creation of energy as the source that links the anti-entropic virucidal effects of sunlight to all biodiversity via what is known to serious scientists, you will not understand what serious scientists know about how to prevent all virus-driven energy theft from linking mutations to all pathology in all living genera
See also: Individual Bromodomains of Polybromo-1 Contribute to Chromatin Association and Tumor Suppression in Clear Cell Renal Carcinoma

The architecture of chromatin is governed, in part, by adenosine triphosphate (ATP)-dependent chromatin remodelers. These multi-protein complexes contain targeting domains that recognize posttranslational marks on histones. One such targeting domain is the bromodomain (BD), which recognizes acetyl-lysines and recruits proteins to sites of acetylation across the genome. Polybromo1 (PBRM1), a subunit of the polybromo-associated BRG1- or hBRM-associated factors (P-BAF) chromatin remodeler, contains six tandem BDs and is frequently mutated in Renal Clear Cell Carcinoma (ccRCC). Mutations in the PBRM1 gene often lead to loss of protein expression; however, missense mutations in PBRM1 have been identified and tend to cluster in the BDs, particularly BD2 and BD4, suggesting that individual BDs are critical for PBRM1 function. To study the role of these six BDs, we inactivated each of the six BDs of PBRM1 and re-expressed these mutants in Caki2 cells (ccRCC cells with loss of function mutation of PBRM1). Four of the six BDs abrogated PBRM1 tumor suppressor, gene regulation, and chromatin affinity with degree of importance correlating strongly to rate of missense mutations in patients. Furthermore, we identified BD2 as the most critical for PBRM1 and confirmed BD2 mediated association to histone H3 peptides acetylated at lysine 14 (H3K14Ac), validating the importance of this specific acetylation mark for PBRM1 binding. From these data we conclude that four of the BDs act together to target PBRM1 to sites on chromatin; when a single BD is mutated, PBRM1 no longer controls gene expression properly, leading to increased cell proliferation.

See also: From Fertilization to Adult Sexual Behavior

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

microRNA polycomb Items: 1 to 20 of 394
microRNA hecatomb No documents match your search terms
Epidemic hecatomb in the New World (1992)

The American population developed, during thousands of years, free of epidemics that had been attacking Europe, Asia and Africa. The European and African migrations, after Columbus’s first trip, produced an epidemic invasion of influenza, smallpox, measles, yellow fever, malaria, diphtheria, typhus, and other diseases that attacked the immunologically virgin populations and produced a very high mortality, with a diminution of the indigenous population of more than 90% in many places. According to historical evidence, the first epidemic was influenza, produced by swine strain of virus, immediately followed by smallpox. The Spaniards mated freely with the Indians producing a mixed race called the Mestizo, who were immunologically more capable of defending themselves against various viruses, bacteria, and parasites brought over from the Old World. Marriage between the races also was sanctioned by Queen Isabella (1503) and Fernando I (1515). With these new genetic immunologic defenses against infections, the Mestizo eventually made up the majority of the population of Indians in the New World.

Virus-mediated archaeal hecatomb in the deep seafloor (2016)

Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.

See: Dispensing with all pseudoscientific nonsense about evolution (2)
 

Alternative splicing of pre-mRNA

Virus-driven downsizing of the human brain (4)

Excerpt:

Chad Lerner

We house our animal mouse models in pathogen free environments (aside from transponson). They still age and die with pathological features. Sorry

Chad Lerner claims to be a Postdoctoral Researcher at Buck Institute for Research on Aging

On Saturday, 4/22/17, which was the day of the “March for Science” he wrote:

You should not have featured me. It is out of context and you have no idea what you’re talking about. You just want there to be a god like the other children . Leave me out of this quackery. Remove my name. Never contact me.

See also: Heading into Today’s March, Here’s When to Doubt a Scientific “Consensus”

 Excerpt: There’s an old legal proverb:

If you have the facts on your side, argue the facts. If you have the law on your side, argue the law. If you have neither, attack the witness. When proponents of a scientific consensus lead with an attack on the witness, rather than on the arguments and evidence, be suspicious.

Chad Lerner attacked me as if I was a witness for Creationism and Americanism. Tomorrow is another day.

See Behavior related genes, dietary preferences and anthropometric traits,which is scheduled for presentation on 4/24/17

Reported as: Could genetics influence what we like to eat?

…little is known about how natural variation in these genes could affect eating behaviors in healthy people. Gene variation is a result of subtle DNA differences among individuals that make each person unique.

