To be intellectually uncomfortable

From one of Uncertain Principles' link dumps comes this piece from Inside Higher Ed: Tolerant Faculty, Intolerant Students. Apparently, despite the myth of the politically stubborn professor forcing his views on poor openminded students, the truth is more like students haranguing each other and professors doing fairly well at not inappropriately expressing political views. (Well, at least in Georgia. The study might have turned out differently if done on CRAZY CALIFORNIAN COLLEGES!!!!1!11!one.)

(I should note that I have only been in actual political discourse once all year, and it was with a student on my hall who fervently supported Ron Paul. Perfectly friendly, civil discussion; I didn't enjoy it because I don't enjoy political discourse, period. I haven't seen any politics in classes, probably because I haven't taken any classes where it's even marginally relevant. Coulomb's Law? Politicize that, bitches.)

The thing that really struck me about this article, though, was one particular quote: universities are a place to go to feel uncomfortable intellectually. Obviously, the article means this with regard to one's political beliefs -- but it's applicable in a much larger sense.

When I encounter something I can't understand, something really confusing, I get anxious and upset. This happens a lot because I'm at a difficult school, and it's to be expected that I will encounter confusing things. But why should I get upset? This is an artifact of tying understanding to Success and Achievement (TM), rather than understanding for its own sake. Even though I went to one of those hippie elementary schools where there are no grades, I suppose I still have kind of a hang-up about 'succeeding' versus being way outside of my comfort zone.

I really admire people who respond to confusing things by first feeling humble, and then feeling happy that they have another puzzle to solve. People who get suspicious if it looks like they understand everything. It's not that I think such people never get frustrated, but that seems like a highly useful mindset for a scientist or intellectual, much more so than getting upset and frustrated. (Certainly, given the complexity of the real world, if you think you understand everything about X, you're almost certainly wrong.) This mindset should also make for a happier person overall. Apart from that, it feels like the right thing to do -- it appeals to the idealist in me.

Universities are a place to go to feel uncomfortable intellectually.

The world is a place to go to feel uncomfortable intellectually!

I'm going to try and embrace this mindset, embrace this mantra. A form of "intellectual asceticism, perhaps?" Hopefully I can change my knee-jerk reaction to the difficult and the confusing.

Perverse, Ugly, Terrible Beauty

Neurophilosophy writes about amyloid plaques and Alzheimer's, showcasing this really interesting 3D rendering of the plaque's constituent protein fibrils -- larger picture with the original article at Discover. The article and the post are really informative and you should go read them because I'm not going to address their content. (Gasp!)

My first reaction on seeing the image was, "How strangely beautiful". Even though this is a picture of a prime suspect in an absolutely horrific disease. Even though it's got a rather menacing fire-and-brimstone color scheme. Even though I shudder at the idea of these nasty little fibrils snaking their way through my brain, withering neurons like the Goo of Death from Princess Mononoke.

It's well established that good, hardworking, well-oiled biology is a joy to behold (if you have the right mindset). Listen to PZ Myers rhapsodize about the time he got a close-up look inside his hand. Read Dr. Sidney Schwab's eulogies to the body unmarred, and to the regal liver and warm, welcoming intestine. You've all seen The Inner Life of the Cell; watch it again and marvel.

It's also pretty well established that diseased, shattered, out-of-control biology is ugly, ugly, ugly. Hear Dr. Schwab, again, on how injuries and cancer ravage and ruin the anatomy that was so lovely. And who hasn't shuddered (inwardly) at the sight of scabs and puckered scars?

But somehow, I find there's a genuine (albeit perverse, ugly, terrible) beauty to diseases and such evil things. In the same way that it's interesting to watch flames blacken and consume a sheet of paper, it's interesting to imagine a cancer burning its way through a tissue. There's an elegance to the way viruses hijack and pervert cells to their own nefarious ends. And so on. I'm not saying that I think diseases are a good thing, or anything that causes pain/death is "nice" or "pretty"; far from it. But can't you see the grace, the sweeping lines, the eye-drawing colors, of those evil amyloid fibrils?


(Having thus far skirted the edge of hell, with these paragraphs I commit my soul to the inferno.)

