Science is hard, therefore God


I took another peek into the nonsense the Discovery Institute is currently peddling. It’s depressingly shallow, a lot of motivated reasoning and twisted use of the evidence. For instance, Kirk Durston has an article titled Could Atheism Survive the Discovery of Extraterrestrial Life?, which, as an atheist who would be thrilled to pieces if we discovered alien life of a completely independent origin, seems peculiar.

Here’s his argument, though. The origin of life on Earth is a hard problem (agreed). Current models, as he understands them, suggest that it was an event of exceedingly low probability, so low that it was extremely lucky that it happened here, but it would be extremely unlikely that it would also happen in multiple places in our universe. Therefore, logic dictates the existence of a supernatural creator. It’s simply, I don’t understand this, therefore god. It also flops inelegantly into a common creationist theme that there are only two possible models, and if I find a weakness in yours, my model is automatically correct, even if my model has even more flaws, which I conveniently ignore.

The centerpiece of these kinds of articles is usually some juicy admission from real scientists that we don’t understand every detail of the origin of life, therefore, ha ha, god exists! It’s annoying, because this is how science works, by identifying problems and working to solve them, and creationists love to pervert that methodology into some kind of admission that science is failing and wrong. They never seem to notice, either, that the only way they can steal some credibility is by quoting the scientific literature, or rather, misquoting it.

Durston provides us with a prime example of this tactic.

A 2011 article in Scientific American, “Pssst! Don’t tell the creationists, but scientists don’t have a clue how life began,” summarized our lack of progress in the lab. Of course, there are plenty of scenarios, but creative story-telling should not be confused with doing science, or making scientific discoveries. With regard to “thousands of papers” published each year in the field of evolution, as Austin Hughes wrote, “This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.”

Evolutionary biologist Eugene Koonin, meanwhile, calculates the probability of a simple replication-translation system, just one key component, to be less than 1 chance in 10^1,018 making it unlikely that life will ever spontaneously self-assemble anywhere in the universe. His proposed solution is a near-infinite number of universes, something we might call a “multiverse of the gaps.”

So three sources: Horgan, Hughes, and Koonin. Is he reporting their work accurately?

He comes closest with his interpretation of Horgan’s article. It is very pessimistic, and is describing the failings of the RNA world hypothesis.

But the “RNA-world” hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. Once RNA is synthesized, it can make new copies of itself only with a great deal of chemical coaxing from the scientist. Overbye notes that “even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.”

This is true. Does anyone believe in a pure, straight RNA world anymore? Not that I know of. The evidence is clear that RNA played a bigger catalytic role in the distant past — we can find vestiges of that role in our cells even now — but the answer is going to be more complicated than just “RNA did it”. And of course, “RNA didn’t do it” doesn’t imply that God did it.

Unfortunately, Horgan’s alternative is panspermia, which even he doesn’t believe.

Of course, panspermia theories merely push the problem of life’s origin into outer space. If life didn’t begin here, how did it begin out there? Creationists are no doubt thrilled that origin-of-life research has reached such an impasse (see for example the screed “Darwinism Refuted,” which cites my 1991 article), but they shouldn’t be. Their explanations suffer from the same flaw: What created the divine Creator? And at least scientists are making an honest effort to solve life’s mystery instead of blaming it all on God.

I also think he is too pessimistic and doesn’t seem to be aware of the breadth of origin of life research. The recent ideas from Martin and Lane about chemistry and proton gradients have been a breath of fresh air, and reveals the flaw in creationist dismissals of our current understanding — we are constantly learning new things, and what seems like an unsolvable problem now may become a trivial obstacle with further discoveries. It’s one of the virtues of not constraining your search space to the pages of a single old book.

The Hughes article gets a prize for being the most egregiously distorted of the three. For one, it’s not about problems in origin of life studies at all — it’s about poor statistical analyses and over-reliance on adaptive hypotheses. Read the abstract; does this sound like a guy who is questioning evolution?

Sequences of DNA provide documentary evidence of the evolutionary past undreamed of by pioneers such as Darwin and Wallace, but their potential as sources of evolutionary information is still far from being realized. A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection (1, 2). Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. But it would be a mistake to dismiss Yokoyama et al.’s (3) study, in this issue of PNAS, of the evolution of visual pigments in vertebrates as more of the same. For, unlike all too many recent papers in the field, this study is solidly grounded in biology.

Hughes also does not propose god as an alternative. We’ve got a better option, one that’s actually supported by the evidence.

As well as natural selection, nonselective (or “non-Darwinian”) mechanisms may play a role in the origin of adaptive phenotypes. The most important non-Darwinian process is chance fluctuation in gene frequency or genetic drift, which can lead to the fixation of selectively neutral mutations (those with no effect on fitness) or sometimes even of slightly deleterious mutations. Kimura coined the term “Dykhuizen-Hartl effect” to describe an originally neutral mutation that later becomes adaptive in a changed environment, including a changed biochemical environment resulting from other amino acid replacements in the same protein.

