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Thread: Optimized amino acids

  1. #181
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by DaveB View Post
    What do you mean by this? Are you talking about the metabolism first hypothesis?
    Not necessarily just simply facts, amino acids in and of themselves do not evolve. There are a number of viable hypothesis that involve the early evolution before LUCA.
    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.

  2. #182
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by DaveB View Post
    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?
    The early sets amino acids were not necessarily 'always being used in certain organisms' until after the evolution of LUCA where the set of 20 was selected for over all other possible sets based on natural selection. I believe the evolution was progressive energy resource driven first dependent energy sources, than the progressive independent iron-sulfur to oxygen-phosphorus driven independent metabolism that naturally selected for the present 20 amino acid sets.
    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.

  3. #183
    tWebber Roy's Avatar
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    Quote Originally Posted by DaveB, earlier
    You simply don't have any evidence that there were life forms that used alternative sets of amino acids.
    Quote Originally Posted by DaveB, now
    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.
    Right. Those organisms use an additional amino acid that isn't in the usual set. They have an alternative set.

    So you know shunyadragon does have evidence for life forms that used alternative sets of amino acids.
    And you know my scenario about post-LUCA amino-acid set evolution is not merely hypothetical, and doesn't require new discoveries.
    Those were lies on your part.

    Alternatively, you could be lying now when you say you knew about pyrrolysine-using organisms all along. It doesn't really matter which.
    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.
    I don't need to explain anything to some-one who isn't interested in honest discussion. Anyway, if you already knew about pyrrolysine, then you might already know that there are lots of cases where organisms lack the aminoacyl-tRNA enzymes for one or more of their amino-acids.

    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?
    Probably the former, though it's obvious why a creationist bletherskite might prefer the latter.
    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

  4. #184
    tWebber lee_merrill's Avatar
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    Quote 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?
    No, I don't know these, you may of course bring them up and we can discuss them. I do seem to recall a mention of synthetase in my searches on this subject, though.

    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)

  5. #185
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    No, I don't know these, you may of course bring them up and we can discuss them. I do seem to recall a mention of synthetase in my searches on this subject, though.
    So, after page after page of arguing about the evolution of the genetic code, you're admitting that you don't even know how much the genetic code evolves? Really?

  6. Amen shunyadragon, Roy amen'd this post.
  7. #186
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by TheLurch View Post
    So, after page after page of arguing about the evolution of the genetic code, you're admitting that you don't even know how much the genetic code evolves?
    Glad to learn if I'm wrong, that's part of the reason for such forums.

    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)

  8. #187
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Glad to learn if I'm wrong, that's part of the reason for such forums.
    I've asked this several times in response to your "happy to learn" posts, but you've never answered it. So i'll try again: if you haven't learned in the first place, why do you make such confident assertions about a topic? Wouldn't it be better to ask questions and learn first? Doesn't it bother you to say things that are untrue?

  9. #188
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by TheLurch View Post
    I've asked this several times in response to your "happy to learn" posts, but you've never answered it. So i'll try again: if you haven't learned in the first place, why do you make such confident assertions about a topic? Wouldn't it be better to ask questions and learn first? Doesn't it bother you to say things that are untrue?
    Well, I state my conclusions if I feel the evidence merits a conclusion, otherwise I will indeed ask questions. And you need to show me that amino acid sets are evolving, before I change my conclusion.

    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)

  10. #189
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Well, I state my conclusions if I feel the evidence merits a conclusion, otherwise I will indeed ask questions. And you need to show me that amino acid sets are evolving, before I change my conclusion.

    Blessings,
    Lee
    Demands such as these reflect the fact that you are 'not willing to learn.'

    You were shown in proteins and DNA is evolving to include new combinations that include up to 22 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.

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