anti-entropic Archives - Scent of Eros

Theistic evolutionists fight back and lose (2)

February 27, 2017

by James Kohl with 2 Comments Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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.

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015

“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and 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.

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

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

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

George Church refutes theistic evolution (3)

February 12, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Fifty years of illumination about the natural levels of adaptation

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

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

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

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

Other factors include whales’ incredibly tight social bonding, which is especially strong within groups of pilot whales.

Social bonding is nutrient energy-dependent and controlled by the physiology of reproduction. In species from microbes to humans, the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones.

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

2005 Feedback loops link odor and pheromone signaling with reproduction

2015 Role of olfaction in Octopus vulgaris reproduction

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

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

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

See: atheism

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

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

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

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

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

Phytoremediation

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

CRISPR

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

Microbiome

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

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

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

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

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

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

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

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

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

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

Light-induced-conformer-intercoversion-of-hydrogen-bond

Dobzhansky 1973 and precision medicine (5)

January 26, 2017

by James Kohl with 2 Comments Adaptations biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

See: Dobzhansky 1973 and precision medicine (4)

Microenvironmental autophagy promotes tumour growth

…non-cell-autonomous autophagy is induced both in the tumour microenvironment and systemically… transformed cells engage surrounding normal cells as active and essential microenvironmental contributors to early tumour growth through nutrient-generating autophagy.

Non-cell autonomous autophagy links non-random natural selection for codon optimality from the nutrient energy-dependent pherormone-controlled physiology of reproduction to biophysically constrained RNA-mediated protein folding chemistry via fixation of amino acid substitutions in supercoiled DNA.

The supercoiled DNA links metabolic networks to genetic networks and chromosomal rearrangements to the transgenerational epigenetic inheritance of morphological phenotypes and behavioral phenotypes. Chromosomal inheritance links the 1933 Nobel Prize winning works of Thomas Hunt Morgan and Erwin Schrodinger to the works of 2016 Nobel Laureates Ben Feringa and Yoshinori Ohsumi. Collectively, their Nobel Prizes explain why Richard Axel and Linda Buck won the Nobel Prize in Physiology or Medicine in 2004 for detailing how the de novo creation of G protein-coupled receptors was linked to healthy longevity in all living genera.

It has become obvious that light induced changes in chirality must be linked from chemotaxis and phototaxis to all biodiversity via the pheromone-controlled physiology of reproduction.

Serious scientists start with the anti-entropic virucidal energy of UV light, and link energy to behavior.

See: CRYPTOCHROME mediates behavioral executive choice in response to UV light

Up-to-date research shows that they may employ dozens of mechanisms including epigenetic, hybridization, cryptic variation, behavioral changes, unreduced gametes, directed crossover, regulated micro-RNAs or RNA splicing, horizontal gene transfer, and even modulation of an organism’s microbiota. None of these mechanisms require a struggle for life and death!

See also this easy to read accurate representation of facts about healthy longevity compared to virus-driven pathology. Jeffrey P. Tomkins, Ph.D. 2015. Viral Genome Junk Is Bunk. Acts & Facts. 44 (4).
See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution

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.

There are certain things that we accept as facts with no alternatives,” according to the site. “The Earth is becoming warmer due to human action. The diversity of life arose by evolution. … An American government that ignores science to pursue ideological agendas endangers the world.

Anyone who accepts the claim that the diversity of life arose by evolution is not a serious scientist. Pseudoscientists who sign up for the march should repeatedly march themselves into a corner for a “time-out” until they learn not to throw temper tantrums or make claims that cannot be supported by experimental evidence of biologically-based facts. All serious scientists know that their claims must link chirality and autophagy to all biodiversity via the physiology of reproduction and supercoiled DNA.
See: Dobzhansky 1973 and precision medicine (6) in prep

Autophagy is the antiphage defense strategy

December 8, 2016

by James Kohl with No Comment Autophagy Ecology Light Energy Model Organisms Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity

The “Antiphage Defense Strategy” in Vibrio anguillarum is called autophagy by many serious scientists. It links nutrient energy-dependent pheromone-controlled quorum sensing to viral latency, healthy longevity, symbiosis, reproduction, and biodiversity from microbial species to humans.

