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

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  • #76
    I see that i misquoted something, and ended up quoting myself. The question was directed at Lee. His lack of knowledge of chemistry raises a number of questions about his competence to make arguments about chemistry himself, or evaluate such arguments made by others.

    Specifically, i'd like to find out what he thinks about the fact that his favored source here made an argument that's specifically tailored to sound compelling to people who don't understand much chemistry.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • #77
      Originally posted by shunyadragon View Post
      Not clear so far you have not cited Szostak's work specifically, in detail and your objections. The diagram is not meaning ful.
      Szostak's diagram is meaningful, and misleading, is the point.

      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


      • #78
        Originally posted by TheLurch View Post
        The question was directed at Lee. His lack of knowledge of chemistry raises a number of questions about his competence to make arguments about chemistry himself, or evaluate such arguments made by others.
        I do understand that if a reaction can proceed, it will proceed! But the heat and UV radiation have to be at specific steps in the chain, also, there are new components added at most of the steps, which I think is not well-represented by a single arrow. And there is no stereochemistry, so it's not really proper to call the result a nucleotide.

        Source: James Tour

        I think it displays to the world a simplicity that is unfounded, and it gives the reader a sense that we are much closer to finding a solution to life’s origin than we really are. Indeed, I specifically said in the talk that one day we might figure out the chemistry for origin of life (OOL), but that day is far from today. We are nowhere close. Szostak feels we are not far from cracking this problem. I differ strongly, and I think the synthetic chemist can be the most skeptical because we know what molecules do and do not do in an abiological environment.

        Source

        © Copyright Original Source



        Blessings,
        Lee
        Last edited by lee_merrill; 04-10-2020, 01:00 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


        • #79
          Points rearranged for what I hope is better clarity.

          Originally posted by lee_merrill View Post
          And there is no stereochemistry, so it's not really proper to call the result a nucleotide.
          On that, you're simply wrong. The term "nucleotide" describes a set of chemical properties, but it doesn't assume a specific stereochemistry.


          Originally posted by lee_merrill View Post
          I do understand that if a reaction can proceed, it will proceed!
          But you said having multiple steps makes it less likely, which indicated you did not, in fact, understand that. Are you now retracting your earlier statement?

          Originally posted by lee_merrill View Post
          But the heat and UV radiation have to be at specific steps in the chain, also, there are new components added at most of the steps, which I think is not well-represented by a single arrow.
          Well, that's not an accurate description of things (the "new" components are actually side products of the earliest reaction or initial reactants, the UV and heat can be present the entire time but are only required at specific steps, etc.). But we can set that aside for now as just a typical Lee-style misrepresentation.

          I'd rather focus on the big picture: we're back to you arguing that, in this specific context, more detail was required in the diagram. Originally, you'd been accusing Szostak of being misleading, but you eventually accepted that his statements were accurate and that complex chemical pathways are sometimes represented by single arrows in some contexts. You then claimed that the whole argument was that this was a context where more detail was required. Then, less than a page later, you were admitting that no, it really wasn't that, and you were back to your original argument that Szostak was being misleading. And now, confronted with some actual chemistry, you're back to just saying that the pathway is "not well represented."

          I don't know if you have memory issues, grasp at any argument just to make an argument, or are trolling me. But why don't we set a few ground rules before you turn this into an endless loop of stupidity?
          Make one argument and stick with it.
          Address any counter arguments in a way that explains why those counterarguments are invalid (ie - do not just change your original argument, or repeat it in other words in the hope that the counterarguments will some how go away.)
          If you can't explain why the counterarguments are invalid, acknowledge that your argument was flawed.
          Complete this process before introducing a brand new argument.

          I'd like to think those are reasonable requests, and will prevent the sort of constantly shifting positions we're seeing here, so i don't think it's a burden to ask you to agree to them.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • #80
            Originally posted by TheLurch View Post
            On that, you're simply wrong. The term "nucleotide" describes a set of chemical properties, but it doesn't assume a specific stereochemistry.
            But I think you need a right-handed sugar to make a real nucleotide.

            But you said having multiple steps makes it less likely, which indicated you did not, in fact, understand that. Are you now retracting your earlier statement?
            Yes, I should have phrased that better.

            Well, that's not an accurate description of things (the "new" components are actually side products of the earliest reaction or initial reactants, the UV and heat can be present the entire time but are only required at specific steps, etc.).
            Yet the "initial reactants" are added one by one, and are you sure that heat and UV light wouldn't interfere with the steps where they are not mentioned?

