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Advances in Chirality and other problems of abiogenesis in the Origins of Life

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  • #46
    Originally posted by lee_merrill View Post
    Well, we're just going back and forth, to no avail, so I'll let you have the last word.

    Blessings,
    Lee
    My last word is when you cite research articles and related publications you should consider them in context of the whole publication and not selective citations.

    This will likely bee and ongoing thread as more research is published concerning the issues of abiogenesis and homochirality.
    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
      More information on the primal proteins in the processes of abiogenesis.

      Source: https://www.sciencedaily.com/releases/2020/06/200622095023.htm



      Origin of life: Which came first?
      An experiment in recreating primordial proteins solves a long-standing riddle
      Date:
      June 22, 2020
      Source: Weizmann Institute of Science

      Summary:
      What did the very first proteins look like -- those that appeared on Earth around 3.7 billion years ago? Prof. Scientists have reconstructed protein sequences that may well resemble those ancestors of modern proteins, and their research suggests a way that these primitive proteins could have progressed to forming living cells.


      What did the very first proteins look like -- those that appeared on Earth around 3.7 billion years ago? Prof. Dan Tawfik of the Weizmann Institute of Science and Prof. Norman Metanis of the Hebrew University of Jerusalem have reconstructed protein sequences that may well resemble those ancestors of modern proteins, and their research suggests a way that these primitive proteins could have progressed to forming living cells. Their findings were published in the Proceedings of the National Academy of Sciences (PNAS).

      The proteins encoded in a cell's genetic material are the screws, springs and cogs of a living cell -- all of its moving parts. But the first proteins, we assume, appeared well before cells and thus life as we know it. Modern proteins are made of 20 different amino acids, all of them essential to protein-building, and all arranged in the form of a polymer -- a long, chain-like molecule -- in which the placement of each amino acid is crucial to the protein's function. But there is a paradox in thinking about how the earliest proteins arose. Because the amino acids needed to make proteins are themselves produced by other proteins -- enzymes. It's a chicken-and-egg kind of question, and it has only been partially answered until now.

      Scientists believe that the very first true proteins materialized from shorter protein segments called peptides. The peptides would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup; the short peptides would have then bound to one another, over time producing a protein capable of some sort of action. The spontaneous generation of amino acids had already been demonstrated in 1952, in the famous experiment by Miller and Urey, in which they replicated the conditions thought to exist on Earth prior to life and added energy like that which could come from lightning or volcanoes. Showing amino acids could, under the right conditions, form without help from enzymes or any other mechanism in a living organism suggested that amino acids were the "egg" that preceded the enzyme "chicken."

      Tawfik, who is in the Institute's Biomolecular Sciences Department, says that is all well and good, "but one vital type of amino acid has been missing from that experiment and every experiment that followed in its wake: amino acids like arginine and lysine that carry a positive electric charge." These amino acids are particularly important to modern proteins, as they interact with DNA and RNA, both of which carry net negative charges. RNA is today presumed to be the original molecule that could both carry information and make copies of itself, so contact with positively-charged amino acids would theoretically be necessary for further steps in the development of living cells to occur.

      But there was one positively-charged amino acid that appeared in the Miller-Urey experiments, an amino acid called ornithine that is today found as an intermediate step in arginine production, but is not, itself, used to build proteins. The research team asked: What if ornithine was the missing amino acid in those ancestral proteins? They designed an original experiment to test this hypothesis.

      The scientists began with a relatively simple protein from a family that binds to DNA and RNA, applying phylogenetic methods to infer the sequence of the ancestral protein. This protein would have been rich in positive charges -- 14 of the 64 amino acids being either arginine or lysine. Next, they created synthetic proteins in which ornithine replaced these as the positive charge carrier.

      The scientists also discovered that in the presence of RNA, that the ancient form of the peptide engaged in phase separation (like oil drops in water) -- a step that can then lead to self-assembly and "departmentalization." And this, says Tawfik, suggests that such proteins, together with RNA, could form proto-cells, from which true living cells might have evolved.

      Prof. Dan Tawfik is the incumbent of the Nella and Leon Benoziyo Professorial Chair.

      © Copyright Original Source

      Last edited by shunyadragon; 06-24-2020, 12:41 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


      • #48
        I do not believe I cited this previously. If I did sorry, but it is an interesting discussion on the chemical evolution of homochirality in abiogenesis.

        Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672030/



        Origin of Homochirality in Biosystems

        Sřren Toxvaerd

        Abstract
        Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous solutions show that the amphiphiles with an active isomerization kinetics can perform a spontaneous break of symmetry during the segregation and self-assembly to homochiral matter. Based on this observation it is argued that biomolecules with a sufficiently strong chiral discrimination could be the origin of homochirality in biological systems.

        1. Introduction
        The homochirality of amino acids and sugar molecules in biosystems is a necessity for life, and the preservation of homochirality over long periods of time in a prebiotic fluid environment is the problem. It is the problem because it is not sufficient to obtain homochirality. Due to the active isomerization kinetics in fluid systems [1, 2], which in general drives a chiral system toward a racemic composition, it is of utmost importance to determine the condition and mechanism for preservation of homochirality in prebiotic systems. From a thermodynamical and physico-chemical point of view biosystems consist of big molecules of homochiral units and in a soft condensed state in an aqueous solution. If the origin of life is not based on an extremely rare event we therefore need an explanation of how to maintain homochirality in such a prebiotic state for millions of years. If the creation of ”simple” biosystems is obtained by a steady state synthesis, the prebiotic fluid state must necessarily have been rather constant over very long times in order to build up the very unique and complicated templates for life, where RNA is probable the original template. Even in a deterministically driven self-organisation such template-molecule is not established “overnight”. This is why a mechanism ensuring the preservation of homochirality for a very long time is needed. A period of time which is much longer than the time in which an (diluted) aqueous solution of an amino acid will racemize [1], i.e. in the order of thousands of years. Sugar molecules are much less stable than amino acids and racemize within hours or days depending on the physico-chemical conditions [2]; however, both key-molecules are central in all biosystems. Almost all theories dealing with homochirality have concentrated on explaining its origin, but, irrespective of whether L-amino acids float to us from Space or are obtained by a kind of autocatalysis, it is irrelevant, as we need to ensure its stability during long periods of time within the fluid state when biosystems were synthesized probably around 4 billion years ago. Finally it shall be emphasized that it is not sufficient to explain the origin and preservation of one of the homociral species in biosystems, e.g. D-sugars. One needs to explain the preservation of D-sugars as well as L-amino acids in a prebiotic fluid state.

        The strong chiral discrimination of some of the central biomolecules offers such an explanation not only for a spontaneously break of symmetry and the origin of chirality [4], but also for the preservation of the homochiral states of D-sugar and L-amino acids.

        . . .

        5. Concluding Remarks
        The molecular evolution takes place as a non-equilibrium ”self-assembling” toward higher degree of complexity. From a thermodynamical point of view this non-equilibrium self-assembling and biosynthesis is governed by the law of thermodynamics and given by the competition between entropy and energy. It is natural to assume that also the origin of chirality and the origin of life is governed by the same two driving forces. J. Monod has discussed the effect of entropy in his book ”Le hasard et la nécessité” [33] where the ”hasard”- or chance of mutations is related to the entropy. According to the prologue in the book the title is due to Demokritos who claimed that ” all what exist in the universe is the fruit of the chance and the necessity”. A thermodynamicist will, however, formulate it as ”all states of matter in the universe are obtained by decreasing the free energy either by decreasing the energy (enthalpy) or increasing the entropy”.

        The law of evolution was formulated by C. Darwin as a selection by ”survival of the fittest”. The success of a mutation and a new species depends accordingly to Darwin on its ability to adapt to the environment; but this law does of course not function for a prebiotic fluid, and the law can not explain why one of of the enantiomers dominates in the evolution if there, at the origin, were a racemic mixtures of chiral pairs.

        Historically there are two kind of explanations of the origin of homochirality. One is that there was a dominance already at the origin of life due to the parity-violating forces [34]. The other explanation is originally formulated by Frank [35] and explains the break of symmetry by autocatalsysis during the synthesis, either e.g. due to enantiomeric autocatalysis during the biosynthesis [31, 32, 36], or due to crystallisation [37] or other autocatalysing mechanism. But as pointed out in the introduction it is not sufficient to explain the origin of chirality, it is even more necessary to explain the preservation of homochirality over long time in a prebiotic fluid at the beginning of the evolution. The principle- or the law which ensures such a break of symmetry and the preservation of chirality is here explained as selfstabilizing chance. It is fundamentally different from the evolutionary principle of survival of the fittest in that the growth of a new species is selfstabilyzing, and the survival of the species does not depend on its ability to adapt to an ”unfriendly” environment which were there at the time of the creation and where the species must ”fight” and fit in in order to survive. The origin of chirality in a prebiotic fluid is obtained by selfstabelizing homochiral domains accordingly to this mechanism. But the selfstabelizing change acts in all the selective steps in the evolution; e.g. at the autochatalytic biosynthesis (the Frank-models). The two laws are complementary as is the two laws of thermodynamics.

