Open thread: ask me questions!

Dear all the CS people who I know glance at this blog: I would love to hear from you! (And, y'know, from anyone else who happens not to study CS.)

I've recently come up short on blog topics, but also had a hankering to explain basic biology items in a way that makes them exciting to people who "hate biology", or are at best indifferent to it.

What would you like to hear about? Is there some old question left over from your intro biology course, to which you've never heard a satisfactory answer? Want quick summaries of recent developments in synthetic biology, or the ways in which biology imitates EE/CS? How about Anthropomorphized Enzyme Comics? Or, perhaps, White Lies Your High School Bio Teacher Told You?

Reply now and you might even get the post before Monday morning! :D

Science Poetry: The Perfume, A. D. Hope

I ran across this gem while trolling randomly through the archives of The Wondering Minstrels. It's the newest incarnation of the archives of an old mailing list, long gone out of service, but at least all the poems and commentary are still there. I'm in the process of going through all the poems, starting from no. 1. It's a wonderful archive, and I highly recommend spending some time there.

"... marked males of the silkworm moth have been known to fly upwind seven miles to a fragrant female of their kind ... the chemical compound with which a female silkworm moth attracts mates is highly specific; no other species seem aware of it. In 1959, the Nobel Laureate Adolph Butenandt of the Max Planck Institute for Biochemistry in Munich succeeded in analysing it. He found it to be an alcohol with sixteen carbon atoms per molecule...."

L. and M. Milne: The Senses of Animals and Men.

0 Chloë, have you heard it,
This news I sing to you?
It's true, my lovely bird, it
Is absolutely true!
A biochemist probing
Has caught without a doubt
The Queen of Love disrobing
And found her secret out.

What drives the Bombyx mori
To fly, intrepid male,
Lured by the old, old story
Six miles against the gale?
The formula, my Honey,
Is now in print to prove
What is, and no baloney,
The very stuff of love.

At Munich on the Isar
Those molecules were found
Which everyone agrees are
What makes the world go round;
What draws the male creation
To love, my darling doll,
Turns out, on trituration,
To be an alcohol.

A Nobel Laureatus
Called Adolph Butenandt
Contrived to isolate us
This strong intoxicant.
The boys are celebrating
And singing at the club:
Here's Bottoms up! to mating,
Since Venus keeps a pub!

My angel, 0, my angel,
What is it you suffuse,
What redolent evangel,
What nosegay of good news?
What draws me like a dragnet
And holds and keeps me tight?
What odds! my fragrant magnet,
I shall be drunk tonight!

-- A. D. Hope [source]

Figure 1: Bombykol, from Wikipedia. "Doesn't that structure make you simply wild with desire?"

I remember hearing stories about this compound, or one very like it, in my organic chemistry class. Apparently, whenever someone wanted to deliver a vial of it across campus, they would be pursued by a gradually accumulating swarm of moths. I like to play that scene in my head. "I'm a synthetic chemist -- I did not sign up for entomological fieldwork!! *panicked fleeing across campus*"

Even supervillains have work-life balance problems

I just got back from seeing Despicable Me with my brother. Although this is not a Pixar movie, it follows Pixar's pattern by being about far, far more than the trailer lets on. (I remember being distinctly unimpressed by the WALL-E trailer, and then I cried my eyes out through the whole thing.) The plot is really fun, and the 3-D is unobtrusive enough to be mostly inconsequential.*

I thought it was pretty cool to see a supervillain (and an older, male supervillain at that) deal with the sort of struggles and discrimination normally associated with working mothers. I haven't experienced these struggles first-hand, of course, but a number of scenes reminded me very strongly of things I'd read -- especially Dr. Isis' blog posts and Allison Pearson's book I Don't Know How She Does It. Seeing parent-discrimination divorced from sexism was quite strange; but then again, I don't doubt that there are fathers in the world who have suffered career setbacks and discrimination because of family demands.

The end of the movie leaves open whether the main character continues the same level of career activity (in the same or a different field), or scales back in order to spend more time with the children. I would have liked to see something indicating that he achieved a productive balance; maybe a montage of newspaper headlines showing him up to something resembling his old tricks, perhaps with the children's collaboration.

Also, as a side note, whoever was writing Margo (the oldest girl) has done their homework on sibling-order effects on personality. I'm an oldest daughter, and though of course I'm not exactly like Margo I found myself identifying with her much more strongly than I was expecting to. (The girls in the movie are not biological siblings. Anyone know if sibling-order effects also happen in families brought together by adoption? It seems plausible -- these effects ought to be mediated in large part by environment... but I'm rambling now, because it's late.)

Go see Despicable Me if you're up for some funny, frivolous action, and so much cuteness that all your teeth will dissolve.


* I'm still cheesed at being made to pay an extra $4 for an effect that, IMO, adds very little to a movie animated in Pixar's style. But there's a cute bit in the credits where some minor characters play around with it, so stick around.

Gunnerkrigg Court takes on animal research ethics

I think I chose a particularly fortuitous time to highlight Gunnerkrigg Court, because it's just started taking on one of my favorite themes, and I think it's being handled very well so far.

First, read the last two pages of the comic: one, two. You don't need much context to see what I'm talking about.

Figure 1: Rock on, Paz.

Now, if I remember correctly, Paz is a character we haven't seen much of yet (her first appearance is basically as an extra), and I'm looking forward to seeing her developed in more detail. I'm very glad to see she's taking (or at least professing) a sensitive, ethical attitude toward animal research. Realistic, too -- I'd swear that Tom Siddell has read the NIH Guidelines. I admire the fact that Paz aspires to reduce or even eliminate the use of animals in her research. Per fantasy conventions, all of these girls are stunningly mature and knowledgeable compared to the average high schooler, but I'm still very impressed by her attitudes and opinions.

(Plus, I'm pleased that she's apparently not white and not a native English speaker. I'm not terribly well informed about racial/identity politics, but nothing about the way she's portrayed jumps out at me as being problematic.)

I will be very interested to see how this plays out. In particular:

• How will the teachers and other students at the Court react to the presence of animal research at their school? Will they even find out, or do they maybe know already? Will we see a range of attitudes, from "Animal welfare is not that important" to "All animal research is morally reprehensible"?


• How will the supernatural entities in the forest react? Will their reaction be shaped more by opposition to the Court in general, or by the fact that many of them are (at least in some sense) animals themselves?


• What is Paz doing, and who is she working with? How did she come by her research assistantship? Is she doing largely self-directed work or is she being used as a pawn by some unscrupulous adults? Is she aware of the broader implications of her work, whatever those turn out to be?


• Is this research actually justifiable/ethical or not? Right now all we have is Paz's word, and we have very little idea what they're actually studying.

I have faith that all of these questions will be answered, if not in as much detail as I would like. Gunnerkrigg Court wouldn't just introduce a subplot like this without exploring it in quite a bit of detail.

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.

Squee!

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...

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?

A sure sign of a healthy lab

Whiteboard, day 1:

THURS 3:30
GROUP MEETING
DANNY

Whiteboard, day 2:

THURS 3:30
GROUP MEETING
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!