Wednesday, July 30, 2008


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?

Tuesday, July 22, 2008


Here's how I make good passwords:

Pick a short keyword that's easy to type -- say, 'left'. Replace some letters with numbers (l3ft) and, for good measure, capitalize some stuff (l3Ft). Now, every time you need to make a password for something, take the name of the thing and stick your keyword on to it somewhere: l3Ftgmail.

This part is fairly well-known (although, still, not enough people use it!!!). What's fun is to make like a linguist and treat your keyword as a real affix. You can affix it anywhere to the name of whatever you need a password for, not just at the beginning or end (prefix or suffix). You can also infix it (gl3Ftmail or gmail3Ftl), or circumfix it (l3gmailFt).

This method doesn't completely specify your password. Sometimes you need to use an acronym for the service instead of the full name (su, or supon, for StumbleUpon), to keep the password from being too long. And sometimes I can't remember whether my YouTube password uses yt, ytube, or youtube. But it doesn't matter, because there are only a few possibilities I need to guess. What's more, this makes it easy to change passwords and still remember them fairly easily -- just move your keyword from prefix to suffix to circumfix to infix...

Sunday, July 20, 2008

Forest-path connectivity

There's a decent-sized blob of public forested space right behind my house. It's crisscrossed with unpaved bike trails -- and a good thing too, because it's difficult to walk through the forest off the trail without getting caught in dense coyote-scrub bushes or masses of poison oak. There's a little pond. From several points you can get a lovely panoramic view of the San Francisco Bay and/or the rest of the forest. All in all, it's quite the concentration of nature for someplace in the middle of a suburb.

One of my mini-projects for the summer is to learn my way around the forest trails. There are maps posted at the trailheads, but I'm challenging myself to use them as little as possible and to figure out the connectivity by myself, for two reasons. One, I'm too lazy to bother making myself a copy. Two, there are a number of "unofficial" trails that are perfectly walkable but aren't on the map. (I suppose the unofficial trails get made when people start riding their bikes down deer tracks or dry creek beds.) So I get to combine physical exercise, nature, and mental exercise. Three for the price of one!

Another point of interest: the forest is in a valley, so it's hard to find a piece of land that isn't steeply sloped (especially once you get away from the surrounding houses). Also, for some reason, the soil is such that trees fall over a lot, but often survive. So the whole place is full of trees with interesting geometries. There are horizontal trees. There are trees that form arches over creek beds -- they don't just sort of bend toward the creek, they actually start growing downward once they get to the other side, so you could almost climb up onto them from either end. Today, I saw a tree that, I kid you not, made four ninety-degree turns, each a foot or two apart.

Timprov, a friend of mine who's a pretty good photographer, is coming over tomorrow and we're going to poke around the woods and take photos of stuff. Should be fun.

Thursday, July 17, 2008

It was the Summer of the Library Books. San Mateo County glowed red...

[The title is an allusion to the pseudo-medieval text on the cover of one of the Redwall books: "It was the Summer of the Late Rose. Mossflower Country shimmered...]

"A red sun rises. Ash has been spilled this night." -- all right, that was worse. I couldn't resist making another allusion, though. All the wildfires in Northern California have been sending so much smoke into the air that, many days, the sky has been silvered over and the sun has turned red long before setting. (I don't remember exactly how long before setting, but the sun's been red while still five or more diameters above the horizon.) It's actually a beautiful sight, for all it's a symptom of fire and destruction elsewhere, and for all the smoke is causing trouble for people with asthma (especially in cities closer to the actual fires).

Other than that, though, mostly the weather has been fantastic. There have only been two days so far that I'd call "uncomfortably hot". Take that, friends back in Boston. It doesn't even matter that my house doesn't have air conditioning! I don't need it!

For the first time in four years, I'm not doing any kind of science research internship thing over the summer. This is mostly because I was too lazy to get myself a lab job, although it's lovely to have all this spare time. And since I have almost nothing but spare time, I've been lavishing attention on my book heap. I've taken an inordinate amount of books out of the library, bought a few from Barnes & Noble, and pulled several out of my family's rather large collection. I even have time to reread books! What a luxury.

(Because I've started to get a little tired of just reading, I'm also teaching myself Scheme in fixnum days.)

Here are some lists of books, with comments. I may write up more details on some of the sciency ones.
(Lists are not in any kind of order, and are not exhaustive (I'll probably remember more and add them later).)

  • The Hobbit, JRR Tolkien. This is a lot more fun than I remember it being when I read it as a kid. Tolkien's prose style is maybe a little difficult for kids -- but this time around I kept wanting to grab a bunch of random kids and read aloud the fun parts, really perform them. On a totally unrelated note, it's also fun to reread The Hobbit after knowing Lord of the Rings; Tolkien is constantly hinting at things. For example, it makes so much more sense that the Necromancer could cause Mirkwood to be nasty and gross if you know that the Necromancer is actually Sauron. And, there are the Dwarves charging into battle yelling "Moria!".

