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James Tour gets to debate origin-of-life chemist!

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  • #46
    Originally posted by TheLurch View Post
    No, i mean the technical details. Show you know enough to understand the basis of his criticism, and can judge whether it's accurate.
    I would like lee_merrill to explain what he understands concerning Szostak's work. It is abundantly apparent he does not understand it.
    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


    • #47
      Originally posted by TheLurch View Post
      No, i mean the technical details. Show you know enough to understand the basis of his criticism, and can judge whether it's accurate.
      Well, the sugars have to show more detail, particularly their chirality, they need to be homochiral (right-handed for life as we know it). Then the diagram as shown is too simple, it leaves out steps in the formation of the molecule, as indicated even by Szostak's comment: "Phosphate catalyzed chemical reactions [plural]".

      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


      • #48
        Originally posted by lee_merrill View Post
        Well, the sugars have to show more detail, particularly their chirality, they need to be homochiral (right-handed for life as we know it). Then the diagram as shown is too simple, it leaves out steps in the formation of the molecule, as indicated even by Szostak's comment: "Phosphate catalyzed chemical reactions [plural]".
        What steps are left out, and do they require things that weren't mentioned by Szostak?
        "Any sufficiently advanced stupidity is indistinguishable from trolling."

        Comment


        • #49
          Originally posted by lee_merrill View Post
          Well, the sugars have to show more detail, particularly their chirality, they need to be homochiral (right-handed for life as we know it). Then the diagram as shown is too simple, it leaves out steps in the formation of the molecule, as indicated even by Szostak's comment: "Phosphate catalyzed chemical reactions [plural]".

          Blessings,
          Lee
          You are both understating and overstating the research by Szostak, and not taking into account Szostak's history of publications, which are many joint publications with many others in peer reviewed publications. A list can be found here: https://molbio.mgh.harvard.edu/szost...lications.html

          How many publications Tour and Behe have published in peer reviewed journals on the subject other than comments and letters 'arguing from ignorance.' A letter in Tour's site to biologists is not a dialogue with biologists concerning abiogenesis.

          A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides. stak
          Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. J Am Chem Soc. 2020 Jan .

          Abstract
          The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2'-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2'-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2'-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2'-deoxy- or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

          Please note that Szostak and others have published many articles, and DO NOT at this point claim how these processes in abiogenesis actually happened. They are working on plausible models for these processes. In other words they only claim a work in progress concerning the natural processes that occurred in abiogenesis.

          Still waiting for the actual peer reviewed publications Tour and Behe have published based on their objections. So far I have seen absolutely none.
          Last edited by shunyadragon; 04-03-2020, 03:00 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


          • #50
            Thanks for the references, now this paper by Szostak gives a reference where we find:

            Source: Nat Chem

            In this synthesis (Fig. 1a, bold, blue arrows), the C2 sugar glycolaldehyde 1 undergoes phosphate-catalysed condensation with cyanamide 2 to give 2-aminooxazole 3. This heterocycle then participates in a C–C bond forming reaction with the C3 sugar glyceraldehyde 4 giving rise to a mixture of pentose aminooxazolines. Reaction of the arabino-configured aminooxazoline 5 with cyanoacetylene 6 then furnishes an anhydronucleoside 7 which on heating with phosphate in urea 8 – a by-product of the first step of the sequence – is transformed into ribo-cytidine-2′,3′-cyclic phosphate 9. UV irradiation then partially converts this nucleotide into uridine-2′,3′-cyclic phosphate 10 and destroys stereoisomeric impurities.

            Source

            © Copyright Original Source


            So 10 listed steps or so. As far as needing other things not mentioned by Szostak, I don't see anything additional that would be required. I note that they state that stereoisomeric impurities are removed, though the stereoisomers might not be enantiomers.