For an evolutionary approach to energy-dependent autophagy that fails to address any aspect of how virus-driven energy theft causes all pathology see: (12/7/16) Part I: Living together: The symbiosis of host-microbial interactions (12/7/16)
See also: 12/7/16

….McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat. V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.

Bobtail squid select bacteria that become luminescent. The squid do not not select archaea. That fact exemplifies how natural selection for energy-dependent codon optimality links top-down causation from the sun’s anti-entropic biological energy to ecological adaptation.
Whether or not you accept this fact, energy-dependent natural selection continues in the context of symbiosis among the most ecologically adapted species.
“The four stages of acceptance: ― J.B.S. Haldane
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.”
Natural selection cannot link mutations to evolution in the context of symbiosis because the interactions among species are far too complex.

…the pattern of microbial exchange is “likely circular in nature.” That means that captive dragons contribute microbes to their environment, and they reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.

Pattern recognition is essential to the understanding of how the microbiome of bobtail squid is linked to symbiosis via the microbiome in all other living genera via the anti-entropic virucidal energy of sunlight.

Search Results for “McFall-Ngai”

Beneficial microbes kill beneficial mutations
1/15/15 Excerpt: McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
and
4) reproduction in their model organisms.
Environment epigenetically shapes the immune system
1/15/15 Excerpt: 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Quantum physics, quantum biology, and quantum consciousness
2/15/15 Excerpt: One would think that the representations of McFall-Ngai that appear to link light-induced amino acid substitutions from the stability of DNA in luminescent microbes to the stability of DNA in squid would invite more attention to details than attempts to pirate ideas about epigenetic links from Turin’s links and my links from quantum physics to Gunther Witzany’s Life is physics and chemistry and communication.

Thermotolerance and Longevity

8/25/15 Excerpt: See also my invited review of nutritional epigenetics. I submitted it by request for a special issue of “Nutrients” and posted the submission to Figshare.com on April 11, 2014, after the submission was returned without review.

Energy-dependent biodiversity (3)

6/25/16 Excerpt: Quorum sensing links the physiology of energy-dependent reproduction and virus-driven energy theft from the microRNAome of and light organ of bobtail squid to the bull sperm microbiome, which links microRNAs in breast milk to human brain development. The bacteria that populate the light organ have already been linked by Bonnie Bassler’s group and Margaret McFall-Ngai’s group to everything known about the physiology of energy-dependent reproduction in all living genera.

Energy-dependent de novo creation and neurogenesis (2)

December 8, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations What's in the News

MicroRNA are very mysterious. They are really relics of the RNA world—pieces of RNA that are highly reactive, very small and which pair and bind other RNA and facilitate catalytic reactions,” Mangone says. “We don’t know much about them—where they come from or how they regulate gene expression, but they are very misregulated in many diseases.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published 14 Jun 2013
Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

My comment: Only if you lived among wolves or among theorists for the past 10 years would you not know that more than 55,000 indexed publications link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. For comparison, all serious scientists also know that virus-driven energy theft links viral microRNAs from mutations to all pathology.
You need only search for “RNA mediated” to find information on how cellular and viral microRNAs are linked from energy-dependent changes to RNA-mediated amino acid substitutions and biophysically constrained protein folding chemistry. For example, this is all it takes to recognize the amount of pseudoscience that is packaged in claims that we don’t know much about microRNAs.
See also: Published to Figshare 10 April 2014

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

See also: MicroRNAs: the future of genomic science?
Excerpt:

The ubiquity of miRNA occurrence is reflected in the current literature, which reports a wide range of potential biomarker applications for this highly conserved molecule.

My comment: MicroRNAs are biomarkers that clearly link energy-dependent biophysically constrained changes in base pairs from RNA-mediated amino acid substitutions to cell type differentiation in all living genera. The energy-dependent links from the innate immune system to the physiology of reproduction also link all metabolic networks to all genetic networks in species from microbes to humans.
See for comparison: A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

…we hypothesize that the novel, human-specific C-terminal sequence of modern ARHGAP11B has a key role in the mechanism by which this protein promotes BP amplification. In this regard, the present data show that this sequence is due to a single C→G base substitution, which creates a novel splice donor site that results in the replacement of the ancestral C-terminal sequence of the ARHGAP11B GAP domain. The present data also demonstrate that this single C→G base substitution underlies the ARHGAP11B-mediated BP amplification implicated in neocortex expansion.

