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The lungfish genome, tetrapods, and junk DNA

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  • The lungfish genome, tetrapods, and junk DNA

    New paper out on the genome of the giant lungfish. I've not had time yet to read the whole thing, but thought i'd share it ahead of that because it's very significant for two reasons:

    One is that lungfish, as part of the lobe-finned fishes, have been proposed to be the closest living species to tetrapods. The fossil record here, including famed intermediates like Tiktaalik, is pretty clear. The genome gives us the chance to test whether the present day evidence is consistent with the fossil record. In news that shouldn't surprise anyone, it is: "Phylogenomic analyses ascertained that lungfish occupy an evolutionary key-position as closest living relatives to tetrapods." They also see some indications of things that would be adaptive for tetrapods pre-existing their split from lobe-finned fishes. These included a limb-like pattern of homeobox gene expression, additional copies of genes associated with air breathing, and more odorant receptors that work in air.

    The second thing is an oddity that's specific to lungfish: their genomes are enormous. This genome is 17x the size of the human genome, and there's no obvious (or even unobvious) explanation for why that extra DNA is needed. Well, we now know where it comes from: mobile genetic parasites are still active in the genome, and most of the extra DNA is simply copies of these parasites inserted between genes and within the introns that are deleted from mature RNAs. This is exactly the sort of thing we'd expect to see if we treat junk DNA as a scientific hypothesis and derive predictions from it.

    May have more once i read the paper, but it's open access, so anyone can have a look for themselves.

    https://www.nature.com/articles/s41586-021-03198-8
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  • #2
    never mind
    Last edited by rogue06; 01-18-2021, 01:10 PM.

    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)
    "Of course, human life begins at fertilization thatís not the argument." --Tassman

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    • #3
      Interesting article. Thanks for sharing.
      "Obama is not a brown-skinned, anti-war socialist who gives away free healthcare. You are thinking of Jesus." Episcopal Bishop of Arizona

      I remember WinAce. Gone but not forgotten.

      Comment


      • #4
        Originally posted by TheLurch View Post
        The fossil record here, including famed intermediates like Tiktaalik, is pretty clear.
        But Tiktaalik is unclear:

        Source: Evolution News

        Simply put, these tracks suggest that tetrapods predated Tiktaalik and thus Tiktaalik is not, as Nature put it elsewhere, a “direct transitional form” between fish and tetrapods.

        Source

        © Copyright Original Source



        The genome gives us the chance to test whether the present day evidence is consistent with the fossil record. In news that shouldn't surprise anyone, it is: "Phylogenomic analyses ascertained that lungfish occupy an evolutionary key-position as closest living relatives to tetrapods." They also see some indications of things that would be adaptive for tetrapods pre-existing their split from lobe-finned fishes. These included a limb-like pattern of homeobox gene expression, additional copies of genes associated with air breathing, and more odorant receptors that work in air.
        Or this could be common design, instead of common descent.

        The second thing is an oddity that's specific to lungfish: their genomes are enormous. This genome is 17x the size of the human genome, and there's no obvious (or even unobvious) explanation for why that extra DNA is needed. Well, we now know where it comes from: mobile genetic parasites are still active in the genome, and most of the extra DNA is simply copies of these parasites inserted between genes and within the introns that are deleted from mature RNAs. This is exactly the sort of thing we'd expect to see if we treat junk DNA as a scientific hypothesis and derive predictions from it.
        Which is fine as far as it goes, I only hope that scientists will not stop at a conclusion of "junk DNA" by default, and will instead continue to look for function.

        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

          Or this could be common design, instead of common descent.

          Blessings,
          Lee
          Or it could be MAGIC! Right Lee? You really need to stop getting your "science" from ID-Creationist propaganda sites like EvolutionNews.

          Comment


          • #6
            Originally posted by lee_merrill View Post
            But Tiktaalik is unclear:
            [quote =Evolution News]...
            Some folks are obviously just incapable of learning.

            Please look up what constitutes a transitional fossil from a reputable source and get back to us.

            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)
            "Of course, human life begins at fertilization thatís not the argument." --Tassman

            Comment


            • #7
              Originally posted by lee_merrill View Post
              Or this could be common design, instead of common descent.
              Or it could be the effect of magical, miniature, invisible blue meanies that roam DNA making changes according to their whims.

              But i'd rather stick to the things we have evidence for. I'm funny that way.
              "Any sufficiently advanced stupidity is indistinguishable from trolling."

              Comment


              • #8
                By the way, Lee, you can consider it a rule in this and any future threads i start that if you quote Evolution News in a thread, then you'll be booted from it. They lie, they lie repeatedly, and they lie shamelessly. I think that, given recent events in the US, i'm going to be taking a bit of a stand against misinformation
                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                Comment


                • #9
                  Originally posted by TheLurch View Post
                  By the way, Lee, you can consider it a rule in this and any future threads i start that if you quote Evolution News in a thread, then you'll be booted from it. They lie, they lie repeatedly, and they lie shamelessly. I think that, given recent events in the US, i'm going to be taking a bit of a stand against misinformation
                  So where is the lie in what I posted from Evolution News?

