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Optimized amino acids

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  • Originally posted by TheLurch View Post
    I have a BA in biochemistry, a PhD in molecular and cellular biology, and have done over a dozen years of post-doctoral and faculty-level research in the biological sciences.

    Don't equate casual phrasing with lack of knowledge.

    EDIT: correcting my own error - apologies for the stupidity.
    If you are that well educated, then there really isn't any excuse for saying this...

    Originally posted by TheLurch
    How much do you know about the process of charging tRNAs with amino acids for translation? Because that's the process that would undergo changes to broaden/alter the amino acid repertoire. It's done by an enzyme, and it's no harder for it to change its substrate specificity than it is for something that, say, digests antibiotics.
    ... because it is simply not true.

    Comment


    • Originally posted by TheLurch View Post
      Given that evolution has been demonstrated repeatedly, it's not something that has to be assumed, so i'm not sure what you're trying to say here.
      Any evolution of the set of amino acids from among other potential sets would have happened before the so-called LUCA and is therefore hypothetical and assumed.

      Comment


      • Originally posted by TheLurch View Post
        Oxygen wasn't present in significant amounts until much later in life's history; oxidative damage wasn't unlikely to be a significant issue until over a billion years after life started. So the phrase "make life possible" is simply wrong, and implies he was either careless, or didn't read or think carefully about the implications of the papers he was citing.
        Rana talks about that and attributes the inclusion of the extra amino acids before they were neededas a sign of foresight by a Creator.

        Didn't you read Rana's post?

        Comment


        • Originally posted by Roy View Post
          You've changed "just-right" to "right". Perhaps "just-right" implies optimality, in which case the first paper could be claiming it's the best possible set.
          "Just-right" is Rana's term. It isn't from either paper.

          Comment


          • Originally posted by DaveB View Post
            Any evolution of the set of amino acids from among other potential sets would have happened before the so-called LUCA and is therefore hypothetical and assumed.
            It is true once the set of 20 dominated, and the alternative sets failed and did not survive primarily due to the efficiency of the ability at energy transfer and reproduction. The references cited previously described the reasons that the set of 20 survived as the most optimal. Actually the set of amino acids have evolved since to a potential of 22 in some amino acid sets.

            Of course, LUCA represents using the set of 20 amino acids with no others surviving, which is the way evolution works. The problem you are 'arguing from ignorance,' which fails to make a constructive argument for either side. The many many examples that only one lineage of species survive and others do not, which is normal for evolution.
            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 DaveB View Post
              "Just-right" is Rana's term. It isn't from either paper.
              In evolution the anecdotal "just-right," nor even "right," are subjective, and have no productive meaning nor context in a scientific argument for falsification of a hypothesis.
              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 TheLurch View Post
                I'll just point out that sterility creates just as strong an evolutionary selection as lethality, so you're clearly wrong.
                Well, whether it's sterility or lethality, the evolutionary blockade is firmly set against evolution of amino acid sets, we don't see them evolving now, so change in this area would be difficult. Difficult as well for LUCA...

                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, whether it's sterility or lethality, the evolutionary blockade is firmly set against evolution of amino acid sets, we don't see them evolving now, so change in this area would be difficult. Difficult as well for LUCA...

                  Blessings,
                  Lee
                  Yes we do as cited.
                  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 DaveB View Post
                    There are many amino acids found on the earth. Perhaps hundreds.

                    The question is why are the relatively few used optimal (in the properties that the researchers tested for)?
                    There are many possible shapes for a fast swimming animal. Maybe millions. The question is; why are the relatively few shapes used, optimal?

                    Comment


                    • Originally posted by DaveB View Post
                      This paper is trying to explain the two different classes of synthetases that are used to process the current set of amino acids. It does nothing to show that life ever used any other amino acid sets.
                      Did you read the full paper, or only the abstract?
                      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


                      • Originally posted by DaveB View Post
                        Any evolution of the set of amino acids from among other potential sets would have happened before the so-called LUCA...
                        Why? What prevents there having been evolution of the set of amino acids since LUCA that either
                        - led to a lineage that went extinct
                        - led to a lineage that hasn't yet been examined
                        - led to a lineage that has been examined, but you aren't aware of?
                        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


                        • Combined reply to two posts.
                          Originally posted by DaveB View Post
                          You are conflating a few exceptions to the Genetic code with changes to the set of amino acids that life uses.
                          No, I'm not.

                          Lee claimed he wanted to hear more about "amino acid systems changing since the last common ancestor" - which includes changes to the genetic code as well as changes to the amino acid set.

                          Originally posted by DaveB View Post
                          You've changed "just-right" to "right". Perhaps "just-right" implies optimality, in which case the first paper could be claiming it's the best possible set.
                          "Just-right" is Rana's term. It isn't from either paper.
                          So Rana misrepresented the authors?
                          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


                          • Originally posted by Roy View Post
                            Why? What prevents there having been evolution of the set of amino acids since LUCA that either
                            - led to a lineage that went extinct
                            - led to a lineage that hasn't yet been examined
                            - led to a lineage that has been examined, but you aren't aware of?
                            The arguments of lee_merrill and Dave B are largely an unethical 'argument from ignorance,' and juggling unscientific shotgun approaches of probability, instead of sound hypothesis that could be falsified.
                            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 lee_merrill View Post
                              But I was asking what other sets exist today, which is what seemed to be being claimed.


                              The best local optimum in the fitness landscape survives, not the best overall optimal solution.

                              Blessings,
                              Lee
                              . . . and I responded that set up to 22 has evolved since and exist today. One of the article I cited described possible alternate amino acid sets. The reason other sets did not survive natural selection and evolve is explained in the articles cited. One of the reasons is that the present set of 20 was only optimal set to survive is the most efficient energy metabolism best suited to life. The evolution from dependent energy sources to independent metabolism of energy for life required the eventual dominant set of twenty. You know natural selection.

                              Do some research for yourself. spoon feeding is getting tiresome.
                              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
                                Do some research for yourself. spoon feeding is getting tiresome.
                                Especially since the baby keeps knocking the spoon away and splattering the food all over the floor.
                                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

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