Reported as: Small Mutation Contributed to Evolution of Bigger Human Brains
Excerpt:

A single base change in a human gene likely played an important role in evolutionary expansion of the human brain, researchers say.

My comment: They claim that a single cytosine to guanine substitution created a novel splice site. They failed to mention that base pair (BP) amplification is nutrient energy-dependent. They also failed to mention that the de novo creation of a novel splice donor site must be linked from the energy-dependent fixation of an RNA-mediated amino acid substitution to the physical landscape of supercoiled DNA via the physiology of reproduction.

Svante Paabo is one of the co-authors who reported this:

Hence, it is not the ARHGAP11 partial gene duplication event ~5 million years ago, as such, that impacted human neocortex evolution. Presumably, ARHGAP11A and ancestral ARHGAP11B coexisted as functionally similar proteins for some time after the gene duplication event. The ability of ARHGAP11B to amplify BPs likely arose more recently from a change that is tiny on a genomic scale but substantial in its functional and evolutionary consequences.

My comment: No experimental evidence of biologically-based cause and effect suggests that any partial gene duplication event ~5 million years ago could have linked a mutation and the altered de novo creation of genes that Svante Paabo (and co-authors) placed into the context of biophysically constrained biodiversity in:

Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

My comment: Natural selection for energy-dependent codon optimality is the only way to link the de novo creation of genes from autophagy to RNA-mediated amino acid substitutions and nutrient-dependent polycombic ecological adaptation.
See: 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.

…the two paralogs displayed similar RNA binding across the transcriptome, indicating that their differential targeting does not derive from their RNA interactions, but from possible different cofactor interactions.

My comment: The cofactors are nutrient energy-dependent microRNAs, which are linked to healthy longevity and all biodiversity and viral microRNAs, which are linked from mutations to all pathology.
See also: Viral and cellular messenger RNA targets of viral microRNAs

…viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

…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 (p. 127).”

…carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

My comment: When did theorists decide to take the light as information and energy out of systems biology and ecological adaptations? Who decided to replace the anti-entropic virucidal energy of light with mutations and evolution?

Phylogenetic similarity sans energy

November 26, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated toxicity Variations

Cites: Sablok and Shekhawat (2008)

Excerpt:

“Microsatellites, often abbreviated as simple sequence repeats (SSRs), are 1 to 5 bp repeat mutation prone motifs. Due to mutation prone specific and high rate of polymorphism, microsatellites (SSR) have become a modern genetic resource tool for the genetic mapping studies, developing and establishing new patterns of molecular breeding and in inferring the phylogenetic and comparative genome analysis. These repetitive stretches are distributed in the coding and non-coding region with a bias towards the noncoding regions.”

My comment: Six years later Caguiat and Tabana (2016) fail to link the sun’s anti-entropic virucidal quantized energy as information in ultraviolet light from hydrogen-atom transfer in DNA base pairs in solution to the SSRs and SNPs. The SNPs link energy-dependent changes in base pairs to the microRNA/messenger RNA balance and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. They use the term “motifs” to link what all serious scientists know about autophagy and cell type differentiation, which protects all organized genomes from virus-driven energy theft.

If they were working with tulips or tobacco plants they might already have examined the extant literature and realized that the varieties of rice exemplify nutrient energy-dependent autophagy in the context of the physiology of reproduction in all living genera. Unfortunately, most theorists are not botanists who understand virus-driven energy theft in the context of protein folding biochemistry in plants.

For example, see: Tulips broken by viruses.

Excerpt:

…colorful patterns are caused by infection with potyviruses, which are filamentous plant viruses with positive-strand RNA genomes.

See also: The virome, microbiome, replisome and supercoiled DNA (November 3, 2015)

Excerpt:

Eventually, someone will get the Nobel Prize that Rosalind Franklin probably would have received had she lived to link the tobacco mosaic virus and poliovirus from pathology in plants to all pathology in mammals via an atoms to ecosystems model of epigenetically-effected non-static DNA structure and function.

Co-author Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine.

