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Advances in the science of abiogenesis

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  • #16
    Originally posted by shunyadragon View Post
    Directed engineering is not Intelligent Design. It just means they were able to do it in the lab through directed engineering,
    Which doesn't help the case for undirected evolution at all - but does support Intelligent Design.


    Good question.

    This is interesting more recent related research:

    Source: https://elifesciences.org/articles/35255



    Ribozyme-catalysed RNA synthesis using triplet building blocks

    Abstract
    RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. To address this apparent paradox, we have re-examined the building blocks used for RNA replication. We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit ‘+’ and ‘–’ strands in segments and assemble them into a new active ribozyme.

    https://doi.org/10.7554/eLife.35255.001

    Introduction

    The premise that some RNA sequences can catalyse and template their own replication - reciprocally synthesizing their own ‘+’ and ‘–’ strands - underpins current thinking about early genetic systems (Crick, 1968; Orgel, 1968; Szostak et al., 2001). Any ancient ribozyme with such RNA replicase capability seems to be lost, but efforts are ongoing to recreate RNA self-replication in the laboratory (Martin et al., 2015) as a critical test of the ‘RNA world’ hypothesis (Gilbert, 1986). Early on, derivatives of naturally occurring self-splicing introns (Doudna et al., 1991; Green and Szostak, 1992; Hayden and Lehman, 2006) as well as later in vitro evolved ligase ribozymes (Lincoln and Joyce, 2009; Sczepanski and Joyce, 2014) were shown to be able to assemble one of their own strands from cognate constituent RNA segments. However, a critical drawback of such systems is their need for specific preformed building blocks of at least eight nucleotides (nt) average length, limiting their potential for open-ended evolution, and precluding their replication from pools of random-sequence oligonucleotide substrates (Green and Szostak, 1992; Doudna et al., 1993).

    In a contrasting approach, RNA polymerase ribozymes (RPRs) have been developed that can use general monomer building blocks (ribonucleoside 5’ triphosphates (NTPs)) in RNA-templated RNA synthesis (Johnston et al., 2001; Zaher and Unrau, 2007; Wochner et al., 2011; Attwater et al., 2013b; Horning and Joyce, 2016), akin to the activity of modern proteinaceous polymerases. However, even the most highly-evolved RPRs (Horning and Joyce, 2016) are substantially impeded by template secondary structures. Such structures are ubiquitous in larger, functional RNAs (including the RPRs themselves) and generally indispensable for function. The strong inhibitory role of this central feature of RNA leads to an antagonism between the degree to which an RNA sequence is able to fold into a defined three-dimensional structure to encode function (such as catalysis) and the ease with which it can be replicated (Boza et al., 2014). This ostensible ‘structure vs. replication’ paradox would have placed stringent probability constraints on the emergence of an RNA replicase and generally impeded the ability of RNA to function as an early genetic polymer.

    We wondered whether this paradox might be avoided through a re-consideration of plausible building blocks for early RNA replication. Models of non-enzymatic polymerisation of all four activated ribonucleotides – the presumed source of the first RNA sequences – yield pools of di-, tri- and tetranucleotide etc. length oligonucleotides (in decreasing abundance) dominating the population alongside longer products (Monnard et al., 2003). Here, we have examined whether substrates of such lengths can support RNA-catalyzed RNA replication, by developing a ribozyme capable of iterative templated ligation of 5’-triphosphorylated RNA trinucleotides (henceforth called triplets). This heterodimeric triplet polymerase ribozyme demonstrated a striking capacity to copy a wide range of RNA sequences, including highly structured, previously intractable RNA templates, as well as its own catalytic domain and encoding template in segments. Its characterization revealed emergent properties of triplet-based RNA synthesis, including cooperative invasion and unraveling of stable RNA structures by triplet substrates, bi-directional (both 5’−3’ and 3’−5’) and primer-free (triplet-initiated) RNA synthesis, and fidelity augmented by systemic properties of the random triplet pools.