All serious scientists know that natural variation in genes is nutrient energy-dependent and controlled by the biophysically constrained physiology of reproduction. The also know this: Feedback loops link odor and pheromone signaling with reproduction
Natural selection for energy-dependent codon optimality links the feedback loops to all biophysically constrained biologically-based cause and effect. There is a model for that: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
This claim makes no sense: “…little is known about how natural variation in these genes could affect eating behaviors in healthy people.”

See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Amino acid modification FA_Epigenetics_Table1

Physicists: Desperate Acts (revisited)

Physicists: Desperate Acts
Light-induced endogenous RNA interference in bioluminescent microbes links Schrodinger’s claims in “What is LIfe?” (1944) from a light-to-chemical pathway of information exchange in all living genera via amino acid substitutions in supercoiled DNA.
All subsequent works on the evolutionary synthesis failed to link  the anti-entropic virucidal energy of sunlight to Darwin’s “conditions of life” from the claims of Schrodinger (1944) or the claims of any other serious scientist.

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also: A theoretical physicist approaches the complexity — and mystery — of quantum gravity head-on

We thought that matter was continuous, and it took quite some time to realize that matter is not continuous,” he explains. “It’s atomic, it’s made by atoms and molecules, by particles. This was only understood about the beginning of the 20th century, not before that. It’s one of those ideas that is very old. It was suggested in ancient times. But it was realized recently.”

“So matter is discrete, and light is discrete, it’s made by photons. A wave of light is actually a cloud of photons. And it’s not surprising, after all, that space itself is sort of a cloud of little teeny small things.
Serious scientists used what is known about subatomic particles to show that all the assumptions of pseudoscientists have always been wrong. The pseudoscientists now must deal with serious scientists who have linked the creation of energy as information to all biodiversity and others who linked virus-driven energy theft to all pathology.
Some of the best among the serious scientists scientists who did that are young earth creationists who have always been right. They somehow knew that gravity did not create itself and most of them began to realize that hydrogen-atom transfer in DNA base pairs in solution must be linked from energy-dependent changes in chirality to autophagy.
When pseudoscientist failed to link chirality from autophagy to endogenous RNA interference and supercoiled DNA, which prevents virus-driven energy theft and genomic entropy in all organized genomes of all living genera, the serious scientists started to ridicule the theorists in parodies.
For a historical perspective on the ridicule, see Was ribosome the first self-replicator?

Two years ago, I asked Matti Pitkanen if differences between biophotons were recognized by the photons at the quantum level of their interactions. His response was a classic example of evading the question with claims that theoretical physicists tout in their pseudoscientific nonsense.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

See for comparison: “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: Why metabolism and what happens in bio-catalysis? Matti Pitkanen (2 February 2017)

  1. The simplest and at the same time most difficult question that innocent student can make about biology class is simple: “Why we must eat?”
  2. …the energies of the hydrogen atom depend on hbareff=n× h in as hbareffm, m=-2<0. Hydrogen atoms in dimension D have Coulomb potential behaving as 1/rD-2 from Gauss law and the Schrödinger equation predicts for D≠ 4 that the energies satisfy En∝ (heff/h)m, m=2+4/(D-4). For D=4 the formula breaks since in this case the dependence on hbar is not given by power law. m is negative only for D=3 and one has m=-2. There D=3 would be unique dimension in allowing the hydrino-like states making possible bio-catalysis and life in the proposed scenario.
  3. The condition that the dark binding energy is above the thermal energy gives a condition on the value of heff/h=n as n≤ 32. The size scale of the dark largest allowed dark atom would be about 100 nm, 10 times the thickness of the cell membrane.

Pitkanen is unable to grasp the fact that the speed of light on contact with water is the source of all binding energy, which links hydrogen-atom transfer in DNA base pairs in solution from endogenous RNA interference to healthy longevity in all living genera via chromosomal inheritance. His attempts to place dark binding energy above the anti-entropic virucidal energy of sunlight is still one of the most foolish attempts I have seen anyone make to deny that the energy in a hydrogen atom has been there from the time God created the heavens and the earth — as detailed in Biblical Genesis.
Matti Pitkänen What new physics do you want to introduce to support your claims about dark energy and dark matter for comparison to the claims of Schrodinger about the anti-entropic energy of sunlight?

I call it adelic physics or number theoretic physics.

Does everyone who knows you except Ulla Mattfolk laugh at your pseudoscientific nonsense?

