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Nice defense of Evolution

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  • #31
    Originally posted by lee_merrill View Post
    Well, it's close enough, if you started with function, which presumably was selected.
    I seem to recall something....
    Oh yes, an entire thread where you unsuccessfully defended the idea that evolution primarily selects for mutations that eliminate function.

    Which of the two ways you've argued would you like to adopt for this thread?

    (For those who aren't Lee, selection is context dependent, and can select for function, non-function, changed function, etc. Axe's work is specifically looking at function without any selection, and so is completely irrelevant to it.)

    Originally posted by lee_merrill View Post
    Multiple point mutations are rare?! I must be misunderstanding you, because a number of genes have multiple point mutations.
    Axe is making multiple simultaneous point mutations. The paper you've linked is irrelevant to that, since it's looking at the mutations accumulated individually over extended time periods.

    Again, i'd like to point out that you don't know enough biology to actually recognize the difference. And so i'll ask again - why do you refuse to accept the extensive evidence you have a poor understanding of biology?


    Originally posted by lee_merrill View Post
    I think it's relevant, since Axe showed that protein space is sparsely populated, making a random walk to another viable protein/enzyme improbable. Selection doesn't save the day, since it is unlikely that there is a selectable path to every new protein.
    No, he didn't. He's shown that a set of simultaneous mutations that disrupt a protein's structure will typically result in a non-functional protein, which we already knew. He's thus concluded that functional structures are sparse within the total space of random proteins, which may be accurate (though we don't know, since we've barely explored that space).

    Where he (and you) go wrong is to conclude that that sparseness means that there are no viable evolutionary paths between different functions. In fact, a large number of mutations are compatible with maintaining structure, while being neutral or altering function. If i remember correctly, Axe had to start making multiple adjacent mutations because when he tried a small number of mutations, they were typically tolerated with no difficulty.

    It's this category of mutation—maintain structure, potentially alter function—that provides pathways to new functions without disrupting the structure.

    Now, if all that were happening were random mutations - which remember, typically happen one at a time, and so are completely unlike what Axe is doing here - you'd rarely end up on on one of these viable pathways. But the whole point of evolution is that selection occurs, and can eliminate any mutations that aren't on a viable pathway.

    In other words, Axe's work actually demonstrates why evolution is so incredibly powerful. He just seems incapable of realizing it.

    Originally posted by lee_merrill View Post
    Which is why his research was published in a peer-reviewed journal while he was at Cambridge?
    His research as published doesn't include the interpretative baggage that the ID movement attaches to it. That's because those interpretations are nonsensical and would never pass peer review.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • #32
      Originally posted by TheLurch View Post
      Which of the two ways you've argued would you like to adopt for this thread?
      But these two arguments are not mutually exclusive, included in the argument here is that the environment stays basically the same.

      Axe is making multiple simultaneous point mutations. The paper you've linked is irrelevant to that, since it's looking at the mutations accumulated individually over extended time periods.
      But the timeframe of mutations doesn't much matter, if the environment stays the same.

      Again, i'd like to point out that you don't know enough biology to actually recognize the difference.
      I do recognize the difference between simultaneous and successive--why do you and others here put everything I say in the worst possible light?

      Where he (and you) go wrong is to conclude that that sparseness means that there are no viable evolutionary paths between different functions. In fact, a large number of mutations are compatible with maintaining structure, while being neutral or altering function.
      Well, that's a bare assertion, I would need to see the data behind it.

      If i remember correctly, Axe had to start making multiple adjacent mutations because when he tried a small number of mutations, they were typically tolerated with no difficulty.
      No, he saw the problem of random mutations in a different light:

      Source: Douglas Axe

      Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution.

      Source

      © Copyright Original Source



      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


      • #33
        Originally posted by shunyadragon View Post
        His publications attacking evolution have been published in Discovery Institute and Biologic Institute associated journals and marginal academic journals. The Biologic Institute is created by Axe himself.
        So we can evaluate his arguments, let's try to do so...

        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


        • #34
          Originally posted by lee_merrill View Post
          So we can evaluate his arguments, let's try to do so...