You know how every time I criticize evolutionary psychology for failing to understand that there’s more to evolutionary biology than just selection, I get a swarm of indignant responses that I must be a creationist? This is the same thing. Hughes is properly pointing out that other forces can drive evolutionary change and criticizing the scientists who seem unaware of that, and for that, Durston thinks he’s a creationist ally…or at least, someone whose words can be twisted to pretend he’s an ally.

What about Koonin? This one is interesting, because Koonin is a brilliant thinker and theorist, and always seems willing to take on sacred cows. His book, The Logic of Chance: The Nature and Origin of Biological Evolution, actually does have a chapter on the mathematical probability of the origin of life, and he does use that 10-1,018 number (but not for the origin of a single component: his point is the coevolution of the multiple components of the transcription and translation apparatus is a difficult problem). It is! In the book, Koonin does suggest that a Multiple Worlds hypothesis might offer an out, but I found that as unconvincing as panspermia or worse, the god did it hypothesis.

The heart of his argument, though, is the power of the Darwin-Eigen cycle. That is, in a replicating system, there is selection for better fidelity of replication, which allows increases in size and complexity by drift, which is then refined further by selection. The existence of this effect means you can get this constant escalation of complexity and information in cells by the interaction of 3 components, fitness, genome size, and replication fidelity. He’s actually making a powerful argument against another key component of creationist ideology, that you can’t get increases in information without a designer. It’s inherent in the system!

However, he also points out that before the Darwin-Eigen cycle can start chugging along, it needs to cross a threshold. You need some minimal genome size, which you could imagine coming together by chance, but you also need some minimal fidelity — if every generation is randomized, the cycle is not going to be able to get a grip — and that requires functionality that is not likely to arise by pure chance processes. Koonin has no problem as a scientist pointing out that you need a certain threshold of complexity to get the engine of selection and drift going, and recognizes that the emergence of a translation system to convert RNA sequences to protein is a crucial, and difficult breakthrough. That chapter in his book is explaining that this really is a hard problem.

But note that Koonin does not argue that the only alternative is a god — gods make no appearances in the book. Nor does he advocate giving up. Maybe there is a solution, he just hadn’t thought of one in 2011.

So, here’s a paper from 2007, “On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization” which Durston does not cite, which proposes pathways by which the breakthrough could have been made.

The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a “frozen accident” or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing.

The authors are Yuri Wolf and Eugene Koonin.

So Durston is incorrect to assume that Koonin gave up with a feeble multiverse of the gaps hypothesis. That a scientist acknowledges the difficulty of an interesting and complex problem is not a prelude to surrendering and going to church; that’s the creationist solution.

It also produced a very interesting paper.

Comments

  1. birgerjohansson says

    BTW, are there other aspects of the early life than this one that (currently) presents major explanatory problems? Since creationists are mentioning this particular problem, I assume they consider it their best bet.
    — — –
    -Nominative determinism for world-views: “Kirk” means “Church”

  2. blf says

    Since creationists are mentioning this particular problem, I assume they consider it their best bet.

    I assume that by “[cretinists’s] best bet” something like “what cretinists ‘think’ is the lying about the ToE most likely to promote the magic sky faeries did it nonsense” is meant. In which case, I ask Why?. That (rephrased) claim-about-cretinists seems to presuppose cretinists are familiar with, and understand, evolutionary disputes and puzzles. (To say nothing of the theory itself.) I am not aware of that being the case for the last hundred or so years.

  3. Owlmirror says

    PZ in the OP:

    Maybe there is a solution, he just hadn’t thought of one in 2011.
     
    So, here’s a paper from 2014, “On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization”

    Um, PZ, this is an embarrassing goof: All of the dates on that paper (Received; Accepted; Published) state 2007 (specifically, May of that year — and that’s a remarkably rapid throughput, although that may be understandable for a hypothesis paper).

    Of course, given the throughput in the publishing business, the chapter from the 2011 book may well have been written long before 2011. But who can say?

    Besides, Google scholar can be queried for a specific author (use: author:"EV Koonin"), and given a date range. I lazily clicked on “since 2013”, even though I could have manually put in 2011, and even with that limit, it looks like EV Koonin (or someone else with those initials) is astonishingly prolific in writing or co-authoring papers in biology, genetics, and related fields.

