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Designer enzymes

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  • Originally posted by lee_merrill View Post
    Again, I was estimating the creation of a ribozyme, not a ribosome.
    By pulling a number straight out of where the sun doesn't shine. Another Dory moment.

    Evolution of Ribozymes in an RNA World
    Muller
    Chemistry & Biology Vol 16, Issue 8, 28 Aug. 2009, pp 797-798

    Overview: Ribozymes (catalytic RNAs) were the center of a presumed RNA world in the early origin of life. In this issue, Lau and Unrau show evidence that an RNA world could have used a similar evolutionary pathway as most proteins do.
    The paper

    A Promiscuous Ribozyme Promotes Nucleotide Synthesis in Addition to Ribose Chemistry
    Lau, Unrau
    Chemistry & Biology Vol 16, Issue 8, 28 Aug 2009, pp 815-825

    Summary: Here we report the in vitro selection of an unusual ribozyme that efficiently performs nucleotide synthesis even though it was selected to perform a distinctly different sugar chemistry. This ribozyme, called pR1, when derivatized with ribose 5-phosphate (PR) at its 3′ terminus and incubated with 6-thioguanine, produces two interconverting thiol-containing products corresponding to a Schiff base and its Amadori rearranged product. Consistent with this hypothesis, removing the 2-hydroxyl from the PR substrate results in only a single product. Surprisingly, as this was not selected for, switching the tethered PR substrate to 5-phosphoribosyl 1-pyrophosphate results in the synthesis of 6-thioguanosine 5′-monophosphate. The discovery that a ribozyme can promote such distinct reactions spontaneously demonstrates that an RNA-mediated metabolism early in evolution could have evolved important new functionalities via ribozyme promiscuity
    Lee will now either lie about this data or ignore it.

    Comment


    • Source: Muller

      The first pathway would have been most important in the beginning of the RNA world, where ribozymes would have to appear de novo from more or less random sequences.

      © Copyright Original Source


      Right, the first ribozyme would have to appear de novo, randomly. Then they state "by amplification of the fittest", which I expect explains "more or less random sequences", and this is offered without any explanation that I can see. But for any amplification of the fittest to occur, there need to be repeated ribozymes, and the probability of that appears to be astronomical.

      And I'm not sure why you posted the second paper, it doesn't seem to address ribozyme genesis at all.

      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


      • Originally posted by lee_merrill View Post
        Source: Muller

        The first pathway would have been most important in the beginning of the RNA world, where ribozymes would have to appear de novo from more or less random sequences.

        © Copyright Original Source


        Right, the first ribozyme would have to appear de novo, randomly. Then they state "by amplification of the fittest", which I expect explains "more or less random sequences", and this is offered without any explanation that I can see. But for any amplification of the fittest to occur, there need to be repeated ribozymes, and the probability of that appears to be astronomical.

        And I'm not sure why you posted the second paper, it doesn't seem to address ribozyme genesis at all.
        Exactly as expected Lee quote-mines and lies about the paper. BTW Dory the first link is the summary of the paper, the second is the paper itself.

        Dory is nothing if not predictable.
        Last edited by HMS_Beagle; 07-20-2019, 05:49 PM.

        Comment


        • Originally posted by HMS_Beagle View Post
          Exactly as expected Lee quote-mines and lies about the paper. BTW Dory the first link is the summary of the paper, the second is the paper itself.
          No, those are two different papers. And you didn't respond to my counterpoint, ad hominems are not a reply.

          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


          • Originally posted by lee_merrill View Post
            No, those are two different papers. And you didn't respond to my counterpoint, ad hominems are not a reply.
            Feel free to explain why you dishonestly quote-mined and lied about the overview article which gave three possible evolutionary pathways for ribozyme. You quote mined the first pathway which was described as extremely unlikely for more complex ribozymes and completely ignored the other two pathways which have supporting positive evidence.

            Nobody likes a liar Lee, especially God.

            Comment


            • Originally posted by HMS_Beagle View Post
              Feel free to explain why you dishonestly quote-mined and lied about the overview article which gave three possible evolutionary pathways for ribozyme. You quote mined the first pathway which was described as extremely unlikely for more complex ribozymes and completely ignored the other two pathways which have supporting positive evidence.
              Well, the other two pathways describe modifying an existing ribozyme, so for the first ribozymes, only the first pathway applies.