          Blessings,
          Lee


          I already have, his work represents an ID agenda and not science, The Lurche has ripped Axe and you in every thread and I respect The Lurche. His publications on ID agenda do not even make the grade in peer reviewed respectable journals.
          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


          • #35
            Originally posted by lee_merrill View Post
            But these two arguments are not mutually exclusive, included in the argument here is that the environment stays basically the same.
            So, in other words, the environment stays the same, and therefore selection doesn't change at all. And we've both seemingly agreed that the mutation pattern isn't a natural one (you claim that this doesn't matter, which is wrong; see below). The combination of no change in selection and no natural mutation pattern makes this pretty irrelevant to natural selection, don't you think?

            Originally posted by lee_merrill View Post
            But the timeframe of mutations doesn't much matter, if the environment stays the same.


            I do recognize the difference between simultaneous and successive--why do you and others here put everything I say in the worst possible light?
            Because it does matter! Each individual mutation would be subject to selection as they happened. Any harmful ones would be eliminated from the population before the second could occur. This could make the second innocuous, or mildly harmful and subject to selection itself. There's a very good chance that NONE of the mutations Axe creates would be present in the final population if they occurred individually.

            This is precisely why this experiment is not relevant to selection. Axe explicitly avoids selection in order to create the combination of mutations he's decided to test, because they'd never be present in the organism if selection were ongoing.

            It's because you can't seem to grasp concepts like this that i think the worst when you phrase something poorly.

            Originally posted by lee_merrill View Post
            Well, that's a bare assertion, I would need to see the data behind it.
            Conveniently, i've found a source for that: Douglas Axe. There are many others, but i have to bring it up here anyway, so see below for it.

            Originally posted by lee_merrill View Post
            No, he saw the problem of random mutations in a different light:

            Source: Douglas Axe

            Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution.

            Source

            © Copyright Original Source

            No right back to you, because i found the reference i was thinking of. It predates yours by 6 years.
            https://www.ncbi.nlm.nih.gov/pubmed/9585527

            "Because the selection system used to score barnase mutants as active or inactive detects activity down to a level that can be approached by nonenzyme catalysts, mutants that test inactive are essentially devoid of enzymatic function. Of the 109 barnase positions subjected to substitution, only 15 (14%) are vulnerable to this extreme level of inactivation, and only 2 could not be substituted without such inactivation. A total of 33 substitutions (amounting to 5% of the explored substitutions) were found to render barnase wholly inactive."
            So, all but 5% of the random mutations in this gene allowed continued catalytic activity. Which is why Axe has had to switch to making multiple simultaneous mutations, since his entire intent is to inactivate proteins.

            You could say his more recent experiments have been intelligently designed to produce a result — inactivation of a protein — that he needed for purposes that are outside the academic literature.


            EDITED TO ADD: Just a general note - i did research in biology for nearly 20 years, and have continued to follow the academic literature since then. It's perfectly fair to ask me to back up what i'm saying with references. But i'd advise strongly against basing your arguments on the assumption i've made a claim that i can't back up.
            Last edited by TheLurch; 11-04-2019, 06:49 AM.
            "Any sufficiently advanced stupidity is indistinguishable from trolling."

            Comment


            • #36
              Originally posted by TheLurch View Post
              Because it does matter! Each individual mutation would be subject to selection as they happened. Any harmful ones would be eliminated from the population before the second could occur. This could make the second innocuous, or mildly harmful and subject to selection itself.
              Though you have to get to new function in order for multiple mutations to be selected positively, and Axe shows that new function is generally far away. So the mutations are probably independent.

              Originally posted by lee_merrill
              No, he saw the problem of random mutations in a different light:

              Source: Douglas Axe

              lthough the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution.

              © Copyright Original Source

              No right back to you, because i found the reference i was thinking of. It predates yours by 6 years.
              https://www.ncbi.nlm.nih.gov/pubmed/9585527

              ...
              So, all but 5% of the random mutations in this gene allowed continued catalytic activity. Which is why Axe has had to switch to making multiple simultaneous mutations, since his entire intent is to inactivate proteins.
              But you don't get to new function, which is what Axe is measuring. New proteins, new folds, how close are they in protein space?

