The Scopes Trial and Flea Medicine

Aww, cute puppies:



The original.

WHAT

[Thanks to Betty Smocovitis's talk for this gem.] Read More...

Website Maintenance with Pandoc and Markdown

I've been struggling for a long time with how to properly and simply maintain a website. The eternal dilemma seems to be this: If you want to keep the HTML simple enough to be readily editable in a text editor, you're stuck with keeping the styling really simple. On the other hand, a nice theme has lots of header and footer material, which makes it a nightmare to deal with editing a page on a regular basis. You can smooth over the problem, but only if you have some heavy server power available to use stuff like PHP or server-side includes, and since my professional website is hosted on academic web servers, I don't have any control over what's happening server-side.

I finally think I've got a solution, using Pandoc. More below the fold.


I've known about Pandoc for a while now -- I'm using it to generate the user manual materials for Logos. But it only just dawned on me that a cautious use of Pandoc could make for a great easy-maintenance website system. So I've got a website tree set up like this:

/
/research
/teaching
/source
/source/research
/source/teaching

In the source directories are a bunch of files with ".mdtext" extension, written in Pandoc's extended Markdown language (the extension of Pandoc's which I use the most is the title block, which lets you do custom page titles).

Then, at the root of the source directory, I have a bash script, which recursively does the following: (1) calls pandoc on every .mdtext file in /source/, using a different HTML header and footer depending on whether or not the page is the main index (which has a slightly different theme), (2) moves the output to the appropriate place in the directory tree, (3) runs HTML Tidy over it to sanitize Pandoc's pretty heinous HTML source, (4, and most importantly) computes the depth in the directory tree at which the .mdtext file is located, builds a string of "../../" characters, and runs sed over the HTML output, replacing $TOP with the dots.

Why are the dots so important? Well, I don't want to use any static path names in my code, since there's multiple addresses you could be using to get to my website (charlespence.net, as well as whatever current host it's on, ND at the moment). So I need to be able to do things like refer to the stylesheet in each document, using a relative path. But the header and footer for all the documents is the same. So I set the href in the link tag to "$TOPstyle.css", and then have the script turn this into "style.css" or "../style.css" or "../../style.css" as the occasion requires.

Finally, I can mount the Notre Dame web host using SFTP and Fuse, and use rsync (rsync -crLO -T /tmp --progress --delete) to copy the files from my local directory to the server mountpoint. And finally I have a website system that makes things easy to maintain!

Watch this space -- I'm planning to put up a little collection of history of biology resources, now that I'm teaching a course this summer and can easily do such a thing.
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Richard Dawkins in Oklahoma

I don't normally just re-post content, but, honestly, this is hilarious. So, Richard Dawkins is going to give a lecture in Oklahoma, and the Oklahoma Legislature decides to condemn him. The video of his response, however, is more than worth the watching. Read More...

Blogging the APA Central: Day 3

I was late getting into Chicago due to a crazy snowstorm, so I only managed to catch the last bit of a morning session on experimental philosophy and naturalism, mostly filled with a talk that was at great pains to establish the following two uncontroversial claims: (i) occasionally, philosophical naturalists speak loosely, which might lead one to believe that they thought that ID and its ilk ('God Hypotheses') were actually scientific, and (ii) if one actually does think that such God Hypotheses are scientific, then one is being self-contradictory in espousing philosophical naturalism. In point of fact, I agree with both. Of course, there hasn't yet been presented a God Hypothesis that actually is scientific, so as of yet the argument is moot.


Over lunch there was a meeting of the North American Nietzsche Society, which featured arguments for (Richard Schacht) and against (Maudemarie Clark) the claim that Nietzsche was a Lamarckian. [Note: for any historians or philosophers of biology, they don't really mean Lamarckian -- they only mean belief in the inheritance of acquired characters. Nietzsche would have been nothing less than an actual Lamarckian, as the inherent notion of progress built into Lamarck's notion of evolution would have driven Nietzsche batty.] A good exchange, one that I regard as rather inconclusive. Perhaps yet another point where Nietzsche couldn't quite make up his own mind.

The highlight of the day was the debate between Plantinga and Dennett on the relationship between science and religion. Plantinga's argument is, of course, bad, but it was presented particularly poorly (and rebutted fairly poorly as a consequence) on this occasion.

