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The book Darwin Devolves

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  • Originally posted by TheLurch View Post
    So you'd expect a lot of gene loss on this lineage, and therefore it's a bit of a trick to use it as an example of evolution only acting by breaking stuff.
    But isn't loss more or less the equivalent of ''breaking''? If you said ''gain'', it would be one thing, but you said ''loss''. Now I'm confused.

    Comment


    • Originally posted by Seeker View Post
      But isn't loss more or less the equivalent of ''breaking''? If you said ''gain'', it would be one thing, but you said ''loss''. Now I'm confused.
      The Lurch may comment further, but I believe "breaking" in this example is better described as "change." Change here is 'adaptive gain.' Part of the fallacy here is the assumption that all "breaking" is unbeneficial "loss."
      Last edited by shunyadragon; 06-18-2019, 07:17 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? 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


      • Originally posted by Seeker View Post
        But isn't loss more or less the equivalent of ''breaking''? If you said ''gain'', it would be one thing, but you said ''loss''. Now I'm confused.
        Sorry, let me clarify. Yes, the polar bear may be an example of a situation where evolution has broken or deleted a bunch of genes (though Behe, as discussed extensively above, didn't actually show that it is). What this paper highlighted is that, given the polar bear's change in diet, you'd expect lots of genes involved in digesting plant matter to be useless, and therefore likely to be lost.

        In other words, the polar bear is likely to tell us little about evolution in general, while specifically confirming what we already know about the fate of useless genes.

        That's point 1. Point 2 is the issue of why Behe chose this example. It could be that Behe, like me, simply wasn't paying careful attention and didn't realize this issue with his argument. Or it could be that Behe just cared about making his argument look good, and cherry picked this example specifically because he knew it would. Given that Behe has, in the past, gone out of his way to ignore counter arguments, play down various data, etc. all to keep promoting his arguments, my suspicion is that it's the latter.
        "Any sufficiently advanced stupidity is indistinguishable from trolling."

        Comment


        • Originally posted by TheLurch View Post
          It would also be an example of Behe cherry picking his example to make his case look good.
          Though the APOB gene in the polar bear was what Behe focused on, to provide an advantage in a high-fat diet, as I recall.

          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


          • Originally posted by shunyadragon View Post
            Part of the fallacy here is the assumption that all "breaking" is unbeneficial "loss."
            Well, yes, that's part of Behe's argument, that breaking genes can provide a selective advantage. I don't think anyone is arguing against that, here.

            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


            • Originally posted by lee_merrill View Post
              Well, yes, that's part of Behe's argument, that breaking genes can provide a selective advantage. I don't think anyone is arguing against that, here.

              Blessings,
              Lee
              Than there is not problem with the "breaking" of genes is a part of the natural evolutionary process.
              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


              • Originally posted by shunyadragon View Post
                Than there is not problem with the "breaking" of genes is a part of the natural evolutionary process.
                Agreed...

                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


                • Originally posted by lee_merrill View Post
                  Though the APOB gene in the polar bear was what Behe focused on, to provide an advantage in a high-fat diet, as I recall.
                  As i recall, there was an entire table listing all the coding region changes altered in polar bears vs. their closest living relatives. Maybe Behe didn't devote much space to this, or maybe it was just brought up in the context of this discussion.
                  "Any sufficiently advanced stupidity is indistinguishable from trolling."

                  Comment


                  • A quote from "Debating Darwin's Doubt", which has relevance to this discussion:

                    Source: Debating Darwin's Doubt

                    The play of forces, and the ensuing annihilation of advantage, is evident in Ohno’s model of duplication and divergence. Where previously it had one gene, duplication provides an organism with two. One gene does the heavy cellular lifting and takes the obvious selective risks; the other is free to explore sequence space and serendipitously find new things to do. Genetic affairs do not get more flexible than this. This is surely a step in the right direction, no? It is by no means clear. Protein perturbation studies indicate that ~40% of all mutations “reduce or completely abolish function,” a substantial portion (8%) leading to the “loss of all functions” (emphasis added). The rate of beneficial mutations, by way of contrast, stands at 103 or 0.1%. Absent selection, any duplicate will be crippled far faster than it will accumulate beneficial mutations.

                    © Copyright Original Source


                    The quote is in reference to this paper.

                    And a quote from the key points of the paper: "Despite buffering effects, the fitness distribution of mutations at the protein level, and for whole organisms, is such that most of the mutations are either neutral or deleterious. This results in the rapid and irreversible non-functionalization of proteins that accumulate mutations under no selection." And we may note that selection will tend to remove deleterious mutations.

