De novo gene creation: Ignoring the experimental evidence

By: James V. Kohl | Published on: November 24, 2016

Regularly Whiffing Essential Oils Can Retrain Lost Sense of Smell

It’s not entirely clear how olfactory training works on a neurological level.

Olfactory training links the experience-dependent de novo creation of G protein-coupled receptors to supercoiled DNA. Conserved molecular mechanisms link food odors and pheromones from the innate immune system to the physiology of reproduction. Simply put, autophagy protects all organized genomes from virus-driven entropy and all pathology via the de novo creation of odor receptor genes.
See for proof: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

The 3D segmentation of high-resolution images provided by SXT reveals an unappreciated interconnectivity between distinct forms of chromatin. The continuous nature of like-chromatin, which is evident even in the nucleolus, supports the existence of non-stereotypic but extensive interactions between different chromosomes, which might have significant regulatory roles in transcription and other nuclear processes.

Natural selection for energy-dependent codon optimality is the obvious link to experience-dependent chromatin remodeling and the de novo creation of species-specific G protein-coupled receptors, which link chemotaxis and phototaxis from the innate immune system to the physiology of reproduction in all living genera. It is obvious to all serious scientists that energy-dependent receptor-mediated biophysically constrained cell type differentiation is the link from angstroms to ecosystems in all living genera. But, in the next sentence, these authors claim (with my emphasis):

Although sequence-specific association of co-regulated genomic loci is appealing, random interactions between loci with shared chromatin properties might be an equally effective way of modulating transcription levels.

No experimental evidence of biologically-based cause and effect supports that ridiculous claim about random interactions. No experimental evidence of biologically-based cause and effect has ever supported similar claims that link anything except the energy-dependent de novo creation of functional protein structures via the modulation of transcription.

Transcription is energy-dependent and biophysically constrained. It links the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and protects all organisms from all pathology via autophagy.

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo was reported as

Imaging Technique Reveals Movement of Genetic Material Within Nucleus

Chromatin functions to package DNA so that it can fit inside of a cell, and forms chromosomes. In the video above, take a trip through the nucleus of a cell; in the video below, DNA reorganization in the nucleus a mouse cell is illustrated.

…it had been thought that chromatin existed as a group of disconnected islands, but the latest report indicated that chromatin is compartmentalized into two areas of “crowding” that comprise a continuous network throughout the nucleus.

The continuous network of chromatin distributes energy as information in the context of hydrogen-atom transfer in DNA base pairs.  Energy-dependent changes in base pairs link quantized energy from angstroms to ecosystems in all living genera via changes in the microRNA/messenger RNA balance. The ability to image the changes has not been linked from chromatin remodeling to RNA-mediated amino acid substitutions and chromosomal rearrangements, because the detailed sequence of biologically-based cause and effect refutes all neo-Darwinian theories. Natural selection for codon optimality comes first, not natural selection for benefical mutations. There is no such thing as a beneficial mutation.

Reported also as: 3-D Imaging Technique Maps Migration of DNA-carrying Material at the Center of Cells

Detailed 3-D visualizations show an unexpected connectivity in the genetic material in a cell’s nucleus, and provide a new understanding of a cell’s evolving architecture.

What architecture evolves? Does it evolve via mutation-driven evolution? How is that possible?

These unique 3-D reconstructions of mouse olfactory cells, which govern the sense of smell, were obtained using X-ray imaging tools at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). The results could help us understand how patterning and reorganization of DNA-containing material called chromatin in a cell’s nucleus relate to a cell’s specialized function as specific genes are activated or silenced.

The 3-D reconstructions govern the sense of smell via the de novo creation of G protein-coupled receptors in the mouse olfactory cells. The cells do not create or recreate themselves. Organization and reorganization of chromatin is energy-dependent.

“We’re trying to understand how the reorganization of chromatin affects gene expression,” Larabell said.

No you are not. You’re trying to avoid admitting that you got caught with your pants down after having missed all the experimental evidence of biologically-based cause and effect that refutes neo-Darwinian nonsense.

“No one’s been able to study this at the human level yet.” This research will hopefully lead to new insights about diseases and disorders that relate to gene expression. Already, the study’s results are being incorporated into models of cell development.