            I'd rather focus on the big picture: we're back to you arguing that, in this specific context, more detail was required in the diagram. Originally, you'd been accusing Szostak of being misleading, but you eventually accepted that his statements were accurate and that complex chemical pathways are sometimes represented by single arrows in some contexts.
            No, I accepted that the ingredients Szostak mentioned were all that was required.

            You then claimed that the whole argument was that this was a context where more detail was required. Then, less than a page later, you were admitting that no, it really wasn't that, and you were back to your original argument that Szostak was being misleading. And now, confronted with some actual chemistry, you're back to just saying that the pathway is "not well represented."
            All these arguments are different aspects of the same argument though. Szostak is being misleading, because the diagram is too simple, the pathway is not well represented.

            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


            • #81
              Originally posted by lee_merrill View Post
              But I think you need a right-handed sugar to make a real nucleotide.
              You think? First I do not believe Szostak's research proposed a solution to that question. There is other research that address this question and I believe we have discussed it previously.

              Such as the following:

              Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151994/



              Structure and function of nucleotide sugar transporters: Current progress
              Barbara Hadley,a Andrea Maggioni,a Angel Ashikov,b,c Christopher J. Day,a Thomas Haselhorst,a and Joe Tiralongoa,⁎

              Abstract
              The proteomes of eukaryotes, bacteria and archaea are highly diverse due, in part, to the complex post-translational modification of protein glycosylation. The diversity of glycosylation in eukaryotes is reliant on nucleotide sugar transporters to translocate specific nucleotide sugars that are synthesised in the cytosol and nucleus, into the endoplasmic reticulum and Golgi apparatus where glycosylation reactions occur. Thirty years of research utilising multidisciplinary approaches has contributed to our current understanding of NST function and structure. In this review, the structure and function, with reference to various disease states, of several NSTs including the UDP-galactose, UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine, GDP-fucose, UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose and CMP-sialic acid transporters will be described. Little is known regarding the exact structure of NSTs due to difficulties associated with crystallising membrane proteins. To date, no three-dimensional structure of any NST has been elucidated. What is known is based on computer predictions, mutagenesis experiments, epitope-tagging studies, in-vitro assays and phylogenetic analysis. In this regard the best-characterised NST to date is the CMP-sialic acid transporter (CST). Therefore in this review we will provide the current state-of-play with respect to the structure–function relationship of the (CST). In particular we have summarised work performed by a number groups detailing the affect of various mutations on CST transport activity, efficiency, and substrate specificity.

              © Copyright Original Source



              The article reviews dome of what is known and not known concerning the potential of the forming neucleotides in abiogenesis. I do not believe it has been determined that the right handed sugars were necessary in the earliest life forms in abiogenesis.

              Yet the "initial reactants" are added one by one,
              No. It just shows the reaction in the a probable proposed model.

              . . . and are you sure that heat and UV light wouldn't interfere with the steps where they are not mentioned?
              If the abiogenesis took place near the ocean floor mid ocean ridges there is non UV light, and the temperatures vary enough around the Mid ocean ridge that temperature is not a problem.


              No, I accepted that the ingredients Szostak mentioned were all that was required.
              OK


              All these arguments are different aspects of the same argument though. Szostak is being misleading, because the diagram is too simple, the pathway is not well represented.

              Blessings,
              Lee
              Again . . . The diagram did not reflect Sxostak's conclusions, and his conclusions are not dependent on the diagram. He published over twenty papers with others to develop a plausible model, and did not make the conclusions you claim he did.

              You still have not specifically cited what your objections are in his research, and not a silly diagram. Arguing what his research does answer is an argument form ignorance.'
              Last edited by shunyadragon; 04-11-2020, 05:52 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


              • #82
                Originally posted by lee_merrill View Post
                But I think you need a right-handed sugar to make a real nucleotide.
                You need that to make the sugar that happens to be used in the DNA we've inherited. You wouldn't necessarily need it for forming the first biochemically active molecules.

                Originally posted by lee_merrill View Post
                Yet the "initial reactants" are added one by one, and are you sure that heat and UV light wouldn't interfere with the steps where they are not mentioned?
                Have you read the actual research paper, or are you just guessing?

                Originally posted by lee_merrill View Post
                All these arguments are different aspects of the same argument though. Szostak is being misleading, because the diagram is too simple, the pathway is not well represented.
                Did you actually look at the paper it comes from? It's an incredibly brief review, meant for a general audience. It does all of planet formation in 3 panels (!). All of geochemistry is handled in one panel. He goes from RNA formation to a proto cell in one panel. It's phenomenally simplified.

                You're seriously telling me that, in this context where absolutely everything is extremely simplified, not having all the steps of a chemical reaction is somehow misleading? You're claiming that all the other massive simplifications in this figure are fine, given it's a brief, general, review, but the one thing you and Tour are obsessing about is an exception, and needs to be the only thing in the entire review shown in detail?