        The selfstabilizing effect which ensures the preservation of homochirality is an energy effect caused by the chiral discrimination and established by the isomerization kinetics. It is autocatalytic as in the Frank model; but it is the homochiral domains which enhances the homochirality. The chance is an entropy effect and plays a role in the spontaneous formation of local domains and the growth of these, and the entropy plays a role at the decisive event when a domain (in a confined geometry) encapsulates other domains of the opposite chirality. There is a qualitative difference between the Frank models for homochirality and the present model in that the Frank autocatalytic models explain the break of symmetry as taking place ”on the fly” of the biosynthesis with a complex autocatalytic kinetics of biomolecules, whereas the present explanation is that the homochirality came first and the self-assembling took place in a chiral ordered fluid.

        © Copyright Original Source

        Last edited by shunyadragon; 07-04-2020, 04:48 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


        • #49
          I note the following:

          "The homochirality of amino acids and sugar molecules in biosystems is a necessity for life..." (p. 2)

          So this reference does state that life requires homochirality, and it proposes that RNA was the start of life.

          "Only for an infinite strong chiral dominance of EDD = ELL = ∞ (d in the figure) does this system end in a pure homochiral fluid." (pp. 8-9)

          "In Table 1 the first criterion [a molecule should exhibit a strong chiral discrimination in favor of homochirality] is only met by glyceraldehyde; but there might very well be other sugar molecules as well as amino acids or other central bio-molecules with a sufficiently strong chiral discrimination in favor of homochirality." (p. 12)

          "Unfortunately, there do not exists data for the chirale discrimination of e.g. D-glyceraldehyde-3-phosphate, D-ribose-1-phosphate or D-ribose-5-phosphate, and it remains to be demonstrated that a concentrated racemic solution of one of these molecules spontaneously behaves homochirally." (pp. 13-14)

          So the title seems to be overstating the conclusion, homochirality has not been demonstrated.

          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


          • #50
            Originally posted by lee_merrill View Post
            I note the following:

            "The homochirality of amino acids and sugar molecules in biosystems is a necessity for life..." (p. 2)

            So this reference does state that life requires homochirality, and it proposes that RNA was the start of life.

            "Only for an infinite strong chiral dominance of EDD = ELL = ∞ (d in the figure) does this system end in a pure homochiral fluid." (pp. 8-9)

            "In Table 1 the first criterion [a molecule should exhibit a strong chiral discrimination in favor of homochirality] is only met by glyceraldehyde; but there might very well be other sugar molecules as well as amino acids or other central bio-molecules with a sufficiently strong chiral discrimination in favor of homochirality." (p. 12)

            "Unfortunately, there do not exists data for the chirale discrimination of e.g. D-glyceraldehyde-3-phosphate, D-ribose-1-phosphate or D-ribose-5-phosphate, and it remains to be demonstrated that a concentrated racemic solution of one of these molecules spontaneously behaves homochirally." (pp. 13-14)

            So the title seems to be overstating the conclusion, homochirality has not been demonstrated.

            Blessings,
            Lee
            This has been true the whole of our discussion the chemical evolution of homochirality occurs in abiogenesis prior to the existence of DNA/RNA life.

            The the necessary chemistry and the potential of chemical evolution of homochirality has been demonstrated by previous research sources as occuring before RNA?DNA life
            The last article cited deals with the chemical evolution of homochirality prior to the existence of RNA/DNA life.
            Last edited by shunyadragon; 07-04-2020, 09:41 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


            • #51
              Originally posted by shunyadragon View Post
              The last article cited deals with the chemical evolution of homochirality prior to the existence of RNA/DNA life.
              "If the creation of 'simple' biosystems is obtained by a steady state synthesis, the prebiotic fluid state must necessarily have been rather constant over very long times in order to build up the very unique and complicated templates for life, where RNA is probable the original template."

              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


              • #52
                Originally posted by lee_merrill View Post
                "If the creation of 'simple' biosystems is obtained by a steady state synthesis, the prebiotic fluid state must necessarily have been rather constant over very long times in order to build up the very unique and complicated templates for life, where RNA is probable the original template."

                Blessings,
                Lee
                If you read the references the chemical evolution of homochirality is prebiotic, before the existence of RNA nor DNA. There is no original templete for RNA. The closest thing is the research into Iron compounds that may form the templete and catalyst for the formation of the first RNA.