See for comparison: A milestone in small RNA biology—piRNA biogenesis from start to finish

Excerpt:

PIWI-interacting RNAs, or piRNAs for short, are a class of ‘small regulatory RNAs’—tiny pieces of nucleic acid just 22–30 nucleotides in length. They may be small, but with their associated Argonaute proteins, piRNAs have the power to ‘silence’ transposable elements, so called egoistic genes found in the genomes of plants, fungi, and animals. piRNA-guided silencing can act on chromatin to block transposon transcription, or by destroying transposon mRNAs in order to block their translation into proteins.

Happy biophysically constrained Thanksgiving (in the USA)

November 24, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Is there any other holiday in the world that celebrates biophysically constrained cell type differentiation in all living genera?
The availability of amino acids and proteins in new genes is nutrient energy-dependent. The de novo creation of genes is biophysically constrained by the innate immune system and the physiology of reproduction. That fact was detailed for a general audience in Biblical Genesis.
Today, all of us can be thankful that the pseudoscientific nonsense of neo-Darwinian theory was replaced earlier in the month with experimental evidence of how new genes are created in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution, single nucleotide polymorphisms, microRNA flanking sequences and RNA-mediated amino acid substitutions that stabilize the naturally fluorescent supercoiled DNA in all organized genomes.
We had this: “…insight coming from re-analyses of translated transcripts in yeast that suggested that de novo gene evolution could even be more prevalent than gene duplication-divergence processes [13]
The energy-dependent de novo creation of genes in the context of duplication and divergence was accurately portrayed like this: “…the exact network of interactions between the nuclear lamina and the genome depends on the protein components of the nuclear envelope, the epigenetic state of the genome, and the availability of specific proteins that interpret these epigenetic signals and mediate interactions with the nuclear lamina.“
Naturally occurring DNA fluorescence in bacteria and dinosaur osteocytes proves that the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution is the basis for the creation of all biodiversity on Earth.

Simply put, God started with the creation of energy contained in hydrogen atoms as information, which is exactly what the Holy Bible says about His Word and the Light (the quantized anti-entropic virucidal energy of sunlight).Schrodinger (1944) linked it to the works that led to the Nobel Prize in Physiology or Medicine (1933) awarded to Thomas Hunt Morgan for linking inheritance to chromosomal rearrangements. Schrodinger and Dirac shared the prize in Physics that year.

If you remember how your sheets smelled after they had been hung out to dry in the sun, you have already experienced an example of purifying selection for energy-dependent codon optimality, which can be placed into the context of the Nobel Prize-winning works from 1933, or not. You can tell atheists and agnostics about the energy-dependent purifying selection before asking them where they think the energy in a hydrogen atom came from, or not.

When a friend asked me about that, I was forced to learn more about subatomic particles, but what I learned does not matter as much now that the energy has been linked to the creation of new genes. The de novo creation of genes is referred to as the “holy grail” of biology.

However, the energy-dependent protection of the new genes from virus-driven energy theft is also important. If energy-dependent protein folding chemistry is not biophysically constrained and protected from energy theft, life on Earth could not exist.

Thank God, for the anti-entropic virucidal effects of ultraviolet (UV) light, which links femotosecond blasts of UV light to energy-dependent RNA-mediated DNA repair outside the context of claims about emergence and evolution. For comparison, see:

Evolution: Dynamics of De Novo Gene Emergence

Conclusion (with my emphasis):

It has been suggested that the seemingly finite amount of stable protein folds observed across all domains of life is indicative of an early origin of all folds [16–18], possibly under different conditions and functions than the ones today [17]. However, entirely new folds have been shown to arise de novo in viruses [19] and new domains are present in recently acquired regions of old genes, as well as in young genes [20]. Until now, de novo evolved genes are largely underrepresented in structural analyses, and it seems that resolving their structure is a challenge that will provide us precious information about the origin of stable folds, molecular functions and the interaction between genome and environment.

Resolving the issues of virus-driven energy theft, which have been underrepresented in claims about the structure of functional DNA requires all serious scientists to include the role of virus-driven energy theft in the context of protein folding chemistry. There has never been a suggestion made by any serious scientist that the de novo creation of genes could occur outside the context of biophysically constrained protein folding chemistry. That’s why all serious scientists have linked energy-dependent changes from angstroms to ecosystems via the creation of genes and the virus-driven energy theft that links mutations to loss of function manifested in all pathology.

