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Apparently, there is still another layer of gene control

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image of DNA/Jezper, Fotolia

From ScienceDaily:

A person’s DNA sequence can provide a lot of information about how genes are turned on and off, but new research out of Case Western Reserve University School of Medicine suggests the 3-D structure DNA forms as it crams into cells may provide an additional layer of gene control. As long strands of DNA twist and fold, regions far away from each other suddenly find themselves in close proximity. The revolutionary study suggests interactions between distant regions may affect how genes are expressed in certain diseases.

According to Scacheri, “The big surprise was when we crunched the numbers and compared the risk associated with the amount of heritability that could be explained by the outside variants. By our calculations, outside variants accounted for a whopping 2-3 times more of the heritability than explained by the current models. That was far more than we had expected.”

According to Scacheri, “The big surprise was when we crunched the numbers and compared the risk associated with the amount of heritability that could be explained by the outside variants. By our calculations, outside variants accounted for a whopping 2-3 times more of the heritability than explained by the current models. That was far more than we had expected.” Paper. (paywall) – Olivia Corradin, Andrea J Cohen, Jennifer M Luppino, Ian M Bayles, Fredrick R Schumacher, Peter C Scacheri. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nature Genetics, 2016; DOI: 10.1038/ng.3674 More.

And all that just sort of happens, the way a room tidies itself if you ignore it.

See also: Even New Scientist now seems to accept that it’s time to rethink how evolution works.

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Comments
Here's another commentary on the same paper:
Scientists discover distant DNA working together to affect disease risk http://medicalxpress.com/news/2016-09-scientists-distant-dna-affect-disease.html
Dionisio
September 24, 2016
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The big surprise was when...
Why is it that some folks are surprised so easily?Dionisio
September 23, 2016
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PaV:
Let’s hear it for the “extended evolutionary synthesis”!
Will they have to extend the extension? :)Dionisio
September 23, 2016
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In 2006, it was already observed that DNA segments interacted with other DNA segments separated by tens of millions of nucleotide bases:
Our observations demonstrate that not only active, but also inactive, genomic regions can transiently interact over large distances with many loci in the nuclear space. The data strongly suggest that each DNA segment has its own preferred set of interactions. This implies that it is impossible to predict the long-range interaction partners of a given DNA locus without knowing the characteristics of its neighboring segments and, by extrapolation, the whole chromosome. (Simonis et al. 2006)
Origenes
September 23, 2016
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I think this is the critical phrase:
Olivia Corradin, PhD, Fellow and Principal Investigator at Whitehead Institute for Biomedical Research, former graduate student in Scacheri's laboratory and lead author of the study explained, "New technologies and DNA sequencing now enable us to evaluate the 3-dimensional organization of DNA within a cell. This gave us the opportunity to assess our hypothesis that multiple DNA variants that are in physical contact with the same gene may help to explain genetic predisposition to disease."
There are other studies now out that have investigated the the 3D "chromatin" structure of the cell, where DNA is sort of 'sheathed.' Apparently--and this study is part of this general area of study--the chromatin structure that is built up can be built up in different ways. And, to add to the Darwinist's woes, it looks like LINE's (you know, "junk") is involved in how this 3D structure surrounding the DNA takes shape, with its 'shape' determining 'expression.' Another day; another bad day for Darwinism. Let's hear it for the "extended evolutionary synthesis"!PaV
September 23, 2016
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A few related notes
Dynamic Genomes in Bacteria Argue for Design - By Ann Gauger - 2015 Excerpt:"Codes within codes within codes – highly efficient and highly intelligent systems – don’t happen by accident and/or selection. The cell might begin with one code, which is incredible in itself. To layer another code in the opposite direction is far and away beyond that. Then to add a third layer of structural dynamics is simply awe-inspiring." http://www.biologicinstitute.org/post/128798433944/dynamic-genomes-in-bacteria-argue-for-design The Multi-dimensional Genome--impossible for Evolution to account for-- by Dr Robert Carter - video (11:30 minute mark) https://www.youtube.com/watch?feature=player_detailpage&v=K3faN5fU6_Y#t=690 Comparing genomes to computer operating systems - Van - May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, We show that both networks have a fundamentally hierarchical layout,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753 Universal distribution of component frequencies in biological and technological systems - February 19, 2013 Excerpt: Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual systems, and their use frequencies vary over many orders of magnitude. We study this frequency distribution in genomes of approx. 500 bacterial species and in over 2 million Linux computers and find that in both cases it is described by the same scale-free power-law distribution with an additional peak near the tail of the distribution corresponding to nearly universal components. We argue that the existence of a power law distribution of frequencies of components is a general property of any modular system with a multilayered dependency network.,,, http://www.pnas.org/content/early/2013/03/21/1217795110.abstract “Three-Dimensional Connections Across the Genome“ Keith Dunaway - ENCODE 2012 Excerpt: These analyses portray a complex landscape of long-range gene-element connectivity across ranges of hundreds of kb to several Mb, including interactions among unrelated genes (Supplementary Figure Y1). Furthermore, in the 5C results, 50-60% of long-range interactions occurred in only one of the four cell lines, indicative of a high degree of tissue specificity for gene-element connectivity http://www.nature.com/encode/threads/three-dimensional-connections-across-the-genome Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks - 25 October 2012 Excerpt Introduction: Long-range chromatin interactions are pervasive in the human genome and serve to regulate gene expression.,, Proximity ligation in combination with next-generation sequencing has recently enabled us to explore genome-wide spatial crosstalk in the chromatin.,,, The observation of most interest was that interacting promoters not only correlate with gene coexpression, but can also regulate each other’s transcriptional states, which blurs the traditional definitions of gene-regulatory elements in the genome. These observations support the notion of a chromatin interactome encompassing a dense repertoire of regulatory elements for transcriptional regulation. http://www.cell.com/cell-reports/abstract/S2211-1247%2812%2900326-9?switch=standard The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin - video (28 second mark) https://www.youtube.com/watch?v=vo3OKSGeFRQ&index=2&list=PL9C519B84FE6C1202 Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. per science daily “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340
bornagain77
September 23, 2016
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Duh! gpuccio said that long ago in this very site. Didn't those folks get his memo? :)Dionisio
September 23, 2016
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