See for review: A Mathematical Model Links Quantum Physics to Quantum Souls (1)

See for comparison: Zaugg Lab

We are applying and developing computational biology tools for integrating large-scale biological ‘omics data to address questions in personalised genomics.

The Zaugg Lab ignores everything known to serious scientists about energy-dependent top-down causation, which is the only way to link quantum physics to biophysically constrained biologically-based biodiversity. Watch them try to do that with a mathematical model, instead.

Loops in DNA affect which proteins are coded 

EMBL scientists unveil how 3D chromatin structure affects RNA splicing

SARCASM ALERT

Q: How does the energy-dependent 3D chromatin structure create itself?

A: Automagically

See: CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals

Read how they link biophysically constrained food energy-dependent alternative RNA splicing to cell type differentiation via 3D chromatin structure without the energy. The food energy is biophysically constrained by autophagy in the context of the physiology of pheromone-controlled reproduction. But they ignore the fact that the energy must be biophysically constrained in the cell membrane via hydrogen-atom transfer in DNA base pairs in solution.

See Long-range coherence and energy storage in biological systems (1968)

Biological systems are expected to have a branch of longitudinal electric modes in a frequency region between 1011 and 1012 sec−1. They are based on the dipolar properties of cell membranes; of certain bonds recurring in giant molecules (such as H bonds) and possibly on pockets of non-localized electrons. In Section 2 it is shown quit generally that if energy is supplied above a certain mean rate to such a branch, then a steady state will be reached in which a single mode of this branch is very strongly excited. The supplied energy is thus not completely thermalized but stored in a highly ordered fashion. This order expresses itself in long-range phase correlations; the phenomenon has considerable similarity with the low-temperature condensation of a Bose gas. General consequences and proposals of experiments are discussed in section 3.

It seems likely that the Zaugg lab will continue to bastardize everything known to serious scientists about biophysically constrained energy-dependent alternative RNA splicing.

See also:

Ruiz-Velasco M, Zaugg JB (2017). Structure meets function: How chromatin organisation conveys functionality. Current Opinion in Systems Biology: 1, Feb 2017,129-136, ISSN 2452-3100

Cakiroglu SA, Zaugg JB, Luscombe NM. (2016)  Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.  Nucleic Acids Res. 44 (17): 8065-8072

Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016) Data-driven hypothesis weighting increases detection power in genome-scale multiple testingNat Methods. Jul;13(7):577-80

Arnold C, Bhat P,  Zaugg JB. (2016) SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. Bioinformatics. doi:10.1093/bioinformatics/btw127

Grubert F*, Zaugg JB*, Kasowski M*, Ursu O*, et al. (2015) Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. 162 (5): 1051-1065
         This article was highlighted in Cell, and Nature Genetics, and also covered by an EMBL press release

For more nonsense about CTCF-mediated effects on chromatin from the January 2018 Active Motif Epigenetics News, see

YY1 Is a Structural Regulator of Enhancer-Promoter Loops.
In the current issue of Cell, Weintraub et al show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF, and propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.
Weintraub A.S. et al: Cell. 2017 Dec 14;171(7):1573-1588.e28. doi: 10.1016/j.cell.2017.11.008. Epub 2017 Dec 7.

See for comparison a search for “Yin Yang” at Autophagy.pro

The food energy-dependent pheromone-controlled enhancer-promoter interactions are the obvious link to gene activation and biophysically constrained viral latency in all living genera.

Highlighted articles and press releases tend to obfuscate the facts that we included in our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation.

From Fertilization to Adult Sexual Behavior

ZFX and ZFY are described as “DNA-binding proteins” and via their binding of sexually dimorphic proteins, chromatin structure and transcription could be modulated in sexually dimorphic ways as a result of females having only ZFX binding events, whereas males would have a mixture of both ZFX and ZFY binding events (Fiddler, Abdel-Rahman, Rappolee, and Pergament, 1995; Lau and Chan, 1989; Zwingman, Erickson, Boyer, and Ao, 1995).

Twenty-one years later, in CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals, the DNA-binding proteins have been represented in the context of the CCCTC-binding factor (CTCF), which supposedly

…is known to establish long-range DNA contacts that alter the three-dimensional architecture of chromatin.

In 1996, we wrote:

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 fact that the sex differences are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction has not been linked to viral latency by theorists. And biophysically constrained energy-dependent viral latency has typically not been linked to healthy longevity.

What went wrong outside the context of ridiculous theories? Did serious scientists forget they were supposed to be fighting against ridiculous misrepresentations by theorists?

See my comments on: Combating Evolution to Fight Disease 2014

2 January 2015 Inching toward the 3D genome

16 Jan 2015 All in the (bigger) family

In the context of the (bigger) family, theorists still seem to think that new species evolve.

Ringing in 2018 with 85 new species

From sea slugs to sharks to flowering plants, spanning 5 continents and 3 oceans, these new discoveries add to Earth’s tree of life.

How could any intelligent person miss the obvious link from the weekend resurrection of the bacterial flagellum in P. fluorescens to UV light-activated endogenous substrates in all living genera. (P. fluorescens gets its name from the fact that it fluoresces on exposure to UV light.)

Watch for the common theme:

See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits (2017)

Summary: Bacteria that eat electrons create uranium isotopes.

Transcriptomic Evidence for the Expression of Horizontally Transferred Algal Nuclear Genes in the Photosynthetic Sea Slug, Elysia chlorotica (2012)

Reported as: The Sea Slug That Eats The Sun  by: Sidney Pierce 15 Jan 2013

See: A Mathematical Model Links Quantum Physics to Quantum Souls (3)

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