              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


              • #37
                Originally posted by lee_merrill View Post
                Though you have to get to new function in order for multiple mutations to be selected positively, and Axe shows that new function is generally far away. So the mutations are probably independent.


                But you don't get to new function, which is what Axe is measuring. New proteins, new folds, how close are they in protein space?

                Blessings,
                Lee
                Function is not defined as 'being what is selectable.'
                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


                • #38
                  Originally posted by lee_merrill View Post
                  Though you have to get to new function in order for multiple mutations to be selected positively, and Axe shows that new function is generally far away.
                  Once again, no he did not show that. He showed that multiple mutations designed specifically to disrupt the structure of the protein produced non-functional proteins. That's it. That's the only thing that was demonstrated. Targeting multiple random changes (10 of them in the paper you cited!) at the sites within a protein that are most likely to be structurally significant doesn't actually tell you anything about how frequent other structures are.

                  Seriously. If that's what you think, explain why in a way that doesn't include "Axe says so".

                  Originally posted by lee_merrill View Post
                  But you don't get to new function, which is what Axe is measuring. New proteins, new folds, how close are they in protein space?
                  First, when you're wrong, it's generally polite to acknowledge that. But i'll take you changing the subject to be a tacit acknowledgement that, as i claimed:
                  a) most mutations are neutral or alter function rather than eliminating it.
                  b) that fact proved a barrier to Axe's early attempts to get the results he wanted, so he had to change his methods.

                  Now, on to your newer errors. Axe was not measuring new function; he was testing the same function that the protein already performed—read the abstract you yourself linked. It's why his work says absolutely nothing about the evolution of new function - the very proteins he created could actually have new functions, and he'd have no idea because he never tested for any. Not even one out of the billions of potential other functions was tested.

                  This is yet another reason why his work is irrelevant to the evolution of new functions.

                  Your inability to read biology abstracts you yourself link is further evidence that you don't understand biology.
                  "Any sufficiently advanced stupidity is indistinguishable from trolling."

                  Comment


                  • #39
                    Originally posted by lee_merrill View Post
                    Though you have to get to new function in order for multiple mutations to be selected positively, ...
                    False. Multiple mutations that enhance the existing functionality may be selected for.
                    ... and Axe shows that new function is generally far away.
                    False. Axe didn't show anything at all about new function, or about genetic distance.
                    So the mutations are probably independent.
                    False. Even if the preceding two claims were correct, this would not follow.
                    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                    MM: First of all, the Bible is a fixed document.
                    MM on covid-19: We're talking about an illness with a better than 99.9% rate of survival.

                    seer: I believe that so called 'compassion' [for starving Palestinian kids] maybe a cover for anti Semitism, ...

                    Comment


                    • #40
                      An interesting example of evolution in regions of uniform environment over time is the tropical rain forests. A large variety of diversification of varieties, subspecies, and varieties of species develop without the necessity of selecting for function. Selection for superior function comes after the genetic mutations over time that create the diversity within the species, and adaption to new environments. It has been demonstrated that the genetic mutations that accumulate within the populations do not do so with the necessity of the result of an adaptive function. New species have been demonstrated to evolve in the Rain forests in this process. The paleontological evidence demonstrates that early mammals and birds evolved in a uniform abundant environments in a similar way evolution takes place in rain forests today.
                      Last edited by shunyadragon; 11-05-2019, 08:25 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


                      • #41
                        So, a bit of meta-discussion about Doug Axe.

                        Most of the Discovery Institute crew are pretty obviously a bit bonkers when it comes to science. Mike Bene is a bit like the black knight, continuing to insist he's right even as valid criticisms of his work pile up. Jon Wells seems to think that a few problems in out-of-date textbooks somehow invalidates the theory the textbooks are describing. Paul Nelson is a young earth creationist that somehow stumbled into a science argument. Steven Meyer is a geologist who's mystified by biology. Dembski i similar but with a math background.

                        The one unifying feature they have is an intense dishonesty. It may not be conscious, but they change their presentations to suit their needs (ID may be science or religion depending on their audience), misinterpret research so consistently that there's no way it could be accidental or stupidity, etc. They're almost certainly lying to themselves to convince themselves about what they're doing (maybe even unconsciously), but they're also lying to everyone else in the process.

