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Nice defense of Evolution

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  • #76
    Originally posted by lee_merrill View Post
    I read Kenneth Miller's book, "Finding Darwin's God".

    Blessings,
    Lee
    OK you read the book. Now what??
    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


    • #77
      Originally posted by rogue06 View Post
      Miller's FDG was written largely as a refutation to Behe, specifically his Darwin's Black Box
      I've read Miller's book - that's not what I remember. My impression was that Miller wrote about how to reconcile evolution with the assumption of a deity.

      I may be wrong though - and I can't find my copy to check
      Last edited by Roy; 11-17-2019, 10:18 AM.
      Jorge: Functional Complex Information is INFORMATION that is complex and functional.

      mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

      Mountain Man: First of all, the Bible is a fixed document.
      Mountain Man: … this is how liberals argue these days, with labels instead of ideas.

      Comment


      • #78
        Originally posted by Roy View Post
        I've read Miller's book - that's not what I remember. My impression was that Miller wrote about how to reconcile evolution with the assumption of a deity.

        I may be wrong though - and I can't find my copy to check
        It is a Christian response to Behe.

        Personally I think his Only A Theory was better.

        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 that’s not the argument." --Tassman

        Comment


        • #79
          Originally posted by lee_merrill View Post
          "He who throws mud is losing ground."

          When you're ready to answer my points, I'm ready to reply some more.
          I'm honestly interested in an answer to the question: given how often you get things wrong or are unaware of key information when it comes to biology, why do you think this is not a Dunning-Kruger situation?

          Saying "you don't seem to know much about biology" shouldn't be an insult. BIology's an incredibly complicated topic, and has been the subject of intensive research for well over a century. I have a PhD in a field within biology, and i'll readily admit there's lots of other fields that i don't know well, and need to read up on before i understand at all. I'm in no way saying that you have some general knowledge deficiency.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • #80
            Originally posted by lee_merrill View Post
            Well, interesting. Yet in the case of the protein Axe worked with, function and folds do seem related.

            Source: Douglas Axe

            ... given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold.

            © Copyright Original Source



            Though as far as I can see, Axe was attempting to measure one function to get an idea how other functions would respond to mutations.
            And how, precisely, would that work? If he's not testing for any functions beyond the one enzymatic activity, or testing for folding, how could he possibly tell anything else? How are these results any more informative than the other protein he looked at where a similar approach left a functional protein?

            The answer comes back to the two points i mentioned above - you need to show both of my statements are wrong. You haven't.

            Originally posted by lee_merrill View Post
            Though I think these results may be consistent, given that a number of mutations are generally required to disable function, as you yourself say: "So, you have to have massive mutational damage before it starts becoming sensitive to additional mutations..."

            Yet the conclusion still stands, that "the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability..."
            Nobody is arguing that thermodynamics doesn't matter. The issue is one of whether thermodynamics plays such a large role that proteins end up locked in place, unable to vary enough to reach new functions. The fact that it takes massive mutational change in order to disable them indicates the answer is no.

            Let's look at this case in Axe's other paper in particular: a situation where any hydrophobic amino acid will do, and you have to mutate 10 of them to kill this one function. So, that means for 9 of the 10, any of the 20 amino acids will do. For the 10th, it's got to be hydrophobic, which means 9 of the 20 amino acids will work. That means there are 4.6 * 10^12 possible amino acid configurations that can be tolerated just at these 10 amino acids alone. For most of the rest of the proteins, any amino acid will do, which gives you an absolutely vast expansion of the configurations that are compatible with the protein's original function.

            So, thermodynamics creates a constraint on this one particular function, but it's an extremely loose one. Nobody has ever tested whether these mutations create additional or entirely new functions, either, so we can't generalize and determine if it creates any sort of barrier to new functions.


            Incidentally, did you notice that Axe had to assume evolutionary relatedness among versions of this protein in different species in order to even do this work?
            An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold.
            "Any sufficiently advanced stupidity is indistinguishable from trolling."

