Uh-oh…poor science alert!

There is considerable interest in a recent paper in PNAS that purports to have found some rather substantial homologies in the proteins that make up the bacterial flagellum. That would be extremely interesting if it were true, but it looks like there are massive methodological problems in the work. Matzke has put up a preliminary criticism; the gang at PT are working on a much more detailed analysis, and if half of what I’m hearing about the paper is true … well, it’s going to be rather thoroughly sunk.

If you are arguing against ID’s favorite example, the flagellum, do not use the data in this paper. It’s about to go kablooieee. Sorry, everyone, but that self-correcting stuff is the way science is supposed to work (and letting error-filled papers make it to press is not supposed to happen, but it does all too often anyway.)

Nick has posted more info — it’s still not the complete argument, but the problem in the author’s interpretation is rather stark.

Once more unto the frame

You’re bored with it? I’m bored with it. All bored now. But since the discussion is still going on everywhere, and I’m frothing rabid (as everyone knows) and always ready to snarl and bite even when (especially when?) I’m beset with ennui, I’ll call your attention to Greg Laden again. He’s pointing out that Nesbit/Mooney have poorly framed — I swear, I never want to use that word ever again — their argument for the evolution-creation conflict, which might explain why they are being so poorly received by some of us who are focused on that ugly mess. That, and the fact that parts of their report read like a pious Discovery Institute press release, which sets our jangled immune systems on fire like a bee sting triggering anaphylactic shock, and no one’s slinging any epinephrine our way.

It looks like they talking about approaches more like we find in Kennith Miller’s “Finding Darwin’s God: A scientist’s search for common ground between god and evolution.” This needs to be clarified, and if this is in fact what they are talking about, then there is something very important that they don’t get, and they need to be flogged, then ignored. If, on the other hand, they are just kind of talking vaguely about this issue and are not explicitly arguing for a god/science chimeric view, then they should be very eager to be educated on this and then to move on with framing but using a very different approach.

We can’t use an approach that brings god into the evolution picture. This is not because of atheism (though that position would make this same argument). It is because it is a) bad science; b) a wedge for bringing various forms of creationism into the classroom and c) illegal.

OK, Greg has put up some very specific issues and questions that fans of the f-word should deal with it. Please do.

Now, since I’ve bored myself again, but since I did mention “rabid” and “flogging”, I’ll recommend that everyone read this article. It’s much more entertaining, even if the thought of 103 literally rabid Christian fanatics gives me the heebie-jeebies. It’s alright if you’d rather talk about that than the f-word, too.

Crud. Laden has added a link to an interview with Nisbet. How would you f-word the idea that the earth goes around the sun for Copernicus? He gives an answer I guess I should have expected.

Lab web pages, anyone?

Pimm is looking for examples of good laboratory homepages — he has links to a few, but is looking for more.

There is actually a conundrum there: most labs don’t want to reveal work in progress on the web (except to a limited extent), they aren’t particularly interested in public PR (something it would be good to change), and they are mostly populated with students and post-docs with a limited tenure and a specific brief that does not include webmastering. Most of the lab web pages I’ve seen out there are simple portals to a cv and maybe a few publication pdfs.

Nisbet and Mooney in the WaPo: snake oil for the snake oil salesmen

Nisbet and Mooney do it again, with an op-ed in the Washington Post … and I’m afraid they’ve alienated me yet further. I am convinced now that theirs is not an approach that I could find useful, even if I could puzzle out some useable strategy from it. In the very first sentence, they claim that Richard Dawkins gives “creationist adversaries a boost” — it’s the tired old argument that we must pander to religious belief. This is their rationale:

Leave aside for a moment the validity of Dawkins’s arguments against religion. The fact remains: The public cannot be expected to differentiate between his advocacy of evolution and his atheism. More than 80 percent of Americans believe in God, after all, and many fear that teaching evolution in our schools could undermine the belief system they consider the foundation of morality (and perhaps even civilization itself). Dawkins not only reinforces and validates such fears — baseless though they may be — but lends them an exclamation point.

We agree with Dawkins on evolution and admire his books, so we don’t enjoy singling him out. But he stands as a particularly stark example of scientists’ failure to explain hot-button issues, such as global warming and evolution, to a wary public.

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Stone soup; or, extracting protein fragments from T. rex bones

Science magazine has an article today on extracting and sequencing proteins from T. rex bones, and I’m already getting email from people wondering whether this is believable, whether it challenges the stated age of dinosaurs, whether this means we can soon reconstruct dinosaurs from preserved genetic information, and even a few creationists claiming this is proof of a young earth. Short answers: it looks like meticulous and entirely credible work to me, these fossil bones are really 68 million years old, and it represents a special case with limits to how far it can be expanded, so scratch “reassemble dinosaur from fragments” off your to-do list.

[Read more…]

George W Bush wins an award!

He should be so proud — he has taken first place in the 2007 Jefferson Muzzle Awards. These are awards given for “egregious or ridiculous affronts to free expression in the previous year”, and little Georgie won it for:

For its unprecedented efforts of discouraging, changing, and sometimes censoring the reports and studies of government scientists in order to make them more supportive of political policies, a 2007 Jefferson Muzzle goes to… the Bush Administration.

It’s a well deserved honor. The description goes on to list several specific instances of Bush administration manipulation of scientific assessment, particularly in areas of climate and environment where scientific conclusions conflict with Republican bidness ties.

Turning science into a party

Lucky Cambridge: a whole bunch of organizations, including Harvard, MIT, and the Cambridge public schools and libraries are collaborating to put on the Cambridge Science Festival—9 days of science activities around the town. That is exactly the kind of broadly supported activity in the service of science education that can make a difference in public perception. It’s an excellent idea…now if only more communities had that kind of concentration of scientific organizations to make that kind of sustained activity possible.

(via Science Made Cool)

Believing and understanding

Larry Moran criticizes a dramatic Youtube video that purports to show how evolution works. He asks if we think this helps or hurts the cause of evolution education. Speaking as an evo-devo guy (forgive me, Larry), I’d also say it hurts. Without understanding the mechanisms of morphological change underlying the simulation, it’s useless. It doesn’t explain anything about the roots of the variation it’s demonstrating or the principles of the propagation of genetic change through a population — funny faces shift generation after generation, with no explanation given. It asserts change without showing how. That is not science.

This is also where I have problems with the Nisbet/Mooney thesis. I presume this kind of simplified, cartoony presentation is what they think we need more of, and that scientists ought to just swallow their pride arrogance and go along with the “framing”…but there’s a point where simplification and flash become the antithesis of good science. I don’t want people to believe in evolution, I want them to understand it.

Would the cartoon help them believe? Maybe.

Does it help them understand? No.

If you want to grasp the goals of scientists (and, tellingly, the goals of atheists), you have to understand that distinction between believing and understanding.