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Optimized amino acids

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  • Originally posted by shunyadragon View Post
    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.
    You simply don't have any evidence that there were life forms that used alternative sets of amino acids.

    Comment


    • Originally posted by shunyadragon View Post
      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.
      I'm not using it to make an argument. I was just pointing out that I didn't change a term that the paper used.

      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?
        Scientific conclusions are always amendable when new discoveries are found, right?

        So, there is nothing that prevents your hypothetical scenario from being discovered.

        Comment


        • Originally posted by Roy View Post
          Combined reply to two posts.
          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.
          It depends on the context of "I would be interested to hear more."

          Here are the relevant quotes.

          Originally posted by lee_merrill
          That's what I mean when I say "highly conserved", we don't see amino acid sets evolving, which indicates that change in this area is fatal to the organism.
          Originally posted by TheLurch
          We do see amino acid systems changing since the last common ancestor, often through horizontal gene transfer.
          Originally posted by lee_merrill
          I would be interested to hear more.
          Originally posted by Roy
          You already did, on page three of this thread.
          The context, as I read it, is that "I'd be interested to hear more" is asking for information about the amino acid system changes that result in evolving amino acid sets.

          Comment


          • Originally posted by The Barbarian View Post
            Originally posted by DaveB
            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?
            Well, let's not change the subject! But fish shapes could conceivably evolve, amino acid sets, not so much.

            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
              . . . 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.
              And as I recall I responded to your posts, and got a response that said "What are your qualifications to critique this research?"

              This is not a way to conduct a discussion.

              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
                And as I recall I responded to your posts, and got a response that said "What are your qualifications to critique this research?"

                This is not a way to conduct a discussion.

                Blessings,
                Lee
                Your response and critique is not a way to conduct a discussion without any relevant qualifications. You would need to cite qualified scientists form literature that critique the article.

                I have emphasized citing peer reviewed scientific articles to support my arguments, and you need to do the same.

                In contrast The Lurch is far more qualified than both of us, and we share the same perspective, and he also has provided references.
                Last edited by shunyadragon; 02-13-2019, 10:47 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


                • Originally posted by lee_merrill View Post
                  Well, let's not change the subject! But fish shapes could conceivably evolve, amino acid sets, not so much.

                  Blessings,
                  Lee
                  Actually amino acids do not evolve. Combinations of amino acids forming proteins evolve in the various possible combinations forming primitive RNA based on the Laws of nature, and adapting to the environment, and potential energy sources as described in the articles cited. The results is LUCA with the best adapted first set of 20 amino acids.
                  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
                    You simply don't have any evidence that there were life forms that used alternative sets of amino acids.
                    Actually, he does. So do I. Shunya has hinted at it several times, as have I, but neither you nor Dory have bothered to do any research to see whether such evidence exists.
                    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?
                    Scientific conclusions are always amendable when new discoveries are found, right?

                    So, there is nothing that prevents your hypothetical scenario from being discovered.[/QUOTE]It's already been discovered. I was just giving you one last chance to reflect that maybe we knew something that you didn't - but instead you've demonstrated that, as suspected, you're just another creationist bletherskite whose ignorance is maintained by so much misplaced arrogance that you don't even bother to do a simple Google/Wikipedia check before posting coprolites.

                    There are lifeforms that use a different set of amino-acids, they obviously do postdate LUCA, and you clearly aren't aware of their existence.

                    Now you could argue that this is only the addition of one amino-acid to the usual set, rather than a completely different set. But overcoming Dory's and your objections doesn't require that completely different set be used, only that it is possible to (I) add new amino acids, (ii) change what amino-acid a codon relates to. There evidence for both of these, but neither you nor Dory knows about that evidence.

                    Your claims that amino-acid sets can't evolved aren't based on knowledge, or even on ignorance (which is curable), but on your unshakeable assumption that you aren't ignorant. As such, any claims you make about the difficulties involved in amino-acid set evolution aren't worth any consideration at all, because - and I will continue to stress this - 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


                    • Originally posted by lee_merrill View Post
                      And as I recall I responded to your posts, and got a response that said "What are your qualifications to critique this research?"