            Blessings,
            Lee
            Last edited by lee_merrill; 04-03-2020, 04:49 PM.
            "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


            • #51
              Originally posted by lee_merrill View Post
              Thanks for the references, now this paper by Szostak gives a reference where we find:

              Source: Nat Chem

              In this synthesis (Fig. 1a, bold, blue arrows), the C2 sugar glycolaldehyde 1 undergoes phosphate-catalysed condensation with cyanamide 2 to give 2-aminooxazole 3. This heterocycle then participates in a C–C bond forming reaction with the C3 sugar glyceraldehyde 4 giving rise to a mixture of pentose aminooxazolines. Reaction of the arabino-configured aminooxazoline 5 with cyanoacetylene 6 then furnishes an anhydronucleoside 7 which on heating with phosphate in urea 8 – a by-product of the first step of the sequence – is transformed into ribo-cytidine-2′,3′-cyclic phosphate 9. UV irradiation then partially converts this nucleotide into uridine-2′,3′-cyclic phosphate 10 and destroys stereoisomeric impurities.

              Source

              © Copyright Original Source


              So 10 listed steps or so. As far as needing other things not mentioned by Szostak, I don't see anything additional that would be required. I note that they state that stereoisomeric impurities are removed, though the stereoisomers might not be enantiomers.

              Blessings,
              Lee
              You missed the point. Szostak is not claiming to have a complete working model nor solution. You have not responded to my my post.

              AGAIN PLEASE RESPOND, and avoid the classic attacking his work with 'arguing from ignorance.'

              You are both understating and overstating the research by Szostak, and not taking into account Szostak's history of publications, which are many joint publications with many others in peer reviewed publications. A list can be found here: https://molbio.mgh.harvard.edu/szost...lications.html

              How many publications Tour and Behe have published in peer reviewed journals on the subject other than comments and letters 'arguing from ignorance.' A letter in Tour's site to biologists is not a dialogue with biologists concerning abiogenesis.

              A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides. stak
              Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. J Am Chem Soc. 2020 Jan .

              Abstract
              The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2'-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2'-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2'-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2'-deoxy- or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

              Please note that Szostak and others have published many articles, and DO NOT at this point claim how these processes in abiogenesis actually happened. They are working on plausible models for these processes. In other words they only claim a work in progress concerning the natural processes that occurred in abiogenesis.

              Still waiting for the actual peer reviewed publications Tour and Behe have published based on their objections. So far I have seen absolutely none.
              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


              • #52
                Originally posted by lee_merrill View Post
                As far as needing other things not mentioned by Szostak, I don't see anything additional that would be required.
                In other words, Szostak's quote was accurate.
                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                Comment


                • #53
                  Originally posted by shunyadragon View Post
                  You missed the point. Szostak is not claiming to have a complete working model nor solution.
                  He is claiming that RNA nucleotides can be formed, with his diagram indicating one simple step.

                  How many publications Tour and Behe have published in peer reviewed journals on the subject other than comments and letters 'arguing from ignorance.' A letter in Tour's site to biologists is not a dialogue with biologists concerning abiogenesis.
                  One letter was in a journal for researchers, along with a letter on his site.

                  A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides...
                  But what does this paper have to do with the topic of the opening post?

                  Please note that Szostak and others have published many articles, and DO NOT at this point claim how these processes in abiogenesis actually happened. They are working on plausible models for these processes.
                  Correct, the point is that their summaries of their current progress is at times, misleading.

                  Still waiting for the actual peer reviewed publications Tour and Behe have published based on their objections. So far I have seen absolutely none.
                  I think it's sufficient to point out the discrepancy between what has been claimed, and what has been done.

                  Blessings,
                  Lee
                  Last edited by lee_merrill; 04-03-2020, 06:16 PM.
                  "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


                  • #54
                    Originally posted by TheLurch View Post
                    In other words, Szostak's quote was accurate.
                    Well, a 10-step process is not well-illustrated by a single arrow!

                    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


                    • #55
                      Originally posted by lee_merrill View Post
                      Well, a 10-step process is not well-illustrated by a single arrow!
                      Context is everything. There's some contexts where a single arrow from glucose to ATP makes sense. There's others where you probably want the entire TCA cycle or electron transport chain drawn out.