    Within the 181 hits, the following look interesting as being similar reviews/hypotheses:

      • Origin and Evolution of the Universal Genetic Code (2017)

      • Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements (2014)

    (And possibly more)

  4. slatham says

    Not that anyone should care, but I’m not a fan of selection-drift cycles as an explanation. Something similar has been proposed for speciation. (By similar, I mean there’s a key and a lock that have to evolve together, or a code and translation system.) But divergent selection was more effective than trying to fix alternative and incompatible alleles/behaviours through drift in sticklebacks, for example. And it “feels” like relying on chance effects in drift is a kind of appeal to a magic black box, even if it’s more applicable to the origin of an RNA world.
    TRends in Ecology and Evolution
    Chapter
    I haven’t read these, but at least the first one, in Box1, shows that genetic bottlenecks don’t lead to genetic incompatibilities. Oh,this is better. Here’s a more applicable one on experiments in Drosophila. I remember Howard Rundle presenting on this, which is why my references all include him:
    Evolution
    Somehow I find a greater affinity in myself for an adaptive mechanism/explanation than one that relies more heavily on chance. Is this just a secular version of determinism? Or are the studies above actually relevant?

  5. Owlmirror says

    This link [Google Scholar for author:"EV Koonin" since 2011] pulls up 271 results.

    This also looks interesting:

      • Origin of first cells at terrestrial, anoxic geothermal fields (2012)

    It’s also possible to check the papers that cite a paper, and use a date to limit results:

    [Google scholar link for papers citing Wolf and Koonin 2007, since 2011 ]

    Which also has a hit by Koonin himself:

      • Viruses and mobile elements as drivers of evolutionary transitions

    Of course, the first hit would be:

      • The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others) (HS Bernhardt, 2012)

  6. jonmoles says

    ‘It’s simply, “I don’t understand this, therefore god”.’
    It’s my belief that every argument for god is an argument from ignorance, albeit that sounds a bit reductionist.

  7. weylguy says

    The typical creationist, confronted with the fact that Planck’s constant (roughly 10^-34) is so tiny, says it’s so small that it can effectively be set to zero. That would make the universe pure Newtonian, which we know just ain’t so. Sometimes very small numbers and probabilities make all the difference in the world.

  8. Scientismist says

    The origin of life on Earth is a hard problem (agreed). Current models, as he understands them, suggest that it was an event of exceedingly low probability, so low that it was extremely lucky that it happened here, but it would be extremely unlikely that it would also happen in multiple places in our universe.

    Yep, this is a pretty old one. I first encountered it as a cause for hilarity in the book “The Self and its Brain” by Sir Karl Popper and Sir John Eccles. Each author, Popper the philosopher of science and Eccles the neurophysiologist, wrote a separate section of the book, but their common theme was that the problems of understanding evolution, especially evolution of consciousness, were so difficult that there must be some kind of pre-existent order or transcendental creative power from which it all sprang. Eccles stated it quite plainly when considering the possibility of contact with extraterrestrial life and intelligences. After explaining that the origin of life was such an unlikely event that it had happened only once on Earth (Really? He knows that for a fact?) and so must have required the help of a transcendental agency, on the very next page he chides Drake and Sagan for suggesting that it might be worthwhile to listen for extra-terrestrial radio signals as a sign of independent civilizations, a possibility which he dismisses as an idea that “can only be entertained by those who are ignorant of the extraordinary hazards of evolution.”

    Yeah, life is so rare that the infinite power of God must have been required to do it; and furthermore, it is so rare that God Himself could only have done it once. I have always been amused at this example of a scientific theory of theological limitations.

  9. Bill Buckner says

    The typical creationist, confronted with the fact that Planck’s constant (roughly 10^-34) is so tiny, says it’s so small that it can effectively be set to zero.

    I thought I had heard every bad argument imaginable. But I never heard that one. Do you have a link to a creationist making that claim? I’d be fascinated to read the rationale. Oh, and a nitpick: You must give units (or lose points)! At least say “roughly 10^-34 in SI units.”

  10. says

    @2 birgerjohansson

    -Nominative determinism for world-views: “Kirk” means “Church”

    Speaking as someone named “Abbey”: screw that.

  11. birgerjohansson says

    Abbey, moving through 180 degrees, that is nominative anti- determinism.

    Re. thirst (durst in Durston) I am not certain… he throught up the argument while plastered?
    His church is in the Arizona desert?
    There are some things man is not meant to know (but women will have no problem working it out).

    PS before the 1940s lots of evolution seemed impossible. But once the details are worked out, everyone will say “it is obvious” about this issue, too.

  12. robert79 says

    I must admit… the one thing that might shake my atheism were if an alien civilisation were discovered, and they also believed in Quetzalcoatl (insert deity of choice here…)

    So I suspect the creationist’s internal logic goes something like this (even though they may not present it so clearly…)
    1) My god exists, and is the one true god
    2) Therefor, any discovered alien civilisation will worship my one true god
    3) This presents a conundrum for atheist thought
    4) Thus, atheists are wrong
    5) and so god exists.
    6) Since god can only be the one true god, if I and a completely independant alien civilisation worship the same god, this must be the one true god.

