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The days of "junk DNA" are over

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  • The days of "junk DNA" are over

    Casey McGrath in Genome Biology and Evolution has an article titled " 'Junk DNA' No More: Repetitive Elements as Vital Sources of Flatworm Variation". The article begins with this sentence:

    Source: Genome Biology and Evolution

    “The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution.

    Source

    © Copyright Original Source


    So a major source of argument for evolution is defunct, if this analysis is correct, and common design instead of common descent becomes more reasonable.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  • #2
    Even before Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome back in the early '70s it was already widely understood that some noncoding DNA had important functions. This is one of those persistent myths like Columbus having proved the world wasn't flat.

    I'm always still in trouble again

    "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
    "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
    "Of course, human life begins at fertilization that’s not the argument." --Tassman

    Comment


    • #3
      Originally posted by rogue06 View Post
      Even before Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome back in the early '70s it was already widely understood that some noncoding DNA had important functions.
      So are you saying evolutionary biologists never said non-coding DNA was an argument for evolution? Just because some non-coding DNA had function was not considered proof back then that "junk DNA" was an incorrect concept.

      Blessings,
      Lee
      "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

      Comment


      • #4
        Larry Moran chimes in...

        Source: Sandwalk

        The latest issue of GBE has a paper by Stitz et al. (2021) that describes some repetitive elements in the platyhelminth Schistosoma mansoni. The authors conlcude that some of these elements might have a function and this prompts them to begin their discussion with the following sentences.

        The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.

        Source

        © Copyright Original Source


        But this is as close as he gets to refuting these sentences in the papers. Merely stating that "junk DNA is alive and well" is not a refutation.

        Blessings,
        Lee
        "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

        Comment


        • #5
          Originally posted by lee_merrill View Post
          Casey McGrath in Genome Biology and Evolution has an article titled " 'Junk DNA' No More: Repetitive Elements as Vital Sources of Flatworm Variation". The article begins with this sentence:

          Source: Genome Biology and Evolution

          “The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution.

          Source

          © Copyright Original Source


          So a major source of argument for evolution is defunct, if this analysis is correct, and common design instead of common descent becomes more reasonable.

          Blessings,
          Lee
          Old and moldy news and not worthy of a thread, and presented in a misleading context that this has any sortof major argument for evolution.
          Glendower: I can call spirits from the vasty deep.
          Hotspur: Why, so can I, or so can any man;
          But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

          go with the flow the river knows . . .

          Frank

          I do not know, therefore everything is in pencil.

          Comment


          • #6
            Originally posted by lee_merrill View Post
            Casey McGrath in Genome Biology and Evolution has an article titled " 'Junk DNA' No More: Repetitive Elements as Vital Sources of Flatworm Variation". The article begins with this sentence:

            Source: Genome Biology and Evolution

            “The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution.

            Source

            © Copyright Original Source


            So a major source of argument for evolution is defunct, if this analysis is correct, and common design instead of common descent becomes more reasonable.

            Blessings,
            Lee
            Thank you for confirming the the ID designer is not omnipotent. Obviously the ID designer is incapable of designing junk DNA. A truly omnipotent designer would be perfectly capable of designing non-functional junk DNA.

            Comment


            • #7
              Shame you couldn't even bother reading the whole article, including the part where it says: "As Grevelding points out, one of the caveats of this study is that the functional predictions of W elements “are mainly based on bioinformatics analyses and have to be substantiated by functional analyses. This is also true for our hypothesis about the mobile character of W elements, which we concluded from genome and structural analysis, but for which we have no direct functional evidence yet.”"

              So, he's declaring it dead without bothering to gather the evidence needed to conclude it's dead.

              There are terms for that sort of behavior. The list of them does not include "being a scientist."

              In any case, we know junk DNA exists, because we've now observed its origin. We've sequenced parent/child genome combinations, and observed many duplications of portions of a chromosome that were not there in the parents, but were present in the offspring. Obviously, this has no function, because the parents were both fine without it - the rest of the human population, in fact, is fine without it. It's simply the product of an error in the process of copying chromosomes.

              Given that set of facts, anyone who declares that junk DNA doesn't exist is necessarily making a rhetorical argument, not an evidence-based one.

              I could write a very long essay on why transposable elements confuse so many people, but i'm on deadline for things at work. Maybe if this discussion remains active until next weekend, i will.
              "Any sufficiently advanced stupidity is indistinguishable from trolling."

              Comment


              • #8
                Originally posted by TheLurch View Post
                Shame you couldn't even bother reading the whole article, including the part where it says: "As Grevelding points out, one of the caveats of this study is that the functional predictions of W elements “are mainly based on bioinformatics analyses and have to be substantiated by functional analyses. This is also true for our hypothesis about the mobile character of W elements, which we concluded from genome and structural analysis, but for which we have no direct functional evidence yet.”"

                So, he's declaring it dead without bothering to gather the evidence needed to conclude it's dead.

                There are terms for that sort of behavior. The list of them does not include "being a scientist."

                In any case, we know junk DNA exists, because we've now observed its origin. We've sequenced parent/child genome combinations, and observed many duplications of portions of a chromosome that were not there in the parents, but were present in the offspring. Obviously, this has no function, because the parents were both fine without it - the rest of the human population, in fact, is fine without it. It's simply the product of an error in the process of copying chromosomes.

                Given that set of facts, anyone who declares that junk DNA doesn't exist is necessarily making a rhetorical argument, not an evidence-based one.