Matti Pitkänen …one must assume that space-time is what topologist calle n-fold covering space. n sheets of covering effectively multiply Planck constant by n to give h_eff. The quantum of action is n-fold since there are n sheets.

I told him that all the assumptions made by others have been wrong.

Matti Pitkänen  It took more than 10 years to deduce this from adelic physics which is fusion of real physics for matter and various p-adic physics for cognition, p = prime.

Matti Pitkänen I think very few laugh to my theory now. If they do so I can safely conclude that they are idiots.

Matti Pitkänen …your understanding of physics could be better. One must distinguish between continuity at space-time level and continuity of matter.

Matti Pitkänen  The cognitive representations defined by the intersections of real and p-adic space-time surfaces as intersection of reality and imagination/cognition are discrete: points have coordinates in extension of rationals. In this sense discreteness makes sense but is has nothing to do with the quantum mechanical discretization of quantum numbers.

Matti Pitkänen …the odor of nutrients is determined by pheromones. Is this true. This would be nice since pheromones could provide information about distribution of h_eff=n*h and thus about the number theoretic evolutionary level of food or potential mating partner. Good odors would correspond to large average n. Bad odors to low value of n and low negentropy.

Matti Pitkänen  TGD predicts both dark matter and energy naturally and this explanation leads to vision about quantum biology and cognition unlike other proposals.

The pre-publication reviews of this book came from people who I think George FR Ellis and others probably believe are serious scientists. I do not believe those people are anything more than theorists. When they include claims about viruses, serious scientists may discuss the reality of pattern recognition with them. But not until then. Energy vs virus-driven energy theft must be considered in the context of adaptive changes in the brain, June 12, 2016

See for comparison: Thomas Hunt Morgan

Morgan contributed to the neo-Darwinian synthesis, despite his criticism of Darwin at the beginning of his career. Much work on the Evolutionary Synthesis remained to be done.

See also: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking
Reported as: Gamma oscillations coordinate food seeking

 “Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

Coevolutionary dynamics of phenotypic diversity and contingent cooperation
Reported as: Study finds mutual reinforcement of phenotypic diversity and cooperation

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism’s observable traits, co-evolves with contingent cooperation when organisms with like traits work together to protect themselves from outsiders, according to a Dartmouth-led study published in PLOS Computational Biology. The study also finds that diversity helps prevent the collapse of cooperation.

Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Reported as: Catalyst mediates energy-efficient proton transport for reversibility

Scientists at Pacific Northwest National Laboratory built a catalyst that mimics nature’s hydrogen-splitting enzymes—working reversibly at room temperature and pressure without added energy. This was achieved by stabilizing the catalyst’s structure by attaching an amino acid…

Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection

Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.

‘Virus-Like Particle’ Method to Make new Polio Vaccines Proven Effective

The investigators have demonstrated that stabilized VLPs can be utilized effectively under controlled conditions. Additional research with model organisms like mice and rats will be necessary and is planned as an important part of crucial procedure of ensuring the safety and efficacy of these new VLPs for use in people.

All experimental evidence of biologically-based cause and effect has shown that controlled conditions are not exemplified in the context of how ecological variation must be linked from natural selection for energy-dependent codon optimality to the physiology of reproduction. Energy-dependent changes must be linked from chirality to autophagy by natural information processing. The control of information processing links energy-dependent endogenous RNA interference from amino acid substitutions in supercoiled DNA to all healthy longevity in all living genera. Negative supercoiling links virus-driven energy theft from mutations to all pathology.

If you would like to learn more about how virus-driven energy theft is linked to messenger RNA degradation and all pathology in species from microbes to humans, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection clearly links energy-dependent RNA-mediated amino acid substitutions to the functional structure that enables the search for nutrients, which are metabolized to pheromones that control the physiology of reproduction in species from microbes to humans.

terrarium-eco-system

Dobzhansky 1973 and precision medicine

MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee

Our findings point to miR-34-5p as novel regulatory component in the complex molecular cascade that governs insect segmentation and to a broader role of miRNAs in the early development due to the detection of mature transcripts from both 5p and 3p arms for several precursor miRNAs. Thus, this work encourages further investigation to pinpoint miRNAs as fine tuners of insect early development.

Anna Di Cosmo‘s group took the lead and already linked all invertebrates to all vertebrates via the conserved molecular mechanisms that link microRNA flanking sequences to all energy-dependent  biophysically constrained biodiversity.

