Brave new epigenomes: the dawn of epigenetic engineering

Reported as:

Opinion: Engineering the Epigenome

Excerpt: .

..until recently, we were not able to assess the influence of individual marks on gene activity because it was only possible to alter chromatin marks globally through mutational approaches or pharmacological inhibition.

My comment: Mutational approaches led to assumptions about cell type differentiation that failed to include the role of viruses, viral microRNAs,  and the nutrient-dependent microRNAs that prevent the accumulation of viral microRNAs from linking entropic elasticity to genomic entropy.

See for contrast: E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity and The octopus genome and the evolution of cephalopod neural and morphological novelties

The sequencing of the octopus genome since linked nutrient-dependent microRNAs to adhesion proteins and cell type differentiation that is perturbed by viruses. That fact links viruses to all stress-induced pathology via perturbed protein folding that is linked directly from nutrient uptake to RNA-mediated DNA repair that controls the damage caused by virues.

Viruses perturb protein folding during thermodynamic cycles of protein biosynthesis and degradation, which is why mutations are linked to disorders, diseases, and early death that could be prevented by what is now known.

See for example: DNA methylation pathways and their crosstalk with histone methylation and Neuroscientist David Edelman on Paradigm Shift (YES) and Origin of ‘3D Organismal Form’ 

RNA-directed DNA methylation and RNA-mediated gene duplication link nutrient-dependent RNA-mediated amino acid substitutions from the biophysically constrained chemistry of protein folding to cell type differentiation in all cell types of all individuals of all living genera. Nutrient-dependent microRNAs clearly support immune system function, which typically protects organized genomes from virus-driven DNA damage. DNA damage is linked to unsuccessful reproduction via everything known about the nutrient-dependent physiology of reproduction.

An approach to healthy longevity can therefore be extended across generations when all scientists integrate what is known about physics, chemistry, and biology via the conserved molecular epigenetic mechanisms of cell type stability. Cell type stability has been virtually ignored by researchers who have focused on genetics and ignored the facts presented in the context of articles like “Beyond neo-Darwinism—an epigenetic approach to evolution.” See also: The Rainbow and the Worm: The Physics of Organisms 3rd Edition

Excerpt:

This highly unusual book began as a serious inquiry into Schrödinger,s question, “What is life? “, and as a celebration of life itself. It takes the reader on a voyage of discovery through many areas of contemporary physics, from non-equilibrium thermodynamics and quantum optics to liquid crystals and fractals, all necessary for illuminating the problem of life.

The link from Schrödinger,s quantum physics to quantum biology via quantum smell to quantum consciousness now includes RNA-directed events, which link microRNAs to cell adhesion in healthy longevity compared to disease.

See: DNA methylation pathways and their crosstalk with histone methylation

Excerpt:

Histone and DNA methylation have important and connected roles in the epigenetic control of gene expression in all three kingdoms of eukaryotic organisms.

See also: Matthew P. A. Fisher’s Quantum Cognition: The possibility of processing with nuclear spins in the brain. 

Abstract excerpt:

We identify the “Posner molecule”, Ca9(PO4)6, as the unique molecule that can protect the neural qubits on very long times and thereby serve as a (working) quantum-memory.

This was reported by John Hewitt as: Neural qubits: Quantum cognition based on synaptic nuclear spins

Excerpt:

The present discussion of regarding curious phosphate phenomena does not pop out fully-formed from in its own void. There is an ample if occaisionally controversial body of experimental findings dealing with magnetic isotope and field effects on the major phosphorylation reactions of life

My comment: This required the experimental evidence that links field effects to the major phosphorylation reactions of life must be placed into the proper context.

See: Is there contextuality in behavioral and social-systems?

My comment: The only way to put context-dependent behaviors into the proper perspective of top-down causation is by starting from the sun’s biological energy. That is how energy links physics to chemistry and biology via conserved molecular mechanisms. Alternatives can be compared in this context.

Neuroscientist David Edelman on Paradigm Shift (YES) and Origin of ‘3D Organismal Form’

See also: Reentry: A Key Mechanism for Integration of Brain Function, which was co-authored by David Edelman’s father.

Unfortunately, it is pointless to attempt to address the links from quantum physics to quantum biology in discussion groups where individuals have never learned enough about biologically based cause and effect to do more that attribute evolution to mutations and/or natural selection.