            Comment


            • #81
              Originally posted by shunyadragon View Post
              OK you read the book. Now what??
              Well, Miller convinced me that Behe had been refuted, notably with a diagram of blood clotting that was a simple "Y". Then I read Behe's book, and realized that I had been had, blood clotting is complex! A simple "Y" does not describe it.

              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


              • #82
                Originally posted by TheLurch View Post
                I'm honestly interested in an answer to the question: given how often you get things wrong or are unaware of key information when it comes to biology, why do you think this is not a Dunning-Kruger situation?
                I don't think I'm so smart! But for arguments presented to the general public, I believe I can understand and present them here, and they seem to hold up pretty well.

                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


                • #83
                  Originally posted by lee_merrill View Post
                  Well, Miller convinced me that Behe had been refuted, notably with a diagram of blood clotting that was a simple "Y". Then I read Behe's book, and realized that I had been had, blood clotting is complex! A simple "Y" does not describe it.

                  Blessings,
                  Lee
                  I do not depend on Miller's book, because it is more a general non-scientific source and old concerning the contemporary research. For the evolution of blood clotting I depend on the contemporary research, for which there are many peer reviewed articles that cover the evolution of blood clotting. I cited three, which you have not provided any specific scientific based responses, and there are many more research articles on the topic.
                  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


                  • #84
                    Originally posted by lee_merrill View Post
                    I don't think I'm so smart! But for arguments presented to the general public, I believe I can understand and present them here, and they seem to hold up pretty well.

                    Blessings,
                    Lee
                    The arguments presented to the general public like Behe's and Miller's book are peer reviewed scientific references, and not good references.
                    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


                    • #85
                      Originally posted by TheLurch View Post
                      And how, precisely, would that work? If he's not testing for any functions beyond the one enzymatic activity, or testing for folding, how could he possibly tell anything else? How are these results any more informative than the other protein he looked at where a similar approach left a functional protein?
                      Well, again, the similar approach and this protein may well be compatible in their results. And testing for one function can be generalized to different proteins and their functions:

                      Source: Douglas Axe

                      How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. 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. Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution.

                      © Copyright Original Source



                      The answer comes back to the two points i mentioned above - you need to show both of my statements are wrong. You haven't.


                      1) You cannot know whether mutagenesis has disrupted a protein's folding without measuring whether it's folded, because many mutations inactivate enzymes without disrupting their structure. Axe has never measured this.

                      2) You cannot know how distant other folds are without determining whether your mutated protein has adopted a different fold. Axe has never measured that either.
                      Well, in this case I would assume that fold and function are related, or else the editors of the Journal of Molecular Biology were duped!

                      Source: Douglas Axe

                      The prevalence of low-level function in four such experiments indicates that roughly one in 1064 signature-consistent sequences forms a working domain.

                      © Copyright Original Source



                      The issue is one of whether thermodynamics plays such a large role that proteins end up locked in place, unable to vary enough to reach new functions. The fact that it takes massive mutational change in order to disable them indicates the answer is no.
                      I don't see how this follows, though, it might take a dozen mutations or more to disable a protein, but that doesn't mean it isn't a long way off to new function.

                      Let's look at this case in Axe's other paper in particular: a situation where any hydrophobic amino acid will do, and you have to mutate 10 of them to kill this one function. So, that means for 9 of the 10, any of the 20 amino acids will do. For the 10th, it's got to be hydrophobic, which means 9 of the 20 amino acids will work. That means there are 4.6 * 10^12 possible amino acid configurations that can be tolerated just at these 10 amino acids alone. For most of the rest of the proteins, any amino acid will do, which gives you an absolutely vast expansion of the configurations that are compatible with the protein's original function.
                      Yes, but the space of distribution of proteins is apparently more vast:

                      Source: Evolution News

                      In the study, after 5-10 mutations, roughly 2 in 3 mutations inactivate a protein. Therefore, 1 in 3 amino acids at each position on average would correspond to a functional sequence. The rarity would then be less than 1/3 to the power of the sequence length. This estimate closely matches the result from Axe’s 2004 β-lactamase experiment that only 1 in 1077 sequences corresponds to a functional fold/domain within the protein. The actual rarity is much more extreme, since almost no sequences are functional after 10 percent of a protein randomly changes.

