New Look & Feel!

So I changed the blog template.

The main thing that bothered me about the old template was that the main text column, the most important part, was of fixed width. Which is annoying if you have a wide monitor. With this new template, go ahead and change the width of your browser window, and the Dendritic Arbor will change right along with you. We strive to provide a customizable reader experience. We strive to be adaptable, plastic, and dynamic, like actual dendritic arbors.

(It also bothered me that approximately 80,000,000,000 other people are using the old template. Then again, this is Blogger, what was I expecting, hmm?)

I chose this particular theme via the complex and deliberate heuristic of seeing which one looked the most like the one Larry Moran picked for Sandwalk. I've been reading his series on protein structure and admiring Sandwalk's look-and-feel. I guess this is the exact same theme as Sandwalk has, just with different colors.

By the way, the protein structure series is excellent and here are links to all its items. There isn't really a 'best' order to read them in, but I've put them in an order that sort of makes sense.

Evolution and Variation in Folded Proteins
Levels of Protein Structure
The Alpha Helix
Beta Strands and Beta Sheets
Loops and Turns
Examples of Protein Structure

EVOLVE: Eyes

I just watched the History Channel's program on the evolution of eyes. Overall it was pretty meh, but there were a couple of interesting parts.
ETA: I didn't liveblog it or take notes, so there are things I forgot. Memory is fallible. I'm human.

My favorite was in the first segment -- the experiments on the jellyfish in the tank. The researchers got a jellyfish with primitive eyespots and shone different colors of light into its tank to see how it reacted. Green light made it "relax", stop swimming, and sink to the bottom of the tank. Purple light made it start swimming really fast, and for some reason it shortened up its tentacles by a factor of 2 or 3. How do they do that? And why do they do that? Is it for speed (shorter tentacles = more drag)?

I was interrupted by a phone call and missed most of the segment on trilobite eyes. My brother, who was watching, informs me that trilobite eyes are made of calcite. Huh.

The segment on the tapetum lucidum (shiny layer in the back of some nocturnal predators' eyes that makes them look all glowy and creepy) was quite good, relative to the other sections. Not so much with the ferocious dinosaur predation or the "T3H STRUGGLE FOR SURVIVAL ZOMGZ", lots of nice creepy glowy-eyed panther shots.

Dragonflies apparently have tens of thousands of lenses in their compound eyes, and have a visual "processing speed" (define please??) ~5x that of humans. Badass.

There was a weirdly long segment of dinosaur obsession. Whenever I see this kind of sensationalism it makes me sad, but I suppose it's only to be expected anymore. The epic, ceaseless struggle for survival! Eat or be eaten! And I imagine, sometime when this episode was being planned, some editor was all "we gotta have dinosaurs in all our nature programs!". Far too much time spent on dinosaurs in a program about eyes. They should have cut this by 90% and spliced in some material on cephalopod eyes, or the design flaws in the human eye, or more than perfunctory detail on intermediate stages between "patch of light-sensitive cells" and "fully evolved eyeball". All of which were either mentioned briefly or omitted altogether.

The other thing that really bothered me about this program was some of the things they felt necessary to explain: Humans are mammals. Vertebrates include reptiles, mammals, and birds. How can kids past kindergarten not know this stuff?

Also -- ok, I would really have liked to see a mention of how wildly different species use a lot of the same genes to control development, and how this interacts with (convergent) (eye) evolution, but this is a ridiculous thing to hope for, given the level of the program. Why are they showing kids-level programming at 10 pm?

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.

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.