Chemistry plus Biology = Abiogenesis:

Discussion in 'Astronomy, Exobiology, & Cosmology' started by paddoboy, Jul 1, 2019.

  1. paddoboy Valued Senior Member

    Even that has more validity then any mythical creationist nonsense.
    Just in case James missed this or was choosy in what he did read...
    "Blind faith" in chemical evolution? Guess who hasn't read the scientific literature!

    Here's 78 scientific papers from the abiogenesis literature, that demonstrate conclusively that "blind faith" doesn't apply. Instead, what applies is direct experimental confirmation that the postulated chemical reactions WORK, and work under the prebiotic conditions postulated to have been present on the early Earth ...

    A Production Of Amino Acids Under Possible Primitive Earth Conditions by Stanley L. Miller, Science, 117: 528-529 (15th May 1953)

    A Rigorous Attempt To Verify Interstellar Glycine by I. E. Snyder, F. J. Lovas, J. M. Hollis, D. N. Friedel, P. R. Jewell, A. Remijan, V. V. Ilyushin, E. A. Alekseev and S. F. Dyubko, The Astrophysical Journal, 619(2): 914-930 (1st February 2005) {Also available at]

    A Self-Replicating Ligase Ribozyme by Natasha Paul & Gerald F. Joyce, Proc. Natl. Acad. Sci. USA., 99(20): 12733-12740 (1st October 2002)

    A Self-Replicating System by T. Tjivuka, P. Ballester and J. Rebek Jr, Journal of the American Chemical Society, 112: 1249-1250 (1990)

    Activated Acetic Acid By Carbon Fixation On (Fe,Ni)S Under Primordial Conditions by Claudia Huber and Günter Wächetershäuser, Science, 276: 245-247 (11th April 1997)

    An Asymmetric Underlying Rule In The Assignment Of Codons: Possible Clue To A Quick Early Evolution Of The Genetic Code Via Successive Binary Choices by Marc Delarue, The RNA Journal, 13(2): 161-169 (12th December 2006)

    Attempted Prebiotic Synthesis Of Pseudouridine by Jason P. Dworkin, Origins of Life and Evolution of the Biosphere, 27:345-355 (1997)

    Carbonyl Sulphide-Mediated Prebiotic Formation Of Peptides by Luke Leman, Leslie Orgel and M. Reza Ghadiri, Science, 306:283-286 (8th October 2004)

    Catalysis In Prebiotic Chemistry: Application To The Synthesis Of RNA Oligomers by James P. Ferris, Prakash C. Joshi, K-J Wang, S. Miyakawa and W. Huang, Advances in Space Research, 33: 100-105 (2004)

    Cations As Mediators Of The Adsorption Of Nucleic Acids On Clay Surfaces In Prebiotic Environments by Marco Franchi, James P. Ferris and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 33: 1-16 (2003)

    Chemistry for the Synthesis of Nucleobase-Modified Peptide Nucleic Acid by R. H. E. Hudson, R. D. Viirre, Y. H. Liu, F. Wojciechowski and A. K. Dambenieks, Pure Appl. Chem., 76(7-8): 1591-1598, 2004

    Computational Models For The Formation Of Protocell Structures by Linglan Edwards, Yun Peng and James A. Reggia, Artificial Life, 4(1): 61-77 (1998)

    Conditions For The Emergence Of Life On The Early Earth: Summary And Reflections by Joshua Jortner, Philosophical Transactions of the Royal Society Part B, 361: 1877-1891 (11th September 2006)

    Darwinian Evolution On A Chip by Brian M. Paegel and Gerald F. Joyce, Public Library of Science Biology, 6(4): e85 (April 2008)

    Early Anaerobic Metabolisms by Don E Canfield, Minik T Rosing and Christian Bjerrum, Philosophical Transactions of the Royal Society Part B, 361: 1819-1836 (11th September 2006)

    Emergence Of A Replicating Species From An In Vitro RNA Evolution Reaction by Ronald R. Breaker and Gerald F. Joyce, Proceedings of the National Academy of Sciences of the USA, 91: 6093-6097 (June 1994)

    Evolution Of Amino Acid Frequencies In Proteins Over Deep Time: Inferred Order Of Introduction Of Amino Acids Into The Genetic Code by Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh, Molecular and Biological Evolution, 19(10): 1645-1655 (2002)