Pseudoscientists who make claims like this have never supported them with experimental evidence of biologically-based cause and effect. Why would anyone include such a claim in the same article that proved the de novo creation of genes was energy-dependent and biophysically constrained via supercoiled DNA, which protects all organized genomes from virus-driven energy theft?

Energy-dependent maternal-to-zygotic transition

November 15, 2016

by James Kohl with One Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Nutrigenomics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Small Non-coding RNAs Associated with Viral Infectious Diseases of Veterinary Importance: Potential Clinical Applications
ON 11/14/16 The co-author Mohamed Samir wrote:

Because our article is among the top 25% most viewed and downloaded articles in the third quarter of 2016 in “Frontiers in Veterinary Science”, The editor of the journal has invited me to host and moderate a new research topic in his journal about miRNAs in veterinary filed. Thanks God.

The topic is virtually guaranteed to bring out the best in researchers who have already linked energy-dependent changes from angstroms to ecosystems in all genera via animal models that make it clear that virus-driven energy theft causes all pathology.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly
Natural selection for codon optimality is an energy-dependent biophysically constrained RNA-mediated sexually differentiated biological function that has been linked to RNA folding and the assembly of functional protein structures in species from yeasts to mammals.
See: Yeast and cancer cells – common principles in lipid metabolism
See also: Signaling from the Cell Surface to the Genome: Pheromone Response in the Sexually Aroused
Yeast Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21 Evolution: A View from the 21st Century
Excerpt:

The two-stage replication proofreading system in E. coli and other bacteria has more complex analogues in nucleated eukaryotic organisms, from yeast to plants and animals.2

Excerpt:

There are two particularly significant facts about the S. cerevisiae mating pheromone response:

• It provides a concrete example of how one cell can communicate through well-defined molecular events with the genome of another cell. This example shows that we cannot consider the genome in any way isolated from the outside world; it is a fully informed cell organelle that works dynamically in response to a wide range of organic and inorganic inputs.

• The yeast pheromone response system utilizes sophisticated and complex sensory and signaling components (such as a G protein-coupled receptor) that researchers have encountered repeatedly in many quite distant organisms [160].

Proof-reading is nutrient energy-dependent and pheromone-controlled in species from microbes to humans. The ab initio creation of energy is linked from the de novo creation of G protein-coupled receptors and cell type differentiation via energy-depnedent chemotaxis and phototaxis. Both are required to find food and to remember where to find it. Nutrient selection is the link to energy-dependent translation of codon identify from the paternal lineage, which involves different cell types. Cell type differentiation is nutrient-dependent and pheromone-controlled in species from microbes to humans.
See also: Learning from Bacteria about Natural Information Processing
See for contrast: 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.

In some species that sexually reproduce, one of the sexually-differentiated cell types is called a spermatozoa. The other is called the ovum. In both energy-dependent sexually-differentiated cell types RNA interference is essential for cellular quiescence. The quiescence links autophagy to the transgenerational epigenetically-effected stability of organized genomes in all cell types.
In our 1996 Hormones and Behavior review, we put RNA-mediated interference (RNAi) into the context of sexual differentiation of cell types via the pheromone-controlled energy-dependent physiology of sexual reproduction.
See: From Fertilization to Adult Sexual Behavior
Abstract excerpt:

The general sense of the word “environment” as something exterior to the person is retained, even if that something influences intraperson processes. In addition, we focus directly on molecular events themselves. Here the “environment” involved can be that within a DNA segment. We also expand the notion of “biologically based sex differences.”

Unlike Jay R. Feierman, others have since recently decided to continue Addressing sex as a biological variable, which is probably what all serious scientists have always done. It is difficult to imagine why anyone who is not a serious scientist would link mutations and/or natural selection to the evolution of sex differences in cell types.
See:

This themed issue of the Journal of Neuroscience Research highlights sex differences of the brain at all scales, from the genetic and epigenetic, to the synaptic, cellular, and systems differences—differences known to be present throughout the life span.

