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Aug 08 2011

How we know things in science, and how we can know things about abiogenesis

Nicked from astrobio.net on the Miller-Urey experiments. That's the actual equipment used

On this blog post over at Greg Laden’s, I’ve made a damn fine effort (if I do say so myself) at explaining the process of scientific inquiry to a pair of commenters who’ve taken issue with the idea that anyone could know anything about the event of abiogenesis — the “Origin of Life”, when the fuzzy boundary between chemicals and life was first breached — that happened on this planet. I’ve agreed with them on a number of points, including Anthony’s main thesis, that there was exactly one way that this universe’s past has unfolded, exactly one “truth” to any event in history, and that as a result, figuring out that exact truth is nearly impossible short of having been there to witness it yourself. He accuses the current scientific establishment of “decadence” (belittling our blog friend DuWayne in the process), and of “ideological materialism” wherein the elite of the scientific world are beholden to assume materialism lest their entire epistemology crumbles beneath them.

Luckily, science doesn’t work that way or we’d have stopped investigating this universe long ago.

The scientific method can be implemented to attempt to model events that it cannot prove with 100% certainty happened in exactly one way. By learning about the past, through the physical and inferential evidence we have available to us, we can develop hypotheses which are testable today. If our hypotheses about the past are correct, we can then correctly predict the results of these experiments, and if the experiments are carefully enough crafted, they can disprove the hypotheses and force us to start over. In the specific case of the abiogenesis event that occurred on this planet, we might never know the exact formula that resulted in our exact lineage. This should not stop us from taking the evidence we have available to us, the direct and inferential physical evidence that shows how this planet was very likely composed chemically in the early pre-biotic environment, and extrapolating from that knowledge that perhaps self-arranging lipids and amino acids might have formed.

The Miller-Urey experiment in 1953 took some of our best guesses about the pre-biotic environment and attempted to verify the Oparin-Haldane hypothesis that it would allow for amino acids to self-arrange. When the experiment was complete, they were proven correct. Amino acids — the building blocks to life itself — formed spontaneously, without direction, in an environment that was like science’s contemporary understanding of the early Earth. If this experiment had failed, it would have put a nail in the coffin of the abiogenesis theory, though not the last one, certainly. The fact that it succeeded suggests one of two things: 1) amino acids might spontaneously emerge in a number of environments, or 2) we got lucky and hit upon the correct way to create amino acids but did not replicate the early Earth, thus disproving abiogenesis. The former is far more likely, for obvious reasons — not ideology, but pure math. If there are a near infinite set of environments that the planet could have had, then there are a near infinite set of environments to test. The problem comes down to one of narrowing — if we know the early Earth had to have ammonia (to provide the organic compounds necessary), then we’ve excised all models that do not include ammonia. Scientists later discovered a photochemical reaction of nitrogen that would provide this ur-Earth with the necessary ammonia. Meanwhile, we narrow our options down significantly with each new piece of evidence.

The fact that better evidence turned up suggesting that the early environment was actually significantly different from the conditions replicated in the Miller-Urey experiment should thus hardly come as a surprise, though the actual early environment is still hotly debated among scientists. Miller tried again in 1983 with the newer data, but came up empty — hardly any amino acids to be found. However, Professor Jeffrey Bada repeated the experiment with an even better approximation of the early environment, e.g. that Miller’s second test had omitted iron and carbonate, and amino acids were once more formed spontaneously through nothing more than pure chemical interactions in the simulated environment. And that certainly isn’t the only such related test.

Two different environments, both resulting in amino acids. Certainly the later test benefits from the extra evidence collected about the early Earth, but getting amino acids in multiple different environments bodes well for our ability to show that every step in the grand staircase toward biology is plausible. We know that the lipid bilayer necessary to create a cell membrane can self-arrange as an emergent property of the lipid’s intrinsic hydrophobia (fear of water) on one side, hydrophilia on the other. They’ll form up all by themselves without prompting, given the right environment. So will RNA nucleotides, meaning if the RNA-world hypothesis is correct, we’re well within our rights to suggest that the hypothesis is the one that best fits the available evidence and make further predictions and experiments from there.