    Formation Of Bimolecular Membranes From Lipid Monolayers And A Study Of Their Electrical Properties by M. Montal and P. Mueller, Proceedings of the National Academy of Sciences of the USA, 69(12): 3561-3566 (December 1972)

    Homochiral Selection In The Montmorillonite-Catalysed And Uncatalysed Prebiotic Synthesis Of RNA by Prakash C. Joshi, Stefan Pitsch and James P. Ferris, Chemical Communications (Royal Society of Chemistry), 2497-2498 (2000) [DOI: 10.1039/b007444f]

    Hyperthermophiles In The History Of Life by Karl O. Stetter, Philosophical Transactions of the Royal Society Part B, 361:1837-1843 (11th September 2006)


    Just a few of the 78 papers.
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  3. Write4U Valued Senior Member

    Wow.....hold on ...Peltzers' first sentence brought me to a standstill.
    Please enlighten me, before I go any further;
    Why does the concept of a "non-biological origin of life" present a problem? Might as well declare the "non-physical origin of the physical universe" was impossible because there were no physics before the BB which gave us physical objects and started acting physically .

    At what stage do we want the origin of life to become biological? Before there were bio-chemicals or after, when bio-chemicals began to act biologically and formed first simple life forms?
    Last edited: Jul 4, 2019
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  5. paddoboy Valued Senior Member


    "I hesitated over Tim Pawlenty, who has argued that intelligent design creationism should be taught in schools. It seems likely he was just pandering to potential voters, however, and Pawlenty has, to his credit, been one of few hardcore rightwingers to take global warming seriously (though he radically toned down his lack of ignorance when he started thinking about running for president).

    Edward Peltzer may not be the most notable member of the creationist movement, but at least he is clearly deranged enough to merit inclusion in our Encyclopedia. Peltzer is a “senior research specialist” at the Monterey Bay Aquarium Research Institute. He is, in fact, an analytical chemist working in oceanography, and has some actual peer-reviewed publications – he even seems fairly knowledgeable about these matters. Since the creationist movement is arduously seeking out anyone with a modicum of scientific credibility who supports their cause, Peltzer is widely used, e.g. in the Kansas Evolution Hearings.

    His contribution to said hearings can be found here. They are revealing; after a lengthy presentation on the problems of abiogenesis, Peltzer spent the last minute launching into an incoherent rant about “the religion of naturalism” in modern science. During cross-examination, he rejected common descent and evolution (hesitant old earth creationism). He has also given talks on the origin of life and the “problems” of scientific naturalism in various creationist venues.

    At least he seems to be doing some worthwhile and actually helpful work related to global warming. Still.

    Diagnosis: Another otherwise intelligent chap who is willing to throw critical thinking and science under the bus if the results don’t fit sufficiently smoothly with his preconceptions. It’s sad, really."

    Two up, two down!!

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  7. Write4U Valued Senior Member

    And Behe makes three......

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  8. Q-reeus Banned Valued Senior Member

    A single innocuous opening sentence stopped you? Then don't keep asking irrelevant questions of me. Keep chatting with and mutually buoying up your like-minded comrades here.
  9. Write4U Valued Senior Member

    I understand your rigor, but logically I disagree.

    That life came from non-life cannot be other than fact. There was no life before the BB, and it took some time after the BB for life to emerge from non-life. Life where there was no previous life, OK?

    There are an infinite number of paths this chronology could take, but there is only one path which denies the overwhelming evidence of the BB and the subsequent creation of physical matter from which still later, Life emerged, driven by exponential variety of chemical processes, forming bio-chemical compounds able to self-assemble into biological organisms. That single opposing path which falsifies all discovered scientific truths and is offered as "devine creation" by an "unknowable but motivated entity", without any evidence whatever.

    OTOH, this simple but delightful and enlightening lecture by Bonnie Bassler, who explains the self-regulating bacterial communities.
    Bacteria are a perfect example of a bio-chemical "link" from purely chemical reactivity to ability for self-duplication and establishing colonies, an evolutionary advantage.

