Cheap DNA sequencing

This is a picture of one DNA sequencing machine: the Applied Biosystems 3730xl DNA Analyzer. It costs a few hundred thousand dollars and it’s starting to show its age, but it’s still the sweetest thing on the market if you want to sequence DNA accurately and fast. Here’s another DNA sequencing machine: RNA polymerase. It’s been around for a few billion years, and you’ve got trillions of them in your body right now, most of them sequencing DNA faster than the fridge-sized 3730xl. If not, you’d be real dead.

One of the reasons I’m optimistic about our ability to understand what’s happening inside the cell is that a cell is already a sophisticated information processing engine. If we can learn how to listen to it as it’s working, we won’t need to blast it to bits and paste its little smithereens back together in a kind of glorified biotech forensics lab. The violence of the language we use is telling. Polymerase chain reactions? Shotgun sequencing? Please. Why don’t we just ask that busy little RNA polymerase to tell us what it’s doing?

Of course that’s easy for me to say, but it turns out that’s exactly what Steve Block is doing in his Stanford lab. By stringing DNA between two tiny polystyrene beads, he can effectively listen to the sound of transcription and infer the sequence. The title of his paper drives home the fact that you can’t get much smaller than this: Single-Molecule, Motion-Based DNA Sequencing Using RNA Polymerase. If you don’t have a subscription to Science (which I don’t) you can read about papers like this in places like Alex Palazzo’s Daily Transcript and then you can go directly to the publishing lab for the paper (PDF).

Misspelled aquaria

This morning, as we were planning to go to the Boston Aquarium, I checked the website, as you do, to verify the Sunday hours. No point in showing up only to discover that it’s closed on Sunday or undergoing massive renovations or some such thing. As I began typing the letters “boston aq” into the Google Toolbar, the following word completions were helpfully suggested to me.

boston aquarium 1330 results
boston aqarium 1140 results
boston aqaurium 856 results
boston aqurium 682 results
boston aquariam 626 results
boston aquirium 64 results
boston aqustics 14 results

I’m not terribly surprised that the word aquarium is so easily misspelled, but I am amazed that the correct spelling accounted for only 28% of the overall result count, not to mention the fact that it very nearly came in second. This is fascinating data, and it illustrates that Google is in possession of the finest set ever made of data on spelling in English. What could schools do with this? For one thing, we’ll be able to watch trends over time. Are we getting better or worse at spelling? It also seems that by correlating a list of frequently used words against frequently misspelled words, we could at least make our spelling tests more practical. Screw up a word like flagellar and nobody gives a damn, but if you write erotic instead of erratic, it might get you in some hot water. Nobody likes an erotic spellor, or mabe they dont realy care much any more, sinse Google can fix it all.

Google will always know what you mean, even if nobody else does, for Google knows what is in your heart.

Incidentally, Boston Acoustics is the name of a speaker company. And yes, Google will indeed suggest that perhaps by aqustics you meant acoustics.

Spider webs, deconstructed

My nominee for the how-in-the-world-did-THAT-evolve-without-intelligent-design award is the web-spinning spider. While I don’t actually believe in intelligent design, it’s always astounding to watch a spider at work. Via Athanasius I came across this spider site that shows web construction movies and a web gallery. There is also an illuminating little essay on how web-spinning works, which ends with this charming fact.

The spider usually replaces the web every night or every other night. … The old web is ingested and recycled into new silk.

I alternate between thinking this is elegant and poetic on the one hand, and absolutely revolting on the other. Think of all the bugs that have been on that old thing. But then I suppose if you liked eating bugs…

Sense-making with Google Trends

From the O’Reilly Radar I came across this fun tip: use Google trends to investigate words with seasonality. What I like about this so much is that it gets at how we make sense of the world. Just as you can use Google images to see what a fleam looks like without knowing what it means or how to translate destornillador without bothering to find out what language it is, you can use Google trends to learn about words that have distinct temporal profiles.

Perhaps you’ve never heard of Beltane, but a quick trend search shows that it stimulates great interest around the end of April every year. Now consider Christmas. Notice that this exhibits the pronounced anticipatory pileup associated with counter-flowing temporal wind. I discussed this effect in detail in an essay about December birthdays. You might think that New Year has a similar profile, but you would only be revealing your cultural chauvinism: New Year casts two shadows, and depending on where you come from it can mean quite different things. Mother’s Day also makes multiple appearances on the calendar.

A typical causal downcalendar decay is evident in this plot of Incredibles. No one had ever heard of the movie The Incredibles, and then suddenly it burst on the scene. We also see a significant Oscar-related spike. For another interesting profile, Tim O’Reilly singled out poor John Kerry as the archetypal example of “falling off a cliff.” Buh-bye John. So sorry.

I could play with this for hours, much as I did with the mesmerizing Name Voyager. There’s something viscerally satisfying about plots like Memorial Day, Labor Day, summer. Got any good ones?

Spooky numerology

Here’s a spooky game to play on Friday: Choose any two digit number you like. That is, think of a number that can be expressed like this

10a + b

where a and b are both single digit numbers. Now add a and b and subtract that sum from your original number, like so:

(10a + b) – (a + b)

I am now going to think about your number. Hmmm. Let’s see.

