How not to examine the evolution of proteins

How not to examine the evolution of proteins

via The Panda's Thumb by PZ Myers on 10/20/11

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.

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^*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.