    Bacteria "talk" to each other via chemicals, a dedicated intra-species chemical communication network.
    The actual words (messages) of bacterial languages are their chemical signatures. Communication among specific kinds. Not unlike the more sophisticated Ant and Bee hive- minds through chemical signalling.

    Could it be that quasi-intelligent mathematical behavior eventually results (evolves) in a sentient intelligent self-awareness? Seems almost too simple to be true, no?
    But then there is always Occam's razor.
    Last edited: Jul 4, 2019
  10. James R Just this guy, you know? Staff Member


    And I'm saying that abiogenesis is just a label, not an "answer". I've already said that scientists are working on an answer and that certain pieces of the puzzle are falling into place, but we're not there yet.

    I agree with you that religion, gods and spaghetti monsters are not scientific explanations of the origin of life. I also agree with the observation that there was no life, then later there was life, on Earth at least. What is lacking is a complete scientific theory of how life came from non-life.

    It's not an answer. It's just a label. Pick it apart: a-bio-genesis. Roughly speaking it translates as "origin of life without biology". Or just another word for "life coming from non-life".

    It's important for you to realise that it is not me who is making claims about this. You are the one making the claim. You're claiming there's a scientific "answer" to the question of how life came from non-life, called "abiogenesis". I disagree with your claim. As the person making the claim, the onus is on you to establish the truth of your claim, perhaps by appealing to appropriate evidence, for example evidence that there is an accepted scientific consensus on just how life came from non-life.

    Understand that it does not follow that if I can't disprove your claim then your claim must be true. Think about it. A Creationist could make a similar argument. Only God can create life from non-life, says the Creationist. If you scientists can't prove that God didn't do it (e.g. by proving that it happened naturally), then God must have done it. See the problem? The onus there is not on the scientists to disprove the Creationist claim. It is up to the Creationists to support their claim. And the same applies to you if you want to claim that Science has all the answers.

    Just to be clear, my own position on this is as follows: I don't know how life came from non-life. That's it. I don't know how it happened. I could expand on that and say that I suspect that science will find a scientific answer sooner or later, but that's not the same as saying that science has an answer now. I could also say that I don't think religion gives any satisfactory answer either, and I could add that religious answers are unsatisfactory precisely because they are unsupported by good evidence. But that's just repeating my previous statement that people who make claims need to prove their claims rather than assume they are true by default.

    Yazata was spot on in what he said. Moreover, I see nothing dishonest in his reply. It seems to me that you just tend to recoil whenever the word "philosophy" is mentioned, as if philosophy is somehow anathema to science and therefore bad. Philosophy, of the secular kind at least, uses a lot of the same tools of reasoning as science. Or, to put it round the other way, science uses tools of reasoning in part provided by and informed by philosophy of various kinds. Calling arguments you'd prefer not to listen to "philosophical semantics" doesn't dismiss those arguments, or even address them. It's just an avoidance tactic. And, like I said, it's not as if your own beliefs are philosophy-free. How could they be?

    I'm not sure what you're referring to with those guys. Depending on what you're talking about, I might or might not agree with you/them.

    You don't need to apologise to me for that. I agree with you that "God did it" is not a scientific explanation.

    My point, again, is that it is just a label, not an explanation.

    Look at what you wrote there: "scientific assumption". How is it science, if it's an assumption you're making? Science is based on observation and experiment, isn't it? What you have there is a hypothesis or a conjecture. Not an unreasonable one, in my opinion, but just a hypothesis nonetheless. There's no Theory of Abiogenesis (yet), where I'm using the term "Theory" in the scientific sense.

    That is not in dispute.

    Agreed. "I can't think/don't know how it happened. Therefore God did it." Bad reasoning.

    Q-reeus disputes that there was no life followed by life? I guess if that's true he can explain his own position. There's little point in my discussing his views with you.

    I'd be happy to call it abiogenesis. That's what the word means, after all. But I suspect that Creationists won't want to use that term, because to them it seems like a term that scientists use to imply that there must be a purely naturalistic explanation for the origin of life, while clearly the Creationists believe in a supernatural origin story. No doubt they would prefer a term like "Creation". Technically, the term "abiogenesis" ought to be a neutral term, because it doesn't make any assumptions about the particular process at work, which is rather different from "Creation". But Creationists prefer to build their assumptions into their arguments from the start rather than following a trail of evidence.

    I agree with him.