                  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


                  • #10
                    Originally posted by lee_merrill View Post
                    So where is the lie in what I posted from Evolution News?

                    Blessings,
                    Lee
                    Everything, and I have cited numerous references in the past where either total self-imposed ignorance, or just down right lying in your references. Your choice.

                    Common dishonesty is the dishonest selective citation, and omission of known scientific evidence.

                    Remember the 'tree galls.'

                    Statements like the following reflect the absurdity of Intelligent Design. There is no evidence to claim Intelligent Design when the evidence is demonstrated as natural origin.,

                    Or this could be common design, instead of common descent.
                    Last edited by shunyadragon; 01-21-2021, 06:33 AM.
                    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? Shakespeareís Henry IV, Part 1, Act III:

                    go with the flow the river knows . . .

                    Frank

                    I do not know, therefore everything is in pencil.

                    Comment


                    • #11
                      Originally posted by lee_merrill View Post
                      So where is the lie in what I posted from Evolution News?

                      Blessings,
                      Lee
                      In all seriousness it would be far easier and shorter to compile a list of the times that they weren't lying. Just go back and look through the various threads where after you uncritically regurgitate their garbage and how it gets dismantled.

                      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)
                      "Of course, human life begins at fertilization thatís not the argument." --Tassman

                      Comment


                      • #12
                        Originally posted by rogue06 View Post
                        In all seriousness it would be far easier and shorter to compile a list of the times that they weren't lying. Just go back and look through the various threads where after you uncritically regurgitate their garbage and how it gets dismantled.
                        But claiming victory is not the same as attaining it.

                        So where is the lie in what I posted from Evolution News?

                        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
                          Originally posted by lee_merrill View Post
                          So where is the lie in what I posted from Evolution News?
                          The lie is that you're using questions about the precise location in the branches by which tetrapods diverged from lobe-finned fishes to question whether the did branch from them at all. The Evolution News post is specifically designed (one might even say intelligently designed) to cause that confusion in its readers.

                          There are an overabundance of fossils of lobe-finned fishes from the time of the split. The fossil and molecular evidence was already clear that they were closely related before this genome was published. The precise details of Tiktaalik's location in this process is just that - a question of details. But Evolution News uses it to try to pretend that this means that the whole picture is missing entirely. It treats people attempting to clarify the actual evolutionary thinking on transitional forms as making excuses, using inflammatory phrasing like "evolutionists often rewrite history."

                          And, based on what you said, you bought the lie entirely.
                          "Any sufficiently advanced stupidity is indistinguishable from trolling."

                          Comment


                          • #14
                            Originally posted by TheLurch View Post
                            The lie is that you're using questions about the precise location in the branches by which tetrapods diverged from lobe-finned fishes to question whether the did branch from them at all. The Evolution News post is specifically designed (one might even say intelligently designed) to cause that confusion in its readers.
                            No, that is not what was said, here it is again: "Simply put, these tracks suggest that tetrapods predated Tiktaalik and thus Tiktaalik is not, as Nature put it elsewhere, a 'direct transitional form' between fish and tetrapods." This is a true statement, your extrapolation was not what was said.

                            The precise details of Tiktaalik's location in this process is just that - a question of details.
                            Source: Evolution News

                            This post has provided clear documentation that leading evolutionary biologists argued that the known ranges of tetrapods and lobe-finned fishes led them to “predict” that a fossil like Tiktaalik would be found in a particular stratigraphic location in the fossil record. When that alleged transitional form was found in that location, they touted it as a confirmed prediction of evolutionary science.

                            © Copyright Original Source


                            So this is not, as you say, just a question of details!

                            But Evolution News uses it to try to pretend that this means that the whole picture is missing entirely. It treats people attempting to clarify the actual evolutionary thinking on transitional forms as making excuses, using inflammatory phrasing like "evolutionists often rewrite history."
                            You left out part of the quote: "When a widely touted prediction of evolution falls apart, evolutionists often rewrite history, soften the 'prediction,' and claim that the harder prediction was never made in the first place." Tiktaalik was widely touted, and it turned out probably not to be a "direct transitional form" as Nature claimed.

                            And no, they don't "pretend that this means that the whole picture is missing entirely". You are again extrapolating.

                            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


                            • #15
                              Originally posted by lee_merrill View Post

                              And no, they don't "pretend that this means that the whole picture is missing entirely". You are again extrapolating.

                              Blessings,
                              Lee
                              Lee does the DI pay you to mindlessly regurgitate this ridiculous anti-science propaganda from Behe, Meyer, Bechly and the other IDiots? Or do you work pro bono in pushing this Creationist nonsense?

                              Comment

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