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Optimized amino acids

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  • #61
    Originally posted by lee_merrill View Post
    The paper the blog is about: Gayle K. Philip and Stephen J. Freeland, “Did Evolution Select a Nonrandom ‘Alphabet’ of Amino Acids?”


    Are you saying the authors of the paper were misguided to use such language?

    Blessings,
    Lee
    Yes. The wording of the abstract was a bit odd, and at present the whole text was not available. Do have a source for the whole text?

    Need more explanation than just the abstract. Based on the abstract this did not involve research nor propose a hypothesis. The abstract proposes that there is a hypothesis that explains the set of 20, but without the full article I could not comment as to what their hypothesis is.

    "Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property."

    What is their hypothesis? Do you have access to the full article that describes the hypothesis they refer to?
    Last edited by shunyadragon; 01-16-2019, 06:54 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


    • #62
      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.
      Says the person who only just found out about variant genetic codes. Why should anyone listen to your opinion?
      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


      • #63
        Originally posted by TheLurch View Post
        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.
        Well, if they evolved all the time, we wouldn't call them highly conserved! And these 20 amino acids are common to all life.

        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


        • #64
          Originally posted by shunyadragon View Post
          "Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property."

          What is their hypothesis? Do you have access to the full article that describes the hypothesis they refer to?
          Their hypothesis is "that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property" such as charge, hydrophobicity, etc. But I don't have access to the full text...

          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


          • #65
            Originally posted by lee_merrill View Post
            But no one I know of is proposing that the amino acid set has been changing substantially! That would imply changes in the codon set, along with a host of other changes to produce different amino acids.

            Blessings,
            Lee
            If you don't mind, I'd offer a small correction to say "use different amino acids" instead of "produce...".

            Expression of proteins (transcription and translation) does not produce the amino acid molecules, it joins them together according to the codon sequence being translated.

            Comment


            • #66
              Originally posted by TheLurch View Post
              Face, prepare to meet palm.

              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?"

              So, the actual scientists who were doing research (rather than the non-scientist who blogged about it) were discussing what you are saying you're not aware of. It's always worth checking the sources when you're reading a blog post....
              The claim that some of the 20 amino acids were early and the others added later is based on the assumption of evolution.

              But even if the claim is true, the additions occurred by the time of the so-called LUCA, and there are extremely few exceptions to the genetic code extant today.

              You don't have any evidence that Lee's claim is incorrect.

              Comment


              • #67
                Originally posted by lee_merrill View Post
                Actually, this was not the article being blogged about, and Fazale Rana does discuss how a subset of amino acids had been proposed. And sorry I wasn't clear, I was talking about amino acid substitutions, which seems to me to involve extraordinary contortions.

                Blessings,
                Lee
                Rana's post deals with both papers, but only the second one is about the optimized nature of the set of amino acids.

                Comment


                • #68
                  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.
                  How much do you know about it?

                  There is not a singular enzyme (aminoacyl trna synthetase) as you suggest. There are a set of them. One for each amino acid. The idea that they can readily change their specificity is not true.

                  Comment


                  • #69
                    Originally posted by Roy View Post
                    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 those are in the existing set of amino acids.

                    Comment


                    • #70
                      Welcome to Tweb!

                      Originally posted by DaveB View Post
                      If you don't mind, I'd offer a small correction to say "use different amino acids" instead of "produce...".

                      Expression of proteins (transcription and translation) does not produce the amino acid molecules, it joins them together according to the codon sequence being translated.
                      Good point, I stand corrected.

                      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


                      • #71
                        Originally posted by lee_merrill View Post
                        Their hypothesis is "that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property" such as charge, hydrophobicity, etc. But I don't have access to the full text...

                        Blessings,
                        Lee
                        I reviewed again the abstract and it's wording, and the publication. No, based on the limited info in the abstract that is not the hypothesis referenced. If you use a research article as a reference I need to be able to access the whole article to understand the context of your claim.

                        I put the wording I objected in context after a careful reading. The conclusion is that the authors stated that there needs to be a falsifiable natural hypothesis to explain the set of amino acids that is non-random, and chance cannot be used to explain the set of amino acids.

                        Considering the publication Astrobiology I can guess the context of what the hypothesis that they are offering to explain the set of 20 amino acids. I have read other proposals for a hypothesis based on the amino acids found on meteorites to explain the source of the amino acids in the desired types to explain the set of 20. This is not new.

                        Nonetheless using this reference to the possibility that ID is an alternative to natural evolution and circumstances, because they cannot occur randomly or by chance does not work. First, these scientists are NOT considering ID an alternative to 'randomness' nor chance. Second, they are proposing a natural hypothesis to explain this in the topic of their publication Astrobiology.
                        Last edited by shunyadragon; 01-17-2019, 05:30 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


                        • #72
                          Originally posted by lee_merrill View Post
                          Welcome to Tweb!
                          Thanks!

                          Comment


                          • #73
                            Originally posted by shunyadragon View Post

                            I put the wording I objected in context after a careful reading. The conclusion is that the authors stated that there needs to be a falsifiable natural hypothesis to explain the set of amino acids that is non-random, and chance cannot be used to explain the set of amino acids.

                            The authors state nothing of the kind. They are not attempting to explain how the set was chosen, they are simply showing that the set is optimized.

                            Here is the sentence in question.
                            Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property.

                            And here is the function of the colon.
                            https://www.grammarbook.com/punctuation/colons.asp

                            A colon instead of a semicolon may be used between independent clauses when the second sentence explains, illustrates, paraphrases, or expands on the first sentence. Example: He got what he worked for: he really earned that promotion.

                            "that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property." explains what the hypothesis is.

                            Comment


                            • #74
                              Originally posted by DaveB View Post
                              But those are in the existing set of amino acids.
                              They are. But changing a codon from one amino acid in the current set to a different one in the current set would be just as disruptive to protein formation as changing a codon to an amino acid not in the current set.

                              Lee's comment:
                              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.
                              is describing as unlikely something that, based on the existence of variant genetic codes, appears to have happened many times.
                              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


                              • #75
                                Originally posted by rogue06 View Post
                                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].
                                The function of the aminoacyl trna synthetase proteins (as well as all proteins) that match a particular amino acid to the right trna (the right anti-codons) depends on the amino acid sequence of the protein which depends on the sequence of DNA nucleotides in the gene.

                                There is no scientific law that requires that any particular sequence of DNA nucleotides exist.

                                Imagine flipping a quarter and letting it land on the ground. You do this 1,000 times and it comes up Heads every time.

                                Your argument is like saying "The outcome was due to the law of gravity".

                                Comment

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