Announcement

Collapse

Natural Science 301 Guidelines

This is an open forum area for all members for discussions on all issues of science and origins. This area will and does get volatile at times, but we ask that it be kept to a dull roar, and moderators will intervene to keep the peace if necessary. This means obvious trolling and flaming that becomes a problem will be dealt with, and you might find yourself in the doghouse.

As usual, Tweb rules apply. If you haven't read them now would be a good time.

Forum Rules: Here
See more
See less

Optimized amino acids

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Optimized amino acids

    From this blog post:

    Source: Reasons to Believe

    It turns out that the set of amino acids found in biological systems possesses the “just-right” properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity. They also showed that the amino acids selected for proteins are a “highly unusual set of 20 amino acids; a maximum of 0.03% random sets outperformed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously.”

    © Copyright Original Source



    As Fazale Rana mentions, one would not expect evolution to select such a highly optimized set.

    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)

  • #2
    Originally posted by lee_merrill View Post
    From this blog post:

    Source: Reasons to Believe

    It turns out that the set of amino acids found in biological systems possesses the “just-right” properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity. They also showed that the amino acids selected for proteins are a “highly unusual set of 20 amino acids; a maximum of 0.03% random sets outperformed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously.”

    © Copyright Original Source



    As Fazale Rana mentions, one would not expect evolution to select such a highly optimized set.
    But we would expect the set found in extant life to be highly optimized since it's been undergoing selection pressure for 3.8 billion years.

    Comment


    • #3
      Originally posted by lee_merrill View Post
      From this blog post:

      Source: Reasons to Believe

      It turns out that the set of amino acids found in biological systems possesses the “just-right” properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity. They also showed that the amino acids selected for proteins are a “highly unusual set of 20 amino acids; a maximum of 0.03% random sets outperformed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously.”

      © Copyright Original Source



      As Fazale Rana mentions, one would not expect evolution to select such a highly optimized set.

      Blessings,
      Lee
      This evangelical blog cite with a fundamentalist agenda is the last source in the world I would respect and consider reliable.
      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


      • #4
        Comment: My knowledge is old, and my Molecular Biology course is almost ancient history. I will have to do some home to comment further.
        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


        • #5
          I gave it some thought and I understand the problem. I have not had the opportunity to go back and read up on the literature to respond in detail.

          All life today has sequences of 20 Amino Acids out of possible 100+{?) Amino Acids that are necessary in the folding and reproduction of DNA. Any other combination of Amino Acids will not work. The argument by fundamentalist Christians like Fazale Rana is a complexity claim that the probability is too low for this issue of specific necessary complexity to take place naturally by evolution/biogenesis.

          I object to these arguments,because like all fundi arguments from complexity and probability they are not scientific arguments based on falsifiable hypothesis that can falsify that something cannot occur naturally, which is compounded by the fallacy of 'arguing from ignorance' of what can or cannot occur naturally.

          I did check up on Fazale Rana, and he indeed has a PhD in Biochemistry, but is a hard core literal Old Earth Creationist,and does not support the ID movement. I believe he believes in an ancient history of the earth as we see in geology, superimposed by a literal special Divine Creation described in Genesis.
          Last edited by shunyadragon; 01-02-2019, 07:53 AM.
          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


          • #6
            Originally posted by HMS_Beagle View Post
            But we would expect the set found in extant life to be highly optimized since it's been undergoing selection pressure for 3.8 billion years.
            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
            "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


            • #7
              Originally posted by shunyadragon View Post
              I object to these arguments,because like all fundi arguments from complexity and probability they are not scientific arguments based on falsifiable hypothesis that can falsify that something cannot occur naturally, which is compounded by the fallacy of 'arguing from ignorance' of what can or cannot occur naturally.
              No, this is an argument based on what we know of natural processes, the scientists in the referenced paper tried to duplicate natural processes by selecting amino acid sets at random.

              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


              • #8
                Originally posted by lee_merrill View Post
                No, this is an argument based on what we know of natural processes, the scientists in the referenced paper tried to duplicate natural processes by selecting amino acid sets at random.

                Blessings,
                Lee
                Yes, even this distorted attempt in the blog to justify an agenda is not valid from the scientific perspective. First, the scientific research outside the fundamentalist community does not support this. Second, this research did not have millions of years like nature does. Third,fundamentally in evolution over millions years the outcome that works is what is selected for. Fourth, without corresponding research outside the fundi agenda I do not have respect nor confidence in their work. Regardless from the scientific I am for multiple sources that confirm research overtime,and this is not the case. Fifth, in review of the literature cited the bold above is not their conclusion, but that of the blog.

                More to follow with references from independent research . . .
                Last edited by shunyadragon; 01-02-2019, 01:21 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


                • #9
                  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.
                  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....
                  "Any sufficiently advanced stupidity is indistinguishable from trolling."

                  Comment


                  • #10
                    Originally posted by shunyadragon View Post
                    Second, this research did not have millions of years like nature does.
                    Yet all nature can do is randomly generate a set of amino acids.

                    Third,fundamentally in evolution over millions years the outcome that works is what is selected for.
                    But what mechanism generates amino acid substitutions, for selection to work on?

                    Fifth, in review of the literature cited the bold above is not their conclusion, but that of the blog.
                    Well, how else would they evaluate sets of amino acids other than by generating sets at random?

                    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


                    • #11
                      Originally posted by TheLurch View Post
                      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, 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
                      "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


                      • #12
                        Originally posted by lee_merrill View Post
                        Yet all nature can do is randomly generate a set of amino acids.


                        But what mechanism generates amino acid substitutions, for selection to work on?


                        Well, how else would they evaluate sets of amino acids other than by generating sets at random?

                        Blessings,
                        Lee
                        Well,ah . . . I question the use of random, but given millions of years to come up with this combination, no problem.
                        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


                        • #13
                          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
                          Hypothetical "seems to" is not very meaningful.

                          What you describe as extraordinary contortions needs explanations, because based on the actual scientific literature I reviewed there are no extraordinary contortions?

                          I believe you are creating bogymen to justify an agenda.
                          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


                          • #14
                            Originally posted by lee_merrill View Post
                            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?

                            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.


                            And there are more than a dozen known variant genetic codes which associate different amino acids with a few codons.

                            So what you don't know of is not only common knowledge in the field but mentioned in both the references cited by that blog post.

                            Your ignorance is not an argument.
                            Last edited by Roy; 01-03-2019, 07:16 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


                            • #15
                              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.
                              So, aside from being wrong about the blog you're citing*, your entire argument rests on personal incredulity. Something "seems to me" to be unlikely, so i'll pretend that it is. Why not ask whether it's unlikely instead, given you're probably not as informed about this topic as others are here?

                              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.


                              *incidentally, that blog post is garbage. It distills down to "i claim that evolution cannot optimize anything past 'good enough', therefore God." Find better sources.
                              "Any sufficiently advanced stupidity is indistinguishable from trolling."

                              Comment

                              Related Threads

                              Collapse

                              Topics Statistics Last Post
                              Started by Hypatia_Alexandria, 03-18-2024, 12:15 PM
                              48 responses
                              135 views
                              0 likes
                              Last Post Sparko
                              by Sparko
                               
                              Started by Sparko, 03-07-2024, 08:52 AM
                              16 responses
                              74 views
                              0 likes
                              Last Post shunyadragon  
                              Started by rogue06, 02-28-2024, 11:06 AM
                              6 responses
                              47 views
                              0 likes
                              Last Post shunyadragon  
                              Working...
                              X