  • This is Your Brain on Music, Daniel J. Levitin. This one had me itching to make funny waveforms to screw around with my auditory perception, and to listen to the pieces of music he mentions with a totally different ear. Unfortunately, I was stuck on an airplane. Quite a ride. I took note of several small things Levitin said about his approach to his area of research, and am planning to write them up.

  • When You Catch an Adjective, Kill It: The Parts of Speech For Better And/Or Worse. Ben Yagoda. This one's good for dipping into because each of the chapters (Adjective, Adverb, Article, Conjunction, Interjection, Noun, Preposition, Pronoun, Verb) is relatively short and stands alone. Yagoda writes as a serious linguist, but not a dry one: he clearly enjoys language for its own sake, as any geek ought to. This is not a writing-advice or prescriptivist book (although it does contain some tidbits of writing advice).

  • How To Dunk a Donut: The Science of Everyday Life, Len Fisher. This is an interesting popular-science book. Rather than describing one small area for the public, Fisher describes applying a "scientific" approach to random topics like "Why do cookies crumble when you dunk them in milk?". I'm somewhat wary, because some of his projects seem to have been solicited by companies who want publicity for their cookies or whatever. Similarly, some of the "scientificness" of his approach seems to consist of wrapping things in numbers and graphs. A very laudable goal, but in some places the description is pretty dense for a book with that goal.

  • Proust Was A Neuroscientist, Jonah Lehrer. This was really well-written and engaging. Lehrer's idea is to show how various artists/musicians/writers (mostly of a certain Paris avant-garde club, it seems) anticipated recent developments in neuro / cognitive science. For example, Walt Whitman's "the body includes and is the soul" lines, and embodied cognition. I thoroughly enjoyed the arts-description parts and the science-description parts. And sometimes the connection between the two was strong and clear, as in the chapter on Proust; not so much in the chapter on, say, Stravinsky (that one felt forced). Still, eminently worth a read.

  • The Time Machine, H.G. Wells. Oh boy, did I ever get the wrong impression from the movie version of this. The book is a lot more realistic and a lot more... quietly horrifying? I don't think it's at all plausible that class separation will lead to humans splitting into two species, but it's thrillingly creepy to imagine humans evolving into either the Eloi or the Morlocks. I guess this one is halfway between dystopia and SF. (And I'm still a fan of the virtual-encyclopedia guy from the movie.)

  • Across the Wall, Garth Nix. I'm a big fan of the Abhorsen trilogy, and the first half of Across the Wall is a shorter story that's part of the canon. The rest of the book is a bunch of short stories outside the canon that I didn't find all that interesting. Nix writes young-adult stuff; Abhorsen aged well, IMO.

  • Autobiography of Benjamin Franklin. Wow! Franklin gets short-shrifted among the Founding Fathers because he didn't do "hero" stuff like command armies or ride at midnight through Massachusetts, because he doesn't look all that dignified and because the things he did do were quietly behind-the-scenes and/or sounded silly (kite, anyone?). But his autobiography is full of all kinds of interesting things, like the brilliant way he basically tricked the people and the legislature into funding a new hospital. And it's packed to the gills with advice that's a little antiquated, but still good. This is a real self-help book, not some lame thing full of whining and words like "self-actualization". I would have liked to hear more about his experiments with electricity.

In Progress
  • Le Ton beau de Marot: In Praise of the Music of Language, Douglas Hofstadter. What can I say? This is a book about translation -- but it's also a book by Hofstadter, which means it's a book about the idea of translation stretched and twisted and abstracted and applied to all different kinds of things, and at the same time it's also a book about poetry and music and elegance and math and computer science and AI and love. The book describes itself as something of a memory of Hofstadter's wife, Carol, and it's touching to read it as the world's longest, most elaborate love letter.

  • Gödel, Escher, Bach: An Eternal Golden Braid, Douglas Hofstadter. This one is also about music and elegance and poetry, but with a much larger dose of logic and math and AI and symmetry and abstraction. It's more work to get through, but it's so worth it.

  • On Food and Cooking: The Science and Lore of the Kitchen, Harold McGee. A really well-written guide to food, "scientific" in that it describes foods using scientific terms, not "scientific" in the sense of nutrition-reductionism. Sort of a Hacker's Guide to Culinary Experimentation.

On Deck
  • I Am A Strange Loop, Douglas Hofstadter

  • Diamond Age, or, A Young Lady's Illustrated Primer, Neal Stephenson

  • Vaccine, Arthur Allen

  • Jonathan Strange & Mr. Norrell, Susanna Clarke

  • On Intelligence, Jeff Hawkins

  • Dante's Inferno (anybody got recommendations about which translator to read?)

Wednesday, July 16, 2008

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.

Tuesday, July 15, 2008

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.