(10a + b) – (a + b) = (10a – a) + (b – b) = 9a

I need perfect silence while I meditate upon the nature of your number… it is… wait, it’s getting clearer now… it is DIVISIBLE BY 9! Pretty spooky, eh? No? Hey, where is everybody going?

Before you run away, go look at this site. milaadesign wizardry. It’s an extremely well-done version of this old mathematical chestnut. They’ve employed some very clever showmanship to obscure the simple math that I spelled out above. First, there is the creepy sound and imagery. The fact that, as an Iranian design firm, they also show the instructions in Farsi just deepens the sense of mystery. But the best hack is the last one. On the last screen you look at a big table of occult-ish symbols and pick out the one next to your number. It looks like all the symbols are different, and after a dramatic pause just long enough for some sort of telepathic voodoo, they reveal your symbol, amid chirping crickets and maniacal cackling. You didn’t have enough time to observe that all the multiples of 9 (i.e. 18, 27, 36, and so on) have this exact same symbol. Finally, for better dramatic effect, they change this symbol the next time you play.

That’s good show business! My hat is off to anyone who can squeeze that much mileage out of a two-bit math hack. (thanks to my sister-in-law Elizabeth for forwarding this one to me)

The Sheep Market

Ever since Amazon’s Mechanical Turk service launched, I’ve been wondering if it would really take hold. If you haven’t heard of it, the Mechanical Turk, which gets its odd name as an homage to an old chess-playing automaton, is a human-in-the-loop web utility offered by Amazon. Want to transcribe some handwritten notes? It’s hard for a computer, but easy for a person, and Amazon has taken all the hassle out of hiring someone for $0.05 worth of work.

But still, how many people would really do it? Apparently not many people are actually taking advantage of the service. On the other hand, I recently came across the best evidence yet that the Mechanical Turk has a future.


Someone has put up the money for people around the world to draw 10,000 sheep. Little badly drawn cartoons of sheep facing left. All on display at The Sheep Market. To the list of things computers find difficult, add pointless doodles. (via Karim via Ben Hyde)

Calder’s circus

I had seen pictures of sculptor Alexander Calder’s tiny toy circus before, and I had read how in Paris in the 1920s the “Cirque Calder” mesmerized the like of Jean Arp, Piet Mondrian, and Jean Cocteau.

He would issue invitations to his guests, who would sit on makeshift bleachers munching peanuts, just like the real circus. With the crash of cymbals and music from an old gramophone, the circus would begin. Many of the individual circus animals and performers include mechanized parts—Calder was originally trained as a mechanical engineer.

Still I couldn’t picture how it all worked. What did the performances actually look like? So I was happy to see that someone has YouTube’d a movie of (a much older) Calder and his wife performing his famous circus. Here is the first clip. Find the others with this search.

Watching Calder’s bucking broncos and weightlifting strong man makes me think that he must have done a lot to inspire people like Arthur Ganson. Follow the link and be sure to look at the “Machine with Wishbone” movie.

The Inner Life of a Cell

Someone I work with went to SIGGRAPH this week and posted a link to a cool movie he saw. SIGGRAPH (which stands for Special Interest Group Graphics) is the biggest computer graphics conference on the calendar, and it happens to be in Boston this year. Anyway, I followed this link and stumbled upon the juiciest, sexiest, most eye-popping movie I’ve seen all year: a speculative visit to the inside of a living cell.

Cellular Visions: The Inner Life of a Cell.

It’s sort of like the movie Fantastic Voyage, only from a molecule’s point of view. Starting on the outside of a white blood cell, you journey deep inside to gawk at some of the insane machinery that makes it work: a bubbling Golgi apparatus, actin fibers spontaneously spinning themselves from the soup, a lonely shuffling motor protein hauling its heavy-laden vesicle cargo up an endless microtubule footpath.

This is the movie I always wanted to make. From a protein’s point of view, the cell is an enormous place, and the process of building it is a mega-engineering project something like the construction of a skyscraper. Cartoony diagrams in biology textbooks just don’t transmit that sense of scale. You zoom through this cell, and you think, “My God! This thing is huge! Who’s in charge? What does that thing do?” The obvious question is: does it really look like that? The answer is a reasonably qualified yes, given their need to tell a visual story. Here is a quote from the press for the movie.

“There are plenty of others in the academic community creating these kinds of animations to illustrate concepts for students and their peers, but they tend to look and feel, well, very academic. The idea with this was to make something different, and there was definitely an effort to make it as cinematic as we could.” In some instances, that meant sacrificing literal accuracy for visual effect. “What we did in some cases, with the full support of the Harvard team, was subtly change the way things work,” Liebler says. “The reality is that all that stuff that’s going on in each cell is so tightly packed together that if we were to put every detail into every shot, you wouldn’t be able to see the forest for the trees or know what you were even looking at.”

I’m looking forward to a lot more movies like this. Proteins are very photogenic. You can see the full eight minute version of the movie (with scientific explanations and no cheesy music) at the XVIVO website. For the record, the process depicted goes by the name “leukocyte extravasation“. It’s not boy-meets-girl, but it’ll do.