I'm quite the Douglas Hofstadter fan, and I'm right in the middle of rereading his book Le Ton beau de Marot: In Praise of the Music of Language. In the introduction, Hofstadter dedicates the book to his wife, Carol, who was "hit from out of left field by a strange and eerie malady with the disgusting name of glioblastoma multiforme... vanishing from our midst almost as suddenly as if she had in fact been hit by a bus, with so much of life still left in her... all cut short by some cell gone wrong." Le Ton beau de Marot is in large part a commitment of their shared soul to paper. The book is stimulating, beautiful, and moving; I cried when I read of her death and his grief. I don't mean to minimize any of that. But I have to disagree with Hofstadter on one point. I don't think the name glioblastoma multiforme is "disgusting". "Strange and eerie", yes, and awful and dreadful (in the sense of inspiring awe and dread). But not disgusting. There's even some euphony, some beauty in the sound of the term.

Of course, I say this as someone who has never lost a close and treasured friend or family member to cancer (and I'm very grateful for that!); I certainly don't blame Hofstadter for describing as "disgusting" a name associated with so much pain and grief. His reaction is completely natural; in fact there would probably be something wrong with him if he didn't react that way. You could as well say that I am incapable of tasting all the bitterness as that Hofstadter is incapable of seeing any of the beauty. Nothing wrong with that.

Gallery of nudibranchs!

Check this out: National Geographic nudibranch photo gallery. It's absolutely amazing.

I've seen a couple of nudibranchs underwater, scuba diving in Hawaii. It's neat to see them live and in context, but it being underwater, it's kind of dim and the colors are washed out. Seeing them in optimal photography conditions like this is really cool.

[h/t Pharyngula]

Grad students declared "security threats" by govt

You have got to be kidding me.

This article, Government Declares Some Grad Students Are ‘Security Threats’, appeared in today's issue of The Tech (MIT's student newspaper). A number of international students working with the Woods Hole Oceanographic Institute are being denied easy access to the ports they sail from because the government considers them, for no reason at all, "security threats".

To get in and out of the ports, you need this RFID card, the "Transportation Worker Identification Credential". Without the TWIC, it's very difficult (though not impossible) to get in and out. Difficult-but-not-impossible is a totally unreasonable restriction to impose on these researchers. It's hard enough not having key-card access to the building that contains the lab you're interning in -- *raises hand* -- and even though it's reasonable to expect a bit more difficulty when you're doing fieldwork, it's not Antarctica these students are requesting easy access to, it's a port. And, I might add, these students are only asking for the same access that their labmates and PIs already enjoy.

As the Dept. of Homeland Security wrote to one student (others received similar letters), “I have personally reviewed the Initial Determination of Threat Assessment, your reply, accompanying information, and all other information and materials available to the TSA. Based upon this review, I have determined that you pose a security threat and you do not meet the eligibility requirements to hold a Transportation Worker Identification Credential (TWIC).” This is what we say to students who come here to carry out government-funded research? We give them grant money and then call them "security threats"?

Two of the students being denied access are from Britain and Germany. Britain and Germany. I thought we were supposed to be all buddy-buddy with these countries? If this is what students from friggin' Britain and Germany have to deal with, how much worst must it be for students from, say, Syria?

My friend Raffi, who's from Canada, mentioned how the Office of International Students is always warning them about how "if you do this you'll get deported. If you do that you'll get deported." Apparently the definition of "security threat" bears this out: you're a security threat if you threaten national or transportation security, if you pose a threat of terrorism, if you have "lacking mental capacity"... or if you simply have the wrong kind of visa.

I'm ashamed to live in a country that funds scientists and then treats them this way.

[Crossposted to LiveJournal]

My Erdős number is 5

Back in high school, when we got around to it (about once a year) the Neighborhood would publish an issue of the Menlo Math Magazine. It was sort of a random collection of real-world-relatedness, whimsy, and interesting problems. Not an academic publication by any standard. But that didn't stop us all from facetiously claiming an Erdős number of 6, when we heard that Mr. T's was 5.

I just found out that mine is actually 5, and this time it's damn near official, not tenuously based on a high school pamphlet. Over the summer of 2005 I worked on the Stanford ALL project. Mostly as unpaid labor, admittedly, but I did sit in on the meetings and I did point us to a couple of valuable data sources. This meant I got to interact with some big names, however briefly.

According to Language Log, the lowest Erdős number known for a linguist is 2, and Geoff Pullum's is 3. A quick Google Scholaring shows that Arnold Zwicky and Thomas Wasow, therefore, have Erdős numbers not greater than 4. And they were both involved in the ALL project, as was I, which makes my Erdős number not greater than 5.

...All right, none of us are actually authors of the paper in question. I appear in the acknowledgement footer on the first page, along with the other students involved in the project. But Zwicky and Wasow appear in the same footer, as does John Rickford (who doesn't have any papers coauthored with Pullum, at least on Google Scholar). (Well, OK, all those big names appear in the references, which I don't.) Their contributions to the project were certainly substantive enough to qualify criteria for what counts as `collaboration'. My contributions were far less substantive, but I still think they counted for something, and if I appear in the same acknowledgements (the same parenthesis in the acknowledgements, even), that's got to be worth something.

