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Optimized amino acids

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  • #16
    Originally posted by shunyadragon View Post
    Well,ah . . . I question the use of random, but given millions of years to come up with this combination, no problem.
    Well, if there were changes then, why don't we see changes now? And mere chance cannot explain the origin of this set of amino acids, is the conclusion of the paper.

    What you describe as extraordinary contortions needs explanations...
    I am not a biologist, but something in the chain of codons -> mRNA -> tRNA would need changing. The new amino acid would need to be useful right away in proteins, as a substitution for the previous amino acid. This I deem unlikely.

    Blessings,
    Lee
    Last edited by lee_merrill; 01-03-2019, 04:01 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


    • #17
      Originally posted by Roy View Post
      The abstract of the Hawaiian team's paper also refers to changes to the set of amino acids available:
      The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Considerable evidence indicates that some of these amino acids were present through nonbiological syntheses prior to the origin of life, while the rest evolved as inventions of early metabolism.
      But this is mere hand-waving, I would hope to see a mechanism proposed.

      And there are more than a dozen known variant genetic codes which associate different amino acids with a few codons.
      Are you saying the same codons code for different amino acids?

      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


      • #18
        Originally posted by TheLurch View Post
        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.
        Well, as above, I wonder why we aren't seeing such changes today.

        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


        • #19
          Originally posted by lee_merrill View Post
          Well, as above, I wonder why we aren't seeing such changes today.
          https://www.pnas.org/content/100/24/13863
          https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868979/

          Again, since you don't know this well, ask.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • #20
            Thanks for the references!

            But this has to do with putative prior evolution, not current-day evolution.

            Source: NIH

            A complete deletion of this gene family is lethal, indicating that the tRNASerGCU is essential in Saccharomyces cerevisiae.

            © Copyright Original Source


            And if I'm reading this right, this paper shows that having a gene copy around which can mutate back to a deleted gene is beneficial, and deleting all the copies is lethal. But this hardly demonstrates evolution of new amino acids!

            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


            • #21
              Originally posted by lee_merrill View Post
              Well, if there were changes then, why don't we see changes now? And mere chance cannot explain the origin of this set of amino acids, is the conclusion of the paper.
              The Fundi Creationist hokus bogus 'mere chance' has nothing to do with science and the scientific literature best explains the origin of the Amino Acids. The Lurch has effectively pulled your pants down, and revealed your agenda and ignorance concerning the reality of the scientific literature.

              I am not a biologist, but something in the chain of codons -> mRNA -> tRNA would need changing. The new amino acid would need to be useful right away in proteins, as a substitution for the previous amino acid. This I deem unlikely.

              Blessings,
              Lee
              Yes, your not a biologist, and the scientific literature best answers your questions to the extent of present, which your blog cite selectively misrepresented.
              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


              • #22
                Originally posted by lee_merrill
                I am not a biologist, but something in the chain of codons -> mRNA -> tRNA would need changing. The new amino acid would need to be useful right away in proteins, as a substitution for the previous amino acid. This I deem unlikely.
                Are you saying the same codons code for different amino acids?
                Yes.

                For example, some flatworms generate
                - methionine rather than isoleucine from ATA;
                - serine rather than arginine from AGA/AGG;
                - asparagine rather than lysine from AAA.

                That you seem unaware of the existence of these variant genetic codes renders your view of what is unlikely irrelevant. Your ignorance is not an argument.