    We really ought to be on the same page regarding this. We both believe that science has the best chance of explaining the origins of life. The major sticking point in our disagreement is that you appear to think that science has already solved the whole problem, whereas I think it hasn't. Thus, you say there is a Theory, and I say there isn't (a Theory in the scientific sense being a well-tested and generally accepted description of a natural process or set of processes).
    Last edited: Jul 4, 2019
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  11. paddoboy Valued Senior Member

    You have a funny attitude q-reeus...funny peculiar, not funny ha ha...You make a big thing when those refuting your position give or receive likes, then accept your own likes from the likes of river, and give them yourself to the likes of MR and river...funny, very funny!
  12. James R Just this guy, you know? Staff Member



    One that is not disputed by anybody, as far as I'm aware. Unless, that is, you regard the creation of life by God as life being created from life, for some reason.

    Brushing over potential problems with the notion of "before the BB", OK.

    I agree that Biblical Creationism - in its literal sense at least - is in conflict with scientifically-established truths. But if biblical creationism is false that doesn't mean that any particular scientific theory of how life started must be true automatically.

    But wouldn't opponents of scientific abiogenesis point out here that bacteria are already alive? How are they relevant to the question of how life got started, then?

    Maybe. Maybe not. The onus of proof is on the claimant to prove the claim.
  13. Write4U Valued Senior Member

    Au contraire, it was perhaps innocuous in appearance, but if you unpack it, it suggests a logical and mathematical contradiction. And that invalidates the premise on which the argument of "abiogenesis" rests.

    Can't have biology before you have biology. Once there was no biology, but there was chemistry. Then there was bio- chemistry but no life and finally there was biology and life. Can't have life before there was life. Error, error.
  14. Write4U Valued Senior Member

    This is what you are disputing, no? If not, what is wrong with use of abiogenesis as the definition of bio-chemicals emerging from inorganic chemical interactions, creating bio-chemical compounds, eventually yielding biology.
    Then why is the use of the term abiogenesis being questioned?

    This is a simple either/or question. There is no middleground.
  15. paddoboy Valued Senior Member

    Playing semantics just as exchemist did, and some similar fence straddling.
    They have an answer...the only scientific answer...they don't have a pathway though.
    Abiogenesis is the obvious scientific answer...knowledge of the methodology and pathway is as yet unknown. Similar gaps also with DM...while we know that it exists, we do not know the exact nature.

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    yep another word that translates to the only reasonable scientific theory/model/process that answers that question, with some gaps still there.
    Í'm not a scientist James, but I have given many articles and papers supporting my position, and as I said, the same thread elsewhere is not creating this sort of pedantic semantic nonsense. Those papers certainly surpass the two by q-reeus by two scientists with obvious religious agendas.
    Note: One at least also dismisses evolution.
    The creationists and IDers positions are unscientific as is all supernatural and paranormal nonsense. I have tried many times to drum that into MR as you should know.
    I certainly accept your reasoning that religious and IDer answers are unsatisfactory, in fact as pointed out, unscientific. I don't believe though that you therefor cannot see that there is only one answer left, one scientific answer that is...Abiogenesis. And I believe I have the vast majority of reputable scientists agreeing.
    Yazata also inferred that I had started this thread just to flame....The exact same thread is also elsewhere with total acceptance, including one Philosopher. What they did reject from the one dissenter was his usual pedant and semantic nonsense.
    I accept that. But I'm not critical of philosophy per se...I'm critical of it being applied in too greater depth and where not needed. Check out some stuff on Lawrence Krauss or the late Stephen HAWKING
    Exactly as is here, near word for word n my side...If you doubt that go and check at SFN under 'comets kick starting life on Earth. It quickly got onto Abiogenesis with my help

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    Which leaves just one scientific explanation.

    We also have scientific assumptions that the universe is isotropic and homegenous.
    Scientifically speaking Abiogenesis is the only reasonable explanation left.

    I hope you check out the same debate at SFN.
  16. Write4U Valued Senior Member

    It most certainly can mean that as just one expression of the infinite expressive potential in the universe. Has there ever been a spontaneous chemical self-assembly creating a new universal chemical potential? Not?
    True, but they are only chemically alive (biochemistry) and not very alive as Bassler demonstrated. Viruses are another example of a quasi living organism.

