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Thread: Origin of life status

  1. #21
    tWebber shunyadragon's Avatar
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    Source: https://futurism.com/left-handed-life



    Life: It is All Left-Handed, and We Don’t Know Why:

    Further testing on meteorites show left-handed amino acids contained within their rocky treasure chests. That gives credence to the theory that life originated in space and was deposited on Earth in meteor and comet bombardment. But, again, we come to the important question… why are left-handed amino acids more common? Why is there a strong bias against right-handed amino acids?

    One possible solution deals with the interaction of light with amino acids in space. This is where circular polarization comes in. Electrical polarization is a fancy way of describing an electromagnetic field that doesn’t change in strength but, rather, changes direction in a rotational fashion. Depending on the direction of the circular rotation, the light itself could potentially unravel molecules of one handedness giving a preference to the lucky left-handed survivors.


    This type of polarization has been observed in the Cat’s Paw nebula, located in the constellation Scorpius about 5,500 light-years away. A team of astronomers at the National Astronomical Observatory in Japan discovered that about 22 percent of the Cat’s Paw was circularly polarized. This suggests that circular polarization may be a common feature of star formation and could potentially have strong implications on the handedness of life that can arise.

    left handed life 2In concert with these findings, astronomers also know that the chemical reactions required to build amino acids can happen in space. If amino acids were forming in the midst of this circular polarization, the handedness favored by the direction of the polarization would certainly form much better and much more frequently than the mirror image.

    Of course, from here the objects in the solar system formed with a bias to left-handed amino acids. When these objects delivered their precious organic materials to Earth, life had more left-handed amino acids to work with than right-handed ones thus explaining why we are all lefties.

    © Copyright Original Source



    We do know chirality is important because for the symmetry of the structure of RNA and DNA all the amino acids must be either right handed or left handed. Life on earth resulted in left handed amino acids resulting in left handed helicies.

    Science is working on possible viable answers to the problem. The problem with the ID advocates is they have falsify the premise that science cannot come up with a possible explanation.
    Last edited by shunyadragon; 05-23-2019 at 02:12 PM.
    Glendower: I can call spirits from the vasty deep.
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    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

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  2. #22
    tWebber shunyadragon's Avatar
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    Another article that deals with the development of left handedness:

    Source: https://www.oatext.com/Abiogenic-evolution-of-ribonucleic-acid-as-a-left-handed-helix-and-its-protecting-substances-on-primordial-earth-A-story-about-evolution-of-ribosome-and-the-origin-of-life.php#Article


    Abiogenic evolution of ribonucleic acid as a left-handed helix and its protecting substances on primordial earth – A story about evolution of ribosome and the origin of life
    Kozo Nagano
    Nagano Research Institute of Molecular Biology, 4-8-24 Higiriyama, Kohnan-ku, Yokohama 233-0015, Japan

    DOI: 10.15761/IMM.1000284

    Abstract

    Origin of life on earth must be started from a story explaining how ribonucleic acids (RNAs) had been accumulated in azoic era. Since the world of nonazoic era could have been full of water, a single molecule of RNA should have been in danger of hydrolysis rather than in a tendency of progressive synthesis. It necessarily requires coevolution of proteins that had been playing a role of protecting RNA from hydrolysis. The present article describes a possibility of a large-scale of confined organic phosphates and methane hydrates under high pressure and temperature deeply hidden into the mantle of the earth. In such conditions, a polymeric form of D-ribose can be made as a left-handed helix connected by base pairs with neighboring strands. In the lattice of left-handed helices of RNA, a lot of spaces or gaps allowed accumulation of various amino acids, from the smallest one such as glycine to not very large as tryptophan. At the 3’ end of a polymeric RNA strand, aminoacylation could also occur. The other essential substances to the origin of life, such as adenine-triphosphates, could have been accumulated together.