    Results

    In vitro evolution of triplet polymerase activity

    We set out to explore the potential of short RNA oligonucleotides as substrates for RNA-catalyzed RNA replication. To do this, we required a ribozyme capable of general, iterative RNA-templated oligonucleotide ligation. Previously-described RNA polymerase ribozymes such as the ‘Z’ RPR (Wochner et al., 2011) can use NTPs to iteratively extend a primer hybridized to an RNA template, but do not accommodate oligonucleotides bound downstream of the primer or accept them as substrates. However, we detected a weak templated ligation activity in a truncated version of the Z RPR comprising its catalytic core domain (Zcore) (Figure 1a), which supported incorporation of oligonucleotide substrates as short as three nt (Figure 1—figure supplement 1) when incubated in the eutectic phase of water ice (Attwater et al., 2010; Mutschler et al., 2015).

    © Copyright Original Source

    So, basically, no, they can't replicate the result of creating self-replicating RNA and, if I'm reading this correctly, actually are showing that the problem is even more difficult than they thought originally.

    Let me reread it later to make sure I get it.

    "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


    "Forgiveness is the way of love." Gary Chapman

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    • #17
      Originally posted by Teallaura View Post
      Which doesn't help the case for undirected evolution at all - but does support Intelligent Design.


      So, basically, no, they can't replicate the result of creating self-replicating RNA and, if I'm reading this correctly, actually are showing that the problem is even more difficult than they thought originally.
      This has nothing to do what can and cannot do. There are two roughly methods: one they are experimenting on what reactions can be engineered to produce a given result, and when natural environments and conditions are created to determine what results can be achieved naturally. The present research deals more with the specific steps and problems in the abiogenesis process.

      Let me reread it later to make sure I get it.
      Please do . . .
      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


      • #18
        Originally posted by shunyadragon View Post
        This has nothing to do what can and cannot do. There are two roughly methods: one they are experimenting on what reactions can be engineered to produce a given result, and when natural environments and conditions are created to determine what results can be achieved naturally. The present research deals more with the specific steps and problems in the abiogenesis process.
        The first is basically retro engineering - that can't answer abiogenesis except via Intelligent Design - so I presume they are using it as a stepping stone. Figure out the processes, then worry about whether or not nature can do them.

        The second has massive problems and doesn't seem related to the papers you cited in this thread so I'll just leave it be.


        Please do . . .
        Chemistry - I'm reading CHEMISTRY!!!


        Get back to you later...

        "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


        "Forgiveness is the way of love." Gary Chapman

        My Personal Blog

        My Novella blog (Current Novella Begins on 7/25/14)

        Comment


        • #19
          Originally posted by Teallaura View Post
          The first is basically retro engineering - that can't answer abiogenesis except via Intelligent Design - so I presume they are using it as a stepping stone. Figure out the processes, then worry about whether or not nature can do them.

          The second has massive problems and doesn't seem related to the papers you cited in this thread so I'll just leave it be.


          Chemistry - I'm reading CHEMISTRY!!!


          Get back to you later...
          Again . . .

          here are two roughly methods: one. 'retro engineering,' they are experimenting on what reactions can be engineered to produce a given result, and when natural environments and conditions are created to determine what results can be achieved naturally. The present research deals more with the specific steps and problems in the abiogenesis process.
          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


          • #20
            Originally posted by Teallaura View Post
            The first is basically retro engineering - that can't answer abiogenesis except via Intelligent Design - so I presume they are using it as a stepping stone. Figure out the processes, then worry about whether or not nature can do them.
            There's a major problem in practical abiogenesis research experiments in that people are effectively trying to duplicate what could happen in the world's oceans in millions of years, and they've got a bathtub and a month.

            So if they optimise environmental conditions and molecular concentrations and ratios in order to favour the reactions they're studying, that's understandable because there's literally no way on earth for them to duplicate the actual conditions. As long as they make it clear in their publications what they did and what the consequences are for how relevant their research is to actual possible history, it's not an issue.

            Oh, and while they may be intelligently designing their experiments to maximise success/usefulness, that's not the same as Intelligent Design.
            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.

            Mountain Man: First of all, the Bible is a fixed document.
            Mountain Man: … this is how liberals argue these days, with labels instead of ideas.