My comment: Epigenetically-effected sex differences in the brain that develop during the lifespan have been linked from nutrient energy-dependent biophysically constrained RNA-mediated protein folding chemistry to fixation of amino acid substitutions such as VAl158Met, which links energy-dependent behavioral transitions from adolescence to adulthood in humans.
See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The function of the amino acid substitution is altered by a single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele display a fourfold decrease in enzymatic activity compared to Val allele carriers. The decrease is accompanied by an increase of prefrontal DA activity. (Lachman et al. 1996; Lotta et al. 1995).
See also: Amino acids and virus penetration
Conclusion:

Theorists have ignored what serious scientists have detailed in the context of energy-dependent RNA methylation and cell type differentiation that must link learning and memory from ecological variation to ecological adaptation via the conserved molecular mechanisms of protein folding biochemistry that link metabolic networks to genetic networks. The amount of ignorance is overwhelming, and the theorists are not attempting to inform themselves.

Even Tim Bredy’s group seems to have fallen behind after publication of Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

They clearly linked energy-dependent RNA-methylation from learning and memory to RNA-mediated cell type quiescence and to sex differences in cell types in species from yeasts to mammals. With publication of Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain, they appear to ignore their prior claims, which link learning and memory in spermatozoa to the ability to find the ovum, which is another biophysically constrained sexually differentiated cell type. That energy-dependent ability of a sperm cell to find an ovum becomes increasingly important in the context of other published works such as this one. Mitochondrial genome and epigenome: two sides of the same coin

That claim made me more interested in seeing what I could find by scanning the table of contents in the Journal of Neuroscience Research :An Issue Whose Time Has Come: Sex/Gender Influences on Nervous System Function

From what initially saw, no one is addressing the facts about how energy-dependent biophysically constrained protein folding chemistry links RNA-mediated amino acid substitutions to supercoiled DNA via the physiology of pheromone-controlled reproduction in species from marine microbes to humans. Perhaps the special issue only claims to be Addressing Sex as a Biological Variable — 20 years after we did that.

See for comparison: From Fertilization to Adult Sexual Behavior (1996)

Excerpt:

See also: Misunderstanding cancer
The fact that detection of accumulated mutations does not provide diagnostic clarity should eliminate theories about accumulated mutations and evolution. How could mutations not be linked to physiopathology, but somehow lead to the evolution of biodiversity. For example, see the conclusion from Mutation-Driven Evolution: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).
I cited several different works from Tim Bredy’s group and am grateful to him for helping to inform me after I asked him about microRNAs in November 2012. All works from Tim Bredy’s group and the works of others can now be placed into the context of this one: Single-nucleotide polymorphism rs948854 in human galanin gene and multiple sclerosis: a gender-specific risk factor

These data demonstrate for the first time an association between rs948854 polymorphism and multiple sclerosis and, further, that this association is sex specific.

Why isn’t someone else linking the energy-dependent change in the base pair to changes in hydrogen-atom tranfer in DNA base pairs in solution in all living genera and linking the changes in base pairs to amino acid substitutions that determine thei differences in all cell types? It’s not just about sex differences and never has been. All cell type differentiation is energy-dependent and all biodiversity is controlled by the physiology of reproduction.

Before you read anything else from the special issue Journal of Neuroscience Research: An Issue Whose Time Has Come: Sex/Gender Influences on Nervous System Function, I recommend that you read Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain

How else are they going to link cell type differentiation in species from microbes to humans via sex differences without including what was known about genetics and molecular epigenetics 20 years ago? No matter how hard they try to ignore the facts we presented in the molecular epigenetics section of our 1996 review and all other facts about energy-dependent cell type differentiation, they cannot escape the fact cell type differentiation is energy-dependent and controlled by the physiology of reproduction.
I’ll let you know more about what I find in other articles from the same special issue when I have time to unravel any attempts to obfuscate facts that serious scientists have always know, like this one: Feedback loops link odor and pheromone signaling with reproduction
See Energy-dependent maternal-to-zygotic transition (in prep)

Epigenetics and autophagy vs mutations and evolution (7)

November 12, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA-directed DNA methylation Variations

