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Optimized amino acids

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  • #46
    Originally posted by lee_merrill View Post
    Are you saying scientists have not touted junk DNA as evidence for evolution? Assuredly they have.
    No, i'm saying scientists understand why some things will be optimized through evolutionary processes and other things won't, or will only be partially optimized. And it has to do (in part) with what's termed effective population size.

    Which you should know if you're going to make arguments in this area.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • #47
      Originally posted by lee_merrill View Post
      Agreed, so the absolute optimum may not be expected to evolve.

      Blessings,
      Lee
      . . . and absolute optimum is not the nature of life on earth nor the evolution of life.

      The purpose of evolution in optimization is survival of lineage of life we describe as species.
      Last edited by shunyadragon; 01-10-2019, 07:27 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


      • #48
        Originally posted by lee_merrill View Post
        Well, I am aware of the ENCODE project, so I tried to make a careful statement, phrasing it in the past.

        Blessings,
        Lee
        OK,but it remains a problem that you are misrepresenting what is considered 'Junk' DNA. Is it out of ignorance or deception as in your advocates at the Discovery Institute.

        Yes, it is evidence of evolution, and no longer considered simply Junk DNA.
        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


        • #49
          Originally posted by TheLurch View Post
          No, i'm saying scientists understand why some things will be optimized through evolutionary processes and other things won't, or will only be partially optimized. And it has to do (in part) with what's termed effective population size.
          Yet evolution will generally find only local optimums, not the highest fitness peak in the entire landscape. Which means seeing a highly-optimized set of amino acids is surprising. And yes, higher population sizes mean more effective searching, if that's what you are referring to, if not, please enlighten me.

          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


          • #50
            Originally posted by shunyadragon View Post
            . . . and absolute optimum is not the nature of life on earth nor the evolution of life.
            Agreed, so finding a highly optimized set of amino acids is surprising.

            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


            • #51
              Originally posted by lee_merrill View Post
              Agreed, so finding a highly optimized set of amino acids is surprising.

              Blessings,
              Lee
              Surprising?!?!? The set of amino acids is simply what evolved and works, and not surprising from a natural perspective.
              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


              • #52
                Originally posted by lee_merrill View Post
                Yet evolution will generally find only local optimums, not the highest fitness peak in the entire landscape. Which means seeing a highly-optimized set of amino acids is surprising. And yes, higher population sizes mean more effective searching, if that's what you are referring to, if not, please enlighten me.
                No, it's not surprising, and once again, you're revealing your ignorance of the topic, because your statement is simply wrong. Whether or not evolution reaches local or global optima depends on the shape of the fitness landscape, the probability barriers between local optima, etc. Do you know the shape of the fitness landscape for amino acid usage? No? Then you shouldn't be surprised.

                Doesn't it bother you to speak so confidently about a subject you clearly don't understand?
                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                Comment


                • #53
                  Originally posted by shunyadragon View Post
                  Surprising?!?!? The set of amino acids is simply what evolved and works, and not surprising from a natural perspective.
                  Originally posted by TheLurch
                  Whether or not evolution reaches local or global optima depends on the shape of the fitness landscape, the probability barriers between local optima, etc. Do you know the shape of the fitness landscape for amino acid usage? No? Then you shouldn't be surprised.
                  Well, the authors of the paper say "we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone", so according to them, selection must have been involved. Yet they went through many sets, and I would say it's unlikely that the set of amino acids (and thus the proteins that can be built) would change very much, and thus the sets of amino acids that could be examined by evolution would be limited.

                  Doesn't it bother you to speak so confidently about a subject you clearly don't understand?
                  Oh, I'm up for correction if I misspeak or misunderstand something.

                  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


                  • #54
                    Originally posted by lee_merrill View Post
                    Well, the authors of the paper say "we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone", so according to them, selection must have been involved. Yet they went through many sets, and I would say it's unlikely that the set of amino acids (and thus the proteins that can be built) would change very much, and thus the sets of amino acids that could be examined by evolution would be limited.