    Introduction

    Fossils have shown that biochemically advanced microbial life had existed on earth over 3 billion years ago. Since the age of earth is believed to be about 4.6 billion years, it would be natural to think that prebiotic molecules of nucleic acids and proteins had been accumulated either shortly after or at the same time of the birth of the earth, the surface of which at that time was magmatic ocean covered by a thick layer of vaporized water molecules and various gaseous molecules, rather rich in hydrogen molecules. Glycine, α-amino-isobutyric acid, alanine, glutamic acid, β-alanine, isovaline, aspartic acid, and leucine were observed in the Murchison meteorite [1]. Although they reported the relative abundance of L-enantiomer, it might not be the cause of the origin of the prevailance of L-enantiomer on the present-day earth [2,3]. In the Yamato-91198 meteorite, serine, threonine, proline, valine, isoleucine, sarcosine, α-aminobutyric acid, β-aminobutyric acid, γ-aminobutyric acid, α-aminoisobutyric acid, α-aminoadiopic acid, various aliphatic carbonic acid, and aliphatic as well as aromatic hydrocarbons were observed. However, no sign of nucleic acids has been observed in meteorites except some purines and pyrimidines. Some of them might have been synthesized by a shock of thunder, while some of them, such as nucleic acids in particular, might have been destroyed on a boiled magmatic ocean. Accordingly, it remains an etigma how nucleic acid had been formed using D-riboses as its main component among many other pentose candidates. The present article tries to present a hypothesis that solves the problem of multiple difficulties to reach the origin of life from the origin of earth.

    Evolution of earth

    The origin of earth has been supposed to be a gathering center of meteorites and comets. A core of comet is usually composed of ice water and dry ice (carbon dioxide) as well as methane, ammonia, silicates, and phosphates. On the other hand, the components of meteorites are mainly reduced metals and metal oxides. Surface temperature of primordial earth would have been pretty high by thermal energy produced by collisions of comets and meteorites, but would have been cooled down when its core became occupied by components of meteorites and its surface was covered by those from comets. The above process in evolution of earth should be referred to as the first stage. The second stage in the history of earth started from temperature elevation in its core by accumulation of thermal energy originated from disintegration of uranium atoms. At this stage, the surface temperature would have been as cool as that of comets. As temperature in the core of the earth was elevated, water vapour would have been concentrated in the atmosphere of the ancient earth, while its surface would have been rather a magmatic ocean composed of exposed hot mantle, on which hot rain would have been falling to make a lot of boiling lakes. The boiling lakes might have grown up to form a boiling ocean. It should be referred to as the third stage. The fourth stage in the history of earth would be in the cooling process. When the first signs of the ancient life existed over 3 billion years ago, the evolution of RNA had already reached a ripening period. The basic hypothesis adopted in the present article is that the evolution of RNA started from the end of the first stage and continued until the end of the third stage.

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    Glendower: I can call spirits from the vasty deep.
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    Frank

    I do not know, therefore everything is in pencil.

  3. #23
    tWebber shunyadragon's Avatar
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    Here is another viable explanation of formation of chirality in abiogenesis:

    Source: https://www.chemistryworld.com/opinion/why-is-life-chiral/3008772.article



    The twists and turns of life

    The mystery of handedness could soon be unravelled

    Why life is chiral has puzzled scientists for well over a century. Louis Pasteur famously discovered molecular chirality in his meticulous experiments in 1848. He separated by hand the mirror-image forms of salts of tartaric acid and saw that their solutions will rotate the plane of polarised light in opposite directions. ‘There is no doubt,’ he wrote in 1860, ‘that there is a grouping of the atoms [in tartrate ions] of an asymmetric type that is not superposable on its mirror image.’

    Pasteur convinced himself that this property of molecular chirality was a barrier separating the living from the inanimate worlds – almost an echo of the vitalistic belief in the specialness of organic nature that Pasteur’s work on microbes and ‘spontaneous generation’ helped to dispel. He set out to find the origin of this handedness of life’s molecules.

    A little madness

    ‘Do such asymmetric agencies arise from the cosmic influences light, electricity, magnetism, heat?’ Pasteur asked. From 1853 he pursued experiments that look not a little cranky now, growing crystals in magnetic fields and plants from seeds irradiated with light ‘inverted’ with mirrors. Jean-Baptiste Biot, who discovered optical activity in organic solutions in 1815, advised Pasteur to abandon his eccentric quest, and even Pasteur himself, normally of a conservative nature, admitted: ‘One has to be a little mad to undertake what I am trying to do now.’