                But this is mere hand-waving, I would hope to see a mechanism proposed.
                Then go read the papers and follow up the references therein.
                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


                • #23
                  P.S. you didn't answer this:

                  If you looked at the research article that was being blogged about, you'd find that these are the first two sentences of the abstract:
                  "All life uses the same 20 amino acids, but only 7–13 early amino acids seem to be indispensable to build functional proteins. Thus, what triggered the introduction of the additional amino acids?"
                  Actually, this was not the article being blogged about,
                  Yes it was. The blog post repeatedly references the work of the German team throughout, whereas the work of the Hawaiian team is only mentioned in a single paragraph. Did you not bother to read the blog post before citing it, or are you purposefully misrepresenting it?
                  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


                  • #24
                    Originally posted by shunyadragon View Post
                    The Fundi Creationist hokus bogus 'mere chance' has nothing to do with science and the scientific literature best explains the origin of the Amino Acids.
                    Unfortunately the "mere chance" arguments that are often presented seem to overlook that very specific scientific laws are at play that often direct an outcome. It's like arguing that if you let go of a ball it is "mere chance" that it just happens to fall to earth rather than float off in any number of possible directions [for the pedantic this presumes that you are on earth rather than in space].

                    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)
                    "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
                    "Of course, human life begins at fertilization that’s not the argument." --Tassman

                    Comment


                    • #25
                      Originally posted by Roy View Post
                      P.S. you didn't answer this:

                      Yes it was. The blog post repeatedly references the work of the German team throughout, whereas the work of the Hawaiian team is only mentioned in a single paragraph. Did you not bother to read the blog post before citing it, or are you purposefully misrepresenting it?
                      But the blog post was about the optimization of amino acid groups, which is the subject of the second reference.

                      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


                      • #26
                        Originally posted by lee_merrill View Post
                        But the blog post was about the optimization of amino acid groups, which is the subject of the second reference.

                        Blessings,
                        Lee
                        . . . which is no problem given millions of years.

                        An important point in the nature of our physical existence is the variability in the outcomes of cause effect are determined by natural laws, and the variability in the out comes described in ones imagination as 'mere chance' or 'random,' or more correctly called fractal relationships, DO NOT determine the outcome of cause and effect relationships. I believe rogue06 made it clear how foolish your line of reasoning is.
                        Last edited by shunyadragon; 01-04-2019, 06:39 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


                        • #27
                          Originally posted by lee_merrill View Post
                          But the blog post was about the optimization of amino acid groups, which is the subject of the second reference.
                          According to the blog post, it's also the subject of the first reference:

                          Source: ibid

                          As it turns out, proteins are built from a specialty set of amino acids that have the just-right set of properties to make life possible, as recent work by researchers from Germany attests.[1]

                          © Copyright Original Source



                          The answer to "Did you not bother to read the blog post before citing it, or are you purposefully misrepresenting it?" appears to be "Both".
                          Last edited by Roy; 01-07-2019, 05:09 AM.
                          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


                          • #28
                            Originally posted by Roy View Post
                            According to the blog post, it's also the subject of the first reference:

                            Source: ibid

                            As it turns out, proteins are built from a specialty set of amino acids that have the just-right set of properties to make life possible, as recent work by researchers from Germany attests.[1]

                            © Copyright Original Source



                            The answer to "Did you not bother to read the blog post before citing it, or are you purposefully misrepresenting it?" appears to be "Both".
                            I'd just like to point out that this quote implies that blog author didn't read the paper he's citing. Far from a set of properties to "make life possible", the paper suggests that the current set was the result of the addition of over five new amino acid over evolutionary time, and therefore life was possible with significantly fewer.
                            "Any sufficiently advanced stupidity is indistinguishable from trolling."

                            Comment


                            • #29
                              Originally posted by TheLurch View Post
                              I'd just like to point out that this quote implies that blog author didn't read the paper he's citing.
                              That's why I wrote "According to the blog post"

                              Citing something unread is standard YEC strategy. Citing something unread that cites something unread is unremarkable.
                              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


                              • #30
                                Originally posted by shunyadragon View Post
                                . . . which is no problem given millions of years.
                                Yet the paper in reference 2 concludes that the current set of amino acids did not come about by chance.

                                An important point in the nature of our physical existence is the variability in the outcomes of cause effect are determined by natural laws, and the variability in the out comes described in ones imagination as 'mere chance' or 'random,' or more correctly called fractal relationships, DO NOT determine the outcome of cause and effect relationships.
                                But I'm not sure what you are saying here, are you saying there are no random causes?

                                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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