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Salk Institute: Brain shows stunning “genomic diversity”

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No, we know… This is not our high school genetics.

From the Salk Institute:

LA JOLLA—Our brains contain a surprising diversity of DNA. Even though we are taught that every cell in our body has the same DNA, in fact most cells in the brain have changes to their DNA that make each neuron a little different.

Now researchers at the Salk Institute and their collaborators have shown that one source of this variation—called long interspersed nuclear elements or L1s—are present in 44 to 63 percent of healthy neurons and can not only insert DNA but also remove it. Previously, these L1s were known to be small bits of DNA called “jumping genes” that copy and paste themselves throughout the genome, but the researchers found that they also cause large deletions of entire genes. What’s more, such variations can influence the expression of genes that are crucial for the developing brain.

The findings, published September 12, 2016 in the journal Nature Neuroscience, may help explain what makes us each unique—why even identical twins can be so different from one other, for example—and how jumping genes can go awry and cause disease.

Gage believes that diversity can be good for the brain—after all, about half of our brain cells have large chunks of missing or inserted DNA caused by L1s alone—but that too much of it can cause disease. More.

See also: Jumping genes? Life continues to ignore what evolution experts say

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10 Replies to “Salk Institute: Brain shows stunning “genomic diversity”

  1. 1
    bornagain77 says:

    Per Jonathan Wells,, “It’s the organism controlling the DNA, not the DNA controlling the organism.”

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,,
    The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism.
    In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,,
    ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view.
    I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.
    http://www.evolutionnews.org/2.....93851.html

    A few more notes:

    Neurons constantly rewrite their DNA – Apr. 27, 2015
    Excerpt: They (neurons) use minor “DNA surgeries” to toggle their activity levels all day, every day.,,,
    “We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell’s identity,” says Hongjun Song, Ph.D.,, “This research shows that some cells actually alter their DNA all the time, just to perform everyday functions.”,,,
    ,,, recent studies had turned up evidence that mammals’ brains exhibit highly dynamic DNA modification activity—more than in any other area of the body,,,
    http://medicalxpress.com/news/.....e-dna.html

    Duality in the human genome – Nov. 28, 2014
    Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.
    The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,,
    According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe.
    http://medicalxpress.com/news/.....enome.html

    The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern – July 2011
    Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,”,,, “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”,,,
    http://www.physorg.com/news/20.....-seen.html

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.”
    leodp – UD blogger

  2. 2
    Dionisio says:

    Our brains contain a surprising diversity of DNA.

    Can someone explain why they keep saying ‘surprising’?

  3. 3
    JoeCoder says:

    So L1 transposons actively edit DNA in our healthy brain cells. Does this also happen in the germline? Does that mean that when two organisms share a deletion it is not necessarily from common descent?

  4. 4
    awstar says:

    I think they’re on to something. Might it be that a Boltzmann-brain was the source of the first living cell?

  5. 5
    gpuccio says:

    Transposons, transposons… 🙂

  6. 6
    gpuccio says:

    From Wikipedia:

    “LINE1 (also L1 and LINE-1) are transposable elements in the DNA of some organisms and belong to the group of Long interspersed nuclear elements (LINEs). L1 comprise approximately 17% of the human genome.”

    Non coding DNA, again! 🙂

  7. 7
    Dionisio says:

    gpuccio:
    You can say here: “I told you so” because you have mentioned these transposons many times for quite some time.
    It seems like you’re about to get vindicated by science.
    Now, one question:
    How do the transposons relate to ID?

  8. 8
    Dionisio says:

    gpuccio @6:

    Non coding DNA, again! 🙂

    Yes, but that’s just 17%
    What about the rest (>80%)?
    🙂

  9. 9
    Dionisio says:

    Are these transposon-related DNA differences neutral or even deleterious? Are there cases of novel functionality observed?

    How do these DNA differences originate?

    Do the transposons get inserted anywhere randomly, though within biochemical constraints?

  10. 10
    gpuccio says:

    Dionisio:

    My point of view has always been clear: transposons are the best candidates as tools of design.

    Tools of design must be potentially random events that can be guided by consciousness at quantum level.

    While traditional mutations can be such a kind of events, transposon activity fits better the scenario (and the existing data).

    Regarding somatic variation in individuals at neuron level, this is simply a rather new finding, and very interesting. I believe it can have functional meaning, but it is too early to say.

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