            Comment


            • #21
              Originally posted by shunyadragon View Post
              Again . . .

              here are two roughly methods: one. 'retro engineering,' they are experimenting on what reactions can be engineered to produce a given result, and when natural environments and conditions are created to determine what results can be achieved naturally. The present research deals more with the specific steps and problems in the abiogenesis process.
              Yeah... that doesn't read any differently this way.


              "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


              "Forgiveness is the way of love." Gary Chapman

              My Personal Blog

              My Novella blog (Current Novella Begins on 7/25/14)

              Comment


              • #22
                Originally posted by Roy View Post
                There's a major problem in practical abiogenesis research experiments in that people are effectively trying to duplicate what could happen in the world's oceans in millions of years, and they've got a bathtub and a month.

                So if they optimise environmental conditions and molecular concentrations and ratios in order to favour the reactions they're studying, that's understandable because there's literally no way on earth for them to duplicate the actual conditions. As long as they make it clear in their publications what they did and what the consequences are for how relevant their research is to actual possible history, it's not an issue.

                Oh, and while they may be intelligently designing their experiments to maximise success/usefulness, that's not the same as Intelligent Design.
                Actually, introducing the attempt is the biggest problem of all - intellect is not a random process.

                But I was merely observing the obvious - I still don't think they replicated the original results (my actual question) and in the first read, this didn't seem nearly as impressive to me as it is to Shuny. I wasn't intending to debate the thing - I'm still trying to digest it.

                On that last point, true, it's not the same thing - but it's also not the same thing as random chance. It's a lot closer to the former than the latter - which is why the first article better supports ID rather than RC. I already conceded it can be used so don't yell but to prove RC, you've (general) got to get a model that doesn't involve intellect - and yeah, it's an incredibly high bar. Higher still when you look at the probabilities, but intellect invalidates random chance if it's present in the final model.

                "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


                "Forgiveness is the way of love." Gary Chapman

                My Personal Blog

                My Novella blog (Current Novella Begins on 7/25/14)

                Comment


                • #23
                  Originally posted by Teallaura View Post
                  Yeah... that doesn't read any differently this way.

                  That is the reality as science researches the different possible ways abiogenesis took place. There is nothing in the research article that describes retro-engineering that would indicate it refers to Intelligent Dsign.
                  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


                  • #24
                    Originally posted by Teallaura View Post
                    Actually, introducing the attempt is the biggest problem of all - intellect is not a random process.
                    Science does not consider 'intellect a random process. Puzzling remark needs claification.

                    On that last point, true, it's not the same thing - but it's also not the same thing as random chance. It's a lot closer to the former than the latter - which is why the first article better supports ID rather than RC. I already conceded it can be used so don't yell but to prove RC, you've (general) got to get a model that doesn't involve intellect - and yeah, it's an incredibly high bar. Higher still when you look at the probabilities, but intellect invalidates random chance if it's present in the final model.
                    The model that does not involve 'intellect' involves the 'Laws of Nature and natural processes' that falsified based on objective verifiable evidence.

                    . . .the discoveries of new evidence and research supports the natural origins and evolution of life.
                    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


                    • #25
                      Source: http://astrobiology.com/2019/09/interstellar-formamide-nh2cho-a-key-prebiotic-precursor.html



                      Interstellar Formamide (NH2CHO), A Key Prebiotic Precursor

                      Formamide (NH2CHO) has been identified as a potential precursor of a wide variety of organic compounds essential to life, and many biochemical studies propose it likely played a crucial role in the context of the origin of life on our planet.

                      The detection of formamide in comets, which are believed to have --at least partially-- inherited their current chemical composition during the birth of the Solar System, raises the question whether a non-negligible amount of formamide may have been exogenously delivered onto a very young Earth about four billion years ago. A crucial part of the effort to answer this question involves searching for formamide in regions where stars and planets are forming today in our Galaxy, as this can shed light on its formation, survival, and chemical re-processing along the different evolutionary phases leading to a star and planetary system like our own.