    There’s always a little madness involved in pondering life’s handedness. Why does DNA have its right-handed double helix, and why are chiral amino acids in proteins only of the left-handed variety? Was this pure chance or determinism? Some have sought an answer in the tiny degree of left–right symmetry breaking evident in the weak force, although it would demand some extraordinarily powerful magnifier (perhaps an autocatalytic feedback in prebiotic amino-acid synthesis?) to make the resulting difference in stability manifest in chemistry.

    Stirring the pot

    At any rate, researchers have proposed that stirring of a solution to create vortices can couple molecular to macroscopic chirality. It sounds unlikely, but it happens. In 1990, Dilip Kondepudi and coworkers reported that they could selectively make almost enantiomerically pure crystals of sodium chlorate (which are chiral, although the molecular building blocks are not) by stirring the solution from which they form.1 And a team at Kobe University, Japan, has reported that right-handed double-helical DNA not only aligns within vortex flows but shows a slight preference for right-handed vortices.2

    This isn’t so mysterious. After all, the energy of turbulent flows is transferred to ever smaller spatial scales before finally being dissipated in friction at the molecular level. I shouldn’t be surprised, though, if hypotheses emerge about the first living entities having opposite chirality in the northern and southern hemispheres of our planet – agitated by the Coriolis force that gives cyclones opposite senses of rotation either side of the equator – before doing Darwinian battle. Do the maths and you’ll find that such influences would be utterly negligible even at the level of organisms, let alone molecules. But that didn’t stop an extraordinary number of people insisting (wrongly), when I wrote recently about the amazing spiral nests of Australian stingless bees Tetragonula carbonaria,3 that they would surely rotate the other way in the north.

    So sure, chiral molecules and crystals seem able to express preferences for stirring. But according to calculations by Alec Owens and colleagues at the Centre for Free Electron Laser Science in Hamburg, Germany, chiral molecules can actually be created by stirring: that is, by spinning the molecules themselves.4

    Twist and pulse

    If you take a pyramidal ‘symmetric top’ molecule like ammonia or phosphine (PH3) and rotate it, you produce chiral motion: clockwise rotation isn’t superimposable on its mirror image. But that kind of symmetry breaking doesn’t make the molecule itself chiral, much as chiral arrangement of SiO4 tetrahedra in optically active quartz doesn’t give these units a handedness. The researchers say, however, that PH3 can be given a chiral structure if it is highly rotationally excited, because in that case the motion actually distorts the molecular structure, due to a Coriolis force acting on the spinning molecules. This force makes one P–H bond shorter than the others, removing the equivalence of the hydrogens. That breakdown of permutation symmetry, coupled with the unidirectional rotation, creates two enantiomers. Then by using a strong static electric field to align the axis of rotation (along one P–H bond), either enantiomer can be generated selectively.

    Such rotationally induced chirality has been mooted before, but not much explored because of the difficulty of producing highly excited rotational states (rotational quantum number J of 40 or so) with a rather narrow and well defined distribution of states. It’s now made possible in principle, though, by the advent of intense, ultrashort laser pulses with the kinds of tailored polarisation needed to excite extreme rotation. Such a pulse, called an ‘optical centrifuge’, should have linear polarisation that not only rotates helically around the direction of polarisation but does so at an accelerating rate, so that the ‘thread’ of the corkscrew rotation gets ever tighter.

    The researchers’ quantum-mechanical calculations indicate that for J=42, rotationally induced chirality should be achievable and observable with realistic experimental parameters. And that’s their goal now.

    References
    1 D K Kondepudi, R Kaufmann & N Singh, Science, 1990, 250, 975 (DOI: 10.1126/science.250.4983.975)

    2 Y Tsujimoto et al, Bull. Chem. Soc. Jpn., 2011, 84, 1031 (DOI: 10.1246/bcsj.20110178)

    3 R M Brito et al, Swarm Intelligence, 2012, 6, 151 (DOI: 10.1007/s11721-012-0068-1)

    4. A Owens, A Yachmenev & J Küpper, 2018 arxiv.org/abs/1802.07803

    © 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.

  4. #24
    tWebber shunyadragon's Avatar
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    Source: http://dirac.ruc.dk/~st/articles/article68print.pdf



    Conclusions . . .

