Chemical evolution:

Discussion in 'Biology & Genetics' started by paddoboy, Aug 7, 2020.

  1. Q-reeus Banned Valued Senior Member

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    Terrific effort there exchemist in expounding how clever and resourceful Nature has been to bypass ID in coming up with nifty chemical cascades such that:
    So with the discovery of chemical cascade reactions, cracking unguided OOL completely is perhaps just over the horizon? A few contra considerations:

    1: Any accompanying homochirality and of the correct sign in any of these RNA/DNA units, amino acids, and lipid building blocks? If not Nature is still screwed.

    2: There must have been many other reaction products apart from the desired ones. Will they magically hold off from reacting with and in effect poisoning the desired products? Hard to believe. A key observation of Edward Peltzer in 'Abiogenesis - The Faith and the Facts'. This issue bears heavily on the feasibility of e.g. RNA/DNA unit unbroken polymerization to the requisite large biologically active lengths. And did I mention homochirality maintained throughout? Which still leaves out the origin of information content required for cell reproduction and repair being somehow encoded in those (hopefully) long chains.

    3: Peltzer also pointed out a simple lipid layer enclosing some notional primitive self-reproducing system (so many begging questions just there) may protect the protocell contents from environmental poisoning, but also works to kill the protocell anyway. That's because it would result in waste product buildup while simultaneously preventing new feed-stock from entering. In addition no feasible clever instruction sets and communications systems to allow protocell division are on offer. Or self-repair for that matter. What a pity - our miracle protocell evidently is doomed to die a very lonely death.

    But hope springs eternal that such 'minor wrinkles' will all be solved in the bye and bye and via purely unguided mechanisms. Keep on dreaming. Keep up the faith.
     
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  3. exchemist Valued Senior Member

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    The point of my story is not that all the problems of the origin of life has been solved, obviously. Don't pretend that is what it is saying.

    The point of the story is what I said it was: it shows that the way this Houston synthetic organic chemist thinks, and the sorts of analogies he comes up with, provide no insight into how nature could have synthesised the building blocks of life. In fact, that way of thinking led people to bark up the wrong tree for 40 years. Only in 2009 did they get this breakthrough, as a result of abandoning that way of doing it.

    So Tour, far from being an authority on abiogenesis as he pretends, is actually impeded, by the silo he has worked in all his life, from understanding how these molecules could have arisen in nature.

    That's the point.

    As for the rest of your post, anyone can come up with a list as long as your arm of all the issues that need to be resolved before we have a model of natural abiogenesis. That it is about the biggest outstanding problem in science is not in doubt. I do not expect more than a few of these issues to be solved in my lifetime. But the fact is that research is advancing rapidly and solutions to the myriad problems are being found, one by one, in the way that science typically does. So it is contrary to the evidence, not to mention absolutely unscientific, to claim it's insoluble.
     
    Last edited: Nov 27, 2020
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  5. Q-reeus Banned Valued Senior Member

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    It's customary to link to the relevant article when reproducing chunks of text from the same. Something you avoided doing in#36. Going on nothing more than Sutherland as name of one researcher and the year 2009, managed to find that far from being totally ignorant of that cascade discovery as you implied, Tour actually commented on it at length. And in the same article you professed to read right through: https://inference-review.com/article/animadversions-of-a-synthetic-chemist
    See refs 41, 42 at bottom, and further up under 'It Stands to Reason', then 'Extrapolation on Steroids', finally 'Dream On'.
    You may disagree with his assessments, but the charge of gross ignorance of Sutherland et. al.'s work rebounds and only makes you look silly.

    PS: Last para under 'Extrapolation on Steroids' reads in part:
    "...The routes afford very simple precursors to just a few of the many molecules within the building block class, and all their precursors were racemic if they even bore any possible stereoisomerism."
    Which answers my question on that in #41. I had little doubt that was the case.
     
    Last edited: Nov 27, 2020
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  7. exchemist Valued Senior Member

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    I copied it from another web forum. It is usually considered bad form to direct users of one forum to another one. But if you want the link, I'll give it (and hope the mods don't mind, given the context

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    ): https://www.religiousforums.com/threads/science-of-abiogenesis-by-popular-demand.193208/page-2

    Yes I did read right through Tour's screed. (I was not lying, hard though you may find that to believe.

