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Thread: Advances in the science of abiogenesis

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    tWebber shunyadragon's Avatar
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    Advances in the science of abiogenesis

    This thread will review scientific articles on the advancements in the science of abiogenesis

    The first article concerns research in the mechanism for the formation of RNA.

    [cite=https://www.wired.com/2009/05/ribonucleotides/]
    LIFE'S FIRST SPARK RE-CREATED IN THE LABORATORY

    A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

    Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn't explain how these ingredients might have formed.

    "It's like molecular choreography, where the molecules choreograph their own behavior," said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

    RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth's history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

    However, though researchers have been able to show how RNA's component molecules, called ribonucleotides, could assemble into RNA, their many attempts to synthesize these ribonucleotides have failed. No matter how they combined the ingredients — a sugar, a phosphate, and one of four different nitrogenous molecules, or nucleobases — ribonucleotides just wouldn't form.

    Sutherland's team took a different approach in what Harvard molecular biologist Jack Szostak called a "synthetic tour de force" in an accompanying commentary in Nature.

    "By changing the way we mix the ingredients together, we managed to make ribonucleotides," said Sutherland. "The chemistry works very effectively from simple precursors, and the conditions required are not distinct from what one might imagine took place on the early Earth."

    . . .

    At each stage of the cycle, the resulting molecules were more complex. At the final stage, Sutherland's team added phosphate. "Remarkably, it transformed into the ribonucleotide!" said Sutherland.

    "Ribonucleotides are simply an expression of the fundamental principles of organic chemistry," said Sutherland. "They're doing it unwittingly. The instructions for them to do it are inherent in the structure of the precursor materials. And if they can self-assemble so easily, perhaps they shouldn't be viewed as complicated."


    *Citations: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Matthew W. Powner, Beatrice Gerland & John D. Sutherland. Nature, Vol. 460, May 13, 2009.

    *"Systems chemistry on early Earth." By Jack W. Szostak. **Nature, Vol. 460, May 13, 2009.
    Glendower: I can call spirits from the vasty deep.
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    tWebber lee_merrill's Avatar
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    Though the sugars need to be all left-handed (or all right-handed), my guess is that they weren't...

    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)

  3. Amen Teallaura amen'd this post.
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    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Though the sugars need to be all left-handed (or all right-handed), my guess is that they weren't...

    Blessings,
    Lee
    Source: https://phys.org/news/2012-01-scientists-clue-chemical-life.html#jCp



    Scientists discover new clue to the chemical origins of life
    January 24, 2012, University of York
    Organic chemists at the University of York have made a significant advance towards establishing the origin of the carbohydrates (sugars) that form the building blocks of life.

    A team led by Dr Paul Clarke in the Department of Chemistry at York have re-created a process which could have occurred in the prebiotic world.

    Working with colleagues at the University of Nottingham, they have made the first step towards showing how simple sugars –threose and erythrose—developed. The research is published in Organic & Biomolecular Chemistry.

    All biological molecules have an ability to exist as left-handed forms or right-handed forms. All sugars in biology are made up of the right-handed form of molecules and yet all the amino acids that make up the peptides and proteins are made up of the left-handed form.

    The researchers found using simple left-handed amino acids to catalyse the formation of sugars resulted in the production of predominately right-handed form of sugars. It could explain how carbohydrates originated and why the right-handed form dominates in nature.

    Dr Clarke said: "There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living -- everything up to that point is chemistry.

    "We are trying to understand the chemical origins of life. One of the interesting questions is where carbohydrates come from because they are the building blocks of DNA and RNA. What we have achieved is the first step on that pathway to show how simple sugars –threose and erythrose—originated. We generated these sugars from a very simple set of materials that most scientists believe were around at the time that life began."



    Read more at: https://phys.org/news/2012-01-scient...-life.html#jCp

    © 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.

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    tWebber shunyadragon's Avatar
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    The basic goals of science concerning Abogenesis at present focus mostly on are: (1) The natural chemical evolution of inorganic amino acids to RNA. (2) The natural chemical evolution of inorganic phosphates to functional organic phosphates that are capable of energy storage and transfer independent outside energy sources, such as the ADP > ATP energy organic energy transfer process. (3) The environment where abiogenesis took place with sufficient energy, and chemistry suitable for abiogenesis. The three dominant environments that meet this criteria are: (1) Alkaline thermal vents on mid-ocean ridges. (2) Terrestrial environments such as volcanic vents clay volcanic vents, or coastal environments. (3) Combinations of the first such as where mid-ocean ridges come to the surface as in Iceland.

    I favor the alkaline thermal mid-ocean ridge vents. I will give my reason with scientific references in future posts.
    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.

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    tWebber lee_merrill's Avatar
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    Source: phys.org

    The researchers found using simple left-handed amino acids to catalyse the formation of sugars resulted in the production of predominately right-handed form of sugars.

    © Copyright Original Source


    So they started with left-handed amino acids for this step, I would still contend that in their starting experiment they did not generate all left-handed amino acids. Note also that even with loading the deck, they couldn't generate all right-handed sugars, which is a requirement for life, AFAIK.

    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. Amen Jedidiah, Teallaura amen'd this post.
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    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Source: phys.org

    The researchers found using simple left-handed amino acids to catalyse the formation of sugars resulted in the production of predominately right-handed form of sugars.

    © Copyright Original Source


    So they started with left-handed amino acids for this step, I would still contend that in their starting experiment they did not generate all left-handed amino acids. Note also that even with loading the deck, they couldn't generate all right-handed sugars, which is a requirement for life, AFAIK.

    Blessings,
    Lee
    I do not believe it is necessary to develop all right-handed sugar nor left-handed amino acids. Thee simply are left-handed amino acids available that will react to produce right handed sugars to form RNA as the reference indicated.

    From the reference cited: "The researchers found using simple left-handed amino acids to catalyse the formation of sugars resulted in the production of predominately right-handed form of sugars. It could explain how carbohydrates originated and why the right-handed form dominates in nature."
    Last edited by shunyadragon; 10-15-2018 at 08:45 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.

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    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    I do not believe it is necessary to develop all right-handed sugar nor left-handed amino acids. Thee simply are left-handed amino acids available that will react to produce right handed sugars to form RNA as the reference indicated.
    Well, mostly right-handed sugars, correct? And RNA was not formed, just sugars:

    Source: phys.org

    What we have achieved is the first step on that pathway to show how simple sugars –threose and erythrose—originated.

    © 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)

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    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Well, mostly right-handed sugars, correct? And RNA was not formed, just sugars:

    Source: phys.org

    What we have achieved is the first step on that pathway to show how simple sugars –threose and erythrose—originated.

    © Copyright Original Source



    Blessings,
    Lee
    This reference only involve the formation of the right-handed sugars by left-handed amino acids. This was in response to your question. The previous reference involved the natural formation 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.

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    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    This reference only involve the formation of the right-handed sugars by left-handed amino acids. This was in response to your question. The previous reference involved the natural formation of RNA.
    They formed ribonucleotides, that would not be 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)

  12. Amen Teallaura amen'd this post.
  13. #10
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    They formed ribonucleotides, that would not be RNA.

    Blessings,
    Lee
    correct . . .

    "Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn't explain how these ingredients might have formed."

    more to follow . . .
    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.

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