See for example: Role of olfaction in Octopus vulgaris reproduction (January 1, 2015)

For a perspective, see: The phylogenetic utility and functional constraint of microRNA flanking sequences (February 18, 2015)

The majority of flanking sequences used in our analyses are composed of non-coding intergenic DNA, suggesting that conservation of these hairpin-loop flanking sequences is independent of either the presence of exonic sequence or protein-coding gene regions.

For the extension to humans, see:

Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits

 …all amino acid substitutions or all promotor variants are not equal, and one can predict the impact based on knowledge of the location and type of substitution.

All cell type specific and tissue type specific amino acid substitutions in all individuals of all living genera are energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction. A long-time antagonist echoed that fact in the human ethology yahoo group, but he took facts about complex traits out of context. See: Practical application of whole-genome sequencing

The complex traits used here are heart and blood related ones, but the concepts are applicable to all complex genetically-sourced traits, including behavioral ones. — Clarence A. ‘Sonny’ Williams

Complex traits are not genetically sourced. The physiology of pheromone-controlled reproduction is clearly the link to the complexity of all nutrient energy-dependent morphological and behavioral traits.
See: No Genetics without Epigenetics? No Biology without Systems Biology?

…a unified understanding of life requires: (1) a view on its component parts, the cells, (2) a view on the life cycles of all cells—their formation, growth, development, and reproduction—as based in chemical reactions among similar sorts of molecules, (3) a view on the way in which amino acids are put together to form proteins, as specified by DNA and RNA according to a nearly universal and precise scheme.

That fact makes it perfectly clear that behavioral traits are not genetically sourced. All traits arise only in the context of systems biology, which links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera. For comparison, Clarence A ‘Sonny Williams wrote:

mutations in gene regulatory regions are the “driving force” behind human brain complexity. 

and

I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.

The facts about systems biology were stated clearly in Dobzhansky’s Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

See also:

For example, 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.

The de novo creation of amino acids has since been linked from chirality to autophagy and healthy longevity via chromosomal rearrangements.
See:
Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Dynamic control of chirality and self-assembly of double-stranded helicates with light
The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

The cycle of interconversion of assemblies and helicities shown here holds promise to design other dynamic systems driven out of equilibrium by light energy.

See also: ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
The de novo creation of amino acids has since been linked from the energy-dependent creation of helicase to the structure of functional DNA. Theories about minimal mutational distances have been replaced by facts that link angstroms to ecosystems in all living genera via biophysically constrained RNA-mediated protein folding chemistry.

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.

They linked energy-dependent metabolic networks to genetic networks by recapitulating Dobzhansky’s claims and in this parody they add: “every angstrom is dynamic from the 5 prime to the three”

See also: Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation

…definitive conclusions about the exact role of the N-tier in helicase mechanism will require higher resolution to identify candidate-specific amino acid residues, followed by direct mutagenesis and biochemical characterization.
 

Although the candidate-specific amino acid residues have not been identified, the energy-dependent creation of RNA-mediated amino acid “residues” links the anti-entropic virucidal energy of sunlight from angstroms to ecosystems in all living genera via chirality and autophagy, which protect all organized genomes from virus-driven entropy in the context of the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution

How social learning adds up to a culture: from birdsong to human public opinion
Conclusion:

For human online cultures, we suggest that it may be useful to consider features of birdsong learning, which have been optimized over millions of generations to give rise to stable polymorphic cultures. Experimenting with implementation of similar features in online communication systems could potentially facilitate the design of more stable and balanced information systems, which can potentially promote distributed self-governance.

Public opinion (above) is based on bird-brained representations of pseudoscientific nonsense about “…balanced information systems, which can potentially promote distributed self-governance.” The information systems are not linked from energy-dependent changes in the microRNA/messenger RNA balance to all biodiversity via the physiology of pheromone-controlled reproduction. Instead the information systems automagically may promote “distributed self-governance” across all species in the context of millions of years of evolution.

In my model of biologically-based cause and effect, top-down causation is linked from natural selection for energy-dependent codon optimality to the physiology of reproduction and all biodiversity via supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

For an example of medication-induced genomic entropy, see: Some Antibiotics Linked to Serious Nerve Damage

The FDA is strengthening its warning that a popular class of antibiotics, called fluoroquinolones, may cause sudden, serious, and potentially permanent nerve damage called peripheral neuropathy.