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    ) Admittedly, though, I made my commentary on it before I had read Sayak's piece explaining the Sutherland work, so I saw no reason to single out Tour's superficial dismissal of it- in a paragraph. Tour can't fault any of the chemistry - which would never have occurred to him to try - so he just resorts to claiming that the conditions required are implausible. Even though he wrote his piece in 2016, he refers only to the original 2009 findings and not to the subsequent 6 years of futher work on refinement and development of the "cascade" that are mentioned in the piece I quoted from.

    I'd actually like to read the original Sutherland papers, but I don't have a subscription to Nature, unfortunately.
     
  8. paddoboy Valued Senior Member

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    Whether it's "over the horizon" or not is irrelevant to the evidence that chemical evolution, over probably hundreds of millions of years, was the process for the origin of life, or Abiogenesis.
    You [and Tour] seem so obsessed with the installing of a God of the gaps excuse. With Tour, that seems to be verging on the fanatical, evident in the "preacher" style of narrative he uses, pushing his excuses.
    In my opinion, the vast majority of scientists, [and me for what its worth] accept Abiogenesis because of how far we have come in the evolution of life, and the the first evidence that organic molecules needed for life can be formed from inorganic components. A simple extrapolation of that fact, taking in the time frame, seems to be far more logical then inventing some hypothetical IDer, magical spaghetti monster. Why would you do that, knowing what already has been achieved and what we know?

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    Oh, the pain of it all! I'll refrain from any ironic Pot, Kettle Black narrative at this time.

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  9. Michael 345 New year. PRESENT is 72 years oldl Valued Senior Member

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    Which you didn't

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  10. exchemist Valued Senior Member

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    This 2015 paper from the Sutherland team seems to be the origin of the flowscheme at the end of my previous link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

    It seems the authors do not claim all this goes on in "one pot" but in a series of pots connected by a flow. We seem to be back to Darwin's warm little pools, but with volcanic minerals around. Intriguing that they can get so much of the relevant chemistry to occur under such mild conditions.
     
  11. Q-reeus Banned Valued Senior Member

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    It was of course the absence of that link to the original Sutherland et. al. work I was referring to in #43, not a link to that of the other forum discussion.
    From 2015 paper's 'Conclusion' in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

    "Although it necessarily has to be painted with broad brushstrokes, the picture that emerges is that of an overall reaction network developing over time in separate streams and pools, according to a dynamic flow chemistry scheme. The various products would be synthesised by subtle variations in flow chemistry history of the streams and the order in which they merged, or ran into pools. Although the overall scheme would not involve all the steps of the reaction network taking place simultaneously in ‘one pot’, the various products would all end up mixed in pools...."

    Specific sequence of events scenario perfectly in keeping with Tour's commentary in 'Animadversions...'. Further supported after a cursory read through the all important Supplementary Material linked to at the end of their paper:
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/bin/NIHMS64646-supplement-SI.pdf
    Lots of very carefully controlled chemistry described there. What you dismiss as 'superficial' re Tour's commentary is imo actually incisive and perfectly relevant.

    And my bet is that Sutherland et. al. here in late 2020 are still stuck with biologically useless racemic mixtures. If that barrier is ever plausibly crossed, the far greater barrier of accounting naturally for the vast DNA/RNA specific encoding sequences absolutely necessary for a functioning cell/protocell to live and reproduce, will need to be crossed. Dream on.

    PS: Tour has similar and very relevant things to say about more recent 'breakthroughs' in OOL research here:
    http://inference-review.com/article/two-experiments-in-abiogenesis
     
    Last edited: Nov 28, 2020
  12. Q-reeus Banned Valued Senior Member

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    Revealing your basic ignorance yet again. No, that's impossible. Organic molecules must contain carbon. Inorganic molecules are devoid of any carbon. Got it? A correct statement is that certain inorganic constituents can be incorporated into organic biomolecules, and certain other inorganic molecules can act as intermediaries in the formation of organic biomolecules.
     
    Last edited: Nov 28, 2020
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  13. Write4U Valued Senior Member

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    Your perspective is somewhat limited.
    The earliest biomolecules were already being formed in cosmic clouds, long before earth or any other solid object formed in the universe.

