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Surgical Management of Ulcerative Colitis

08 July 2008 in geekery, medicine, surgery | No comments

I’m supposed to be giving a 10-minute talk on the surgical management of ulcerative colitis this Thursday at teaching conference, so (as always) I’m posting my presentation online in case anyone else can use it. For all statistics, I’ve included references in the primary literature when possible and references to Sabiston otherwise (the footnotes are clickable hyperlinks). You can navigate through the presentation using the arrow keys, or you can mouse over the lower right-hand corner of the slides and some controls should pop up. If you’re so inclined, pressing “t” will toggle between presentation mode and my scanty speaking notes.

This is also my first attempt at using Eric Meyer’s S5 presentation format with John Manoogian’s Glossdeck theme, and they’ve been really great so far! S5 uses a nice mix of JavaScript, XHTML, and CSS to make simple, standards-compliant presentations that can play in any modern browser. Though I haven’t experienced this yet, I’m told that the images won’t scale well at resolutions other than 1024×768. I have to say that it’s really nice to be able to write a presentation in a text editor rather than something intensely visual like PowerPoint or Keynote. Like writing LaTeX markup instead of word processing, it lets me focus on content rather than style. It’s also nice to use when I’m trying to work in little snippets throughout the day, using whatever workstation I happen to be near. As a side note, I’d originally planned to test out Google Presentations, but the site was down for a while this afternoon and the thought of a server failure during the conference almost made me pee my pants.

Update, 10 Jul 2008: This talk was well-received by a group of surgeons renowned for their merciless pimping, so you may get some mileage out of it. The meta-analysis referenced on the DALM slide was particularly good fodder for discussion.

Med Schools Should Support Free Software

07 July 2008 in geekery, medical education, public schools, undergraduate education | No comments

Font Variations with LaTeX

I’ve always been a little unsure why medical schools (and schools in general) don’t make more extensive use of free or open-source software (that’s free as in speech, not free as in beer). It seems like a win-win situation to me: schools don’t have to pay for huge installations of expensive software, and professors and students can keep their data in open document formats that will not become obsolete. The PDFs, PostScript files, and plain text files I wrote in the mid-1980s are still easy to open and work with - can you say the same for all those old WordPerfect files? After putting so much effort into creating decent lecture notes and presentations, professors shouldn’t have their hard work suddenly rendered incompatible with the latest tools. This issue is particularly important for medical schools and hospitals, where increasingly large quantities of patient information are being stored in proprietary formats accessible only through closed-source programs. Vanderbilt, for example, uses an electronic medical record system that only functions well in Internet Explorer. Thus, every workstation in the hospital must run Windows (which undoubtedly costs the medical center thousands of dollars a year), and the systems administrators must upgrade operating systems and reprogram the EMR according to Microsoft’s release schedule. This approach lacks foresight - while the information itself is (I hope) actually stored in an open-format database, access to that information depends on a notoriously unstable and insecure operating system and browser.

And beyond these practical issues, there’s also a compelling moral and philosophical argument to be made. Schools should be institutions that encourage curiosity, innovation, and the free exchange of knowledge - all ideals that run directly against the spirit of proprietary software. Proprietary software is locked down with copyrights and patents, preventing students and professors from reading or modifying its source code. Free software, on the other hand, generally comes with an invitation to re-use, modify, or improve the code to benefit the community. By using free software, even schools and students who are uninterested in programming can express their support for freedom of thought.

Now, I’m not suggesting that every school and medical center immediately switch to Linux and ditch all proprietary software (though that would be an excellent goal). Instead, there are some easy and painless substitutions anyone can make.

  1. Switch the default browser from Internet Explorer to Firefox.
  2. Install OpenOffice rather than Microsoft Office, and encourage faculty and students to make the same switch on their personal computers.
  3. Install GIMP rather than Photoshop. Or install GIMP rather than nothing, which seems to be the current standard (who in their right mind uses PowerPoint to edit images?).

For the more adventurous (or the more tech-savvy):

  1. Use LaTeX for document preparation. Your documents will be better-structured and more beautiful (the image in this post is an example of the gorgeous output LaTeX is capable of).
  2. Use S5 rather than PowerPoint or Apple’s Keynote.
  3. Use Debian GNU/Linux for the ultimate in stable, free computing bliss.

Mapping Human Cognition, Validating Free Journals

05 July 2008 in geekery, medicine, neurology | No comments

For the first time in quite a while, a scientific paper is getting lots of ink just for being cool - and it’s not attempting to debunk medical dogma, attacking cherished religious beliefs, or drumming up any scandal at all. As far as I can tell, everyone just thinks it’s really interesting. The authors of the paper, published in PLoS Biology, used functional and structural MRI to construct a map of connections between areas of human cortex. If you’re like me, this sounds pretty humdrum; after all, didn’t we already know most of this? The gory details of the authors’ methods and findings are so stupendously dry that it’s actually pretty difficult to tell what the big fuss is about (and before anyone says anything, I did eventually read the whole paper…with some difficulty). But the important thing to realize is that the authors aren’t just saying, “Look, these two areas are both involved in recognizing faces. They must be part of the face-recognition-sensation-memory-integration circuit! Nifty, eh?” Instead, they’ve actually mapped structural connections between functional areas of cortex. Now they can say, “Look, we know that areas A and B are both involved in recognizing faces; that’s not news. We’ve taken this a big step further and shown that A and B are physically connected via C, D, E, and F in the following circuits: blahdey-blahdey-blah. In fact, we’ve shown that the ABCDEF network is probably the brain’s central integrating network and we’ve mapped all its most important connections.” This type of map should permit the kind of mathematical modelling that’s common in computer science and AI applications.

I’m geeky enough to think that this is really sweet. But it’s great that the New York Times agrees - it’s rare that a paper with so few immediate practical applications and so little attached scandal gets much ink. Granted, the NYT Science section is not exactly the cover of USA Today, but this paper even made Metafilter’s top posts of the day. Oddly enough, though, the NYT article didn’t touch on the authors’ decision to publish in PLoS Biology rather than a more traditional, big-name journal (like one of the Nature group’s journals). PLoS is open-access and publishes everything under the Creative Commons Attribution License, which basically means that readers can do whatever they want with the work as long as they credit the original authors. This is quite unusual in scientific publishing, where the usual model is to charge ludicrously high fees for read-only access. This article’s publication also comes on the heels of Nature’s criticism of PLoS’s publication model and the flurry of discussion it prompted online. As a strong supporter of open science and free (as in speech, not as in beer) journals, I think it’s great that the authors chose to publish in a manner that supports perpetual, free access to research funded with public monies.