See also: There is nothing inevitable or natural about chronic disease

Causation at the molecular level, deep inside the body, appears to be beyond our current reach

See for comparison: Understanding and accounting for relational context is critical for social neuroscience

George Ellis:

This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc

I wrote:

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).” — Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
See also: Methylation Maestro

So are many others who do not understand how energy-dependent changes in chirality must be linked from autophagy to supercoiled DNA in the context of the physiology of reproduction and fixation of RNA-mediated amino acid substitutions.

They have failed to link the National Microbiome Initiative to the Precision Medicine Initiative via RNA-mediated protein folding chemistry and are trapped in theories with no explanatory power.

If you ask one of them about the virus-driven energy theft of quantized energy, which is linked to all pathology, they will run away. They cannot stand to think about how the potential of hydrogen (pH) must be linked from sunlight to all biodiversity via the claims of Schrodinger in What is Life? (1944)

rp_levels-of-organization.jpg

Science journalists or paid propagandists? (2)

Excerpt:

Riffell is interested in how chemical signals, like smells, affect behavior. Explore further: Researchers show that the mosquito smells, before it sees, a host.

This was reported last year in “Science” and on January 6, 2017 as Orchids mimic human body odor to attract mosquitoes
The year-long delay aroused my suspicion because everything known to serious scientists since 1996 has linked food odors and pheromones to reproduction in species from microbes to humans.
See for example: Insect pheromone in elephants (1996)

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.

See also: Feedback loops link odor and pheromone signaling with reproduction (2005)
See also: Schedule 2016 and this search for pheromones: The Role of Pheromone Differences in Lineage Maintenance

…sex-specific pheromones used by plethodontid salamanders may play a role in sexual incompatibility and therefore the maintenance of isolated, genetically distinct populations.

…relative ratios of specific pheromone isoforms were compared across groups.

Species-specific pheromones must first epigenetically effect the nutrient energy-dependent hormone-organized function of the invertebrate and vertebrate brain. Then, pheromone isoform composition can affect energy-dependent male behavior or energy-dependent female behavior.
The evolutionary origins of social insect queen pheromones: honesty and dynamics of fertility signal production in a socially polyphenic Halictid bee.

…the evolution of these signaling channels given the potential for destabilizing dishonest signal production remains somewhat unclear. Fertility signal evolution may be at a nascent stage in primitively social insect societies…

They invented a nascent stage in an attempt to explain the nutrient energy-dependent pheromone-controlled behavioral development after claiming that facts about virus-driven destabilization of signal production were unclear.
Estrogen implantation alters putative pheromone composition in male brown tree snakes

Previous work in another snake species demonstrated that both estrogen implantation and testosterone removal (castration) could induce female pheromone expression in male red-sided garter snakes. It was thus the goal of this study to use estrogen implantation to manipulate putative pheromone expression in male brown tree snakes and determine the effect of implantation on male attractiveness. We implanted male brown tree snakes (n=7) with silastic implants (1 cm) containing estradiol and found that implanted males had significantly altered expression of long-chain methyl ketones, specifically the longer, monunsaturated ketones.

The hormone-dependent production of sex differences in pheromones has been linked from sex difference in yeasts at the advent of sexual reproduction to all sex differences in all cell types of all species that sexually reproduce.
Influence of female orientation and pigmentation on male positioning during courtship

We can modify the dummy’s appearance, pattern of motion, and pheromone coating. Males will robustly court the dummy, enabling us to delineate the relative contributions of visual and other sensory cues to male courtship behavior.

It is fascinating to see anyone pretend that the courtship behavior might depend on visual or other sensory cues without attesting to the facts about the classical conditioning of odor-driven changes in behavior that link chemotaxis to phototaxis in all living genera, not just organisms with eyes.
Cooperation and conflict in social insect societies: from genes to pheromones

Our studies provide novel insights into genomic, epigenomic, physiological and chemical mechanisms that regulate the variation in pheromone production and responses to these pheromones that shape social behavior in honey bees. We have extended these studies to other social insects (bumble bees, paper wasps, and fire ants) to begin to examine the evolution of the genomic pathways underpinning chemical communication and reproductive dominance…

Anna Di Cosmo’s group already linked everything known about ecological variation to ecological adaptation in species from marine invertebrates to terrestrial vertebrates in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

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).

Attempts to put facts like these back into the context of “…the evolution of the genomic pathways underpinning chemical communication and reproductive dominance…” are doomed to fail. There is no experimental evidence of biologically-based cause and effect that can be linked to the evolution of one species from another.
See also: Science journalists or paid propagandists? (3)