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Clever vid on DNA Loop-the-Loops

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From The Scientist :

Hi-C yielded a dizzying array of contacts between different regions of the genome. The researchers used algorithms to determine the genome’s structure. Defining loops as regions of DNA demarcated by two loci that were more frequently in contact with one another than with other loci in between them, the researchers broke the genome down the into contact domains—regions of the genome in which loci tend to interact with each more than with other genomic regions. In many cases, contact domains are contained within loops.

“The contents of the loop tends to interact with itself,” explained study coauthor Suhas Rao, a researcher at the Center for Genome Architecture. Loci within contact domains also tend to have relatively uniform histone modifications. Finally, the researchers found that the genome can be divided into at least six subcompartments, or regions that segregate into similar sectors of the nucleus.

Altogether, the team identified around 10,000 loops—far fewer than previously estimated. “I was shocked, frankly speaking, when I saw that number,” said Ren, who himself once estimated that there were more than 1 million loops in the human genome.

“I think much depends on how you define a loop,” said Giacomo Cavalli, who studies chromatin and cell biology at the Institute of Human Genetics in Montpellier, France, and was not involved in the study.

And whether it is all just a big accident depends on how you define a big accident.

The question that comes to the fore is precisely the one the ID theorists raise: Can pure randomness create highly specified information, neatly compressed, as we are instructed to believe?

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3 Replies to “Clever vid on DNA Loop-the-Loops

  1. 1
    bornagain77 says:

    a few related notes:

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role – September 2012
    Excerpt: The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said.
    There also is a sort of DNA wiring system that is almost inconceivably intricate.
    “It is like opening a wiring closet and seeing a hairball of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.”
    There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — (several) feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.
    http://www.nytimes.com/2012/09.....wanted=all

    “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/t.....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-repor.....h=standard

    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/re.....160649.htm

    Biological Information – Not Junk After All 11-29-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=xO-7kVBA_JM
    In the book “Biological Information: New Perspectives” the chapter entitled “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information” discusses the various functions of DNA and finds that non-functional DNA is a small minority.

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2.....ellig.html

    DNA – Replication, Wrapping & Mitosis – video
    https://video.search.yahoo.com/video/play;_ylt=A2KLqIGeLYxUeBoA16j7w8QF;_ylu=X3oDMTByZWc0dGJtBHNlYwNzcgRzbGsDdmlkBHZ0aWQDBGdwb3MDMQ–?p=dna+replication+wrapping+mitosis&vid=7a17fb94b5784b10db359f21e2b35dba&l=2%3A19&turl=http%3A%2F%2Fts4.mm.bing.net%2Fth%3Fid%3DVN.608042274282998271%26pid%3D15.1&rurl=http%3A%2F%2Fvimeo.com%2F33882804&tit=DNA+-+Replication%2C+Wrapping+%26+Mitosis&c=0&sigr=10p1lm48p&sigt=115pkvign&age=0&fr2=p%3As%2Cv%3Av%2Cm%3Asa&hsimp=yhs-001&hspart=mozilla&tt=b

  2. 2
    Querius says:

    The origami theme of the video is brilliant!

    Contact domains in 3D loops and nuclear subcompartments add yet another dimension to the previously underestimated complexity of DNA, which includes multiple sections of overlapping DNA code.

    As a result, the Darwinist paradigm of “junk DNA,” becomes more and more remote, despite the tenacious apologetics to the contrary.

    This development once again demonstrates with *actual facts and observations* that the ID paradigm of treating something that looks like it’s designed as if it were designed is pragmatically and scientifically superior to assuming that it’s evolutionary “junk.”

    -Q

  3. 3
    Mung says:

    would you be interested in my forthcoming book, Feng Shui and the Genome: Proof the Intelligent Designer of Life was Chinese?

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