                      The present review primarily addresses the chemistry of formamide in the interstellar medium, from the point of view of (i) astronomical observations, (ii) experiments, and (iii) theoretical calculations. While focusing on just one molecule, this review also more generally reflects the importance of joining efforts across multiple scientific disciplines in order to make progress in the highly interdisciplinary science of astrochemistry.

                      Ana López-Sepulcre, Nadia Balucani, Cecilia Ceccarelli, Claudio Codella, Francois Dulieu, Patrice Theulé
                      (Submitted on 25 Sep 2019)
                      Comments: Review, 5 figures
                      Subjects: Solar and Stellar Astrophysics (astro-ph.SR); Earth and Planetary Astrophysics (astro-ph.EP); Astrophysics of Galaxies (astro-ph.GA)
                      DOI: 10.1021/acsearthspacechem.9b00154
                      Cite as: arXiv:1909.11770 [astro-ph.SR] (or arXiv:1909.11770v1 [astro-ph.SR] for this version)
                      Submission history
                      From: Ana Lopez-Sepulcre
                      [v1] Wed, 25 Sep 2019 20:59:32 UTC (1,250 KB)
                      https://arxiv.org/abs/1909.11770
                      Astrochemistry, Astrobiology

                      © 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


                      • #26
                        Originally posted by shunyadragon View Post
                        Science does not consider 'intellect a random process. Puzzling remark needs claification.



                        The model that does not involve 'intellect' involves the 'Laws of Nature and natural processes' that falsified based on objective verifiable evidence.

                        . . .the discoveries of new evidence and research supports the natural origins and evolution of life.
                        The problem is that the model is designed, which introduces intellect into the modelling. It's a skew that's devilishly difficult to control for.

                        Also, science doesn't think - quit anthropomorthizing, it's silly.

                        "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


                        "Forgiveness is the way of love." Gary Chapman

                        My Personal Blog

                        My Novella blog (Current Novella Begins on 7/25/14)

                        Comment


                        • #27
                          Originally posted by Teallaura View Post
                          The problem is that the model is designed, which introduces intellect into the modelling. It's a skew that's devilishly difficult to control for.

                          Also, science doesn't think - quit anthropomorthizing, it's silly.
                          It is your anthropomorphizing that is silly. Nothing in the research articles and the references indicates any sort of designing from any source other than natural origins and Laws of Nature. The model is not designed as in Intelligent Design.
                          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


                          • #28
                            Originally posted by shunyadragon View Post
                            It is your anthropomorphizing that is silly. Nothing in the research articles and the references indicates any sort of designing from any source other than natural origins and Laws of Nature. The model is not designed as in Intelligent Design.
                            Come on, Shuny, you know better. The mere act of modelling introduces intellect - because the model will reflect programming choices. Only people make those choices so the is no anthropormorphizing on my part.

                            "He is no fool who gives what he cannot keep to gain that which he cannot lose." - Jim Elliot


                            "Forgiveness is the way of love." Gary Chapman

                            My Personal Blog

                            My Novella blog (Current Novella Begins on 7/25/14)

                            Comment


                            • #29
                              Originally posted by Teallaura View Post
                              Come on, Shuny, you know better. The mere act of modelling introduces intellect - because the model will reflect programming choices. Only people make those choices so the is no anthropormorphizing on my part.
                              Come on Teallaura, you know better, scientists in any discipline do no consider 'design' issues in the manner the bogus scientists of the Discovery Institute consider 'design.'

                              Your bogus argument is based on a religious agenda, and science does not have any religious agenda one way or the other.
                              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


                              • #30
                                Originally posted by Teallaura View Post
                                Come on, Shuny, you know better. The mere act of modelling introduces intellect - because the model will reflect programming choices. Only people make those choices so the is no anthropormorphizing on my part.
                                Just out of curiosity, how do you feel about situations where the conditions chosen for the modeling are based on those planetary scientists have concluded are likely to be present on the early Earth? That's really quite constrained for the researchers, and doesn't give them a lot of choice in terms of what they can set up in their model reactions — there's not much "intellect" involved, to use your terminology. But it does depend on the scientific conclusions of other people (although those are also quite constrained, obviously).
                                "Any sufficiently advanced stupidity is indistinguishable from trolling."

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