There is only one model of cell energy-dependent cell type differentiation during the development of all morphological and behavioral phenotypes in species from microbes to humans.
See for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

One of the precursors to Alzheimer’s disease, which attacks the brain’s nerve cells, is a loss of smell, so understanding this connection to olfactory nerve cells could perhaps serve as a diagnostic tool and perhaps unlock a deeper understanding of the degenerative disorder.

Who is claiming that this energy-dependent connection to the de novo creation of genes in olfactory nerve cells is not already understood by all serious scientists? Why are they lying about what is already known?

“This work highlights the power of multidisciplinary research,” said Mark Le Gros, associate director of the NCXT and a physicist who was responsible for the design and construction of the X-ray microscope. Le Gros, the lead author in this research, added, “This is an example of work that required a combination of molecular biologists and cell biologists with physicists and computer scientists.”

It highlights the ignorance of theorists. See for example: Search Results for “alzheimer”
For a historical perspective on the ignorance of theorists who are among the molecular biologists and cell biologists with physicists and computer scientists who published a paper that ignored all the accumulated experimental evidence of biologically-based cause and effect, see: Learning from Bacteria about Natural Information Processing

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

See also: From Fertilization to Adult Sexual Behavior
We included a section on molecular epigenetics, and nothing about the facts that we detailed has changed at any level of examination that links energy-dependent changes from angstroms to ecosystems in all living genera.

The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).

See also The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity Published September 30, 2015
Their cited works link energy-dependent chromatin interactions from the determinants of nucleosome organization to G+C content and intrinsic nucleosome occupancy, which is linked to biophysically constrained cell type differentiation via chromosomal inheritance in primary human cells. The terms “promoter elements” and “self-renewal” are used to obfuscate the fact that energy-dependent RNA-mediated amino acid substitutions differentiate all cell types in all living genera in the context of autophagy and polycombic ecological adaptations. The nutrient energy-dependent fixation of the RNA-mediated amino acid substitutions in supercoiled DNA is not mentioned in the context of autophagy, which must be linked to physiology of reproduction. The game of hide the facts about virus-driven energy theft and all pathology continues to be played by experts who do not want anyone to know what they missed when they invented their theories and taught others to believe in them.
Reported Nov 22, 2016  as: Researchers uncover a survival mechanism in cancer cells

The results showed an inverse relation between H1.0 and the division of cancer cells: “As the H1.0 levels fall, the greater the potential of uncontrolled division of cells. In contrast, high levels of the protein prevent this process. We found that the disappearance of protein H1.0 is characteristic of cancer stem cells and it is necessary to maintain the ability of partition and the potential for growth creation.”

Virus-driven energy theft is clearly linked to the disappearance of H1.0 via everything known to serious scientists about autophagy. Energy-dependent RNA-directed DNA methylation stops the proliferation of undifferentiated cell types is all living genera and it links amino acid substitutions from biophysically constrained protein folding chemistry to supercoiled DNA and all biodiversity. Reports of negative supercoiling in bacteria link virus-driven energy theft from the creation of archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA via the conserved molecular mechanisms of epigenetic top-down causation that links food odors from pheromones to the physiology of reproduction.
See also: How keeping active pays off in the olfactory system
open access with comments at Neuroscience: How keeping active pays off in the olfactory system

Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?
Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338. DOI: 10.3402/snp.v2i0.17338.

The article elucidates how the environment can broadly influence gene expression through an epigenetic effect chromatin – the way DNA is package and organized. This allows the environment to influence sensory function, to tune the olfactory sense to better suit the surrounding environment, because these environmentally regulated chromatin changes are coupled to cell longevity. This results in a change in the distribution of cells in the tissue that have made particular stochastic choices, where the stochastic choice is which olfactory receptor to express, without affecting the mechanism of stochastic gene expression.

I have since modeled nutrient-dependent pheromone-controlled adaptive evolution and uploaded the text and diagram, which are available here:… I was advised I should have previously declared ownership of the domain and my commercial involvement in marketing products based on animal models of common molecular mechanisms in species from microbes to man.

I have since published “Nutrient-dependent/pheromone-controlled adaptive evolution: a model” https://www.socioaffectiveneuro…

Model organisms exemplify the fact that the epigenetic effects of olfactory/pheromonal input result in nutrient-dependent amino acid substitutions and changes in phenotype associated with the pheromone-controlled physiology of nutrient-dependent reproduction. Included are example in microbes, nematodes, insects, other mammals, and a human population that adaptively evolved in what is now central China during the past ~30,000 years.

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