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Something from no thing

Posted on August 7, 2014 by James Kohl.

The Bridge From Nowhere How is it possible to get something from nothing? BY AMANDA GEFTERAUGUST 7, 2014

Excerpt: “Evolution has trained us to find causal patterns at any cost. As our ancestors wandered the African savanna, the ability to suss out effects from their causes marked a line between life and death. She ate that speckled mushroom and then fell ill.” 

My comment: Thank you for your explanation of how pattern recognition may be beneficial to serious scientists.

Creation enabled our nutrient-dependent ability to find causal patterns that cost us nothing. The fact that everything is connected to everything else is perfectly clear. It led some people to realize that eating some things can make us ill, which supports the claim that health and illness are nutrient-dependent. The fact that reproduction also is nutrient-dependent links what organisms eat to their species survival. 

We’ve since learned that “Feedback loops link odor and pheromone signaling with reproduction” via amino acid substitutions and cell type differentiation in species from microbes to man. Thus, anyone who believes that mutation-initiated natural selection led to the evolution of biodiversity — or that “Evolution has trained us…” to do anything — probably does not believe in causal patterns of biophysically-constrained biologically-based cause and effect that cost us nothing to believe in. For example, it costs nothing to believe light-harvesting functions link amino acid substitutions that differentiate cell types in plants and animals.

Similarly, it costs us nothing to believe that docosahexaenoic acid links the phrase “Let there be light!” to a quantum theory for its irreplaceable role in neural cell signaling via ecological variation that links quantum physics to quantum biology and ecological adaptations manifested in the increasing organismal complexity of brains.

Taken together, these facts suggest it costs us nothing to believe that ecological adaptations are manifested in the morphological and behavioral diversity of species from microbes to man via conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in organized genomes.However, evolutionary theorists seem to somehow have not been trained to find causal patterns that molecular biologists have known about for more than 50 years. See for example: Biology, molecular and organismic  “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.”

Apparently, evolution …


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Epimutations: Attacking pseudoscientific dogmas

Posted on August 6, 2014 by James Kohl.

Our principle aim in the lab is to attack scientific dogmas.

Pseudoscientific dogma: “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.”

My comment: I’ve tried to get along, REVISITED:  11 Simple Rules For Getting Along With Others “6. Avoid openly trying to reform people. Every man knows he is imperfect, but he doesn’t want someone else trying to correct his faults. If you want to improve a person, help him to embrace a higher working goal — a standard, an ideal — and he will do his own “making over” far more effectively than you can do it for him.” This suggestion does not seem to apply to evolutionary theorists who now substitute the term “epimutation” for amino acid substitutions and use sRNA rather than microRNA to avoid the obvious connection from the microRNA/messenger RNA balance to amino acid substitutions that differentiate the cell type of all cells of all individuals of all species.

See for example: Antifungal drug resistance evoked via RNAi-dependent epimutations.

Open reform of evolutionary theorists ridiculous perspectives  is required. Others must tell them enough is enough or they will continue to misrepresent biologically-based cause and effect and link disorder to the orderly increasing complexity of morphological and behavioral phenotypes. They want mutations and natural selection to be the link,  or epimutations to be the link, or whatever else they can think of to avoid admitting that they cannot think in terms of biologically-based cause and effect.

When will others be able to understand information like this:  “In Ostrinia moth species, substitution of a critical amino acid is sufficient to create a new pheromone blend (Lassance et al., 2013).

The problem for theorists appears to be a widely-touted example of what they think is natural selection via predation in fawn to pepper-colored moths.  The example is ridiculous and based on pseudoscientific nonsense, The moth larvae ate lead- and manganese-contaminated leaves that caused a nutrient-dependent pheromone-controlled color change. Thus, the color change was an ecological adaptation in the moths.

What about birds? Evolutionary theorists misrepresent the nutrient-dependent pheromone-controlled ecological adaptation in the moths. They tell people the nutrient-dependent pheromone-controlled ecological adaptation …


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Order and disorder: Ecological adaptations not mutations

Posted on August 2, 2014 by James Kohl.

In the context of order and disorder that includes what is known about quantum physics and light-induced amino acid substitutions in plants and animals, as well as the control of the functional rearrangement of influenza hemagglutinin, I’m beginning to see even more confusion/obfuscation enter the picture of biophysically-constrained ecological adaptations.

The nutrient-dependent ecological adaptations are now being put into the context of mutation-initiated natural selection and the evolution of biodiversity (i.e., “Evolution for Dummies”).

ECOLOGICAL ADAPTATIONS (not mutations)

Nutrient-dependent changes in the microRNA/messenger RNA balance are readily linked from ecological variation to ecological adaptations via conserved molecular mechanisms that eliminate mutation-initiated natural selection and evolution from consideration. However, since no experimental evidence of biologically-based cause and effect has shown that mutations are ever fixed in the organized genomes of any population of any species, researchers now refer to the amino acid substitutions that are fixed in the genome as if they were epimutations (translation: epigenetically-effected mutations).