RNA interference (RNAi) fails to protect all cell types from virus-driven energy theft. The effect on some cell types cannot be controlled. That’s because nutrient energy-dependent endogenosymbiosis and the pheromones-controlled physiology of reproduction protect the organized genomes of species from microbes to humans. Billions of waster dollars have been spent with no end to the waste in sight — until the Trump administration stops it.
As that begins to happen, see: tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence (open access)
Excerpt: Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria.
My comment: Natural selection for energy-dependent biophysically constrained RNA-mediated protein folding chemistry is the coordinated system that links autophagy to supercoiled DNA. Pseudoscientists, atheists, and the YEC admins on “The Battlefield” FB group do not want anyone to know that energy-dependent pheromone-controlled metabolic networks and genetic networks clearly exemplify that fact. Supercoiled DNA prevents virus-driven energy theft, which links mutations to all pathology via the conserved molecular mechanisms of RNA-mediated amino acid substitutions and cell type differentiation. That fact has been known to all serious scientists for several decades.
Instead of helping others learn about the facts, some people would like you to believe that a newly discovered genetic code controls the future of energy-dependent healthy longevity in species from microbes to humans. If it’s a new code, their ignorance can be excused. If it’s new, they could not be expected to know about it.
But energy-dependent natural selection for energy-efficient codon optimalitly is nothing new. It’s the survival mechanism that prevents virus-driven energy theft from causing all pathology in all living genera. It’s called autophagy.
Reported as: Newly discovered genetic code controls bacterial survival during infections
Those amino acids are delivered to the ribosome by tRNA. Like other types of RNA, tRNA consists of a sequence of four main ribonucleosides—A, G, C, and U. (U in RNA substitutes for the T found in DNA.) Each tRNA molecule has an anticodon that matches an mRNA codon, ensuring that the correct amino acid is inserted into the protein sequence. However, many amino acids can be encoded by more than one codon. For example, the amino acid threonine can be encoded by ACU, ACC, ACA, or ACG. In total, the genetic code has 61 codons that correspond to only 20 amino acids.
My comment: Bacterial survival is nutrient energy-dependent and pheromone-controlled in the context of metabolic networks and genetic networks that clearly link chemotaxis and phototaxis to the physiology of reproduction in species from microbes to humans. Energy-dependent alternative splicings link the microRNA/messenger RNA balance to all morphological and behavioral phenotypes in all living genera via Darwin’s “conditions of life” and everything known about energy-dependent cell type differentiation or virus-driven energy theft, which links mutations to all pathology.
See for comparison: Panayiotis Stavrou‎ to Religion: Science & Psychology
PLEASE SOMEONE TELL ME THIS IS A JOKE… A POE, SOME BANTER…SOMETHING??? American politician and former member of the United States House of Representatives made this ridiculous observation on television.
6.57 video

6.37 video

My comment: From the dawn of Creation, this energy-dependent coordinated system of codon usage (autophagy) has linked the sun’s anti-entropic virucidal energy to biophysically constrained protein folding chemistry via RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and all pathology in all living genera.

That fact may play a role in linking claims like the one Michele Bachmann and others have made about the importance of including consideration for God’s ongoing direction in the life of all creatures that He created.

Atheists will always think the claims of theists are unreasonable, which may sometimes be true. However, atheists cannot support their claims with experimental evidence linked to biologically-based cause and effect. That has always been true.

The atheistic alternative is to credit emergence and evolution via mutations to all pathology without acknowledgement of any anti-entropic force such as sunlight, which is directly and indirectly linked to all healthy longevity in all living genera via RNA-mediated DNA repair.

For comparison, there is no model of biologically-based cause and effect that suggests healthy longevity emerged and evolved from anything. The innate immune system has always been considered the link from the epigenetic landscape to the physical landscape of supercoiled DNA by all serious scientists.

Epigenetics and autophagy vs mutations and evolution (3)

November 11, 2016

by James Kohl with No Comment Adaptations Autophagy Ecology Model Organisms Variations

On the Origin of Species voted most influential academic book in history

Excerpt:

Darwin used meticulous observation of the world around us, combined with protracted and profound reflection, to create a book which has changed the way we think about everything – not only the natural world, but religion, history and society,” he said. “Every researcher, no matter whether they are writing books, creating digital products or producing artworks, aspires to produce something as significant in the history of thought as Origin of Species.

My comment: What led others to abandon Darwin’s “conditions of life” and to place natural selection first? How can anyone believe that life emerged and then evolved when Darwin never observed that. Yet, those same people tout his observations in the context of refutations of their ridiculous theories by serious scientists who know that all life on earth is energy-dependent and that Darwin’s “conditions of life” require Schrodinger’s anti-entropic force: sunlight.