                If so, i question your judgement.
                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                Comment


                • #83
                  I'm going to be honest, I'm not even sure what people are arguing about at this point.

                  Comment


                  • #84
                    Interesting article likely previously posted.

                    Source: https://www.sciencealert.com/amyloid-protein-self-replication-abiogenesis-contrasts-rna-world



                    Scientists Discover a Self-Replicating Protein Structure, And It Could Have Built The First Life on Earth

                    MIKE MCRAE4 MARCH 2018

                    Roughly 4 billion years ago an assortment of complex organic compounds went from being mere carbon soup to replicating biochemistry – the first steps to life on Earth.

                    The order of these steps has been a source of debate for decades. Now, a recent discovery about a common protein structure could help tip the balance, bringing us closer to understanding just how we came to be here.


                    Researchers from Eidgenössische Technische Hochschule (ETH) in Zürich have demonstrated that short strands of amyloid protein structures can direct the selection of amino acids to build even more amyloids.

                    If the word amyloid doesn't sound familiar, they're a protein structure that's increasingly being found all over the place in nature.

                    Part of the reason it's so common is that the amyloid has a special kink in it called a cross-β fold - this allows it to stick together into long, thin structures called fibrils.

                    You might have come across them in relation to Alzheimer's disease – that 'stickiness' can sometimes cause clumps of amyloid beta to aggregate in the brain and lead to the degeneration of neural tissues.

                    In fact it's this tendency to clump and cause disease that for a long time led scientists to consider amyloids to be a biological aberration.

                    But now it looks like its talents may have actually contributed to kick-starting life itself billions of years ago.

                    Just two years ago the ETH team found that peptides, which are chains of amino acids shorter than a typical protein - in this case just 5 to 14 units long - could spontaneously form amyloid structures in the presence of carbonyl sulphide.


                    Fibres made up of amyloids had already been shown to act as enzyme-like catalysts, prompting the scientists to wonder if their possible formation on ancient Earth played a role in helping other organic compounds come together in the days before cells.

                    Here the researchers take their hypothesis one step further by investigating whether amyloid sequences might also catalyse the construction of other peptides.

                    The team designed sequences of amyloids to act as the equivalent of DNA primer strands, and mixed them in with select quantities of other amino acids and a few helper chemicals.

                    By comparing the peptide sequences that resulted in these mixtures with ones that lacked designed 'primer' amyloid structures, the researchers found there was a huge advantage to having the amyloids in there.

                    "This ability also potentially applies to the amyloid itself – meaning the molecules can self-replicate," says chemist Roland Riek.

                    When it all boils down to it, life is special thanks to its ability to make imperfect copies of itself. Make enough copies, and some will do an even better job at replicating next time.


                    If we rewind the clock, we eventually get to a tricky question; was the simplest form of life based on replicating strands of nucleic acid as it is today, or replicating protein fragments?

                    Both benefit from catalysts - compounds that help speed the whole process up.

                    Proponents of the 'RNA world' hypothesis point to the physical properties of RNA to act as the original catalyst, building better and better nucleotide sequences using RNA machines until amino acids could be recruited later down the track.

                    We know RNA-like bases were around 4 billion years ago. But there have been questions over the availability of key elements needed to build the molecules, leading others to wonder if we should be looking down other paths.

                    Self-replicating protein fragments would pave the way for nucleotide chemistry, if only somebody could show how amino acids could form and help generate new peptides - and amyloids could be an answer.

                    "Additionally, amyloids are much more stable than early nucleic acid polymers, and they have a much simpler abiotic synthesis route compared to the complexity of known catalytic RNAs," says researcher Jason Greenwald.


                    To be fair, these were highly controlled laboratory conditions. It's a leap to go from tweaking proteins to generating life.

                    But the principle stands - short peptide sequences shaped like amyloids have what it takes to speed up the generation of similar amino acid sequences.

                    As with most things in biology, the origins of living chemistry are unlikely to be simple. Metabolic processes, RNA generation, and amyloid replication all could have been competing, clashing, and blending to form the first life in a primitive biochemical tango.

                    "We will never be able to prove which is true – to do so, we would have to turn back the last 4 to 4.5 billion years of evolution," says Riek.

                    "However, we suspect that it was not one, but multiple molecular processes with various predecessor molecules that were involved in the creation of life."

                    This research was published in Nature Communications.

                    © Copyright Original Source

                    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


                    • #85
                      Originally posted by Terraceth View Post
                      I'm going to be honest, I'm not even sure what people are arguing about at this point.
                      Hilarious! Me neither. But it's not the first thread in which this happens to me.

