How not to examine the evolution of proteins

Posted 20 October 2011 by PZ Myers

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.

19 Comments

DS · 20 October 2011

It's so cute when creationists try to ape the behavior of real scientists. Like "publishing" real "papers" in real "peer-reviewed" "journals". Don't they know that once it's out there the difference between this and real science will be glaringly obvious. Man, who was the reviewer for this crap? He must not know anything about ... what? OH. Never mind.

And if they can't even be bothered to suggest an alternative in their own journal, it's no wonder no one takes them seriously. They don't even take themselves seriously.

harold · 20 October 2011

DS said: It's so cute when creationists try to ape the behavior of real scientists. Like "publishing" real "papers" in real "peer-reviewed" "journals". Don't they know that once it's out there the difference between this and real science will be glaringly obvious. Man, who was the reviewer for this crap? He must not know anything about ... what? OH. Never mind. And if they can't even be bothered to suggest an alternative in their own journal, it's no wonder no one takes them seriously. They don't even take themselves seriously.

I also notice that a great deal of their imitation "science" can be viewed as a variation on the old "a tornado doesn't create a 747 in a junkyard therefore no evolution" meme. Here, at the very core of it, that's what we've got. Create a straw man version of "what would have to happen" for certain proteins to evolve from ancestors. Then argue that it's "too improbable" for "it all to happen at once (or within a reasonable period of time)". The related fallacy is to calculate the probability of a particular outcome when the probability of any outcome should be calculated. "It's impossible that anyone won the lottery by natural means, because prior to the draw, the odds were ten million to one against winning". People like Ann Gauger and Doug Axe, who have strong mainstream science training, are incredible. I can think of three possible explanations for them - and they're all weird. 1) So blinded by self-serving bias and psychological issues that they can't see their own errors. Typically, this blinding is somewhat imperfect, so that there is cognitive dissonance, a negative emotional response to mainstream science, and an obsessive need to contradict and deny mainstream science. This is probably the explanation for most creationist behavior. 2) Extremely specific learning disability with regard to abstract concepts related to probability, but otherwise high functioning (*this one wouldn't explain why they set up a straw man problem to begin with - it would only explain the analysis of the problem - but I'll include it - conceivably this might be an enabling feature*). 3) Hyper-specialized con men who prefer the moderately easier and moderately better paid life as a "DI Fellow" to the life of an academic or industry scientist; willing to lie in this specific area but able to restrain themselves from openly illegal financial fraud or other more dangerous temptations. It's my purely subjective inclination to suspect that some such people exist; of course, this can never be documented unless they themselves come clean. A Straussian justification that "the common people can't handle the truth" might be an enabling mechanism.

https://www.google.com/accounts/o8/id?id=AItOawkDp_xo0moKWxtwldHdblYB7LXvm8qaRoo · 20 October 2011

The argument presented by Axe and; Gauger in their paper is isomorphic to the classical "crocoduck" creationist argument.

Do they think no one will recognize it?

Matt G · 20 October 2011

Especially funny is how they feel the need to explain that 10^27 is "10 with 27 [sic] zeros after it." Thanks, we're not children (although perhaps that is your intended audience...).

https://www.google.com/accounts/o8/id?id=AItOawkDp_xo0moKWxtwldHdblYB7LXvm8qaRoo · 20 October 2011

A question for management:

Why hass the comment software started to give me the name "A Masked Panda (aRoo)"? This has never been my name under any account used to sign on to PT, or anywhere else for that matter.

==Olorin

Scott F · 20 October 2011

"Science". You're doing it wrong.

Mike Elzinga · 21 October 2011

*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.

Sheesh; not even the decency to be Steves.

TomS · 21 October 2011

Matt G said: Especially funny is how they feel the need to explain that 10^27 is "10 with 27 [sic] zeros after it." Thanks, we're not children (although perhaps that is your intended audience...).

I assume that your "[sic]" is meant to refer to the fact that "10 with 27 zeros after it" is 10^28?

Kevin B · 21 October 2011

Mike Elzinga said:
*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.
Sheesh; not even the decency to be Steves.

Ah, but they're part of a separate group. Project Steve demonstrates that there are more scientists named Steve signed up in support of evolution than there are people signed up on the DI's dissenters list. The Sean Carroll Collective are pointing up the fact that the number of scientists named Sean Carroll publishing in peer-reviewed journals is larger than the total number of Intelligent Design researchers doing likewise.

Karen S. · 21 October 2011

Why hass the comment software started to give me the name “A Masked Panda (aRoo)”?

Maybe they think you're part beagle?