                        Axe at least once upon a time seemed to be doing biology, and basing his arguments on his own research. So, i'd kind of given him the benefit of doubt. His arguments were dumb, and based on an unjustified extrapolation of his work, but i figured he's at least trying to put some substance behind it. But looking over his stuff in more detail thanks to Lee has made it clear that he's no better than the rest of them.

                        One of the truisms about science is that you have to go where the data leads you. That seems to be the exact opposite of what Axe is doing. As far as i can tell, he set out to conclude that functional proteins were rare, and he's adjusted his research to try to fit that conclusion. That's why he started by making random mutations and then, when that mostly left function intact, he's moved on to making large numbers of mutations, simply because that's what he needs to do in order to inactivate the protein. He then uses this to leap to conclusions about the existence of functional proteins in general, even though he never tests for anything other than the original function of the protein he's working with.

                        In other words, once i've been compelled to look more closely, it's become clear that Axe is no better than the rest of them.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • #42
                          Originally posted by TheLurch View Post
                          Once again, no he did not show that. He showed that multiple mutations designed specifically to disrupt the structure of the protein produced non-functional proteins. That's it.
                          So he hoodwinked the editors of the Journal of Molecular Biology? What you just stated would not seem worthy of publication.

                          Targeting multiple random changes (10 of them in the paper you cited!) at the sites within a protein that are most likely to be structurally significant doesn't actually tell you anything about how frequent other structures are.
                          Sure it does, varying the areas of structure in the protein would be the way to find out how the structure can vary, this seems almost self-evident.

                          Source: Douglas Axe

                          Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site.

                          © Copyright Original Source



                          But i'll take you changing the subject to be a tacit acknowledgement that, as i claimed:
                          a) most mutations are neutral or alter function rather than eliminating it.
                          b) that fact proved a barrier to Axe's early attempts to get the results he wanted, so he had to change his methods.
                          Well, I disagree, but I don't think every point needs disputing. Most mutations are neutral or deleterious, for instance, correct?

                          Axe was not measuring new function; he was testing the same function that the protein already performed—read the abstract you yourself linked.
                          Yes, but his work provides a way to estimate the prevalence of protein sequences adopting functional enzyme folds. Just quoting from the title. This gives us an idea of the distance to new 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


                          • #43
                            Originally posted by Roy View Post
                            False. Multiple mutations that enhance the existing functionality may be selected for.
                            I think that's compatible with what I said--I agree.

                            False. Axe didn't show anything at all about new function, or about genetic distance.
                            See above, in my reply to The Lurch.

                            Originally posted by lee_merrill
                            Though you have to get to new function in order for multiple mutations to be selected positively, and Axe shows that new function is generally far away. So the mutations are probably independent.
                            False. Even if the preceding two claims were correct, this would not follow.
                            Well, if it's a long way to new function, with multiple mutations, then the mutations are probably not positive together. Thus they are probably neutral or deleterious, and thus independent.

                            Blessings,
                            Lee
                            Last edited by lee_merrill; 11-06-2019, 07:30 PM.
                            "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


                            • #44
                              Originally posted by shunyadragon View Post
                              An interesting example of evolution in regions of uniform environment over time is the tropical rain forests. A large variety of diversification of varieties, subspecies, and varieties of species develop without the necessity of selecting for function.
                              Surely function was being selected for throughout! A uniform environment does not mean that selection ceases.

                              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


                              • #45
                                Originally posted by lee_merrill View Post
                                Surely function was being selected for throughout! A uniform environment does not mean that selection ceases.

                                Blessings,
                                Lee
                                Simply no. function has not been selected throughout. Genetic drift results from mutations creating genetic diversity throughout the history of life does not necessarily relate to function. Genetic diversity for evolution is greatest in many environments that do not change over hundreds of thousands if not millions of years like rainforests. Adaptive function does arise from the genetic diversity due to mutations.
                                Last edited by shunyadragon; 11-06-2019, 10:04 PM.
                                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

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