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.

The art of linking

For some reason I find it really irritating when I'm reading a blog post on some interesting topic, and every third word is a link. Especially when some of them are duplicates* or semi-duplicates (e.g. linking to Foo and also to the blog post that brought Foo to your attention, or to several other people's commentaries on Foo and on each other's commentaries!).

I am generally in favor of Wikipedia-style linkage as a means of optionally explaining terms that may need explaining. Nice and inline. They don't interrupt the flow unless the reader needs them to. (This is less generally true of blog links. On Wikipedia, you know any blue link will take you to a factual description of X. A blog link could point to anything, and you can't always tell from the URL.) Surgeonsblog is very good at this, with links to informative pages that explain various jargon terms.

An alternative strategy is to write easier and harder versions of your post, and let the audience choose -- but I've only seen this well implemented once, in Tailsteak's retelling of a poignant D&D story. Since the story is about D&D, the options to offer the audience are fairly clear: "Never heard of it", "Some familiarity", and "Know it like the back of my hand". Whereas people's understanding of some complicated science thing may not divide itself so neatly into levels**. And it only gets worse if you're discussing two or more topics interweavedly. What are you supposed to do then, write a separate blog post for each permutation?
(You'll notice, by the way, that the main difference between the three versions of Tailsteak's story is that the "Never heard of D&D" variant begins with a paragraph describing RPGs in general; the bodies of the three versions are basically identical. A simple link to Wikipedia might have sufficed, but I rather like the three-versions trick.)

* Some kinds of link-duplicating are good. Mind Hacks is in the habit of duplicating all the links in a post into a little pile at the bottom of the post. This can also be a subtle way to suggest reading the links in a certain order, possibly a different order from how they were presented in the post proper.

** I have another post brewing about being stuck between the level of popular-science writing and the level of professional scientists.

======================

I strive to clarify what all my links are, in the text of the post.

Good: I recently read Lewis Thomas' essay Autonomy, which I thought was a really interesting take on the way our bodies operate independently of conscious control.
Bad: Here is a link to a really interesting essay I read, about the way our bodies operate independently of conscious control.

Notice also the use of Google-friendly link text -- helping Google index things properly. Googling things like "here", "this", "this page", etc. is an interesting exercise.

======================

Here's a more coherent listing of the irritating links from the beginning of this post. They're a selection of random interesting things I've run across in the past week or so.

• "Human Guinea Pig" feature on Slate magazine: a Slate writer puts herself in interesting situations for fun and profit. I enjoyed the day in the life of a daycare staffer.


• A brilliant and creepy New Yorker article about itching, starring a woman who involuntarily scratched right through her skull.


• Three lights in the sky for the price of one: fireworks, comet, thunderstorm. Amazing photograpy.


• PDF of Chapter 1 of In Defense of Food, Michael Pollan's new book.


• A collection of in-jokes in (mostly) computer books, which has inspired me to look up "self-reference" in the index of any sufficiently geeky book I come across for the rest of my life.


• Kurt Vonnegut writes on writing style, with advice that certainly gives me a lot to think about.

Sign of the times

I finished my last final exam today (woo!!!), so now instead of staying up late studying, I get to stay up late sorting through all my junk and packing some of it in boxes with copious amounts of duct tape -- aka 'packing'. I'm moving to a new dorm on the other side of campus next year, and I'm heading back home to California on Saturday, so I have to hurry up and get all my stuff boxed and hauled across campus before then.

Just now, I was making safety sheaths for a set of cooking knives I bought and never used (because they're mediocre quality, and I just used my pocket knife for everything anyway). Take several sheets of paper, wrap around, duct tape, fold the end over, duct tape again, et voila. It works surprisingly well. For day-to-day storage, these sheaths work fine as is; for longer-term storage, duct tape the knife handles to the sheaths so they don't slip out.

Clearly, though, it is a sign of the times, of the era of online publishing, that I used printouts of PNAS papers to do this. It's the rare, rare paper that I'll print out to read, what with PDFs and having an institutional subscription to everything. Anymore, the only papers I print are ones that I need to read and reread in quite a bit of detail -- say, if I've got to write an essay that addresses the content of that paper specifically. (Intro Psych, I'm looking at you!)

Yes, kids, science saves lives! It keeps you safe! Were it not for science, how would I keep myself from being slashed up by kitchen knives??

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]

[Buddhism|Hinduism|Catholicism|*ism] is the new black

Cosmo: "Choosing a religion is like choosing a MySpace wallpaper"

...WTF?

In what sense can religion meaningfully be chosen? Ideally, everyone discovers what they believe when they look at the world around them and come to an incontrovertible conclusion. Of course this is not going to happen. Conclusions change, and it's impossible to be 100% sure of anything, given the fallibility of human minds. And for a lot of people it's going to be too much work to really figure out what they think, rather than just hopping onto the nearest appealing ready-made philosophy.

[...Ok, I'll bite. I am a hard agnostic: I believe that the nature of deity is both unknown and unknowable. (I used to be a soft agnostic -- wasn't sure whether nature of deity was knowable or unknowable). I believe in questioning but remembering the limits of our understanding, and retaining a sense of wonder.]

I'm honestly not sure what to think of this article (other than the obvious "oh, look, more dreck from Cosmo").