                Non of the references I cited research the chemistry of the prebiotic chemical evolution of homochirality prior to the existence of RNA.
                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


                • #53
                  Originally posted by shunyadragon View Post
                  If you read the references the chemical evolution of homochirality is prebiotic, before the existence of RNA nor DNA.
                  And that's fine, the point remains, no homochirality, no life.

                  There is no original templete for RNA. The closest thing is the research into Iron compounds that may form the templete and catalyst for the formation of the first RNA.
                  No, they're saying, as I understand them, that RNA is the first bioactive molecule, and no homochirality, no RNA.

                  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


                  • #54
                    Originally posted by lee_merrill View Post
                    And that's fine, the point remains, no homochirality, no life.


                    No, they're saying, as I understand them, that RNA is the first bioactive molecule, and no homochirality, no RNA.

                    Blessings,
                    Lee
                    These are your assertions, of course, but have no relationship to the references cited where homochirality evolved in a prebiotic chemical evolution before the existence of RNA.
                    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


                    • #55
                      Originally posted by lee_merrill View Post
                      I note the following:

                      "The homochirality of amino acids and sugar molecules in biosystems is a necessity for life..." (p. 2)

                      So this reference does state that life requires homochirality, and it proposes that RNA was the start of life.

                      "Only for an infinite strong chiral dominance of EDD = ELL = ∞ (d in the figure) does this system end in a pure homochiral fluid." (pp. 8-9)

                      "In Table 1 the first criterion [a molecule should exhibit a strong chiral discrimination in favor of homochirality] is only met by glyceraldehyde; but there might very well be other sugar molecules as well as amino acids or other central bio-molecules with a sufficiently strong chiral discrimination in favor of homochirality." (p. 12)

                      "Unfortunately, there do not exists data for the chirale discrimination of e.g. D-glyceraldehyde-3-phosphate, D-ribose-1-phosphate or D-ribose-5-phosphate, and it remains to be demonstrated that a concentrated racemic solution of one of these molecules spontaneously behaves homochirally." (pp. 13-14)

                      So the title seems to be overstating the conclusion, homochirality has not been demonstrated.

                      Blessings,
                      Lee
                      Again, your are dishonestly selectively citing sources and adding your own layman editorial editing to justify your agenda as documented in the past.

                      Again . . . "My last word is when you cite research articles and related publications you should consider them in context of the whole publication and not selective citations.

                      This will likely bee and ongoing thread as more research is published concerning the issues of abiogenesis and homochirality."
                      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


                      • #56
                        2020 has been a big year for published articles on the abiogenesis of homochirality.

                        Source: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007592



                        The origin of biological homochirality along with the origin of life
                        Yong Chen, Wentao Ma

                        Abstract


                        How homochirality concerning biopolymers (DNA/RNA/proteins) could have originally occurred (i.e., arisen from a non-life chemical world, which tended to be chirality-symmetric) is a long-standing scientific puzzle. For many years, people have focused on exploring plausible physic-chemical mechanisms that may have led to prebiotic environments biased to one chiral type of monomers (e.g., D-nucleotides against L-nucleotides; L-amino-acids against D-amino-acids)–which should have then assembled into corresponding polymers with homochirality, but as yet have achieved no convincing advance. Here we show, by computer simulation–with a model based on the RNA world scenario, that the biased-chirality may have been established at polymer level instead, just deriving from a racemic mixture of monomers (i.e., equally with the two chiral types). In other words, the results suggest that the homochirality may have originated along with the advent of biopolymers during the origin of life, rather than somehow at the level of monomers before the origin of life.

                        Author summary


                        People have long been curious about the fact that central molecules in the living world (biopolymers), i.e., nucleic acids and proteins, are asymmetric in chirality (handedness), but as the relevant background, the chemical world is symmetric in chirality. Now that life should have originated from a prebiotic non-life background, how could this dissymmetry have occurred? Previous studies in this area focused their efforts on how the chirality-symmetry may have been broken at the monomer level (i.e., nucleotides or amino acids), but have achieved little advance over decades of years. Here we demonstrate, by in silico simulation, that instead, the required chirality-deviation may have been established along with the emergence of biopolymers at the beginning stage in the origin of life–just deriving from a chirality-symmetric monomer pool. The process is actually not only an issue of chemistry but also an issue involving evolution–thus previously difficult to reveal by pure lab work in this area. By modelling the evolutionary process, the present computer simulation study provides significant clues for experiments in future.

                        © 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

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