(Naturally, this all comes with the caveat that we've been counting non-strictly-mathematical publications, but that has plenty of precedent.)

It makes a fella proud to be a scientist

Pharyngula linked to this amazing video that "compares creationism and science". Really, it's no comparison. [3:54]



You could watch it without the music -- none of the strictly visual beauty would be lost -- but instead, I highly recommend turning your speakers up to eleven, putting the video on fullscreen, and inviting all your officemates to come watch. Better yet, invade a conference room or a lecture hall for five minutes. It'll be worth it.

I found it incredibly affecting. Some parts had me cheering and yelling "SCIENCE: IT WORKS, BITCHES!". And some had me tearing up. I felt like a little kid again, all "when I grow up I wanna be a scientist!" I'm damn proud to be a part of it (or at least to be on track to become part of it).

Black vs. white backgrounds (also, chalk)

(No, this post is not about race).
The other night, I and my friend 4pq1injbok were discussing the compelling, overarching, enormously important issue of black text on white ground vs. white text on black ground. (Woo, having spare time!)

Of course, each option is appropriate in different contexts. If you're printing something out, you better have a good reason to do it in white on black, because that wastes so much ink/toner. But for viewing on screens (including projection screens), I vastly prefer black on white because it reduces glare and seems to make my eyes less tired. Mostly the former. Glare is a problem especially on very large projection screens: you can dazzle (in a bad way) an entire lecture class with a white-backgrounded Powerpoint, especially if the projector is having an off day. Not fun early in the morning.
What troubles me, then, is that there seems to be some kind of unspoken rule in academia that you can't use black backgrounds, and I'm not entirely sure why. I watched a dry run of a job talk a couple summers ago, and in the midst of everybody commenting on every facet of every slide, my mentor explained to me that there's just a certain way scientific presentations are done, which includes black text on white ground. The Google example is telling, in one sense -- Google is renowned for the "clean" look of its pages, which I'm sure has a lot to do with being white-backgrounded. Perhaps there's a lot of pressure from older academics who are more comfortable with print on paper. Perhaps, also, it makes pictures easier to see, but you can fix that with a relatively narrow white border. I think we should take a hint from the movie industry; when was the last time you saw the end credits in black on white?

(Also, using black backgrounds probably saves energy -- I don't know any numbers, but the savings must be considerable for large screens. There's even Blackle, an almost entirely black version of the Google homepage. Supposedly if everyone used it, we'd save ~750 MWh a year (hat tip for the calculation to ecoIron).)

Chalkboards are the only common medium I could think of where the default is light text on dark ground. (Not to say there aren't others; it's just that I couldn't think of them.) Nothing profound about it; chalkboards are this way because CaCO3 is white, and slate is dark gray. But it does raise an interesting question. Suppose you draw two circles on the board, and fill one in with chalk while leaving the other one empty. Which is black, and which is white? Do most people just seem to naturally agree, or is there some kind of consistent convention, or is there no consistency at all?
In my music theory class, and anywhere I've seen musical notation on a chalkboard, the convention is that quarter notes are filled/white while half and whole notes are empty/black. In print, it's the other way around, at least with regard to absolute colors. But in this case, you can define it in terms of filling, not color, so it's a bad example. I'm rather tempted to crash a game theory class on the day they discuss chess/checkers, or some kind of visual arts/design class on the day they discuss positive vs. negative space, or take a poll of professors, or some such.
Related linguistic issue: on the Improbable Research blog, a prof rants about the suckiness of Crayola's new chalk, complaining that "the new pieces are thinner, shorter, and don't write as dark", using "dark" to denote degree of whiteness. But "don't write as well" lacks specificity, and "don't write as lightly" would be interpreted the wrong way around. Sounds like "heavily" (or perhaps "cleanly") might be the way to go.

And finally (and randomly): hooray for profs who know how to use colored chalk well, to highlight information and obscure noise, without overusing it. More on this subject if I ever get around to reading Tufte's books.

Ping!...Pong!...

Many, many thanks to Coturnix, of A Blog Around The Clock, for linking here!

I realize this happened several days ago. I plead guilty of falling out of the habit of checking my Technorati page because nothing ever happened on it.

And, I may as well take this opportunity to apologize for the recent lack of activity. Homework is no excuse; there are lots of people out there who are busier than MIT undergrads (though you'd have a hard time getting some of my friends to agree to that)