                      Now, you can argue that, in the context of the piece at issue, a more detailed pathway would be appropriate. But that doesn't seem to be the argument Tour is making here, does it?
                      "Any sufficiently advanced stupidity is indistinguishable from trolling."

                      Comment


                      • #56
                        Originally posted by lee_merrill View Post
                        I think it's sufficient to point out the discrepancy between what has been claimed, and what has been done.

                        Blessings,
                        Lee
                        There are no discrepancies, and you have not shown to be competent in the science in question. You are dishonestly misrepresenting the peer reviewed research of not only Szostak but all the other researchers and the journals they published in. Again, you are arguing from ignorance' with a religious agenda supported by Tour and Behe that have absolutely no peer reviwed literature to support your assertions. These are facts you cannot deny. All you can do is dishonestly stone wall.

                        You missed the point. Szostak is not claiming to have a complete working model nor solution. You have not responded to my my post.

                        AGAIN PLEASE RESPOND, and avoid the classic attacking his work with 'arguing from ignorance.'

                        You are both understating and overstating the research by Szostak, and not taking into account Szostak's history of publications, which are many joint publications with many others in peer reviewed publications. A list can be found here: https://molbio.mgh.harvard.edu/szost...lications.html

                        How many publications Tour and Behe have published in peer reviewed journals on the subject other than comments and letters 'arguing from ignorance.' A letter in Tour's site to biologists is not a dialogue with biologists concerning abiogenesis.

                        A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides. stak
                        Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. J Am Chem Soc. 2020 Jan .

                        Abstract
                        The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2'-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2'-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2'-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2'-deoxy- or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

                        Please note that Szostak and others have published many articles, and DO NOT at this point claim how these processes in abiogenesis actually happened. They are working on plausible models for these processes. In other words they only claim a work in progress concerning the natural processes that occurred in abiogenesis.

                        Still waiting for the actual peer reviewed publications Tour and Behe have published based on their objections. So far I have seen absolutely none.
                        Last edited by shunyadragon; 04-03-2020, 08:44 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


                        • #57
                          Originally posted by lee_merrill View Post
                          Well, a 10-step process is not well-illustrated by a single arrow!

                          Blessings,
                          Lee
                          The published work of Szoztak considered his research a work in progress, and a plausible model, and NOT a complete solution to the problem. That is the reason I sited his latest research article. It remains a fact that you are misrepresenting the conclusions of his research, by claiming he made conclusions he did not make.
                          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


                          • #58
                            Originally posted by TheLurch View Post
                            Now, you can argue that, in the context of the piece at issue, a more detailed pathway would be appropriate. But that doesn't seem to be the argument Tour is making here, does it?
                            Well, I think it is:

                            Source: James Tour

                            But all of the above is minor compared to Szostak’s showing that in a single step, heat and light can make a compound that resembles a dehydrated nucleotide .... There are so many steps involved in such a transformation.

                            Source

                            © 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


                            • #59
                              Originally posted by shunyadragon View Post
                              It remains a fact that you are misrepresenting the conclusions of his research, by claiming he made conclusions he did not make.
                              But how have I claimed he made conclusions he did not make?

                              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


                              • #60
                                Originally posted by lee_merrill View Post
                                Well, I think it is:

                                Source: James Tour

                                But all of the above is minor compared to Szostak’s showing that in a single step, heat and light can make a compound that resembles a dehydrated nucleotide .... There are so many steps involved in such a transformation.

                                Source

                                © Copyright Original Source



                                Blessings,
                                Lee
                                Yout think?!?!?! I doubt it.

                                Well, ah . . . citing Tour is not citing Szostak the source, and Tuor has published absolutely 'nothing' with actual research on the subject. Szostak stated clearly in his work he is developing a plausable model.

                                Still waiting. . . for you to do something else and not necessarily complete as all the steps are known beside misrepresenting Szostak without any knowledge on the subject, and citing Tour who has not published anything in the way of research to actually refute Szostak.
                                Last edited by shunyadragon; 04-04-2020, 05:15 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

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