    5. The Abiogenesis

    The Abiogenesis, or the origin of life, is probably not a result of a series of single events, but rather the result of a gradual process with increasing complexity of molecules and chemical reactions.

    This article argues, however, that there are some ”milestones” and order in the evolution of the complex molecular biostructures and networks of chemical reactions. One of the elements in the Abiogenesis is the establishment by time of an aqueous emulsion of homochiral compact proteins. The homochirality can be obtained by the isomerization kinetics and preserved by the compact secondary and tertiary structures of the proteins in aqueous emulsions with low water activity (e.g. high ionic concentrations) (Toxvaerd, 2017).

    Another link in the evolution is the establishment of a metabolism. The first step in the Glycolysis is the stereospecific phosphorylation of Glucose to D-Glucose-6-phosphate. RNA and DNA, are correspondingly phosphor polyesters, so the phosphorylation is central for the establishment of the metabolism as well as the genetics. The synthesis of peptides and carbohydrates have appeared simultaneously in the prebiotic aqueous environment. A stereospecific phosphorylation can be obtained by proteins, which by change acted as enzymes for phosphorylation of D-glucose and D-Ribose only and thereby established the D-carbohydrate world.

    Whereas one today can find a few examples of D-amino acid units in biosystems, L-carbohydrates does not appear. The explanation for this lack of L-carbohydrates and dominance of peptides with units of L amino acids today can very well be the same as the explanation for the formation and preservation of homochiral carbohydrates given here: the existence of the stereospecific enzymes like Hexokinase and Ribokinase together with a stereospecific catabolism of L-carbohydrates is sufficient to establish the homochirality in the metabolism and to remove the L-carbohydrates and proteins with D-units.

    Can this order in the evolution be verified? Perhaps not, the prebiotic world has disappeared on planet Earth. But there is a chance that frozen ice in cavities in the rocks beneath the evaporated oceans on planet Mars contains prebiotic materials, which can reveal the start of the Abiogenesis.

    © Copyright Original Source



    The following is the abstract of the research by Toxvaerd, 2017:

    Source: https://www.researchgate.net/publication/323571442_The_start_of_the_Abiogenesis_Preservation_of_homochirality_in_proteins_as_a_necessary_and_sufficient_condition_for_the_establishment_of_the_metabolism


    Abstract

    Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the metabolism and the genetics. The Abiogenesis, or the origin of life, is probably not a result of a series of single events, but rather the result of a gradual process with increasing complexity of molecules and chemical reactions, and the prebiotic synthesis of molecules might not have left a trace of the establishment of structures and reactions at the beginning of the evolution. But alternatively, one might be able to determine some order in the formation of the chemical denominators in the Abiogenesis. Here we review experimental results and present a model of the start of the Abionenesis, where the spontaneous formation of homochirality in proteins is the precondition for the establishment of homochirality of carbohydrates and for the metabolism at the start of the Abiogenesis.

    © Copyright Original Source

    Last edited by shunyadragon; 05-23-2019 at 02:56 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.

  5. #25
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    The following reference goes into considerable detail concerning the problem of left and right handed proteins and abiogenesis, and one of the developments that developed a possible solution. This is oe reference on how scientists are working to resolve the problem. It is not a complete unsolvable mystery.

    Source: https://www.quantamagazine.org/chiral-key-found-to-origin-of-life-20141126/


    Scientists now have an enzyme that doesn’t need a chiral world. Researchers, including Joyce himself, are still trying to understand the implications. The findings open the possibility that chirality emerged after life first evolved. “Maybe we didn’t need to break symmetry,” said Blackmond.

    © Copyright Original Source

    Yet we read "But, he said, “I am skeptical that life began in this way.” Szostak argues that this scenario would require both left-handed and right-handed RNA enzymes to have emerged at the same time and in the same place, which would be highly unlikely."

    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)

  6. #26
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Source: https://futurism.com/left-handed-life



    Life: It is All Left-Handed, and We Don’t Know Why:
    Of course, from here the objects in the solar system formed with a bias to left-handed amino acids. When these objects delivered their precious organic materials to Earth, life had more left-handed amino acids to work with than right-handed ones thus explaining why we are all lefties.