    Louis Allamandola
    Dr. Louis Allamandola, Senior Scientist in the Space Science Division, is the founder and director of The Astrophysics & Astrochemistry Laboratory
    Significant contributions made by the The Astrophysics & Astrochemistry Laboratory include:
    1. determining the mid- and far-infrared properties of over 800 PAHs in their neutral and charged forms under astrophysical conditions and making this collection available to the community at large (www.astrochem.org/pahdb),
    2. the demonstration that biogenic organic molecules can be made under the harsh, abiotic conditions in extraterrestrial ices implying they are widespread throughout the Galaxy and cosmos,
    3. the recognition that polycyclic aromatic hydrocarbon ions containing nitrogen are common in space, resolving long standing astronomical mysteries associated with infrared emission bands and optical absorption bands that are widespread throughout the universe,
    4. the identification of many of the known molecular species frozen in interstellar/pre-cometary ices, and
    5. the recognition that a significant fraction of the carbon in the interstellar medium is carried by both microdiamonds and organic materials.
    http://www.astrochem.org/bios/allamandola.php
     
  14. Q-reeus Banned Valued Senior Member

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    And I was referring to earliest origins of organic biomolecules? No. Another non sequitur of yours.
     
  15. paddoboy Valued Senior Member

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    And your own ignorance in ignoring the facts we do have, along with obtuse arguments when someone dares attempt to deflate your mythical beliefs, here and elsewhere, are even more obvious.
    Although obvious you did have many fooled for quite a while before coming out of the closet, in relation to this matter.
    https://link.springer.com/article/10.1007/BF00927014

    https://www.khanacademy.org/science...-earth/a/hypotheses-about-the-origins-of-life

    "In 1953, Stanley Miller and Harold Urey did an experiment to test Oparin and Haldane’s ideas. They found that organic molecules could be spontaneously produced under reducing conditions thought to resemble those of early Earth.
    Miller and Urey built a closed system containing a heated pool of water and a mixture of gases that were thought to be abundant in the atmosphere of early earth (\text{H}_{2}H2start text, H, end text, start subscript, 2, end subscript\text{O}Ostart text, O, end text, \text{NH}_{3}NH3start text, N, H, end text, start subscript, 3, end subscript, \text{CH}_{4}CH4start text, C, H, end text, start subscript, 4, end subscript, and \text{H}_{2}H2start text, H, end text, start subscript, 2, end subscript). To simulate the lightning that might have provided energy for chemical reactions in Earth’s early atmosphere, Miller and Urey sent sparks of electricity through their experimental system".
     
  16. paddoboy Valued Senior Member

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    The force [gullibility] is strong in this one...and of course Tour!
     
  17. Q-reeus Banned Valued Senior Member

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    Incapable of admitting your error, the usual strategy of going on the offensive ensues. Except it's just rambling nonsense. The article you link to is 46 years old! Your searching for any article that looks like it might be contra to my position is altogether too random and careless. And what is this supposed 'coming out of the closet' all about? Have you gone totally mad?
    Added by you after that in email notification. Another stab in the dark at refuting me. It fails also. Tour's critiques are essentially all correct, but totally misunderstood or simply reflexively rejected by those committed to the atheistic/materialist worldview.
     
  18. paddoboy Valued Senior Member

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    And still holds today.
    Like I said, Tour is a fanatical nut as I showed, and obviously you adoring him because it fits your agenda, would certainly have you disregard all evidence to the contrary...point in hand...the overwhelming thoughts are that Abiogenesis did take place and is the only scientific answer available, not withstanding your usual conspiracy nonsense.

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    Not at all...it is in only relatively recent times, your ID gullibility has been shown. [along with others]

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    Yes, yes, as I predicted, more conspiracy crap...the big bad mainstream science adherents.
    Uhh? Sounds rather paranoid q-reeus, but then again.............
     
    Last edited: Nov 28, 2020
  19. Q-reeus Banned Valued Senior Member

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    No you haven't shown any such thing. And frequent recourse to 'fanatical nut' or 'usual conspiracy nonsense' and similar unjustified/skewed put-downs is an extremely poor way to argue a case. But a leopard can't change it's spots.
    I didn't join up at SF with the intention of discussing ID vs blind evolution. At a certain point I decided to join the debate. To construe that as 'coming out of the closet' is stupid and offensive. But that's part and parcel of paddoboy's MO.
    No conspiracy there at all. Only in your head. And btw, societies have nearly always been run by conspirators, ever since the dawn of civilization. Naive to think otherwise.
     