None of this is, you’ll notice, an attempt at building a narrative of “how things definitely happened”. People will often demand such a thing, knowing that they cannot themselves replicate experiment results, nor comprehend their interconnectedness with other such experiments if they’re even aware of these other experiments, nor suss out how all the pieces of the puzzle ultimately fit together. I understand this drive — the drive to build a narrative that is easily digested — because every human being has it. It is that drive that frees up one’s mind to contemplate other things, like immediate survival concerns or reproduction or the pursuit of leisure. It is that drive that one combats when arguing with people who cling tenaciously to their received dogmas. The temptation is great to replace one dogmatic narrative with another. But the scientific worldview demands that we understand that our understanding of this universe may never reach 100% certainty about any single topic or event, but as we slowly polish and chip away at the theories we have built, we can bring them to within impressive degrees of certainty that put any former, more dogmatic, effort at explaining the universe to shame.

The level of certainty that Andrew believes we are expressing about the study of abiogenesis is galling, and his repeated insistence that scientists are engaging in myth-making betrays his lack of understanding of the process. That we don’t know a great many things about the actual abiogenesis event on this planet means nothing, ultimately, in the study of how it might have happened. It is like asking that we know everything about the daily life of the very first ape to climb down out of the trees, or else the theory of evolution is about building a just-so narrative. I’m personally content to allow the process of scientific investigation to grind down all the possibilities until there are but a few left, and we can choose which one fits all the evidence best, until such time that new evidence overturns the model and we are forced to revisit.

That’s how science works, you see. And science does indeed work.

(To within a reasonable degree of confidence.)

15 comments

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  1. 1
    Dan Johnson

    Wonderful post! Now where’s our little friend from the hills of Nebraska…

    I’m making some guesses about his arguments against materialism, and the guesses make me not want to read his comments for fear some of the stupidity might leach through the computer.

    Why do we assume that materialism is the basis for reality? Because it works. Other worldviews don’t work. They may be “internally consistent”, but that doesn’t mean a damned thing when you want realistic expectations of repeatability and predictability.

  2. 2
    cass_m

    Well said.

  3. 3
    Garnetstar

    Great comment. And, thank you so much for your long, reasonable discussion with unreasonable people on Greg’s thread. I quit trying early on, figuring that reasoning with someone who did not arrive at their opinion through reason is impossible. Your posts added a lot of value.

    As a result of your untiring comments, I’ve found your blog, and like it so much that now I’m reading it every day. Thanks!

  4. 4
    Jason Thibeault

    Dan: yeah, that’s the difference between philosophical and methodological materialism. As I said over on that quagmire of a comment thread, evidence is paramount, and we have enough evidence showing materialism to be correct that it’s fine to use it as our methodological default for future hypotheses. If we have to rule out the supernatural every time we investigated something, we’d never have managed to do so since the supernatural is de facto something that provides no evidence, and we would have stalled developmentally at the very start.

    Garnetstar: Well, I don’t have “red meat” posts every day, but happy to have you aboard nonetheless! Thanks! My gaining a reader is probably the only good thing to have come from that mess of comments.

    Cass_m: Saw you over at Almost Diamonds too, and the thought occurred to me to ask, if you don’t mind: how did you discover me and Stephanie, and which one did you discover first? She and I have been colluding to try to increase one another’s traffic (she’s easily my favorite blogger), and that kind of metric — who you discovered first — is difficult to come by.

  5. 5
    DuWayne

    What frustrates me about this sort of misunderstanding of science, is that it is not just limited to nuts like Anthony, who have a specific agenda. I will grant that I don’t run into it nearly as often, but there are all too many skeptics who also completely fail to grasp what science is and how science is done. What really bothers me, is that there are a number of them who would also have little or no problem with the label “ideological materialist.” It would appear – at least from where I am sitting, that there are a lot of folks on both sides of the religious/skeptical divide who embrace this notion of a science/materialism as ideology paradigm.

    This shit makes me really uncomfortable, because I spent all too damned many years wallowing in ideological bullshit. The last thing I want to see is my career choice and lack of religious belief turned into the same sort of fucking bullshit.

  6. 6
    Dan Johnson

    Exactly, DuWayne. It’s the same old post-modernist bullshit from the same mental masturbators. They have no interest in being correct; they just want to feel intellectually superior.

  7. 7
    sinned34

    I’ll accept their argument that naturally-occurring abiogenesis could not have occurred unless scientists recreate exactly how it originally happened the same day creationists are able to recreate their god “poofing” animals into existence ex nihilo.