                    Oh, I'm up for correction if I misspeak or misunderstand something.

                    Blessings,
                    Lee
                    Which paper?

                    'Chance alone.' cannot explain anything, nor does it cause anything, and it is not the basis of scientific explanations. Laws of Nature are the explanation and the natural process of evolution over millions of years.
                    Last edited by shunyadragon; 01-13-2019, 08:50 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


                    • #55
                      Originally posted by lee_merrill View Post
                      Well, the authors of the paper say "we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone", so according to them, selection must have been involved. Yet they went through many sets, and I would say it's unlikely that the set of amino acids (and thus the proteins that can be built) would change very much, and thus the sets of amino acids that could be examined by evolution would be limited.
                      Do you have any reason to think it unlikely or limited beyond "I would say"? If not, all you have is an argument from not-an-authority, which isn't even good enough to qualify as a fallacy.

                      Your ignorance is not an argument.
                      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


                      • #56
                        Originally posted by Roy View Post
                        Do you have any reason to think it unlikely or limited beyond "I would say"? If not, all you have is an argument from not-an-authority, which isn't even good enough to qualify as a fallacy.

                        Your ignorance is not an argument.
                        To echo this with a specific - do you (Lee) know how many additional (beyond the 20 in use) amino acids are produced by cells as metabolic byproducts, intermediates in chemical reactions, etc.? If you don't (and I certainly don't, and i was a biochem major), then you don't have any sense of how difficult it would be to add a 21st amino acid.

                        This is the second time on a single page (!) that you've tried to make an argument without even knowing the fundamentals that underly the issue. (See the fitness landscape comment above). It's not that you don't know the relevant probabilities - it's that you don't even know which probabilities would be relevant.

                        You say you're open for correction? Try this: before making an argument, understand the subject you're arguing about. Or, if you can't be bothered to do that, ask someone here to explain it to you, rather than putting out an ignorant position for us to shoot down.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • #57
                          Originally posted by TheLurch View Post
                          To echo this with a specific - do you (Lee) know how many additional (beyond the 20 in use) amino acids are produced by cells as metabolic byproducts, intermediates in chemical reactions, etc.? If you don't (and I certainly don't, and i was a biochem major), then you don't have any sense of how difficult it would be to add a 21st amino acid.
                          Lee didn't even know that the genetic code isn't universal. He's not interested in learning things that might adversely affect his preconceived ideas.
                          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


                          • #58
                            Originally posted by shunyadragon View Post
                            Which paper?
                            The paper the blog is about: Gayle K. Philip and Stephen J. Freeland, “Did Evolution Select a Nonrandom ‘Alphabet’ of Amino Acids?”

                            'Chance alone.' cannot explain anything, nor does it cause anything, and it is not the basis of scientific explanations. Laws of Nature are the explanation and the natural process of evolution over millions of years.
                            Are you saying the authors of the paper were misguided to use such language?

                            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


                            • #59
                              Originally posted by TheLurch View Post
                              To echo this with a specific - do you (Lee) know how many additional (beyond the 20 in use) amino acids are produced by cells as metabolic byproducts, intermediates in chemical reactions, etc.? If you don't (and I certainly don't, and i was a biochem major), then you don't have any sense of how difficult it would be to add a 21st amino acid.
                              No, I don't, but the amino acid set is highly conserved, and thus it would be difficult for it to evolve.

                              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


                              • #60
                                Originally posted by lee_merrill View Post
                                No, I don't, but the amino acid set is highly conserved, and thus it would be difficult for it to evolve.
                                No, you don't know that. In fact, nobody knows that, because it's false. Highly conserved things evolve all the time. DNA polymerases are highly conserved, yet mammals have evolved multiple versions to handle various sorts of DNA damage.
                                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                                Comment

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