                      Comment


                      • #86
                        Originally posted by Terraceth View Post
                        I'm going to be honest, I'm not even sure what people are arguing about at this point.
                        The purpose of the thread is very obvious as the sky is Carolina blue on a clear day at noon from the perspective lee_merrill is that it is very very unlikely that abiogenesis can happen naturally without Divine intervention through intelligent design. From the perspective of lee_merrill, Behe and Tour there is an abundant of dishonest misusing. misrepresenting, and abusing science to justify a religious agenda.

                        This has been repeated more frequently than 'Groundhog Day' in the movie'
                        Last edited by shunyadragon; 04-12-2020, 08:42 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.

                        Comment


                        • #87
                          Originally posted by shunyadragon View Post
                          The article reviews dome of what is known and not known concerning the potential of the forming neucleotides in abiogenesis. I do not believe it has been determined that the right handed sugars were necessary in the earliest life forms in abiogenesis.
                          I think the paper talks about sugar transport within a cell, not abiogenesis. And you need non-racemic sugars for life.

                          No. It just shows the reaction in the a probable proposed model.
                          Step by step, reactants and heat and UV light are added, this should be clear.

                          If the abiogenesis took place near the ocean floor mid ocean ridges there is non UV light, and the temperatures vary enough around the Mid ocean ridge that temperature is not a problem.
                          Except temperature would tend to disintegrate constituents as well as create them.

                          ... and [Szostak] did not make the conclusions you claim he did.
                          I claim he stands by his diagram, which is oversimplified.

                          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


                          • #88
                            Originally posted by TheLurch View Post
                            You need that to make the sugar that happens to be used in the DNA we've inherited. You wouldn't necessarily need it for forming the first biochemically active molecules.
                            Well, we're talking about the origin of life as we know it.

                            Have you read the actual research paper, or are you just guessing?
                            I'm asking you if heat and UV light would interfere with the reactions at various points, that they would not seemed to be your claim.

                            You're seriously telling me that, in this context where absolutely everything is extremely simplified, not having all the steps of a chemical reaction is somehow misleading? You're claiming that all the other massive simplifications in this figure are fine, given it's a brief, general, review, but the one thing you and Tour are obsessing about is an exception, and needs to be the only thing in the entire review shown in detail?
                            I think he's oversimplifying here, "some scientists believe that RNA emerged directly from these reactive chemicals, nudged along by dynamic forces in the environment." (Source, emphasis mine). That, followed by a simple diagram would be an oversimplification.

                            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


                            • #89
                              Originally posted by shunyadragon View Post
                              Interesting article likely previously posted.

                              Source: https://www.sciencealert.com/amyloid-protein-self-replication-abiogenesis-contrasts-rna-world



                              Scientists Discover a Self-Replicating Protein Structure, And It Could Have Built The First Life on Earth

                              To be fair, these were highly controlled laboratory conditions. It's a leap to go from tweaking proteins to generating life.

                              This research was published in Nature Communications.

                              © Copyright Original Source

                              Well, that's refreshing. Tour I believe only hopes that other origin-of-life researchers would be as forthright.

                              … from the perspective lee_merrill is that it is very very unlikely that abiogenesis can happen naturally without Divine intervention through intelligent design. From the perspective of lee_merrill, Behe and Tour there is an abundant of dishonest misusing. misrepresenting, and abusing science to justify a religious agenda.
                              No, this thread is to discuss whether origin-of-life researchers overstate their results. See the opening post, Tour would be happy if OOL researchers came up with an OOL scenario. I believe it is too improbable, but Tour is agnostic--and that would be a topic for another thread.

                              Blessings,
                              Lee
                              Last edited by lee_merrill; 04-12-2020, 12:00 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


                              • #90
                                Originally posted by lee_merrill View Post
                                I think the paper talks about sugar transport within a cell, not abiogenesis. And you need non-racemic sugars for life.


                                Step by step, reactants and heat and UV light are added, this should be clear.
                                Except temperature would tend to disintegrate constituents as well as create them.
                                Tend to? Heat and UV how much? Heat and UV in and of itself does not destroy life. If you propose this you need to specifically define the heat and UV. Life exists right at the extreme heat of the mid ocean ridge fumerols.


                                I claim he stands by his diagram, which is oversimplified.

                                Blessings,
                                Lee
                                You need to cite Szostak specifically in text and put the diagram in context of his research. Remember his work proposes a plausible model not a conclusive model. In other words a work in progress.

                                Your religious agenda does not allow for any alternatives.
                                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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