  8. 8
    ildi

    I assumed Anthony’s underlying assumption is that God intervened twice in creating his bffs: first, the Big Bang; second, abiogenesis. Scientists may be able to replicate the markers of abiogenesis in the lab, but that will only ever be a sad reflection of God’s unique action. This way you can have your scientific cake and eat your theology, too.

  9. 9
    Jason Thibeault

    ildi, I’m not sure that’s his goal. He’s stated a few times that he’s not a theist, but he’s not explicitly called himself an atheist. I strongly suspect he’s anti-atheist in that he sees “new atheists” as being dogmatic materialists.

    The problem with Anthony’s argumentation is less that he’s right about how we might (probably) never know with 100% certainty exactly how the event of abiogenesis occurred on this planet, than it is that he assumes that anyone using inferential evidence to narrow down the possibilities is engaged in pure mythmaking along the same lines as those theists that built their hypotheses thousands of years ago and stuck to them in the face of mountains of evidence to the contrary. The problem is entirely one of strawman arguments and a tenuous-at-best grasp of the scientific method.

  10. 10
    ildi

    Well, he had this to say on Joshua Rosenau’s web page a couple of weeks ago:

    That said, evolution is the best available explaination of an enormous amount of evidence, there is no other phenomenon in science which has more evidential support. As I said, if you want to challenge it on the basis of science, you’ve got your work cut out for you. If you believe that God created life on Earth, through the mechanism made manifest in that evidence, that’s not an invalid idea, though you can’t insert it into science because science couldn’t deal with the idea of the divine creation of life, science couldn’t deal with the idea.

    I believe in God, I believe God created the entire universe and everything about it. I believe that God is not susceptible to the network of causality that contains the subject matter of science. I believe it is an act of idolatry to turn some human conception of God into a mere thing that can be subjected to science. The insistence that God can be seen through science is an act of desecration. That God might be seen in the majesty of the universe is not the same thing, it is an acknowledgement that God is only knowable, in an absurdly miniscule part, through living experience of a kind far to broad and far too complex for science.

  11. 11
    Jason Thibeault

    Excellent find, ildi. I don’t frequent Roseneau’s blog mostly because it tends to harbor people of Anthony’s ilk. It’s interesting that he’s arguing much the same way there — that you can’t go from “dead elements” to “life”. If he’s a theist, it certainly explains everything that’s transpired at Greg’s blog. And it paints him in a horrible light where he’s had every opportunity to admit he’s a theist and that’s where his own prejudices lie. Not that it will matter to him — we’re just materialist ideologues and therefore have a dog in the race to show he’s disingenuous in his argumentation. :p

  12. 12
    DuWayne

    I strongly suspect he’s anti-atheist in that he sees “new atheists” as being dogmatic materialists.

    No, no, no. He sees most, if not all of us, as credulous, illogical, ideological materialist.

    The problem is entirely one of strawman arguments and a tenuous-at-best grasp of the scientific method.

    Now, now…Don’t be misusing the invocation of “strawman” or other logical fallacies…

    Wow, that’s really easy if you’re a ignorant, lying, hypocritical asshat.

  13. 13
    ildi

    I was intermittently following the Greg Laden comment thread; when I saw Anthony bring up the “unless you have actually been there” canard, it set off my spidey sense, since that tends to be the creationist line. I wandered to Josh’s site following links on the scientific illiteracy issue and saw that comment, which confirmed my hunch that he had a religious agenda.

    I think he is a good example of someone who is not scientifically illiterate, but seems to consciously draw a line in the sand where the scientific method must not even be applied, and magic must be the answer, and anyone who thinks otherwise is a dogmatic materialist. The interesting thing is seeing the wide variety of points at which theists draw this line, from the YEC/flood story/Biblical literalists on one end to “God created the universe and started a process that after billions of years resulted in us.” I think a good scientist can compartmentalize in this fashion (they will pick a field where it’s ok in their mind to be a methodological naturalist); I just don’t think an excellent scientist can.

  14. 14
    Jason Thibeault

    You guys might like to know that Anthony just darkened the comment thread of my post on Cosmos 2. He couldn’t look at the recent comments or scroll down just far enough to see him mentioned by name, so he just started commenting in the top thread. I have threatened him with a ban if he continues to comment about things other than Cosmos 2 there, and have pointed him here. To help him make the mental shift necessary, I will post his comments below.