Plantinga's main points, with my editorial commentary:

1. The claims that the earth is ancient and that descent with modification are the mechanisms of the evolution of life are compatible with theistic belief. [I agree.]
2. The claim that the mutations which underly evolution are completely unplanned and unguided is incompatible with, at least, Christian theistic belief. [I'm not sure if I agree or not. I probably don't. But I don't have a horse in that race, so I'm not very concerned with this claim. At least in part, Plantinga's argument here seems to rely on the claim that a mutation-directing God is not part of an organism's environment, which seems absolutely preposterous.]
3. Further, evolutionary theory doesn't require such completely random mutations. [Indeed, in some sense. See Dennett's reply below.]
   
4. The claim that evolution undermines the argument from design, and thus the only really tenable reason for believing in God, is false, due to the work of people like Michael Behe. [Oh jeez. Yeah, he really did refer to Michael Behe. Dennett will tear this to shreds in a little while.]
5. The claim that evolution is a particularly bad case of the problem of evil isn't valid, because it's no worse an example of the problem of evil than anything else. [This is probably true.]
6. The claim that positing a theistic designer is unnecessary, in the Ockhamist sense, is false. [Plantinga's defense of this seems to hinge on the claim that there's no "further Ockamistic cost" for someone who already believes in God to posit a designer. That's true, but that's also completely evasive of the point.]
7. Even if evolution were contrary to theistic belief, theistic belief wouldn't automatically become irrational or unwarranted. [If by this he means it wouldn't become any more irrational or unwarranted than it already is, then I agree with that. Its warrant seems to have little to do with empirical fact.]
8. Conclusion of this first part of the talk: the supposed conflict between theistic religion and evolution is, in fact, a chimera.

So much for Part I. Now for Part II.

1. The probability that our cognitive faculties are reliable (i.e., that the content of most of our well-formed beliefs is true), given that naturalism and evolution are both true, is quite low. [This seems to me to be a really problematic claim, for lots of reasons. First of all, Plantinga said nothing in his talk about what the content of a belief is, how that content can be true or false, and so forth. I'll come back to this claim with the help of Dennett, below.]
2. If you accept that the probability is low, you have a defeater for every belief. [I don't see how this is true whatsoever. I accept that the probability of my own existence is low. I was born premature, and required quite a bit of medical intervention to reach adulthood. In this sense, the probability that I have reliable cognitive faculties is pretty small. I don't thereby have a defeater for my beliefs. Plantinga seems to think this follows straightforwardly.]
3. This defeater can't be defeated. [Because, I take it, any such defeat would be an argument, which would rely on other premises, which would be defeasible by the defeater already proposed. In other words, if you accept the position I'm trying to attack, you automatically become ineligible to do any philosophy in your own defense. Honestly...]
4. If you have a defeater for R, you have a defeater for every belief you have, including naturalism and evolution. [Fine, probably true.]
5. Therefore, the conjunction of naturalism and evolution is self-defeating and can't be accepted.
6. Plantinga backs up the first claim with some really hasty philosophy of mind, all reliant on the premise that adaptiveness -- in the sense in which our cognitive faculties would have had to be adaptive in order for them to evolve in our ancestors -- doesn't entail truth. [As far as I'm concerned, this claim is transparently false. If it isn't, Plantinga's going to have to give me a very careful account of beliefs, belief content, truth ascription, natural selection, and adaptiveness that makes the point. For my money, here's a good counterargument: (1) on most accounts, the content of our beliefs is fixed by repeatable, causal, physically law-based processes; (2) these processes create correlations between our mental states and the contents of the environment; (3) insofar as these correlations are established by these processes, they reflect the contents of the environment accurately. Now if Plantinga means something else by truth than accurate correlation with environmental stimuli, he'd better tell me what it is.]

Now, Dennett moves in. Three of Plantinga's premises, he says, are accurate, but not in the way Plantinga needs them to be for his argument.

1. Evolution is compatible with theistic belief. This is true, Dennett argues. Theism is one of a class of reasonably silly beliefs that are nevertheless compatible with evolution. Thus, as supporters of evolution, we have no contradiction upon which to base a rejection of theism. (After all, Dennett argues, finding actual evidence of intelligent design is really, really hard -- compare the "design" of a greyhound with the "design" of a cheetah -- and it's equally really hard to conceptualize natural selection.) On the other hand, with respect to evolution, we can see that theistic design hypotheses are entirely gratuitous. Thus, we have no real reason to accept them.
2. Evolutionary theory doesn't imply that mutations are random, in the sense of being uncaused. This point of Plantinga's is just flatly correct, despite what some very good evolutionary biologists (like Monod) thought.
3. Evolutionary theory, by itself, doesn't deny divine design.
   