  13. What a Maroon, living up to the 'nym says

    I agree with this sentence:

    creative story-telling should not be confused with doing science, or making scientific discoveries.

    I assume this is why the babble was never used as a textbook in any of my science classes. Or history, for that matter.

  14. says

    I don’t know about Durston, but some Christian types don’t believe there are aliens. After all the Bible doesn’t mention life elsewhere, and if there was they’d need Jesus to redeem them from sin, which couldn’t happen because reasons. So if beings claiming to be aliens showed up they’d of course be demons pretending to be aliens.

  15. rietpluim says

    The title of this post is the best summary of the creationist position I’ve ever read.

  16. latveriandiplomat says

    Personally, I would love it if we found independent abiogenesis on Mars, Europa and Enceladus, a hat trick of stomping this “gap” into the ground.

    Just because we haven’t figured out abiogenesis, doesn’t mean it’s not common under the right conditions, And if those conditions are deep sea volcanic vents,which Earth, Mars, Europa, and Enceladus have or had in the past. And in a few decades, we might have evidence for exactly that.

  17. birgerjohansson says

    Re @ 14
    Should be “lots of aspects of evolution seemed impossible”.

    The point being, the problems get solved If you wait a while.
    As for the extra- terrestrials, they will be our distant descendants.
    Because, Fermi Paradox.

  18. birgerjohansson says

    Re@ 16
    I de not find the bible that creative.
    An anthology of fanfic to the old testament.
    JRR Tolkien is far superior.

  19. consciousness razor says

    latveriandiplomat:

    Personally, I would love it if we found independent abiogenesis on Mars, Europa and Enceladus, a hat trick of stomping this “gap” into the ground.

    I doubt that would change anything. Some people would think they’ve got evidence for gods, whether the whole universe is teeming with life, it’s extremely rare, or anything in between.

    – Oh, life got started only once on this single planet? Wow, look how rare and special it is. Must have involved some kind of miracle. Thus, goddidit.
    – Life is ubiquitous? Wow, look how the whole universe seems devoted to producing it, as if that’s what somebody wanted it to be like. Thus, goddidit.

    Try to imagine what it would be like to have both of those views. But don’t try too hard … might hurt yourself.

  20. mnb0 says

    @12: “I thought I had heard every bad argument imaginable.
    I think I can beat it. A few weeks ago I had the following exchange on a Dutch creacrap site (Logos.nl):

    Creacrapper: “Evolution Theory does not yield testable predictions.”
    MNb: “Make sure dogs remain isolated from grey wolves for another 10 000 years and they will have become a separate species.”
    Creacrapper: “Evolution is NOT about speciation! It’s about adding information!”

    If you can read Dutch I’ll look up the link.

  21. says

    “I don’t understand lightning, therefore Thor” has already demonstrated that this mode of “reasoning” tends to be unfruitful.

    As a note: “I don’t understand this, therefore X” seems to be how a lot of conspiracy “theories” work.

  22. says

    sez latveriandiplomat @19: “Personally, I would love it if we found independent abiogenesis on Mars, Europa and Enceladus, a hat trick of stomping this “gap” into the ground.”
    Sadly, consciousness razor @22 has the right of it: Creationists’ position is not based on evidence. Rather, their position is based on their unshakable Faith that ‘somehow, somewhere, somewhen, Evolution is wrong’. Whatever evidence is discovered, Creationists will view that evidence through the filter of that Faith… and they’ll ignore that evidence until such time as somebody comes up with a line of reasoning which begins with that evidence and ends with “—therefore, Evolution is wrong”.

  23. KG says

    Horgan is the postmodernist numpty who declared, some time in the mid-nineties in Scientific American, that fundamental physics was no longer science because it was no longer making significant empirical advances. That was before the discovery of the accelerating expansion of the universe, the Higgs boson and gravitational waves, to name but three.

  24. Rob Grigjanis says

    KG @26: I think Horgan’s point was about theory, not observation. The existence of gravitational waves was not in serious doubt for decades before LIGO detected them. The Higgs discovery gave a mass to plug into equations which had been around for decades. No paradigm shifts in either case. As for accelerating expansion*, with or without it the theoretical basis is still the Friedmann equations.

    Still, Horgan is/was full of shit, because the thing about paradigm shifts is that they have a way of sneaking up on you. LHC and space telescopes may yet have surprises in store. They may not, but to claim that they won’t is just dangerously stupid for a science writer.

    *which may be only at the 3 sigma level.

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