                      This is not a way to conduct a discussion.
                      It's an excellent way to handle some-one who demonstrates with every post that they have neither the knowledge nor the intellect to make meaningful comments.
                      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


                      • Ok, since i've been ignoring this while sick, it seems like a good chance to back up to some basic stuff. Lee, without resorting to internet searches, can you answer the following questions:
                        How many different sets of amino acids are currently in use? (Or, put differently, how many distinct genetic codes are there?)
                        What is the name of the class of enzyme responsible for matching amino acids to genetic codes?
                        Has that enzyme class shown signs of recent evolution?

                        These all seem relevant to your claim that the genetic code hasn't evolved. Do you actually know them?
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • Originally posted by TheLurch View Post
                          Ok, since i've been ignoring this while sick, it seems like a good chance to back up to some basic stuff. Lee, without resorting to internet searches, can you answer the following questions:
                          How many different sets of amino acids are currently in use? (Or, put differently, how many distinct genetic codes are there?)
                          What is the name of the class of enzyme responsible for matching amino acids to genetic codes?
                          Has that enzyme class shown signs of recent evolution?

                          These all seem relevant to your claim that the genetic code hasn't evolved. Do you actually know them?
                          Excellent questions!!!!
                          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 Roy View Post
                            Actually, he does. So do I. Shunya has hinted at it several times, as have I, but neither you nor Dory have bothered to do any research to see whether such evidence exists. Scientific conclusions are always amendable when new discoveries are found, right?

                            So, there is nothing that prevents your hypothetical scenario from being discovered.It's already been discovered. I was just giving you one last chance to reflect that maybe we knew something that you didn't - but instead you've demonstrated that, as suspected, you're just another creationist bletherskite whose ignorance is maintained by so much misplaced arrogance that you don't even bother to do a simple Google/Wikipedia check before posting coprolites.

                            There are lifeforms that use a different set of amino-acids, they obviously do postdate LUCA, and you clearly aren't aware of their existence.

                            Now you could argue that this is only the addition of one amino-acid to the usual set, rather than a completely different set. But overcoming Dory's and your objections doesn't require that completely different set be used, only that it is possible to (I) add new amino acids, (ii) change what amino-acid a codon relates to. There evidence for both of these, but neither you nor Dory knows about that evidence.

                            Your claims that amino-acid sets can't evolved aren't based on knowledge, or even on ignorance (which is curable), but on your unshakeable assumption that you aren't ignorant. As such, any claims you make about the difficulties involved in amino-acid set evolution aren't worth any consideration at all, because - and I will continue to stress this - your ignorance is not an argument.
                            Not only was I aware of Pyrrolysine, I'm also aware of Selenocycteine.

                            The organisms that use Pyrrolysine have genes for a specific tRNA and aminoacyl-tRNA-synthetase for Pyrrolysine. And, it doesn't replace an existing amino acid/codon mapping, it codes to one of the stop codons.

                            You need to explain how either one (tRNA or aminoacyl-tRNA-synthetase) could have been selected for without the other one existing. They work together.

                            Is this a case of an additional amino acid being added to the set or a case of discovering an amino acid that was always being used in certain organisms?

                            Comment


                            • Originally posted by shunyadragon View Post
                              Combinations of amino acids forming proteins evolve in the various possible combinations forming primitive RNA...
                              What do you mean by this? Are you talking about the metabolism first hypothesis?
                              Last edited by DaveB; 02-14-2019, 09:43 AM.

                              Comment


                              • Originally posted by TheLurch View Post
                                Ok, since i've been ignoring this while sick, it seems like a good chance to back up to some basic stuff. Lee, without resorting to internet searches, can you answer the following questions:
                                How many different sets of amino acids are currently in use? (Or, put differently, how many distinct genetic codes are there?)
                                A couple of weeks ago he didn't even know that there were variant genetic codes.
                                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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