Theorists tend to use the term de novo when they don’t know.

If they don’t know how energy-dependent structures and functions are created, functional structures are created de novo.

See for example:  Lymphotoxin-Dependent B Cell-FRC Crosstalk Promotes De Novo Follicle Formation and Antibody Production following Intestinal Helminth Infection

If theorists don’t know what causes mutations, the mutations are de novo mutations.

See for example: Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures

My comment: The energy-dependent de novo creation of functional structures readily extends what is known about viruses and energy theft to the creation of de novo mutations that cause all pathology. Serious scientists have linked the energy-dependent creation of nucleic acids from angstroms to ecosystems. They have linked virus-driven energy theft to all pathology via the creation of viral nucleic acids. Nucleic acids do not create themselves. Their creation is energy-dependent. Viruses steal the energy that links hydrogen-atom transfer in DNA base pairs in solution to pH and healthy longevity.

See, for instance: DNA and RNA structure: nucleic acids as genetic material

Excerpt:

Asking what holds two strands of DNA together presupposes there’s some other force trying to pull the strands apart. There is, and that force is none other than heat. Heat, after all, is just random motion of molecules, and the force of this vibrational motion depends on temperature.

Remember this:

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

See also: Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79

Excerpt:

KOS63 and its variants have a mutation present in the TATA-box promoter region of the membrane protein US9, as well as a substitution at position 58 in the US9 gene. This substitution introduces an early stop codon, and truncates the last 32 residues of the US9 protein (Macdonald et al., 2012; Negatsch et al., 2011). This mutation removes the stop codon and elongates the neighboring open reading frame of US8A, a protein of undetermined function (Macdonald et al., 2012; Negatsch et al., 2011).

My comment: If you don’t know the difference between a mutation and an amino acid substitution, you know nothing about how energy-dependent RNA-mediated cell type differentiation is biophysically constrained in the context of thermodynamic cycles of protein biosynthesis and degradation.  But, you are among the majority.

See for comparison to what others do not know about energy-dependent cell type differentiation: Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design

Excerpt:

Comparative Model Studies Reveal That Nature Chooses the Simplest and Robust Design of Feedback Regulation.

Conclusion:

 …enhancer elements may also help on recruiting histone modification enzymes, leading to coupling between the two layers of regulation. Future studies will reveal these possible fine-tuning elements and address its implications in other processes of gene regulations.

My comment: In other words, nature fine-tunes itself by choosing which genes must be regulated by feedback. Serious scientists joke about such ridiculous misrepresentations.

Structural diversity of supercoiled DNA (parody)

Chemists know (parody)

See also: New Insights into the Mysteries of Smell

Excerpt: 

In the new study, Dr. Xing and colleagues used these existing experimental data to create a computational model of how olfactory receptor expression can be both uniform across a single neuron, yet very diverse across the entire population of neurons. They then used this model to correctly predict several additional findings that have been demonstrated by other research groups, demonstrating that their model is valid.

My comment to the Neuroscince News site: Their model seems irrelevant compared to what is known about the biophysically constrained chemistry of energy-dependent protein folding.I plan to present this tomorrow at this free online conference.

http://www.labroots.com/virtual-event/genetics-genomics-2016

RNA-mediated physics, chemistry, and molecular epigenetics

Abstract: Olfaction and the innate immune system link energy as information from the epigenetic landscape to the physical landscape of supercoiled DNA. The sun’s biological energy is the source of the information that links angstroms to ecosystems via physics, chemistry, and molecular epigenetics.

RNA-mediated protein folding chemistry and amino acid substitutions link the anti-entropic quantized energy of sunlight from the virucidal effects of ultraviolet (UV) light to healthy longevity via biophysically-constrained energy-dependent hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation.

Biomarkers link energy-dependent differences in base pairs and amino acid substitutions to biosignatures across the healthy life span. RNA-mediated amino acid substitutions also reveal the increasing complexity of interactions among cell types as pathology progresses. For comparison, successful reproduction links energy from supercoiled DNA to protection of all organized genomes from virus-driven energy theft and pathology.

This model links the sun’s biological energy from top-down causation in microbes to the most recent model of bottom-up gene activation and cell type differentiation in vertebrates. Citations to extant literature provide examples of what is currently known about how ecological variation leads to biophysically constrained cell type differentiation in the context of nutritional epigenetics and Precision Medicine, which clearly link metabolic networks and genetic networks to pharmacogenomics.

———————-

Summary: In the series of five blog posts “RNA-mediated physics, chemistry, and molecular epigenetics” (1-5), I included citations to experimental evidence of biologically-based cause and effect. The citations link energy-dependent changes from angstroms to ecosystems because that is what serious scientists do.

RNA-mediated physics, chemistry, and molecular epigenetics (5) 5/10/16

RNA-mediated physics, chemistry, and molecular epigenetics (4) 5/9/16

RNA-mediated physics, chemistry, and molecular epigenetics (3) 5/9/16

RNA-mediated physics, chemistry, and molecular epigenetics (2) 5/6/16

RNA-mediated physics, chemistry, and molecular epigenetics 5/4/16

Serious scientists do not link computer models of biologically-based cause and effect to cell type differentiation without an energy source. That’s what pseudoscientists do.

If the switch on a pseudoscientist’s computer is turned off, or their computer gets infected by a virus that steals its energy to replicate, pseudoscientists no longer have a model of anything. They have only their ridiculous theories, and the ridiculous theories of pseudoscientists do not link energy-dependent life to biodiversity via what is known to serious scientists.

See for comparison: Feedback loops link odor and pheromone signaling with reproduction and Combating Evolution to Fight Disease.

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