Friday, July 30, 2010

Watch out for the mad biologist!

One of my favorite webcomics is Gunnerkrigg Court. It's a mixed fantasy, SF, and school story with some characters who are pretty badass for their apparent age (middle/high school). Antimony and Kat, the two main characters, play a crucial, growing role in trying to preserve peace and increase cooperation between their school (the Court) and the adjacent forest -- but they're also just two girls capering in a world that's often a lot bigger than they realize. It's framed as technology versus magic/divinity, but I have a feeling it runs a lot deeper than that.

I highly recommend reading it, even though it starts out just a little slow -- the 'real' threads start soon enough.

But why am I highlighting it now? I'm super excited, because in among all the magicians and mad roboticists, I think we may have our first mad biologist character.

Should I say that again? Mad. Biologist. Character.


Err, I would totally include a small click-to-embiggen preview image of the comic, but I can't figure out how to make Blogger do that. I have been thinking of migrating to Wordpress...

Monday, July 19, 2010

But why is the sky blue?

Here's a sampling of the random questions I've encountered in the past week that have piqued my interest. I feel like these should be answerable with a little effort (by someone other than me, since my brain is stuck in corners), but they're also fun to just speculate about.

It's a commonplace that Benadryl makes you drowsy. kcr noted that it only seems to make him drowsy when it isn't busy fighting off an actual allergic reaction. Are the antihistamine and sleep-inducing activities of Benadryl different? Does one compete with the other?

Why do martial arts seem to be optimized for fighting other practitioners of that same martial art? I don't know anything about how martial arts develop, but my intuition says something like this: it's dangerous and impractical to always practice by getting in real fights, and if you're going to make a new variant on an existing style, then practicing against others of that style is a decent proxy for being in real fights. Of course, this runs into the bootstrapping problem of where did the first formalized martial art come from... but humans have been punching each other for so many years that I feel like basic instinct can serve as a starting point. (How do you go about designing a martial art for "real combat"? I know these exist -- mumble military mumble something.)

What's the most cost-effective way to make ice cream using a dry ice and ethanol bath?

Monday, July 12, 2010

A sure sign of a healthy lab

Whiteboard, day 1:

THURS 3:30

Whiteboard, day 2:

THURS 3:30
Oh DANNY boy

Paper attached to whiteboard, day 3:

Oh Danny boy, pipets, pipets are calling,
From bench to bench, and in the TC hood.
The gels are gone, and all the yields are falling;
'Tis you, 'tis you must make the data good.

So come ye back, where we cells are abiding,
Or when the lab is lonely as the grave.
'Tis here we'll be, in log-phase swift dividing...
...if you will please not put us in the autoclave!

Friday, July 2, 2010

Bacteria break symmetry too

It's amazing what you can learn on the internet, especially when looking for something totally unrelated! :)

Caulobacter crescentus is a really cool little bacterial species with a funky two-phase lifestyle. The "stalked cells" attach themselves to rocks or whatever in the freshwater environments where these guys live. When a stalked cell divides, part of it remains a stalked cell and part splits off into a "swarmer cell". The swarmer cells swim around like more 'normal' bacteria.

Check out some images of these dudes. (Blogger's image uploader is misbehaving so you guys get a link to Google Images. Sigh.)

They're a fascinating organism to study because their cell division is asymmetrical. If you think back to the high-school-biology version of mitosis... well, it seems like a totally symmetrical process, right? There would seem to be no reason for a particular set of molecules to end up in one daughter cell and not the other, because everything's floating freely around in a droplet of water anyway. But in an asymmetric division like this, the two daughter cells have to develop in different ways. The stalked cell has to keep maintaining its stalk, but the swarmer cell has to grow a flagellum and start making the necessary sensory proteins to swim toward yummy-smelling food molecules. And not only that, but there's a correct orientation for this difference and an incorrect one. It would be kind of awkward if the new stalked cell started trying to swim away, and the swarmer cell floated around trying vainly to anchor to something.

So there must be some sophisticated mechanisms at play here. Notably, it's not that the two daughter cells end up with different genes -- after all, the swarmer cell will later settle and put down roots as a stalked cell. What matters is the presence (or absence) of proteins and other molecules that regulate those genes, so the stalked cell can keep making stalk proteins while the swimmer turns those genes off and turns on the ones for making a flagellum.

This asymmetric division isn't just some strange bacterial phenomenon. Every multicellular creature goes through this kind of process as it grows from a single cell (a fertilized egg) to whatever elaborate body it has as an adult. Figuring out the origins of symmetry-breaking in cell division is one of the major problems of developmental biology.

It also has to do with stem cells, by definition. The vast majority of cells in your body are "terminally differentiated" -- that is, they've gone from nondescript round blobs to fully elaborated cells with sophisticated morphology, heavily optimized for doing whatever job it is they need to do. But the 'terminally' part means they stop dividing once they reach maturity. So if you lose some mature cells, you need to get new ones from a renewable pool of immature cells. These are stem cells. The key defining feature of a stem cell is that it can divide asymmetrically. One of its progeny will be a precursor cell, traveling inexorably down the path to neuron-hood or white-blood-cell-hood or whatever. The other will be a new stem cell, all set to keep hanging in the lazy infinite loop of waiting until it's needed again.