  20. Write4U Valued Senior Member

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    18,597
    And pray tell, what was this all about?

    My correction of your limited perception of Universal abiogenetic chemistry is perfectly appropriate.
    Read Robert Hazen instead of this Tour guy, with his "synthetic chemistry". There is no such thing as synthetic chemistry that has not already been produced by natural processes.
     
    Last edited: Nov 28, 2020
  21. Write4U Valued Senior Member

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    18,597
    Pray tell Q-reeus, how old is the Universe and when did the first chemical reactions take place?

    Mind that Earth, a minor planet with ordinary chemistry, has performed 2 trillion, quadrillion, quadrillion, quadrillion chemical experiments in some ~4.5 billion years. Now multiply this by the number of similar planets in the Universe.

    And you dare speak of synthetic chemicals as produced by a couple of scientists in a 30 x 30 sterile lab?

    Get REAL!
     
  22. Q-reeus Banned Valued Senior Member

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    Damm it you added that late! Well I can't make it any easier than what you quoted. Thinking on it some more may result in enlightenment.
    Sure. If you say so.
    Tour is a world renowned synthetic organic chemist. As in synthesis of molecules from simpler progenitor ones. That artificial and synthetic CAN be used interchangeably at times, has confused you here.

    We all know how enthralled you are with Hazen and his take on how abiogenesis can happen 'naturally'. His 'large numbers guarantees success' arguments are naive and ignore many factors making those large numbers look ridiculously small. I much prefer Tour and others who clearly understand the huge barriers facing unguided abiogenesis.
    Your #58 brings nothing new to the table. Are we done?
     
  23. Write4U Valued Senior Member

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    If you and Tour understand abiogenesis so clearly, then why are you compelled to introduce mysticism into the equation?

    Clearly, you do not understand the definition of the therm "evolution" from simple to more efficient complex forms.

    Outline of evolution

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    A diagram showing the relationships between various groups of organisms
    Contents
    Earliest Earth (−4540)

    Earliest water

    Earliest life

    LHB meteorites

    Earliest oxygen

    Atmospheric oxygen

    Oxygen crisis

    Earliest fungi

    Sexual reproduction

    Earliest plants

    Earliest animals

    Ediacaran biota

    Cambrian explosion

    Tetrapoda

    • Introduction to evolution – non-technical overview of the subject of biological evolution
    • Evolution – change in the heritable characteristics of biological populations over successive generations
    • Evolution as fact and theory – A discussion of the meaning and usage of the terms evolution, fact and theory
    Basic principles[edit]
    • Macroevolution – Evolution on a scale at or above the level of species
      • Speciation – Evolutionary process by which populations evolve to become distinct species
        • Natural speciation
          • Allopatric speciation – Speciation that occurs between geographically isolated populations
          • Peripatric speciation – Speciation in which a new species is formed from an isolated smaller peripheral population
          • Parapatric speciation – Speciation within a population where subpopulations are reproductively isolated
          • Sympatric speciation – A process through which new species evolve from a single ancestral species while inhabiting the same geographic region
        • Artificial speciation
          • Animal husbandry – Management, selective breeding, and care of farm animals by humans
          • Plant breeding – The art and science of changing the traits of plants in order to produce desired characteristics
          • Genetic engineering – Direct manipulation of an organism's genome using biotechnology
        • Hybrid speciation – Form of speciation involving hybridization between two different species
      • Despeciation – The loss of a unique species of animal due to its combining with another previously distinct species
      • Anagenesis – Gradual evolutionary change in a species without splitting
      • Extinction – Termination of a taxon by the death of the last member
    • Microevolution – change in allele frequencies that occurs over time within a population
      • Artificial selection – Process by which humans use animal and plant breeding to selectively develop particular phenotypic traits
      • Natural selection – Mechanism of evolution by differential survival and reproduction of individuals
        • Sexual selection – Mode of natural selection involving the choosing of and competition for mates
      • Mutation – Alteration in the nucleotide sequence of a genome
      • Gene flow – The transfer of genetic variation from one population to another
      • Genetic drift – The change in the frequency of an existing gene variant in a population
     

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