See for example my facebook group comments:

Re: Neuroscientist David Edelman on Paradigm Shift (YES) and Origin of ‘3D Organismal Form’

Also, watch biologically uniformed trolls try to address the facts about ‘3D Organismal Form” in the discussion of Neural qubits: Quantum cognition based on synaptic nuclear spins

My comment: Suzan Mazur concludes this week’s addition to her expose of neo-Darwinian nonsense with this claim:

My comment: I’m convinced that she is taking a considerate approach to finalizing this series with something that attests more fully to the amount of pseudoscientific nonsense that neo-Darwinian theorists have forced on the unsuspecting masses.

Obviously, the rules of the game haven’t changed. Ecological variation must lead to nutrient-dependent RNA-mediated ecological adaptation via the biophysically constrained physiology of reproduction or ecological variation leads to extinction via mutations that perturb RNA-mediated protein folding chemistry.

If Ms. Mazur was Schrodinger, the cat already would be alive and well outside the box that theoretical physicists put it into when they ignored Schrodinger’s comments about sunlight as the most likely anti-entropic link to answering the question “What is Life?”

Mae-Won Ho and others know that light is the nutrient source that protects life from virus-driven extinction. The direct effects are manifested in photosynthesis, with indirect effects on species survival that link symbiosis to the nutrient-dependent physiology of reproduction in all living genera. Why is David Edelman focussed on the role of visual input and its indirect effect on hormones that affect behavior when others have linked olfaction and pheromones from the morphological and behavioral phenotypes of species from octopuses to humans via what is currently known about molecular epigenetics?

My comment: In the light of evolution and our ability to see it… “The cat was picked in honour of a thought experiment, proposed in 1935 by the Austrian physicist Erwin Schrödinger, in which a hypothetical cat in a box is both alive and dead, as long as no one knows whether or not a poison in the box has been released.”

See: Entangled photons make a picture from a paradox

In the context of that thought experiment, it appears the cat could have been inside and outside the box at the same time.

What this suggests to me is the David Edelman’s perspective on the importance of visual input to the octopus will fall prey to details about the importance of olfaction in the context of quantum physics and quantum biology. I’m not sure Suzan Mazur will take us quite that far, but I am sure that Anna Di Cosmo’s work will help others to do so.

See for example: Role of olfaction in Octopus vulgaris reproduction

Stephen Hawking should see GGGGCC repeat expansion in C9orf72 compromises nucleocytoplasmic transport, reported as: Nuclear transport machinery is compromised in ALS!

His focus on theoretical physics has probably caused him to miss some important information on links between nutritional epigenetics and the transgenerational epigenetic inheritance of predispositions for all neurodegenative diseases. However, the big bang cosmology industry and evolution industry continue to ensure that most people will never realize that everything from atoms to ecosystems is RNA-mediated.

The sequencing of the octopus genome links the innate immune system of all genera to RNA-mediated cell type differentiation via what is now known about nutrient-dependent microRNAs and adhesion proteins in healthy longevity compared to virus perturbed genomic entropy via the accumulation of viral microRNAs.

The octopus genome and the evolution of cephalopod neural and morphological novelties

Excerpt:

Surprisingly, our phylogenetic analyses suggest that the squid and octopus protocadherin arrays arose independently. Unlinked octopus protocadherins appear to have expanded ~135 Mya, after octopuses diverged from squid.

My comment: No experimental evidence suggests that their results can be placed into the context of evolution or linked to divergence of any species at any time during the history of this planet.

See again: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity Reported as: Reprogramming Cancer Cells Back to Normal Cells

Excerpt:

…PLEKHA7 maintains the normal state of the cells, via a set of miRNAs, by tethering the microprocessor to E-cadherin and p120. In this state, E-cadherin and p120 exert their good tumor suppressor sides.

My comment: The role of nutrient-dependent microRNAs and E-cadherin in the maintenance of cell type integrity can be compared to what happens when the accumulation of viruses alter the integrity of cell types by stealing the nutrient-dependent energy they require for proper protein folding.

One more time, see: Neuroscientist David Edelman on Paradigm Shift (YES) and Origin of ‘3D Organismal Form’

 Suzan Mazur:

What would you say about the following driving biological evolution toward increasing complexity?: (1) adhesive interactions among cells, which your father was studying, (2) infection of cellular organisms by viruses, bacteria or fungi plus symbiosis, (3) the constructal law of flow systems–

David Edelman:

It’s a combination.

My comment: Given the fact that the combination must link quantum physics to quantum biology, any attempt to link the combination to biologically-based cause and effect must start with top-down causation and link the sun’s biological energy to cell type differentiation in all cells of all individuals of all living genera. If not, researchers like David Edelman will never have anything more than a theory that cannot link atoms to ecosystems via what is currently known to serious scientists about physics, chemistry, and molecular epigenetics.

Keep Reading