Nice to know I'm doing it right

I talked briefly with M_____, the department's vice-chair in charge of instruction today, making official what she already knew--that I would no longer be teaching at Davis after this quarter. I felt rather apologetic telling her, since I knew that she didn't have instructors lined up for introductory bio in summer I, summer II, or either of the two sections introductory bio in the fall, or for introductory microbio in the fall. I'm making her already difficult job even harder.

Although M_____ knew of my intentions, the department chair did not. According to M______, when she mentioned my departure at a recent chairs' meeting, the department chair said words to the effect of "Well, ****! What are we going to do when we need to get a competent instructor for any random class on five days notice?!"

I guess I've established a niche here.

Monday Musical Offering

Bach's Italian Concerto, second movement. Click here for first movement.

I love this piece. I first learned it when I studied with Naomi Sparrow as an undergrad, and I was surprised to find that it was still sort of "in my fingers" twenty-some years later. However, I think I had to un-learn a bit--I've come to the conclusion that when I was young, I was musically an idiot with good hands. I'm musically smarter now, but my hands are not so good.

Out with the old quarter, in with the new

So the new quarter starts tomorrow. I guess the students had a spring break, but between finishing grading and getting the revised syllabus etc ready, it didn't seem that different from any other week. Barely enough time to compose and translate into Maori this quarter's haka, let alone give it a decent rehearsal with the TAs. The audience (Bis2A--introductory biology) is 270 frosh. As always, it sounds much better in the Maori. The translators do a bang-up job, and they tell me they even rescued the pun in the last line of the opening.

Freshlings!
Your ears are full of ear-buds
Your eyes are full youtube
Yours mouths are full of gossip
Your hands are full of text
Your noses are full of
Let'snot go there.

Your head is full of AP trivia
You know the name of every part
of the Krebs cycle
You know the name of every enzyme
In the pentose phosphate shunt
ooooooooo!

I do not care
no no no
I do not care
Please forget all that
I do not care
learn to think of the unknown
and write a decent paragraph.

Post Mortem

Winter Quarter 2011 is finally, finally done. Or perhaps I should say, it’s all over but the whining.

Every quarter, there are some students whose world was rocked in a really positive way, and whether frosh or senior, these students are so gratifying to work with. I generally know these students pretty well. They are highly interactive, come to office hours, ask lots of questions, and seem to relish sparring with new ideas and the lecturers who present them.

Every quarter, there’s also the tail on the other side of the bell curve. I don’t know these students at all until after grades are submitted, but once they find out they’ve somehow gotten a D or an F, they really make themselves known. Somehow, despite the barrage of questions I ask every day in class, the midterms, the projects, the review questions, and all the other means of feedback, they remained unaware that they were bombing the class—so I never saw them, never got an email, never heard a question, their graded exams remained uncollected. Only after the grades have been submitted do they acquire an awareness that they need to pass the class in order to graduate or avoid expulsion. And so, I get a handful of emails wondering if there’s anything that can be done, surely there was some mistake, I forgot there was an assignment, I missed class those days, I worked so hard…

When I’m grading, I always try to “temper justice with mercy.” I generally feel like crap giving an F. I view it as partly being a failure of my efforts—was there something I failed to do that would have gotten them to pay attention and think? I have to tell myself, as I tell the desperate students, that making that grade was their quarter’s work.

The other part of the post mortem is about my quarter’s work—I’ve yet to teach the perfect class. So, I spent an hour talking with Dr. D___ about what I’d do differently next time. Ironic, since this class was a one-off for me. Not wasted effort though. It’s always useful to be conscious of what one’s doing and how it can be done better.

Friday Flora

Yet another orchid. Angraecum distichum, an epiphyte native to central Africa. It's teeny tiny, the flower smaller than a centimeter.
There are some non-orchid things out and blooming, but the last week as been so almighty rainy that everything outside is just soggy and miserable looking. And who's gonna complain about orchids?

This about says it all...

And it even mentions one of my favorite eukaryotes, Fuligo!

From the ever-wonderful XKCD. (Click on it to make it legible.)

Oozing along with Beggiatoa (part II)

(See part I).
So, as my student asked, how do they do that--oozing along so hypnotically?

