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Thread: Optimized amino acids

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    tWebber lee_merrill's Avatar
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    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)

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    tWebber HMS_Beagle's Avatar
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    Quote 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.

  3. Amen JimL amen'd this post.
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    tWebber shunyadragon's Avatar
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    Quote 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.

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    tWebber shunyadragon's Avatar
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    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.

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    tWebber shunyadragon's Avatar
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    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 at 06:53 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.

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    tWebber lee_merrill's Avatar
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    Quote 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)

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    tWebber lee_merrill's Avatar
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    Quote 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)

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    tWebber shunyadragon's Avatar
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    Quote 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 at 12:21 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.

  10. #9
    tWebber TheLurch's Avatar
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    Quote 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....

  11. Amen shunyadragon, Roy amen'd this post.
  12. #10
    tWebber lee_merrill's Avatar
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    Quote 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)

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