   • This is true, but only in a very qualified way. Consider two different explanations of a scenario, where one describes a very plausible naturalistic hypothesis, and one ascribes a very simple divine hypothesis. There's just no reason to accept the design explanation.
4. Naturalism and Plantinga:
   
   • First, if we deny naturalism, Plantinga's doing an injustice (!) to Behe, by placing him among theologians or philosophers, and not scientists.
   • Further, Behe's work is a crock. Here's a selection of quotes from Dennett:
     
     • Behe's work is "neither serious nor quantitative"
     • It is a "transparent concoction of bad science and bad rhetoric"
     • It is "hugely disingenuous propaganda"
   • And Dennett already refuted Behe once, with the help of Haig (from Harvard) at a Notre Dame conference. He's not going to do it again.
   • No matter how hard the Discovery Institute looks for intelligent design, they aren't going to find any skyhooks.
5. Naturalism and evolution
   
   • The claim that the probability of reliable cognition given naturalism and evolution is low is simply false.
     
     • First of all, we can measure the reliability of sense organs and correct when they become unreliable. (Wear glasses much?)
     • Our brains are syntactic, not semantic engines. We clearly track truth syntactically, and such truth-tracking is adaptive. What more do you want? [Parallels my objection above.]
     • After a question by Michael Tooley, challenging Plantinga on this premise: all of the most plausible accounts of brain states have them causally correlated to the environment. Where's the problem here if there's laws of nature doing causal work for us?
6. Finally, after Murray Gell-Mann told Dennett that the Christian fish was an acronym, he pressed Dennett to come up with an acronym for his Darwin-fish pin. Dennett came up with: "Delere Auctorem Rerum Ut Universum Infinitum Noscas": Destroy the author of things in order to understand the infinite universe.

Plantinga replied and a short Q&A session followed, in which nothing really substantive took place. Among the humor was Plantinga's claim that Behe hasn't been refuted (?!!?).

And thus ended the APA. A good time was had by all.
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Blogging the APA Central: Days 1 & 2

After the first two days of this year's Central APA, I should probably jot a little note here about the proceedings.


Thursday afternoon I sat in on Michael Tooley's John Dewey Lecture, which, after a brief bit of biographical detail, wound up being on one of my favorite philosophical problems. Tooley offered the conclusions, at least, of proofs of the following two premises: (i) if we have a reductive (e.g., Humean) conception of natural law, there's good reason to think we'll never be able to justify induction, and (ii) if we have a strong (i.e., Armstrong/Tooley) conception of natural law, we get a reasonably straightforward justification of induction -- probabilities climb fairly simply with observed instances. I'm looking forward to going through these proofs in fuller mathematical detail.

After the talk, I got a chance to meet Prof. Tooley, as well as famed Spinoza scholar Edwin Curley and Iowa's Evan Fales. I also got the chance to talk with Stephanie Lewis, wife of the late David Lewis, who is both an astute philosopher (far moreso than her self-description as "amateur metaphysician" would imply), and, perhaps more importantly, an incredibly kind and genial woman whom it was a joy to chat with.

After a set of quick talks on reduction, multiple realizability, and complex systems, it was back to South Bend for the night.

Today started with a nice set of talks on causation; my personal favorite being Luke Glynn's discussion of how we might salvage orthodox theories of probabilistic causation (by accepting conditional probabilities as primitive and being careful about our synthesis of objective chance and determinism). After lunch there was an interesting session on the relationship between human freedom and brain and behavioral science, which, for me, mostly served as a primer on the current state of compatibilism, since the free will literature is somewhere I have close to zero experience.

Finally, I attended Peter van Inwagen's Presidental Address. It was mostly combinations of various arguments of Peter's that I'd heard before -- in particular, his claim that the existential quantifier is univocal due to its relationship with counting, combined with his insistence that metaphysical claims, like the truth or falsity of mereological fusions, are valid, non-trivial philosophical problems worth being solved. In this instance, he was defending himself against arguments of van Fraassen -- that many metaphysical problems turn on vagueness in language -- and Putnam -- that the way we count (i.e., whether or not to include fusions in our counts of what there is) is a convention that determines (changes) our use of the existential quantifier. A good paper, very much in van Inwagen's style.

Watch this space tomorrow evening for a report on the Dennett-Plantinga debate on science and religion!
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