                      Source

                      © Copyright Original Source



                      Incidentally, did you notice that Axe had to assume evolutionary relatedness among versions of this protein in different species in order to even do this work?
                      Didn't he look at homologous domains, though?

                      Source: Douglas Axe

                      Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold.

                      © 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


                      • #86
                        Originally posted by lee_merrill View Post
                        I don't see how this follows, though, it might take a dozen mutations or more to disable a protein, but that doesn't mean it isn't a long way off to new function.
                        I can respond to the rest later, but you're -this- close to getting it here. What would Axe have to do to actually determine if it's a long way off to a new function? TEST FOR NEW FUNCTIONS.

                        Which he didn't do.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • #87
                          Originally posted by TheLurch View Post
                          I can respond to the rest later, but you're -this- close to getting it here. What would Axe have to do to actually determine if it's a long way off to a new function? TEST FOR NEW FUNCTIONS.

                          Which he didn't do.
                          Agreed.
                          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


                          • #88
                            Originally posted by TheLurch View Post
                            I can respond to the rest later, but you're -this- close to getting it here. What would Axe have to do to actually determine if it's a long way off to a new function? TEST FOR NEW FUNCTIONS.

                            Which he didn't do.
                            Well, I thought we agreed that testing for new function would be prohibitive. So we would need some other way to estimate the distance between functions, which I believe Axe attempted, and succeeded well enough that the editors of the journal thought his work worth publishing.

                            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


                            • #89
                              Originally posted by lee_merrill View Post
                              Well, I thought we agreed that testing for new function would be prohibitive. So we would need some other way to estimate the distance between functions, which I believe Axe attempted, and succeeded well enough that the editors of the journal thought his work worth publishing.
                              Right, so he doesn't know what the actual distance is. Instead, he's derived one imperfect estimate based on a single protein. Obviously, he would have gotten a completely different answer had he tried to do that with the far more mutation-tolerant protein he had used in his earlier work.

                              I have a copy of the full text of the paper, but it seems unnecessarily verbose. At some point when i have the time, I intend to look at how precisely he derived a number for a distance. From what you quote from Evolution News, the estimate starts with a heavily mutated protein, and uses that as the starting point for its calculation of the frequency (note the 1/3), and then compares that figure to the total of every possible amino acid configuration of that length.

                              One, it's laughably bogus to start the calculation without compensating for the other mutations needed. Two, this assumes that absolutely no other functions are present in any proteins of the same length, which is simply wrong. Finally, it assumes that mutated versions of the protein can't possibly have a different function. Every single aspect of that is comically wrong.

                              So, i'm assuming this is just a product of the fact that, as usual, the people at Evolution News have no understanding of biology and so misunderstood the paper. I'll know once i look.


                              Didn't he look at homologous domains, though?
                              And how do you think that homology is defined?
                              "Any sufficiently advanced stupidity is indistinguishable from trolling."

                              Comment


                              • #90
                                Originally posted by TheLurch View Post
                                From what you quote from Evolution News, the estimate starts with a heavily mutated protein, and uses that as the starting point for its calculation of the frequency (note the 1/3), and then compares that figure to the total of every possible amino acid configuration of that length.
                                I think there's been a misunderstanding, Evolution News was referencing the paper by Tokuriki and Tawfik.

                                One, it's laughably bogus to start the calculation without compensating for the other mutations needed. Two, this assumes that absolutely no other functions are present in any proteins of the same length, which is simply wrong. Finally, it assumes that mutated versions of the protein can't possibly have a different function. Every single aspect of that is comically wrong.
                                I think what they must be doing is defining a general measure for all proteins, or at least all globular proteins.

                                Source: Evolution News

                                The authors demonstrate that their results apply generally to globular proteins (e.g., enzymes and components of molecular machines).

                                © Copyright Original Source



                                And how do you think that homology is defined?
                                Sequence similarity, I would say.

                                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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