                    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


                    • Originally posted by lee_merrill View Post
                      A quote from "Debating Darwin's Doubt", which has relevance to this discussion:

                      Source: Debating Darwin's Doubt

                      The play of forces, and the ensuing annihilation of advantage, is evident in Ohno’s model of duplication and divergence. Where previously it had one gene, duplication provides an organism with two. One gene does the heavy cellular lifting and takes the obvious selective risks; the other is free to explore sequence space and serendipitously find new things to do. Genetic affairs do not get more flexible than this. This is surely a step in the right direction, no? It is by no means clear. Protein perturbation studies indicate that ~40% of all mutations “reduce or completely abolish function,” a substantial portion (8%) leading to the “loss of all functions” (emphasis added). The rate of beneficial mutations, by way of contrast, stands at 103 or 0.1%. Absent selection, any duplicate will be crippled far faster than it will accumulate beneficial mutations.

                      © Copyright Original Source


                      The quote is in reference to this paper.

                      And a quote from the key points of the paper: "Despite buffering effects, the fitness distribution of mutations at the protein level, and for whole organisms, is such that most of the mutations are either neutral or deleterious. This results in the rapid and irreversible non-functionalization of proteins that accumulate mutations under no selection." And we may note that selection will tend to remove deleterious mutations.

                      Blessings,
                      Lee
                      Considering that most mutations are already neutral to then say that most are either neutral or deleterious is effectively meaningless. It would in fact be just as accurate to say that most are either neutral or beneficial.

                      Moreover, the selection process takes place at a higher level -- does it improve or impair an organism's chances to survive, reproduce and leave progeny. If the latter then over time they will be increasingly weeded out as those without the mutation out reproduce them. Likewise if the mutation improves their chances then they will out produce those without it.

                      This is basic evolutionary theory and has been demonstrated repeatedly.

                      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


                      • Originally posted by lee_merrill View Post
                        A quote from "Debating Darwin's Doubt", which has relevance to this discussion:

                        Source: Debating Darwin's Doubt

                        The play of forces, and the ensuing annihilation of advantage, is evident in Ohno’s model of duplication and divergence. Where previously it had one gene, duplication provides an organism with two. One gene does the heavy cellular lifting and takes the obvious selective risks; the other is free to explore sequence space and serendipitously find new things to do. Genetic affairs do not get more flexible than this. This is surely a step in the right direction, no? It is by no means clear. Protein perturbation studies indicate that ~40% of all mutations “reduce or completely abolish function,” a substantial portion (8%) leading to the “loss of all functions” (emphasis added). The rate of beneficial mutations, by way of contrast, stands at 103 or 0.1%. Absent selection, any duplicate will be crippled far faster than it will accumulate beneficial mutations.

                        © Copyright Original Source


                        The quote is in reference to this paper.

                        And a quote from the key points of the paper: "Despite buffering effects, the fitness distribution of mutations at the protein level, and for whole organisms, is such that most of the mutations are either neutral or deleterious. This results in the rapid and irreversible non-functionalization of proteins that accumulate mutations under no selection." And we may note that selection will tend to remove deleterious mutations.

                        Blessings,
                        Lee
                        Ditto . . . repeatedly dumped by The Lurch, Rogue06 and I. Repeating trash science again and again just makes you more and more a fool with a religious agenda like Behe.
                        Last edited by shunyadragon; 03-22-2020, 07:01 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? 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


                        • Originally posted by rogue06 View Post
                          Considering that most mutations are already neutral to then say that most are either neutral or deleterious is effectively meaningless. It would in fact be just as accurate to say that most are either neutral or beneficial.

                          Moreover, the selection process takes place at a higher level -- does it improve or impair an organism's chances to survive, reproduce and leave progeny. If the latter then over time they will be increasingly weeded out as those without the mutation out reproduce them. Likewise if the mutation improves their chances then they will out produce those without it.

                          This is basic evolutionary theory and has been demonstrated repeatedly.
                          Also, many changes in duplicated genes occur in their regulatory DNA, not in their protein coding sequence. So, this is doubly irrelevant.
                          "Any sufficiently advanced stupidity is indistinguishable from trolling."

                          Comment


                          • Originally posted by lee_merrill View Post
                            Agreed...

                            Blessings,
                            Lee
                            Glad you agree that there is no problem with the natural evolutionary process over time.
                            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


                            • Originally posted by rogue06 View Post
                              Considering that most mutations are already neutral to then say that most are either neutral or deleterious is effectively meaningless. It would in fact be just as accurate to say that most are either neutral or beneficial.
                              According to this paper, about half of the mutations are neutral, and about half are deleterious. So most gene duplications will provide only degraded genes for selection to work with (we can disregard neutral mutations, which are invisible to selection).

                              Moreover, the selection process takes place at a higher level -- does it improve or impair an organism's chances to survive, reproduce and leave progeny. If the latter then over time they will be increasingly weeded out as those without the mutation out reproduce them. Likewise if the mutation improves their chances then they will out produce those without it.
                              Agreed...

                              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


                              • Originally posted by TheLurch View Post
                                Also, many changes in duplicated genes occur in their regulatory DNA, not in their protein coding sequence.
                                Well, I think the paper was referencing protein coding duplications: "the fitness distribution of mutations at the protein level". But surely mutations in regulatory DNA fit this profile too, where most mutations are neutral or deleterious.

                                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

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