How to examine the evolution of proteins »« Standing up to William Lane Craig

How not to examine the evolution of proteins

The Discovery Institute has me on a mailing list for their newsletter, Nota Bene. That’s probably unwise: usually I just glance at it, see another ignorant bit of fluff from Luskin or Nelson or one of the other usual suspects, and I snigger and hit ‘delete’, but sometimes they brag about how they’re really doing science, and I look a little closer. And then I might feel motivated to take a slap at them.

The latest issue contains an article by Ann Gauger, babbling about her recent publication disproving Darwinism, written with her colleague Douglas Axe, published in their tame ‘science’ journal, Bio-complexity, and edited by Michael Behe. It’s not work that could survive in a real journal, I’m afraid.

The work focuses on a diverse family of enzymes, the PLP-dependent transferases. These are all paralogs, or genes produced by duplication and divergence, as determined by their similar sequences. They picked two members of this family that use different substrates and catalyzed different reactions, and asked how they could possibly have evolved from each other…and they did it all wrong. The mistakes they made were fundamental, obvious, and amazingly stupid.

  • The cousin problem. You should have picked up on the key problem from my short description above: they picked two extant proteins and then asked how they could have evolved from each other. Imagine if I picked one of my many cousins — say, the tall, red-headed Mormon fellow from Oregon, or the slender fan of horses in California — and started enumerating our many differences and declared that I couldn’t possibly have evolved from either of them. You would rightly stop me and suggest that maybe my problem is that I didn’t evolve from my cousins — that maybe the smarter approach would be to look at our respective parents, and the grandparents we have in common, and trace the lines of descent.

    And you’d be right, of course. A more sensible way of looking at this problem is to start with a valid premise, and examine parental and grandparental states. Gauger and Axe don’t do that at all. They speculate about the huge number of possible intermediate states between two cousins, and decide that there are so many possibilities that the path from one to another is so improbable that it couldn’t have happened in the history of the planet. You might be able to say the same thing about me and my very different cousin, if you disregarded the fact that there actually were known intermediates.

  • The bridge hand problem. Creationists pull this one all the time. Here’s the situation: you are dealt 13 cards in a hand of bridge. What’s the probability that you’ll get the hand you’ve got? Obviously, the probability of getting a hand is 1.0, but the probability of getting any one specific arrangement of 13 cards is less than one in 635 billion. The silliness of the creationists is to point at a number like that and announce that the arrangement must have been designed. Gauger pulls this same stunt.

    …we calculate that the waiting time for a bacterial population to acquire seven specific mutations in a duplicated gene, none of which provide any functional benefit until all seven are present, is something like 1027 years. That’s a ten with 27 zeros after it. To put this in perspective, the age of the universe is believed to be on the order of 1010 years.

    If I played bridge very, very fast, dealing out one hand every minute, that means I’d still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 102 years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We’re here.

  • The talentless critic problem. Let’s pretend that the prior problems don’t exist (I know, that’s an awfully big hypothetical leap to make, but try). Let’s pretend therefore that the Gauger and Axe paper actually accomplishes what they claim: that neo-Darwinian mechanisms are inadequate to explain the origin of the family of PLP-dependent transferases. Now what? They’re here, obviously — how did they get here? They don’t say. They don’t even speculate; “intelligent design” is a phrase studiously avoided. Lord knows, their experiments and simulations aren’t even designed to reveal alternative mechanisms. This is their conclusion:

    …answers to the most interesting origins questions will probably remain elusive until the full range of explanatory alternatives is considered.

    Yeah, but…if Ann and Doug aren’t considering them in their papers, let alone putting together experiments to test them, why should I? And given that their protocols are so deeply flawed and built on faulty premises, I don’t think they’ve ruled out natural evolutionary mechanisms at all. I’ll be much more interested when they actually try to explore their unstated “explanatory alternatives” and show me a novel mechanism.

  • The much more attractive friend problem. I was surprised at one thing: usually creationists assiduously avoid the possibility of comparisons by, for instance, shutting off comments and not bothering to cite their critics, but in this case, Gauger actually links to a paper by Carroll*, Ortlund, and Thornton. It’s a terrible tactical mistake. Gauger and Axe are saying, “Ooh, we shit in a pot and we couldn’t even get mushrooms to grow in it,” and then pointing to the flourishing, hugely productive garden that Thornton has cultivated and saying, “…and they’re doing it all wrong.” It’s crazy. It just tells me my time is much better spent reading PLoS than Bio-complexity.

That other paper is so much better than the creationist paper, let’s talk about it.


*Sean Michael Carroll. No, not the physicist Sean M. Carroll who works at CalTech, and not the developmental biologist Sean B. Carroll at Madison, but another Sean Carroll at Harvard. It’s so confusing. If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

Comments

  1. says

    Sean Michael Carroll. No, not the physicist Sean M. Carroll who works at CalTech, and not the developmental biologist Sean B. Carroll at Madison, but another Sean Carroll at Harvard. It’s so confusing. If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

    Good grief – there are three?! I was confused enough when I thought there were only two.

  2. Ichthyic says

    If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

    besides, I thought the idea was to clone Steves, not Seans?

  3. Ichthyic says

    PZ; have you done a piece on how ASR works and has been used yet?

    that might be a useful primer for this paper.

  4. Dhorvath, OM says

    I really liked how you explained the bridge hand bit, that one has always bugged me.

  5. Pierce R. Butler says

    That other paper is so much better than the creationist paper, let’s talk about it.

    The link in this sentence produces an endless recursion. What are the odds of that?