I loathe the aspect that promotes religiosity for appearances' sake. If you're going to take "a shot of Catholicism, a sprinkle of Buddhism, a pinch of Hindu teachings — or whatever else you're in the mood for that day", why even bother? All you're doing is quote-mining to justify what you already (want to) believe. Practicing confirmation bias. Enough of that: just believe what you believe, and stop gilding it.

I'm all for the aspect that promotes having your own worldview, instead of blindly accepting whatever some robed old guys with books say, or whatever your parents said. Anything that promotes seeking and questioning is a good idea.

In the same vein, I'm all for anything that diminishes the absolute blind fanaticism with which a lot of people follow their religions. Even if you simply accept a pre-made worldview, there's nothing that says you need to accept it to the extent that you need to go kill people or spread malicious lies and hatred because of it. But I hate to like the Cosmo article simply for this reason. There is something wrong with the world if Cosmo's viewpoint is the lesser of two evils.

Trivia-heap syndrome

Part of the reason I think a lot of hard scientists look down on biology is that introductory biology is so often poorly taught in a particular way. Intro physics is almost entirely problem-solving, and intro chemistry is similar, with maybe a bit more memorization (Quick! How many valence electrons does aluminum have?). But biology frequently ends up being taught as a large heap of random terms and facts, almost entirely without any unifying themes or methods of thought -- just a disconnected jumble.

I've dubbed this "trivia-heap syndrome".

Any biologist (or, hell, anyone who's gotten past the required intro course) can tell you that biology is not about memorizing terms and facts, any more than physics is about blocks sliding down inclined planes. But as Chad Orzel says in that post: "To some degree, this is inescapable-- those repeated exercises are used to establish a pattern of thought that is a necessary prerequisite for moving on to more interesting material." A similar thing could be said of biology: to some degree, it's necessary to memorize a lot of terms and random facts and unconnected processes and so on, before you can get to the interesting work of studying how they interact and how they can be manipulated.

But this is actually true of every field, not just biology (or other fields prone to trivia-heap syndrome); it's just not as apparent. Consider intro mechanics again: all about things falling, hitting each other, rotating, etc etc. In order to do interesting things, you first have to know what balls, rods, strings, pulleys, blocks, inclined planes, and gravity are. You also have to understand the basic types of things they can do: move, rotate, accelerate, come into contact, break, exert forces on each other. Of course these are trivial things to know, because we've all been exposed to simple objects and their motions since we were born -- and this is why intro mechanics courses don't begin with a couple weeks of definitions and memorization. The only difference between that and biology is that we're not exposed from birth to genes and proteins and cells and their interactions. The world teaches us the trivia-heap for physics, but we have to be taught about biology's trivia-heap.

All right, so the trivia-heap is an unavoidable evil whenever you're starting in a new field. Fine. But never fear, there are still ways to get around trivia-heap syndrome. As soon as you know a very few things, you can start thinking about them in terms of experiments to be done and puzzles to be solved, instead of facts and descriptions. What would happen if this particular thing were mutated in this way? What effect would that have on the cell? How could you (the experimenter) tell that this was in fact the case? What if you got the opposite observation -- what might have gone wrong? Here's a simple system you're interested in; outline an experiment to find out whether this particular part of it works this way or that way. This is both interesting and a lot more like what actual biologists do; certainly much more so than the typical dreck of "Define a gene", "Outline how a gene gets translated to protein" that most high-schoolers get shoved down their throats. That's lazy teaching for you (or the creeping horror of bad standardized curricula for things like AP tests, which reduces to the same thing).

I learned a decent bit of biology just by reading random things. I can practically recite The Cartoon Guide to Genetics, by Gonick & Wheelis (that link is to the updated edition, not the old-school edition I read). I also took an introductory class at one of those academic summer camps. The net result was that I came into my high school biology class already knowing about half the stuff we would cover, which just made the trivia-heap syndrome that much more painful. A lot of my classmates struggled with memorizing things. Very few people did well on the "lab practical", in which we had to plan and carry out experiments to identify a mystery substance -- precisely because we spent so much time on trivia-heaping and so little time on problem solving / sensible experiment design. MIT's intro biology course (7.013), by contrast, is like a breath of fresh air. It's not entirely free of trivia-heap syndrome, but there's a gigantic emphasis on solving puzzles, considering what-ifs, proposing experiments, and interpreting results. (`Gigantic' emphasis relative to other intro biologies, of course.)

Granted, even MIT's intro biology problem-solving is simplistic, and occasionally feels like doing an inclined-plane problem in physics (especially when I know a decent bit about a particular system, and I can tell the problem vastly oversimplifies the situation, even if I don't know exactly how). But now we're back to Chad Orzel, inclined planes, and "establishing patterns of thought". There is a certain intuition of biological ways and means, of how cells/genes/proteins work in broad strokes, that is immensely valuable but hard to obtain. This intuition is something like a toolkit of abstractions over specific examples, but I'd venture to say it's not something that can be taught explicitly in the abstract, the way math can. The analogous thing in physics, again, is something the world teaches us from birth: unsupported objects fall, if you push something its speed changes; that sort of general idea about how things operate. I've developed my biological intuition somewhat, through reading and studying (and sometimes working directly with) boatloads of examples, and I think that's just about the only way it can be developed. But it's something every experimenter (or bioengineer!) needs in spades, and it's something the general public could also really use.

So, to sum up: the trivia-heap is sometimes a necessary evil, but trivia-heap syndrome is eminently avoidable. Emphasize puzzle-solving and experiments, instead of facts and definitions, and it'll do everyone a heap of good.