              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


              • Originally posted by lee_merrill View Post
                Well, the other two pathways describe modifying an existing ribozyme, so for the first ribozymes, only the first pathway applies.
                The first ribozymes were described as simple with as little as only three conserved nucleotides. I guess you "accidentally" overlooked that.

                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.
                The fact is you got caught lying about the evidence which blows your "it's too improbable to evolve" nonsense right out of the water. Same as always for Dishonest Dory.

                Comment


                • Originally posted by HMS_Beagle 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?

                  The fact is you got caught lying about the evidence which blows your "it's too improbable to evolve" nonsense right out of the water.
                  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



                  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


                  • Originally posted by lee_merrill View Post
                    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?
                    Keep up the quote mining and lying about the evidence Lee. Jesus is just busting his buttons with pride.

                    No, I'm not saying it's too improbable to evolve, I'm saying it's too improbable to form randomly.
                    So we're right back to your stupid "it's too improbable" calculation which doesn't take into account non-random feedback from evolutionary processes.

                    Notice how since he can no longer deny the evidence Lee starts his backpedaling and word twisting to get out of the huge hole he dug for himself. A command performance by Dory!

                    Comment


                    • Originally posted by lee_merrill View Post
                      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?


                      No, I'm not saying it's too improbable to evolve, I'm saying it's too improbable to form randomly.
                      It does not form randomly, it forms by natural processes according to laws of nature, as cited in the articles you failed to respond to. To form randomly it would conclude that natural processes are random, and they are not. You are consistently misusing the concept of randomness to justify your agenda.

                      Source: Muller

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

                      © Copyright Original Source



                      Blessings,
                      Lee
                      Simplistic quotes without coherent argument concerning his math is meaningless considering he makes the same unethical use of statistics, and chemistry as you, and as cited and . . .

                      You still have failed to respond to the references that explain ribosomes in abiogenesis, and the referenced thread where I busted ID proponents unethical us of probability..
                      Last edited by shunyadragon; 07-20-2019, 09:32 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


                      • Originally posted by lee_merrill View Post
                        Oh, but I asked for your calculations...
                        Got sent out of town on work for a bit, so have been out of action.

                        Allow me to introduce you to basic statistics. If something has happened, then the probability that it can happen is defined as 1. (Same with the probability that something will happen if it always happens.) Maybe you can tell me what calculation you'd do to demonstrate that?
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • Originally posted by lee_merrill View Post
                          Source: Muller

                          The first pathway would have been most important in the beginning of the RNA world, where ribozymes would have to appear de novo from more or less random sequences.

                          © Copyright Original Source


                          Right, the first ribozyme would have to appear de novo, randomly. Then they state "by amplification of the fittest", which I expect explains "more or less random sequences", and this is offered without any explanation that I can see. But for any amplification of the fittest to occur, there need to be repeated ribozymes, and the probability of that appears to be astronomical.
                          And yet you provided a paper here that showed a pool of random sequences contained multiple enzymatic activities. Which suggests the probability is much better than your calculation. How could this be?

                          Very simple: there's more than one sequence with the same enzymatic activity.

                          The reason for that comes down to basic biochemistry. These sequences have a lot of internal base pairing and, in most cases, all that matters is that the bases pair - their precise identity is irrelevant. The length of the base paired sequences are often flexible, too. As a result, there are huge families of sequences that can form the right structure for catalytic activity.

                          So Lee's probability is based on a completely flawed understanding of biochemistry.
                          "Any sufficiently advanced stupidity is indistinguishable from trolling."

                          Comment


                          • Originally posted by TheLurch View Post
                            Allow me to introduce you to basic statistics. If something has happened, then the probability that it can happen is defined as 1.
                            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.

                            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


                            • 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.

                              Blessings,
                              Lee
                              It remains regardless that the probability is for the event nothing more. If you follow The Lurch's posts, that is what he is describing. That is what my references in the other thread I cited described, and why the ID calculated probability is flawed and unethical use of statistics, which includes Muller's misuse of probability.
                              Last edited by shunyadragon; 07-21-2019, 04:38 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


                              • Originally posted by TheLurch View Post
                                These sequences have a lot of internal base pairing and, in most cases, all that matters is that the bases pair - their precise identity is irrelevant. The length of the base paired sequences are often flexible, too. As a result, there are huge families of sequences that can form the right structure for catalytic activity.
                                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
                                "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

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