I'm sure it is a very complicated process that determines how scientists know when to quit a particular theory. Theories don't die easily because scientists often have a lot invested in them. As Quine-Duhem showed (a fun example) it's not a simple matter to falsify a theory. As they suggest, it's easy to contrive adjuncts to the existing theory to prolong its life. However, at some point the contrivances become so mountainous that something happens. Scientists become disenchanted with it. One has to wonder if this is beginning to happening with the Darwinian theory of evolution.

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It's been fashionable to ignore and mock Steve Fuller (or, at least, his arguments) but rarely have I seen any good commentary that actually examines the content of his arguments (Judge Jones, in his Dover decision, briefly mentioned Fuller's argument but didn't engage it at all). I've written about Fuller's argument for teaching ID in schools before, but I'm going to repeat it here for a couple of reasons. First, it has virtually been ignored despite the dearth of arguments against it (and if somebody knows of an argument against it, I'd love to know about it). Second, people have been talking about Fuller recently, due to his post at Crooked Timber. Third, a little controversy never hurt anybody.

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Ed Brayton is commenting on Baylor's controversial decision to deny tenure to Francis Beckwith, who has published extensively on philosophy and law. Brayton believes that the decision was due to the internal politics at Baylor, and criticizes the "inevitable conspiracy theories and blame mongering from the ID crowd", whom he's sure will claim that the decision was based on Beckwith's acceptance of intelligent design defense of the constitutionality of teaching ID. However, so far the only one raising "conspiracy theories" is his fellow critic, PZ Myers, who says that yes, intelligent design was a factor in the decision:

[A]lthough it is nearly impossible to speculate on what's going on in tenure committees - he could have been denied tenure on the whim of some old fart with a grudge - it's hard to imagine that the politics of Intelligent Design did not play some small part in it. Beckwith tied his fortunes to those of the Discovery Institute and the ID movement, and at the very least we can say that that was not enough to salvage his tenure at Baylor. In fact, given that he has a respectable publication record and seems to be a personable fellow, it's hard to avoid the speculation that they might have wanted to steer Baylor away from the disaster of Intelligent Design. A solid record of publishing large quantities of something that is being shown to be utter crap is not helpful to one's tenure chances.

Some people have defended Baylor's decision by claiming that Beckwith lacked collegiality, but as Brayton points out:

I think the reason they gave for that denial - lack of collegiality - is patently absurd. You would be hard pressed to find a nicer, more engaging person. We have had many disagreements over the last few years, including times when I have been harshly critical of his work, and he has never failed to reply with civility and collegiality even to someone he had no reason to view as a colleague. The alleged basis for this claim is a ruse, but not an unexpected one - you certainly can't expect them to deny him tenure and blame it on internal political struggles, can you?

Southern Appeal is critizicing Baylor, as is First Things. Meanwhile, Kathy Hutchins suggests that just like the slaves in the movie Spartacus, all academics should stand up, saying "I am Francis Beckwith".

Francis Beckwith has studied philosophy and law, and has written books and articles about the constitutionality of abortion and the teaching of intelligent design. Despite what Rod Dreher calls "a stellar publication record", Baylor University has decided to deny him tenure. Beckwith is also a contributor to the conservative blog Right Reason, where his fellow blogger Maxwell Goss is on it. I've been unable to find any statement from Baylor, so Right Reason is probably the best place to look for updates.

Update: "Graduate Student X", who's at Baylor, writes about this in The American Spectator.

For my 200th blog, I offer something different. Periodically, there are people in cyberspace who have a complaint about something they think I said. More often than not, such complaints are rooted in stereotype or taking things out of context. For example, recently someone complained that I became upset anytime an atheist spoke up to offer an opinion. Yet when I asked the person to document this complaint, he could not find any examples.

So if you have a complaint about me or about something I have written on this blog, my web page, or on an internet forum, here is the chance to publicly air those complaints. Maybe your complaints are valid. If so, it will become apparent to most readers. As such, I can either apologize or dig myself deeper into the hole. On the other hand, maybe your complaints are rooted in misunderstanding. In that case, it would be helpful for me to explain the nature of this misunderstanding.

Have a complaint? Welcome to the MikeGene Complaints Dept. How can I help you?

Death and contingency in the game of life

Penny D. & Phillips M.J., "The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?", Trends in Ecology and Evolution 19(10):516-22 (2004) [PDF]

The picture of mammals hiding in caves and crevices until a meteor wiped out the dinosaurs and allowed our furry ancestors to populate the planet has long been the consensus, both in popular science books and in the halls of academia. But in this article David Penny and Mathew J. Phillips, two evolutionary biologists from the Massey University in New Zealand, warn against conflating different questions. In particular, they say, the proposition that a large meteor struck the planet about 65 million years ago is distinct from the proposition that it was this event that led to the extinction of dinosaurs. As Penny and Phillips note, "there is widespread querying among the geological and paleontological communities of any 'sudden and unexpected' demise of dinosaurs at the K/T boundary."