We don’t know. That’s the bottom line. Beggiatoa is really common, but it turns out to be kind of difficult to study in the lab—traditional laboratory work requires getting a pure culture of nothing but Bedgy, and that seems to be pretty near impossible. So it’s been difficult to answer even fairly basic questions about this guy.

We do have a bit of a clue, courtesy of another creature from the same mud sample:

It’s a cyanobacterium, a type of bacterium that does the traditional kind of photosynthesis. It kind of looks similar, and it oozes along in the same way. You can even see that it sort of spirals along like Bedgy does. Unlike Bedgy, you can grow cyanobacteria in a pure culture in the lab, and study how they do stuff—like move along oozily.

We still don’t know exactly how this cyanobacterium (and Bedgy) moves, but at least we have some clues. One set of clues comes from Egbert Hoiczyk and his coworkers, who propose what they call the “slime-extrusion” model. Each cell in that long chain of cells is girdled with a ring of pores, which they think are "slime jets". Each cell produces a lot of slime and pumps it out of the pores. Outside of the cell, the slime picks up water and expands dramatically, like a dried sponge taking up water. The expanding slime pushes the cell along.

This model has some appeal; Hoiczyk did some impressive microscopy examining these slime jets. They’re distinctive protein structures that are neatly positioned to connect the inside of the cell where slime is made with the outside world. They also note a correlation between the presence of slime jets and the ability to glide in other types of cyanobacteria (alas, they did not check on Bedgy).

There’s another line of evidence supporting the slime-extrusion model, and that is actual evidence that slime is extruded. Hoiczyk simply put India ink (a suspension of very fine, black particles) in the mix with his cyanobacteri, and watched them go:

You can see streamers of ink-stained snot trailing off of the chains of cyanobacterial cells. But this isn’t proof that jets of slime are pushing these cells along—it could be these are streamers of snot trailing after these cells as they move along by some other means. If the model is wrong, thinking that the slime is pushing the cells along could be like thinking that the plume of exhaust is pushing a car along.

An alternative to the slime-extrusion model is raised by a group led by David Adams. According to this “peristaltic” model, the slime is mainly a lubricant that helps the cell move. The work is done by fibers that lie just beneath the cells’ outer membranes; these fibers contract in waves that move along the length of the cell. These fibers have been chemically characterized, and also nicely examined by electron microscopy. Nicely, the fibers are all aligned in a lengthwise spiral, causing the cells to spiral along as they glide.

We still don't know whether either of these models really describes how cyanobacteria move, let alone whether or not that has anything to do with the way that Bedgy moves. It would be nice to do some experiments to tinker with the slime jets and see if that affects motility. It would be nice to see whether or not Bedgy even has slime jets. The best we can say is that the way Bedgy moves looks like the way these cyanobacteria move, and that Bedgy has some genes for slime synthesis that kinda, sorta look like the cyanobacterial genes.

For now, though, we can dip into almost any pond, find this beautiful pearl necklace, and just sit back and wonder.


Egbert Hoiczyk and Wolfgang Baumeister (1998). The junctional pore complex, a prokaryotic secretion organelle, is the molecular motor underlying gliding motility in cyanobacteria. Current Biology 8:1161–1168. Electron micrographs of slime jets, ink-stains of slime, and circumstantial evidence for the slime extrusion model.


Marc Mußmann, Fen Z. Hu, Michael Richter, Dirk de Beer, Andre Preisler, Bo B. Jørgensen, Marcel Huntemann, Frank Oliver Glockner, Rudolf Amann, Werner J. H. Koopman, Roger S. Lasken, Benjamin Janto, Justin Hogg, Paul Stoodley, Robert Boissy, Garth D. Ehrlich (2007). Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments. PLOS Biology 5 (9): e230. The suggestion that Beggiatoa has slime-producing genes similar to gliding Cyanobacteria.


Nicholas Read, Simon Connell, and David G. Adams (2007). Nanoscale Visualization of a Fibrillar Array in the Cell Wall of Filamentous Cyanobacteria and Its Implications for
Gliding Motility. Journal of Bacteriology 189 (20): 7361-7366. Striking images of the fibers that support the peristalsis model of cyanobacterial motility.

(The literature on this subject is pretty thin, and the dates are old; it's obviously not a subject that attracts much interest, cool as it is.)