For example, in this article about epimutations, microRNAs also are referred to as small RNAs and labeled sRNAs with this mention of what a small RNA is. “Most of these sRNAs average 21–24 nucleotides in length…”

A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides). Thus, the quantum leap from biophysically constrainted light-induced amino acid substitutions to the nutrient-dependent microRNA/messenger RNA balance that controls genome stability via epigenetically-effected amino acid substitutions is replaced with the concept of epigenetically-effected mutations, which are called epimutuations.

By mixing the theory of mutation-initiated natural selection and the evolution of biodiversity with biological facts about how ecological variation leads to epigenetically-effected ecological adaptations manifested in biodiversity, the senior author of the “epimutations” article sets the stage for his claim to be “the first” to find something new and important.

It could be like the discovery of other molecular phenomena like introns or microRNAs, where it all began with just one example,” said Heitman. “We think this discovery may turn out to be generalized fairly quickly.

What discovery? They link nutrient-dependent microRNAs from ecological variation to ecological adaptations in the context of conserved molecular mechanisms in species from microbes to man.

The researchers think these epimutations could be employed in a variety of situations, enabling an organism to adapt to an unfavorable environment and then adapt again when conditions improve.

DISCOVER THIS!

Nutrient-dependent epigenetically-effected alternative splicings of pre-mRNA, …


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Chromosomal rearrangements and hibernation

Posted on July 31, 2014 by James Kohl.

Prepped for the Long Sleep

Hibernation-related proteins are common even in non-hibernating animals, a study shows.

By Jyoti Madhusoodanan | July 30, 2014

Article excerpt: “These genes clustered on the same chromosome fairly near to one another, leading the researchers to at first believe they were conserved throughout mammalian evolution. But the researchers did not find these genes in the mouse, rat, dog, chicken, and human genomes.”

My comment: In the context of mutation-initiated natural selection and the evolution of biodiversity, do mutations lead to conserved chromosomal rearrangements in some mammals but not in others? I ask because of comments by PZ Myers from his attack on John A. Davison, which prefaced his attack on me.

Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species:

In my model, the allelic differences between species of mammals and all vertebrates and invertebrates are nutrient-dependent and pheromone-controlled like they are in other species from microbes to man. Ecological variation leads to nutrient-dependent alternative splicings of pre-mRNA and pheromone-controlled amino acid substitutions that differentiate cell types, which are manifested in morphological and behavioral phenotypes.

What experimental evidence of biologically-based cause and effect led to PZ Myers attacks, and why didn’t he tell anyone about the biological basis for his ridiculously pseudoscientific opinion?

How can scientific progress be made if people like PZ Myers do not explain how experimental evidence led to their claims that serious scientists, like Dobzhansky are cranks?   “…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.” (1973)…


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microRNAs differentiate neuronal cell types

Posted on July 31, 2014 by James Kohl.

microRNAs: key triggers of neuronal cell fate

Excerpt: “In light of the fact that miRNAs have very precise expression patterns depending on the cell type, tissue and/or developmental stage; it is challenging to generalize a single mechanism to regulate their expression and to identify the target genes that each miRNA has during each stage of neurogenesis. Thus, the combination of bioinformatic tools and experimental techniques will help in the study of miRNAs role in early neurogenesis and how they, their target genes, and their regulators are integrated within the regulatory gene expression networks that determine each particular neuronal phenotype.”

My comment: In my model, the nutrient-dependent microRNAs (miRNAs) are the key triggers of all cell type differentiation in all cells of all individuals of all species. The epigenetically effected miRNA/messenger RNA (mRNA)  balance controls cell type differentiation by the metabolism of nutrients to species-specific pheromones. The physiology of reproduction is controlled by pheromones, which allows ecological variation to lead to ecological adaptations via the supply of nutrients. Simply put, microRNAs differentiate cell type via the pheromones that control the nutrient-dependent physiology of reproduction, which controls nutrient-dependent biodiversity.

Although it is becoming clear that Convergent microRNA actions coordinate neocortical development via cell type differentiation that is nutrient-dependent and pheromone-controlled, not all researchers agree that cell type differentiation should be removed from the context of mutation-initiated natural selection and the evolution of biodiversity. For example: in  A critical appraisal of the use of microRNA data in phylogenetics, the authors seemingly claim “…a Bayesian statistical approach that explicitly models the process of miRNA evolution may reveal the uncertainty of phylogenetic studies…” See also: Flaws emerge in RNA method to build tree of life.

By focusing on the evolution of microRNAs and statistics that link them to differentiation of cell types during different developmental stages in different species, the nutrient-dependent nature of the microRNAs that differentiate the cell types of all individuals in all species during their development is removed from consideration. There is no mention of nutrient-dependent pheromone-controlled epigenetic effects on microRNAs that link food odors to changes in the microRNA/messenger RNA balance and amino acid substitutions that differentiate cell types.

Thus, the most parsimonious and well detailed explanation of how ecological variation results in nutrient-dependent pheromone-controlled cell type differentiation via amino acid substitutions: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems, is replaced prior to its …


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