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    But actually I skipped ahead a little bit. That example of bacterial communication was offered in context of evolving sentient intelligence from functional hive-intelligence.
    Well, being that this is a exercise in logic, it is up to both parties to make the most persuasive logical and scientifically supported argument which is acceptable by intelligent human quorum sensing....

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    But I do also understand your adherence to strict scientific standards, whereas I see it more as a mathematical (logistical) probabilistic problem of astronomical proportions.
    Last edited: Jul 4, 2019
  17. James R Just this guy, you know? Staff Member


    No. I have never disputed the notion of life coming from non-life. What I dispute is the notion that there is a well-accepted and mature scientific theory about how that happened.

    There's nothing wrong with that, from my point of view. But that's a hypothesis or conjecture, not a theory.

    Notice that I haven't put forward any hypothesis regarding the origin of life in this thread. I'm quite willing to be shown evidence that some chemical process or other produced life from non-life, if such evidence exists. In fact, I'd be excited to see such evidence. Similarly, I'm quite willing to look at any evidence that a supernatural Creator God caused life to spring from non-life, if there's any evidence for that proposition.
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  18. paddoboy Valued Senior Member

    OK my error above. After reading again I now see you were referring to Krauss and Hawking, not the other forum. Krauss in particular, wrote a book on this isue and actually was peppered with criticism from all round the world...Yazata certainly would be aware I suggest.

    Let me also say now, at the risk again of being accused of conspiracy with you, that I'm not being stubborn with this issue. My position is certainly solid as I believe that as I have been saying, it is the only scientific position to take.
    I'm also not just a religious ID basher. Except and only when they start criticising science unjustly. And experience has always shown me that when that happens, you can bet your short n curlies that religion/ID or similar is at the core of their attempted derision.
    The core to my concrete position on this rests with the fact that what I have claimed is also what the mainstream claim. That along with what I believe to be logic and common sense, the many many papers that also support that position is what grounds me on this.
    Why did i post that subject here? Certainly not to specifically shit stir as exchemist and Yazata appear misinformed about, but because it created interest elsewhere and so I thought it might here. It did, with different results though. exchemists position in my opinion was simply to help an old mate. That's why I find his conduct quite questionable, including calling me a crank.
  19. Write4U Valued Senior Member

    I believe that Robert Hazen makes a very persuasive case of the evolutionary chemical processes which yield the ability to form complex patterns and that some patterns develop their own dynamic potentials, such as movement from purely chemical reactive processes. The flagella is but one complex bio-chemically evolved pattern which offer a functional automotor propulsion system. A crossover from inanimate matter to dynamic animate (bio-chemically driven) living matter.

    But my argument of biology from purely chemical origins rests firmly on the concept of the bio-chemical functions of the trillions of microtubules in all eukaryotic living organisms.

    IMO, they form the self-referential information network in biological systems. An emergent functional excellence from evolving sensory awareness. A self-evident natural phenomenon.
    Last edited: Jul 4, 2019
  20. James R Just this guy, you know? Staff Member


    Sorry to labour the point, but I still don't think you're understanding what I'm getting at.

    Your analogy with the dark matter problem is an interesting one to consider in more detail, because it raises the same kinds of issues.

    In the case of abiogenesis, we have the generally-accepted fact that life came from non-life somehow. In the case of dark matter, we have the general scientific consensus that there is some unseen source of gravity in galaxies (in particular). To the hypothesis that life came from non-life through some kind of natural chemical process we assign the label "abiogenesis". To the hypothesis that the unseen source of gravity is some form of invisible matter we assign the label "dark matter".

    Having assigned these labels, is it fair to say "Problem solved. We're all done here. Nothing more to see. Move along!"? Of course not. The next step is to formulate hypotheses to attach an explanation to the label. Maybe dark matter is WIMPS. Maybe it is MACHOS? Maybe it is supersymmetric particles? Maybe it is massive neutrinos. So, investigate further. Observe. Study. Try to rule out some of the hypotheses to narrow the focus down on what this "dark matter" stuff actually is.