  6. johncryan says

    There’s a problem with that “none of which provide any functional benefit until all seven are present”, isn’t there? Evolutionary models don’t, after all, predict mutations which do not of themselves provide some functional benefit (i.e., confer increased competitive fitness) at the time they arise will likely be selected for and conserved over generations, waiting around for additional future mutations which might suddenly make them useful.

  7. frustum says

    I think from their point of view, as dumb as it is, the bridge hand explanation doesn’t apply.

    The way they see it, a given protein isn’t just the result of contingent evolution — it is a very specific end result which was preordained by God. Therefore, they feel justified in calculating the odds of obtaining that specific hand. They have already declared that any nearby variant must be totally useless, so they are being consistent in assuming only one specific form will ever do. Consistently wrong, but consistent all the same.

  8. Kevin Anthoney says

    That’s a ten with 27 zeros after it.

    Nice of them to explain that in a supposedly scientific paper.

  9. says

    There’s a problem with that “none of which provide any functional benefit until all seven are present”, isn’t there? Evolutionary models don’t, after all, predict mutations which do not of themselves provide some functional benefit (i.e., confer increased competitive fitness) at the time they arise will likely be selected for and conserved over generations, waiting around for additional future mutations which might suddenly make them useful.

    wut.

    of course evolutionary models predict that. most mutations are entirely neutral, meaning they make no difference either way. There’s about 150 of those per person. And sometimes, these neutral mutations spread across a significant portion of the population. When that happens a lot to an isolated population, you get speciation by genetic drift, without any significant changes in how beneficial the new genome is in relation to the old one.

  10. PaulM says

    IDiots:

    …is something like 10^27 years. That’s a ten with 27 zeros after it.

    Maybe it’s nitpicky but I think they will find that the number is a ten with 26 zeros after it (just as 10^2 is a ten with one zero after it).

    Explaining what 10^27 is in a scientific paper is quite funny. But trying to explaining it and getting it wrong is just slapstick.

  11. Yoav says

    @johncryan #8
    That’s why gene duplication has such an effect. You have one copy of the gene that provide the original function to the cell while the other one can accumulate mutations without severe consequences. If one of these mutations happen to reduce the specificity of the active site so it can now bind another substrate even if inefficiently and with lower specificity you may now have a positive selective pressure that will result in a new enzyme that bind and metabolize the new substrate.
    The Tawfik lab at the Weizmann Institute are working on some of these mechanisms, you may find it interesting.

  12. says

    Their publication disproving science:

    We don’t know what we’re talking about but we use lots of scientific words, therefore science is false and magic is true.

    This is good enough for their target audience which is willing to believe any bullshit if it doesn’t make their dead Jeebus cry.

  13. k-dub says

    I’ve always suspected that the probability of getting hit by a rain drop–a specific rain drop–must be nearly incalculable; therefore, it never rains. QED.

  14. Alex, Tyrant of Skepsis says

    They speculate about the huge number of possible intermediate states between two cousins, and decide that there are so many possibilities that the path from one to another is so improbable that it couldn’t have happened in the history of the planet.

    Their schtick is literally the equivalent of walking into a maze, then contemplating how hard it is to go back outside, thus concluding that there is no way that one could have gotten there by natural causes. It’s the “too stupid to climb mount improbable – pedestrian edition”.

    It’s almost unbelievable that they still run on the same class of idiotic mistakes that Behe and Dembski have already embarrassed themselves with in their first oevres. It seems they have built a career out of abusing basic combinatorics and statistics to death in ways no-one before dared to imagine. That is a dubious claim to fame.

  15. Matthew says

    k-dub-

    Excellent metaphor! I’ll be using that liberally in place of the bridge hand (which I usually use).

    Has no one explained this error to Behe? I can’t believe how often this crap gets recycled.

  16. Alex, Tyrant of Skepsis says

    Has no one explained this error to Behe?

    You assume that his intention is to be an honest scientist. That’s not the case.
    If Behe were susceptible to reason, he would never have published such tripe. He is not interested in correcting his mistakes, for that would mean that his arguments evaporate instantly.

  17. Brad says

    That’s a ten with 27 zeros after it.

    Nice of them to explain that in a supposedly scientific paper.

    Aaand they even got that wrong. 10^27 is a one with 27 zeros after it. Or a ten with 26 zeros after it.

  18. Brad says

    Bleh. That’s what happens when you reply to a comment (Kevin Anthoney @10) without reading the subsequent comments (PaulM @12 covers the same point.)

    [Goes back to lurking]

  19. says

    This is some journal. BIO-Complexity.

    Axe has published HALF of the papers in it! Ever!
    That means, he has published 3 papers…

    I want my own journal. I could let my friend pub in it and we would all be famous(er).

    BTW, the comment from Schneider on the BIO-Complexity article fracking his evolution prog is a fun read. (but not the BIO-Complexity article; it’s unreadable)

  20. khms says

    If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

    besides, I thought the idea was to clone Steves, not Seans?

    Martins, I believe. We’ve had a software project locally a decade or two ago that was called UMS, for Universal Messaging System if I recall correctly (related to MausNet, which is where I came in; you probably can’t recognize it, but the red stuff on the right side of my avatar picture is source code I wrote for MausNet back then), but it was often called the Universal Martin System, because all developers and testers where guys named Martin something.

    And living this close to the Bielefeldverschwörung (the guy who ran the machine through which I got my first Internet access claimed to come from there … of course, he also worked for the government …) – well.

  21. says

    I got challenged by an ID enthusiast after citing this article, and I’m stumped. I downloaded the paper by Axe and Gauger… and I can’t find where they cite the paper by Carroll, Ortlund, and Thornton.

    I’ve tried a couple variations, a few searches… and I can’t find the cite PZ is talking about in the paper itself. Is it in the “Nota Bene” announcement that referred to the paper?