Food energy-dependent cell type differentiation (2)

By: James V. Kohl | Published on: June 6, 2017

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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.