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Thread: Designer enzymes

  1. #151
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    That's a good point, So let's say all the nucleotides are flexible, it's twice as probable that a given nucleotide will work, and calculate 297 cubed, which is 1 in 4 x 1087.

    Blessings,
    Lee
    No. This not the probability of the timing of a single event. There are literally untold millions of events to achieve the needed result according to the LAws of Nature. There are limited options on the outcome based on the chemistry.

    Did your calculations take into account the limited number of outcomes of each event determined by the chemistry?
    Last edited by shunyadragon; 07-21-2019 at 03:16 PM.
    Glendower: I can call spirits from the vasty deep.
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    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 . . .

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  2. #152
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    That's a good point, So let's say all the nucleotides are flexible, it's twice as probable that a given nucleotide will work, and calculate 297 cubed, which is 1 in 4 x 1087.
    You're also assuming that only a single length will do, and only one structure can produce the enzymatic activity. Neither of those assumptions are justified.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  3. #153
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    It's important to keep in mind the timeframe in which you view an event. If I roll snake-eyes, the probability of that, viewed in the timeframe before the event, is 1/36. Viewed after the event, it's 1. What people are generally interested in is the probability viewed in the timeframe before the event.
    The probability that you could roll snake eyes is 1 both before and after the roll.

    Remember how this all started. You're trying to claim that the evolution of the interactome is wildly improbable. But evolution produces protein interactions all the time. Given that there's a probability of 1 that proteins within a cell will interaction, i'm completely confused about the claim that any particular set of interactions is wildly improbable.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  4. #154
    tWebber Roy's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Right, it's a catalyst for replicating RNA, so the ribozyme doesn't replicate.
    Since ribozymes are RNA, it's a catalyst for replicating itself.

    Dory once again trips over his own ignorance.
    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

    mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

  5. #155
    tWebber Roy's Avatar
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    Quote Originally Posted by lee_merrill View Post
    The first ribozymes were described as simple with as little as only three conserved nucleotides.
    Well, three conserved nucleotides doesn't mean you can make a ribozyme out of three nucleotides! I picked a ribozyme that was proposed to be involved in the RNA world, do you have a different specific candidate?
    He gave you a specific candidate:

    "An example for a small ribozyme is the recently discovered aminoacylating ribozyme with three conserved nucleotides (Chumachenko et al., 2009); this ribozyme would have been a frequent guest in an RNA world."

    You ignored it.


    No, I'm not saying it's too improbable to evolve, I'm saying it's too improbable to form randomly.
    Source: Muller

    Low probabilities like these present a major hurdle for many ribozymes to appear in an RNA world.

    © Copyright Original Source

    Quote-mining again, Dory?

    Why don't you fail to explain why the probability that Muller gives in that same paragraph - once in 3*1018 - is 30 orders of magnitude higher than the probability you gave a couple of pages previously?

    And when you haven't done that, you can fail to explain why you calculated the probability of a specific ribozyme sequence and ignored not only the other ribozymes that could do the same job, but also the known sequence variability in that one.

    And when you haven't done that, you can fail to calculate the probability of the abovementioned aminoacylating ribozyme forming randomly.
    Jorge: Functional Complex Information is INFORMATION that is complex and functional.

    mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

  6. #156
    tWebber TheLurch's Avatar
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    Quote Originally Posted by Roy View Post
    Why don't you fail to explain why the probability that Muller gives in that same paragraph - once in 3*1018 - is 30 orders of magnitude higher than the probability you gave a couple of pages previously?
    There really is a trend here that every time someone checks the references Lee provides, they end up undercutting his argument.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  7. #157
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by TheLurch View Post
    You're also assuming that only a single length will do, and only one structure can produce the enzymatic activity. Neither of those assumptions are justified.
    Well, the length can vary, say +/- 10%, without affecting the number much, and I'm assuming any structure will do, so that's not an issue.

    The probability that you could roll snake eyes is 1 both before and after the roll.
    Not before the roll, no. That is why when you draw a full house you can say "Wow, that's improbable!"

    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. #158
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by Roy View Post
    Since ribozymes are RNA, it's a catalyst for replicating itself.
    Some ribozymes are self-replicating, but not the one I selected.

    "An example for a small ribozyme is the recently discovered aminoacylating ribozyme with three conserved nucleotides (Chumachenko et al., 2009); this ribozyme would have been a frequent guest in an RNA world."
    I meant specific as in showing the nucleotide sequence.

    Why don't you fail to explain why the probability that Muller gives in that same paragraph - once in 3*1018 - is 30 orders of magnitude higher than the probability you gave a couple of pages previously?
    So this shows that even an drastically higher probability presents severe problems for the RNA world scenario.

    And when you haven't done that, you can fail to explain why you calculated the probability of a specific ribozyme sequence and ignored not only the other ribozymes that could do the same job, but also the known sequence variability in that one.
    I did do that, see above in my response to TheLurch.

    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)

  9. #159
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Some ribozymes are self-replicating, but not the one I selected.
    Not an adequate explanation. Why only select one?

    I meant specific as in showing the nucleotide sequence.
    Not meaningful in response to Roy's question.

    So this shows that even an drastically higher probability presents severe problems for the RNA world scenario.
    Only in your imagination. No, because your calculations have no relationship to the probability of the outcomes for the formation of RNA, because it does not take into consideration the fact that the formation of RNa is determined by the laws of nature, natural processes and the environment.
    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. #160
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Well, the length can vary, say +/- 10%, without affecting the number much...
    Do you know the minimum size of this ribozyme? If not, you've got no idea whether what you're saying is relevant or not.

    Quote Originally Posted by lee_merrill View Post
    and I'm assuming any structure will do, so that's not an issue.
    No, you're most certainly not. Every calculation you've done so far has been predicated on this particular ribozyme, which has a specific structure. If there are multiple other structures that can perform a similar function, then each of the vast families of molecules they represent need to be included in your calculation.

    Do you ever get tired of the fact that others understand your arguments better than you do?

    Quote Originally Posted by lee_merrill View Post
    Not before the roll, no. That is why when you draw a full house you can say "Wow, that's improbable!"
    Read what i wrote again, this time carefully. Now ponder why what i said was correct.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  11. Amen shunyadragon, Roy amen'd this post.

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