Matt G · 21 October 2011

TomS said:
Matt G said: Especially funny is how they feel the need to explain that 10^27 is "10 with 27 [sic] zeros after it." Thanks, we're not children (although perhaps that is your intended audience...).
I assume that your "[sic]" is meant to refer to the fact that "10 with 27 zeros after it" is 10^28?

Yep. The least of the paper's problems, of course. And anyways, what's an order of magnitude between friends?

https://www.google.com/accounts/o8/id?id=AItOawkDp_xo0moKWxtwldHdblYB7LXvm8qaRoo · 21 October 2011

Maybe they think you're part beagle?

How did you know that I am a retired legal beagle? (patents, copyrights, trademarks)

https://www.google.com/accounts/o8/id?id=AItOawkDp_xo0moKWxtwldHdblYB7LXvm8qaRoo · 21 October 2011

And anyways, what’s an order of magnitude between friends?

Would you like designer fries with that order?

Sean McCorkle · 21 October 2011

Matt G said: Especially funny is how they feel the need to explain that 10^27 is "10 with 27 [sic] zeros after it." Thanks, we're not children (although perhaps that is your intended audience...).

(To paraphrase Scott F above) Math. Ur doin it wrong.

386sx · 21 October 2011

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

Well, that's supposed to be their job. So the paper stops just short of doing their jobs. Intelligent Design is an Intelligent Design stopper as well as a science stopper. Lol, hilarious.

386sx · 21 October 2011

Intelligent Design. That's an "I" followed by approximately 17 or 20 or so letters or something.

Gary_Hurd · 22 October 2011

I think a recent article in Science is germane; "Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments" Qiucen Zhang, Guillaume Lambert, David Liao, Hyunsung Kim, Kristelle Robin, Chih-kuan Tung, Nader Pourmand, Robert H. Austin, Science 23 September 2011: Vol. 333 no. 6050 pp. 1764-1767

“It is surprising that four apparently functional SNPs should fix in a population within 10 hours of exposure to antibiotic in our experiment. A detailed understanding of the order in which the SNPs occur is essential, but it is unlikely that the four SNPs emerged simultaneously; in all likelihood they are sequential (21–23). The device and data we have described here offer a template for exploring the rates at which antibiotic resistance arises in the complex fitness landscapes that prevail in the mammalian body. Furthermore, our study provides a framework for exploring rapid evolution in other contexts such as cancer (24).”

To review: Multi-site mutations, functional mutations, TEN HOURS, why sequential mutations are functional, and more likely than simultaneous ones (although 4 in ten hours is pretty quick), and with medical applications.

https://me.yahoo.com/a/kYQj4.Y6hsNHh2hA4cxjQS4Dobc-#0cdad · 25 October 2011

harold said: 1) So blinded by self-serving bias and psychological issues that they can't see their own errors. Typically, this blinding is somewhat imperfect, so that there is cognitive dissonance, a negative emotional response to mainstream science, and an obsessive need to contradict and deny mainstream science. This is probably the explanation for most creationist behavior. 2) Extremely specific learning disability with regard to abstract concepts related to probability, but otherwise high functioning (*this one wouldn't explain why they set up a straw man problem to begin with - it would only explain the analysis of the problem - but I'll include it - conceivably this might be an enabling feature*). 3) Hyper-specialized con men who prefer the moderately easier and moderately better paid life as a "DI Fellow" to the life of an academic or industry scientist; willing to lie in this specific area but able to restrain themselves from openly illegal financial fraud or other more dangerous temptations. It's my purely subjective inclination to suspect that some such people exist; of course, this can never be documented unless they themselves come clean. A Straussian justification that "the common people can't handle the truth" might be an enabling mechanism.

I think its mostly 1. The fundamentalist christian meme tells them that people who aren't "born again" are blinded to the truth of the Bible by Satan, and its not possible to discern the truth unless you view the world biblically. Thus they can tell themselves that they are doing "real science"; correcting for the satanic influences on their observations by incorporating a biblical worldview.

Flint · 28 October 2011

Gauger and Axe KNOW, instinctively and intuitively, that evolution could not have produced these proteins. So it would be implausible to expect them to stumble on the most likely evolutionary pathways, out of all conceivable pathways. To do so would require a model under which evolution happens. I don't see that they're making stupid mistakes here, at least not so directly. Think of someone who lost his keys. Where does he look for them? If he ALSO lost his memory, his search space is suddenly impossibly large.

Theory informs research. Myers is actually complaining here that the research Gauger and Axe are doing, uninformed as it is by evolutionary theory, is therefore full of fundamental mistakes. But there is only one "mistake" that I can see - failure to stand on the shoulders of giants.