Sunday, August 29, 2010

What's wrong with the cartoon eukaryotic cell? [Unusual Cells pt. 1]

I'm starting a series of posts based on a class I taught about "Unusual Cells" for Splash. Eventually, each post will include links to all the others.

The point of this series is to understand the wild and crazy unusual cells that populate the world (and that populate us!). But we should first understand the usual cell... or, perhaps, we will find that there is no such thing as a usual cell.

Consider the cartoon eukaryotic cell that we all know and, presumably, love:

Figure 1: Typical eukaryotic cell. I'll refrain from listing the organelles, in order to prevent yawning; if you're curious, check Wikipedia, where this image is from.

So... what's wrong with this cell? Here's a sampling of some of the answers my Splash students have given me:
  1. You can't see the DNA

  2. You can't see the proteins

  3. It's cut in half (yes, some of them are smartasses)

  4. There are no membrane proteins

The answer I'm really looking for is this:

It's empty!

(To be fair, Splash students pretty much always get this one too, and it's a general case of the answers I gave above except for #3.)

There's nothing in this cell! Yes, the major organelles are there, but where is the cytoskeleton? It's just that tiny little fiber (#7), which you can barely even see. Real cells are just packed with stuff. Structural proteins, membrane proteins, highways of vesicles wandering to and fro...

Now, of course, this is kind of a necessary evil. We can't include all that stuff in cartoons of the cell that are supposed to show the major organelles, because it would just be a distraction. Visual noise. For example, check out this slice of a more realistic watercolor:

Figure 2: You can see a bit of the Golgi (yellow stacks) in this picture. The geodesic-dome-looking thing is a protein framework that's making a vesicle bud out from the Golgi. [Source]

Seriously, check out the whole thing. It's beautiful. If I could get a quality print of this I would hang it above my bed. But even this is far from showing everything. The empty space between all those blobs is filled with crazy amounts of ions, small molecules, and of course water.

For a different perspective, check out these photos of cells in which the cytoskeleton has been labeled with green fluorescence. Yep, that's just the cytoskeleton... it reaches everywhere, helping the cell maintain its shape and move around (just like the human skeleton), and giving direction to packages of important chemicals as they motor their way hither and thither (something like the human circulatory system).

To do: find out what percentage of the membrane surface area is proteins. I know this is in one of my textbooks somewhere.

Monday, August 23, 2010

Perhaps I should flip a coin?

I'm working out my class schedule for the upcoming semester, and I've run into a bit of a dilemma. Two classes are at the exact same time. Both clamor for my attention. Both are only offered in the fall, and this is my last year. They are as mutually exclusive as it is possible for two classes to be.

  • 7.32 Systems Biology: This field is a sister to synthetic biology. I'm interested in to the point of wanting to pursue it in grad school. The Silver lab, where I'm working, is a systems biology lab in more than just name (although it's certainly not typical, being focused on engineering). Networks! Switches! Stochastic behavior! Dynamics! Oscillators! Pattern formation!

  • 21A.212 Myth, Religion, and Symbolism: This class looks like it's going to hit one of my biggest avocational buttons. Despite being atheist/agnostic/nonreligious (damn labels), I've always had a fascination with the power of ritual and storytelling -- the roles they play in our lives and how they adapt to non-religious contexts. How did I manage to not notice this class existed before?


I want to study systems biology in grad school. Therefore, I should get started. Taking this class may help me with my continuing work in the Silver lab, and might even help me get into a good grad program.


I will have plenty of time to study systems biology in grad school. (And if I really get an itch, I can always pick up Uri Alon's book.) I should take this chance to explore a humanities topic that I'm really interested in, while I'm still an undergrad, because time is short.


So, what do I do? Both of these arguments are fairly convincing to me. Which one wins? Or, are there other arguments I've missed?

Sunday, August 22, 2010

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

Sunday, August 15, 2010

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 Chloƫ, 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*"

Monday, August 9, 2010

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.

Wednesday, August 4, 2010

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.