    © Copyright Original Source

    Yet we read:

    Source: Quanta Magazine

    Yet most biologists and chemists are skeptical of these astrophysical theories. The bias they create is just too minute. The theories create “a beautiful union between life and nonlife,” said Marcelo Gleiser, a theoretical physicist at Dartmouth College. “But the problem is that those interactions are very weak and short-range.” According to Joyce, the effect of these physical forces would be lost in the noise of chemical reactions. “Such a small asymmetry in the universe is not enough to move the needle,” he said.

    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)

  7. #27
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Yet we read "But, he said, “I am skeptical that life began in this way.” Szostak argues that this scenario would require both left-handed and right-handed RNA enzymes to have emerged at the same time and in the same place, which would be highly unlikely."

    Blessings,
    Lee
    Yes but . . .

    That is not the point of that particular research reference. The point is the 'chemical mechanism' and chemical pathways that is a possible result of left handed amino acids, and not the way the 'chemical mechanisms' and chemical pathways took place.

    The different research projects involved represent different possible 'chemical mechanisms' and chemical pathways that could result in left handed amino acids required for symmetry of the RNA/DNA helices.

    Of course, this where your 'arguing from ignorance' comes in. I am still waiting for the Fundamentalist Christians do the actual research concerning the organic chemistry of abiogenesis and evolution instead of sitting in the easy chair with the TV control every Monday morning.

    Remember for for the ID hypothesis to be viable it has to falsify and demonstrate that natural processes cannot succeed in abiogenesis, and the science of evolution.
    Last edited by shunyadragon; 05-24-2019 at 01:27 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.

  8. #28
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Another article that deals with the development of left handedness:

    Source: https://www.oatext.com/Abiogenic-evolution-of-ribonucleic-acid-as-a-left-handed-helix-and-its-protecting-substances-on-primordial-earth-A-story-about-evolution-of-ribosome-and-the-origin-of-life.php#Article


    Abiogenic evolution of ribonucleic acid as a left-handed helix and its protecting substances on primordial earth – A story about evolution of ribosome and the origin of life
    Kozo Nagano
    Nagano Research Institute of Molecular Biology, 4-8-24 Higiriyama, Kohnan-ku, Yokohama 233-0015, Japan

    DOI: 10.15761/IMM.1000284

    Abstract

    Origin of life on earth must be started from a story explaining how ribonucleic acids (RNAs) had been accumulated in azoic era. Since the world of nonazoic era could have been full of water, a single molecule of RNA should have been in danger of hydrolysis rather than in a tendency of progressive synthesis. It necessarily requires coevolution of proteins that had been playing a role of protecting RNA from hydrolysis. The present article describes a possibility of a large-scale of confined organic phosphates and methane hydrates under high pressure and temperature deeply hidden into the mantle of the earth. In such conditions, a polymeric form of D-ribose can be made as a left-handed helix connected by base pairs with neighboring strands. In the lattice of left-handed helices of RNA, a lot of spaces or gaps allowed accumulation of various amino acids, from the smallest one such as glycine to not very large as tryptophan. At the 3’ end of a polymeric RNA strand, aminoacylation could also occur. The other essential substances to the origin of life, such as adenine-triphosphates, could have been accumulated together.

    © Copyright Original Source

    Alas, under "Evolution of Ribosome" we read "On the other hand, the structures of the present-day ribosome are too big." And I don't see a description of chiral genesis in this article, especially not in the parts you quoted.

    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)

  9. #29
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    That is not the point of that particular research reference. The point is the 'chemical mechanism' and chemical pathways that is a possible result of left handed amino acids, and not the way the 'chemical mechanisms' and chemical pathways took place.

    The different research projects involved represent different possible 'chemical mechanisms' and chemical pathways that could result in left handed amino acids required for symmetry of the RNA/DNA helices.
    But your own reference says that is unlikely!

    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)

  10. #30
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Here is another viable explanation of formation of chirality in abiogenesis:

    Source: https://www.chemistryworld.com/opinion/why-is-life-chiral/3008772.article



    The twists and turns of life

    The researchers’ quantum-mechanical calculations indicate that for J=42, rotationally induced chirality should be achievable and observable with realistic experimental parameters. And that’s their goal now.

    © Copyright Original Source

    Yes, but they are using laser pulses! This would seem to be a laboratory-only experiment, not generally applicable to prebiotic earth.

    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)

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