    Anthony McCarthy Leveler:
    Jason, I had an e-mail saying that you believed you had found the ultimate refutation of what I’d said at Laden’s blog in part of a refutation I’d given to a creationist at Thoughts From Kansas. However, when I looked I saw that you left off the entire refutation of the creationist that came immediately before the passage you used.It reads, in context:

    Scientism is the belief that only that information produced by science is valid.


    Science is the study of physical evidence, the collection of data about physical evidence, it’s measurement, the analysis of that and the results of that analysis published, the review of that analysis of that information by others able to adequately evaluate it and it’s continually being susceptible to future challenge. It is also the contingent acceptance of that information, the necessity of assuming that information is accurate based on the review of it by competent people. It should also be the knowledge of the limits of science, which is incompetent to deal with anything except those things which can be successfully subjected to its methods. It should also be the knowledge that there are many known phenomena and ideas which can’t be subjected to those but which don’t suffer the fate of non-existence or falsification of those things due to science not being able to process them. It should also be the acknowledgement that science has bred an astonishing amount of arrogance in a large number of its practitioners and its fans that is the very essence of scientism.
    Those arrogant sci-fans are just another variety of fundamentalists.

    That said, evolution is the best available explaination of an enormous amount of evidence, there is no other phenomenon in science which has more evidential support. As I said, if you want to challenge it on the basis of science, you’ve got your work cut out for you. If you believe that God created life on Earth, through the mechanism made manifest in that evidence, that’s not an invalid idea, though you can’t insert it into science because science couldn’t deal with the idea of the divine creation of life, science couldn’t deal with the idea.

    That,Jason, is where I’m coming from, a position of actual skepticism instead of pseudo-skepticism, not pretending that belief is knowledge and not pretending that you can use religion to do science with or that science can deal with anything but physical evidence,that when scientists go beyond what is supported by physical evidence what they produce is belief, not knowledge.

    I hadn’t intended to use the sci-ranger part of the conversation in what I’m writing but I may now.What I believe had nothing to do with the argument I made at Laden’s blog except in so far as I admitted that I believed that all life on Earth had a common ancestor based on what genetic and evolutionary science had discovered.What you believe is obviously the entire thing for you and for Raging Bee (the “Pagan” materialist), Greg Laden and the rest of you.Which is very useful to understanding how the “skeptical” and sciency are pretty clueless, how they mistake ideological dogma for science.

    Jason Thibeault:
    No Anthony, you insipid little troll, the ultimate refutation of what you wrote at Greg’s is right here, three posts down from the one you decided to leave your brain droppings err “thought crime” on here. What’s at Greg’s is an explanation of why you argue how you argue. It is not a refutation of any of your arguments, it’s an explanation. Comment in THIS post about Cosmos 2, or get thee banned.

    Anthony McCarthy Leveler:
    Jason, I just figured I should point out that you lied about what I said by omitting a good part of it. I will use this too

    Jason Thibeault:
    You know I did no such thing. I said you’re a theist. Is that a lie?

    And this post is about Cosmos. I’ll say it again — you’re off topic, and I’ve even provided you with a more appropriate post to talk about your particular prejudices. Post in this post about something other than Cosmos again, and you’re banned. Second and final warning.

  15. 15
    DuWayne

    You know, I really don’t tend to get annoyed about what some random asshat has to say about me – I really don’t. I have even gotten to the point where I just don’t care what obnoxiously vile things random asshats say about groups of people, though in that case I tend to get depressed that people actually think that way. But I do get moderately irritated when people refuse to actually say what they believe (in the context of that sort of discussion) or provide evidence to support their assertions when they say shit about me (or anyone else).

    I am exceedingly amused thought, that he is going to blog about this, us and specifically you. You are so totally FUCKED!!1!1!!! Jason, you ideological materialistic fucking science ranger!!!!!111!!!1!

    (I want to know if you get a special badge or patch for being a science ranger – that might actually be kind of cool…Earthlings)

  1. 16
    Lousy Canuck » Blog Archive » Abiogenesis, chirality and narrowing down the alternatives

    [...] the great “mythmaking” that is the scientific process, discovering things about events long lost to history is done [...]

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