                I could write a very long essay on why transposable elements confuse so many people, but i'm on deadline for things at work. Maybe if this discussion remains active until next weekend, i will.
                Despite claims to the contrary you are correct in that we've known, even prior to the term "junk DNA" being coined, that while some noncoding DNA has important functions (such as to produce noncoding RNA components) there is incontrovertible evidence that a good deal of DNA has no function.

                For instance, Marcelo A Nóbrega demonstrated that you can remove significant portions of DNA, and even replace it with randomized sequences, with no detectable effect on the organism (Megabase deletions of gene deserts result in viable mice). This could only be possible if large sections of our DNA were noncoding.

                Btw, it appears that the term "junk science" is going the way of "missing link" in that the term is being increasingly abandoned due to the confusion it has caused, slowly being relegated to the popular press and colloquial use among scientists. The preferred term is now "noncoding DNA."

                I'm always still in trouble again

                "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
                "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
                "Of course, human life begins at fertilization that’s not the argument." --Tassman

                Comment


                • #9
                  Originally posted by rogue06 View Post
                  Btw, it appears that the term "junk science" is going the way of "missing link" in that the term is being increasingly abandoned due to the confusion it has caused, slowly being relegated to the popular press and colloquial use among scientists. The preferred term is now "noncoding DNA."
                  The problem is that no single term encompasses all the detail of the stuff that doesn't encode proteins - it's easiest described in a Venn diagram. You have noncoding DNA that's junk, noncoding DNA that encodes functional RNAs, noncoding DNA that is structural (centromeres and telomeres), and noncoding DNA that regulates the activities of the coding bit.

                  The other complicating factor is that none of these designations is permanent. Junk DNA can end up forming new genes or getting incorporated into existing ones, or forming new regulatory sequences (this is especially true of transposable elements, which often encode proteins). Existing coding DNA can pick up mutations and be converted into junk. Transposons, when they relocate, often include regulatory DNA, and can influence the expression of nearby genes, or have their activity influenced by the gene's regulatory DNA.

                  Given that no single term works, it really behooves everyone to actually define what they're talking about.
                  "Any sufficiently advanced stupidity is indistinguishable from trolling."

                  Comment


                  • #10
                    Originally posted by TheLurch View Post
                    The problem is that no single term encompasses all the detail of the stuff that doesn't encode proteins - it's easiest described in a Venn diagram. You have noncoding DNA that's junk, noncoding DNA that encodes functional RNAs, noncoding DNA that is structural (centromeres and telomeres), and noncoding DNA that regulates the activities of the coding bit.

                    The other complicating factor is that none of these designations is permanent. Junk DNA can end up forming new genes or getting incorporated into existing ones, or forming new regulatory sequences (this is especially true of transposable elements, which often encode proteins). Existing coding DNA can pick up mutations and be converted into junk. Transposons, when they relocate, often include regulatory DNA, and can influence the expression of nearby genes, or have their activity influenced by the gene's regulatory DNA.

                    Given that no single term works, it really behooves everyone to actually define what they're talking about.
                    This gets to the idea that some "junk DNA" sequences can be future sources for evolution through exaptation: Junk DNA as an evolutionary force


                    As an aside, I find exaptation or co-opting to be one of the most interesting and often overlooked mechanisms in evolution.

                    I'm always still in trouble again

                    "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
                    "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
                    "Of course, human life begins at fertilization that’s not the argument." --Tassman

                    Comment


                    • #11
                      Hello, I am an amateur to this subject, but deeply interested in DNA understanding.

                      The article says: 'additional progress in S. mansoni manipulation may be needed before the authors’ current hypotheses can be definitively confirmed'

                      The stated information is promising for a breakthrough.
                      In any science a century may pass until a hypothesis has a step towards confirmation. Today's technology and experience makes leaps in many fields.

                      DNA understanding is obviously one of the major for past and future of humanity.

                      Comment


                      • #12
                        Originally posted by TheLurch View Post
                        So, he's declaring it dead without bothering to gather the evidence needed to conclude it's dead.
                        No, he's saying more work needs to be done, but the work done so far merits some preliminary conclusions.

                        In any case, we know junk DNA exists, because we've now observed its origin.
                        And no one is saying there is no junk DNA. The point is that junk DNA, as a mainstay argument for evolution, appears to be done for.

                        Blessings,
                        Lee
                        "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

                        Comment


                        • #13
                          Welcome to TheologyWeb, Lariliss!

                          Originally posted by Lariliss View Post
                          The stated information is promising for a breakthrough.]
                          Yes, their conclusions do look promising, if I'm understanding you correctly.

                          Blessings,
                          Lee
                          "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

                          Comment


                          • #14
                            Originally posted by lee_merrill View Post
                            No, he's saying more work needs to be done, but the work done so far merits some preliminary conclusions.
                            And yet, as you said, the article begins with the phrase:

                            The days of ‘junk DNA’ are over,”


                            Does that sound like someone making some "preliminary conclusions" to you?

                            Originally posted by lee_merrill View Post
                            And no one is saying there is no junk DNA. The point is that junk DNA, as a mainstay argument for evolution, appears to be done for.
                            Can you explain how "junk DNA" has been this "mainstay argument for evolution"?

                            I'm always still in trouble again

                            "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
                            "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
                            "Of course, human life begins at fertilization that’s not the argument." --Tassman

                            Comment


                            • #15
                              Originally posted by rogue06 View Post
                              Can you explain how "junk DNA" has been this "mainstay argument for evolution"?
                              Also, you're going to have to unpack how "junk DNA clearly exists" and "junk DNA is no longer evidence for evolution" are consistent.
                              "Any sufficiently advanced stupidity is indistinguishable from trolling."

                              Comment

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