This is particularly relevant when reviewing Stephen Jay Gould's argument for contingency in evolution, in which he claimed that re-running the tape of life would result in a wildly different biota. One of the examples he used was the extinction of the dinosaurs and the rise of mammals. Mammals weren't any fitter than dinosaurs and wouldn't have prevailed, had it not been because a meteor crashed into Earth and shook things up. But, as Penny and Phillips point out, "[t]here is as large body of earlier work about the potential competitive advantages of mammals and/or birds over earlier reptilian groups", based on such traits as lactation, specialized teeth, brain size, and endothermy. In short, "[o]nly if we disregard mammalian and avian physiology could we maintain that there were no potential of mammals over, for example, the smallest dinosaurs."

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From Evolution News & Views I've just heard that the Lancaster School District in southern California has adopted a "Science Philosophy" policy. The policy, which has been supported by the groups Integrity in Academics and Quality Science Education for All, states that "[e]volution … should be taught as theory, as opposed to unalterable fact", and encourages to "[d]iscussions that question the theory … as long as they do not stray from the current criteria of scientific fact, hypothesis and theory." For links to the policy and the groups that supported it, go to Evolution News & Views.

I have long made it clear that I don't support teaching intelligent design in school, and although this policy doesn't mention intelligent design, I still think that it's a bad idea. First of all, it is regrettable that the policy is being pushed by public activist groups, instead of by the scientific community. The people backing it will probably reply that the policy should be judged on its own merits instead of by its supporters, and that discussion-based learning does improve the education of the Californian students. It's certainly correct that a policy should be judged on its own merits, and since I'm not any kind of expert on education, I will, for the sake of argument, also concede the second point. Assuming this, allow me to explain why I still think that the Californian policy will damage intelligent design in the long run.

It is a fact that many ID critics are scared of the ID movement and are trying to convince the scientific community to share this fear. It was only the other day that we saw Texan biologist Sahotra Sarkar telling an audience about the ID movement's desire to turn America into a theocracy, and back when Hector Avalos was trying to discredit ID-friendly astronomer Guillermo Gonzalez, he was citing concerns about Gonzalez being a sort of undercover agent, placed in Iowa State University by the ID movement.

Obviously the policy in California isn't going to result in a theocracy, but many in the ID critic community will interpret it as yet another sign of how dangerous the ID movement is. And when talking to scientists, asking them to sign petitions or to be "vigilant" about opposing those undercover ID supporters, they can point to this case as supporting their paranoia.

It doesn't take a genius to see that such an environment isn't going to foster an objective, open-minded exploration of intelligent design. So, if you think there's something to that intelligent design stuff and would like to see it studied, take the battle out of the classrooms.

The existence of evil is a popular argument against design. Take the Type III secretory system (TTSS), which is embedded as a subsystem within the bacterial flagellum. Since the TTSS is associated with some nasty infectious diseases, some might scoff that the design of the TTSS means the designer is a malevolent being. Perhaps. But as I have argued before, the TTSS is best viewed not a pathogenic device, but as a device that elicits symbiosis. In fact, the distinction between mutualism and parasitism (with or without the TTSS) can be more fuzzy than many appreciate.

A recent study drives this basic point home clearly. There is a filamentous fungus that exists in a beneficial symbiotic relationship with a grass. What does a take to turn this nice relationship into a pathogenic relationship? A mutation in one gene.

I was checking out the anti-ID blog, The Panda's Thumb, when I found this post, "What We're up Against". An elementary school teacher in Colorado has been suspended for showing her students a video featuring sock puppets performing the opera Faust. Apparently, it's a running feud that started between the teacher and a group of parents that started when she banned Christmas songs from the school's winter concert, and the parents reciprocated by complaining about the Faust video. Of course, there's absolutely no evidence that concerns about intelligent design were involved, but the author of the post comes up with some way to link the two together.

However, the best part is the first comment to the post, from "k.e.":

Time to get the Bhurkas out, the theocratic Christo-Taliban regime is here, next they will be banning kite flying and music in hair salons.

If anyone needs me, I'll be in my bomb shelter, organizing the ammunition and preparing for the Coming Theocracy.

Once you label me, you negate me. - Soren Kierkegaard

This post by Nick Matzke on Panda's Thumb made me laugh (moreso than usual). This sentence, in particular, seemed odd:

All of this is worth pointing out because the ID Movement at large has been complaining that methodological naturalism is an unfair constraint on science, and in particular critics of the decision in Kitzmiller v. Dover, such as Alvin Plantinga and Steve Fuller, have been asserting that methodological naturalism is an arbitrary, recently invented constraint - Fuller has even gone so far as to say it was constructed as an anti-creationism tool in the 1980's.

What I found odd wasn't the sentence itself, but the first link in the sentence. While talking about the "ID movement at large" he linked to a number of articles and blog posts that criticized the concept of "methodological naturalism" (MN) in some way or another. There's nothing too strange in this, except that the first link was to this blog post by Hugo Holbling. It would be pretty difficult to call Hugo (who has written an excellent introductory series to philosophy, BTW) a member of the "ID movement at large." I've never seen him write anything that criticizes evolutionary theory, I've never seen him write that he accepts the basic ideas of ID, he has criticized ID, and he has flat out denied being a part of the ID movement.

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