    Do we have a Theory (in the scientific sense) of dark matter? No, at the present time we don't. At best we have a number of competing hypotheses slugging it out in the battlefield of ideas and data, to determine an eventual best-candidate theory of dark matter. Do we have a theory of abiogensis? No, we don't. At best we have a number of competing hypotheses about the possible origins of life and there's still a lot of work to do before we can even start talking about a best-candidate theory of abiogenesis.

    You say that "abiogenesis is the obvious scientific answer", but it isn't an answer. Not yet. It's more like a bunch of educated guesses. Same goes for dark matter. There's no "obvious scientific answer" that solves the dark matter problem yet, either. There's a bunch of different ideas, and a certain amount of evidence that favours some ideas more than others, but that's all.

    Okay. You say there's a reasonable scientific theory or model that answers the question of how life came from non-life. In a nutshell, then, give me the outline of that theory or model. Just the basics. No need to go into huge detail, but you'll need to do better than wave your hands in the vague direction of yet-to-be-specified chemical processes and as-yet-undetermined steps.

    I mean, for example, if there was a theory of dark matter, I should be able to sum it up in a statement like "Dark matter consists of massive neutrinos that are left over from the big bang" or something similar. Since I don't think there is one, the best I could come up with in the current circumstances would be more along the lines of "Some scientists think dark matter might be X; others think it might be Y; some think it could be Z; nobody knows for sure."

    Nor am I an expert in chemistry or biology.

    To me, the papers you have cited suggest that we're possibly making some progress towards a theory of abiogenesis. We're assembling some pieces of the puzzle, to use an analogy I used earlier. But all those papers don't add up to a completed puzzle.

    I haven't yet looked at the sources that Q-reeus is relying on here, but I don't expect that doing so will persuade me that natural abiogenesis is impossible. Nor do I expect that they will provide any evidence to support the conjecture that a supernatural being or force caused/causes life to start.

    Evolution is a Theory, in the proper sense. It requires much more than mere assertion to dismiss a Theory.

    Creationism is religious dogma dressed up to look like science. ID, at least in the form put forward by its religious proponents, turned out to be little more than a poorly-disguised attempt to rebrand Creationism. At best, ID is bad science. Conjecture largely unsupported by evidence.

    As I said before, it does not follow that if religion and ID are wrong, therefore some particular scientific theory of abiogenesis must automatically be right. For all we know, all the current scientific hypotheses regarding abiogenesis might be wrong, too. To compare, for all we know all the current hypothesised explanations of dark matter might be wrong, too.

    What stuff should I check out? I've seen Krauss talk in person. I've read a couple of his books. I've read some of Hawking's stuff. There's endless amounts of material I could potentially "check out" on those guys. Anyway, is this some kind of argument from authority that you're trying to make?

    The discussion you're having in parallel on some other forum is none of my concern. You chose to bring this discussion here, so if there's something relevant you feel a need to bring over it's up to you to bring it. It's your argument. Why should I do all the work?

    Okay. So tell me the correct scientific explanation for abiogenesis. Again, just a brief summary in a sentence or two should be enough, for starters.

    Those arguments go along the lines of "For the sake of argument, let us hypothesize that the universe is isotropic and homogeneous. If we assume that is true, we can then make predictions X, Y and Z about how the universe should look, which we can check against real-world observations. If those observations match the predictions, then it is probably fair to say that the hypothesis is a reasonable one to make."

    What we don't do is say something like "The only possible scientific theory is that the universe is homogeneous, because the idea that God made the universe inhomogeneous is mythological nonsense."

    Certainly the notion that life came from non-life via some kind of natural process is the only reasonable explanation left once we rule out the notion that life came from non-life due to supernatural intervention. But saying life came about via "some kind of natural process" is a very long way from saying "We know how life came about".
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  21. Write4U Valued Senior Member

    How long would you be willing to wait for evidence, in the face of existing evidence of abiogenesis.
  22. Write4U Valued Senior Member

    True, it's an ongoing process and IMO, there is evidence of abiogenesis if we look back far enough into the history of abiogenesis on earth.

    How would you weigh CRSPR technology on the scale of life?

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    Last edited: Jul 4, 2019
  23. Write4U Valued Senior Member

    Abiogenesis is a universal chemical function just like Evolution is a universal physical function. Both universal functions produce new animate and inanimate patterns which did not exist before, although many patterns are based on continuation of universal common denominators.

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