Sunday, November 28, 2010

First ski of the year

Skiing has some similarities to playing the violin. It's really easy to do it badly. And, when you do it just right, it feels so amazingly good that you are instantly hooked. You're desperate for the next fix, so you struggle and try and spend and go to all sorts of lengths in search for that perfect instant.

Today was the first ski of the year for the Real Doctor and myself. California has had a series of cold, wet storms blow through, and last night it was cold enough that it snowed down to 3,000 ft in elevation. 7,000 feet up at Donner Pass, where we ski, there was eight feet of snow and the morning temperature was in the teens. We got to the ski area around 10 in the morning, and the temperature was about 25 degrees--absolutely perfect. "Blue wax" conditions like these are rare in California, where klister is the rule for most of the season, so it was a struggle to avoid the irrational exuberance that is normal for the first ski of the year. I am only a little sore.

As they say, if you can walk, you can ski. However, you'll ski very badly. Skiing well is nothing like walking, and my muscles have been forgetting all about how to ski for the last 8 months. So most of the day was spent just trying to remember...hip up like so...weight over there, then over there...don't look at your skis, look at the trees!...and so on.

Friday, November 26, 2010

Friday Flora

The Real Doctor has been acquiring plants at an alarming rate due to a titration problem. It started with a couple of interesting orchids being purchased from Santa Barbara Orchid Estates; these few required some indoor lighting set-up. However, the indoor lighting set-up, despite being small, still had some extra space. So, more plants were purchased. However, the number of plants exceeded the room on the indoor lighting set-up. So, a larger indoor lighting set-up was purchased. (Note the persistent use of the passive voice; this absolves all concerned from any agency or blame). However, the only reasonable larger indoor lighting set-up involves three shelves illuminated by four-foot fluorescent lights. So, the capacity of the indoor lighting set-up now vastly exceeds the number of plants. Clearly, more plants must be acquired.

Fortunately, I like plants. Especially funky cacti that look like they are desperately trying to be rocks, until they let loose with blooms like this:

Ariocarpus kotschoubeyanus (Northern Mexico, S. of the Rio Grande)

Wednesday, November 24, 2010

Just in time for Thanksgiving

The turkeys have made another appearance. It's the same flock of four, and they're still clueless about how to deal with traffic. When I saw them this morning, one was paused in the middle of the road, holding up traffic. A car tried to pass at the same instant the turkey decided to finish crossing the street. The bird ended up running alongside the car for a while, confused as to why it couldn't run around the car. This agitated the three other birds, who couldn't see their pal, so they started some concerned gobbling. The incident was resolved when all four birds flew straight up, then onto the roof of a two story house.

We haven't seen them for over a month, and I was thinking that maybe they went and joined their brethren on the American River Trail, or (given their inability to figure out cars) they had shuffled off this mortal coil. However, I'm thinking they may be a permanent part of the 'hood. As neighborhood fauna, I prefer them to the cats that infest our yard.

Monday, November 22, 2010

Like Senioritis

I commiserated with K. today. Like me, she is a lecturer at the university. It's near the end of the quarter and we're both more tired than we expected to be. We have both taught our classes many times before, so we could easily phone them in. However, we both are always trying to get them to work better. We tinker with this, adjust that, experiment with the other, and so on. The bulk of the class remains the same, but so much work is spent on the fiddly improvements that it wears you out. It's kind of like Greg LeMond said about bicycling--it never gets any easier, you just go faster. Teaching's always all-consuming, you just hope that you do it better.

We both have spent a lot of time and energy to improve our courses. She has attended workshops in college teaching, and done amazing things with introductory biology at Davis. She has even written her own textbook. She teaches something like 1500 students every year. Like me, K. has been told by the university that there won't be employment for us next year.

So, we're tired, largely because of challenges we're making for ourselves. We try not to think about the end of our jobs--as soon as we do, we both find ourselves just not caring. Why should we bother? We decided that we're in danger of a sort of professional senioritis. K. is looking for something that motivates her (other than riding a horse). I'm probably in denial, keeping thoughts of an uncertain future at bay by giving myself more work to do.

Monday Musical Offering

A bit of gypsy-flavored schmaltz. A couple of weekends ago we had our violin teacher's "adult student" recital at our house. The Real Doctor will not permit recordings of her playing, and recordings of my performance are not permitted by the Geneva Conventions. However, Kris here plays pretty well.

Friday, November 19, 2010

Underneath a sky of genes

I vividly remember my first DNA prep. I had just started working in Sharon Long’s lab and was being led through the basics, and the DNA prep is one of the most humdrum things done in any microbiology lab. You grow up a few milliliters of bacterial cells in culture broth, concentrate them, and use a combination of chemicals to break them open. They release their DNA and all the other goop that is contained in the cell—so the next step is to get rid of all the other goop. At the last step, you have a clear solution containing the cells’ DNA. You add a bit of ethanol, and magic occurs: the DNA that was dissolved in the solution is no longer soluble. It precipitates, making what looks like a delicate dust-bunny of spider silk floating in a test tube of clear liquid. I had been studying DNA in classes for years, but I’d only seen it in pictures. Here, I started with living things and half an hour later I had a visible tangle of their essence. Nowadays, I teach students how to do this, and even though I spend most of my time thinking biology, I still get a buzz out of this.

We are in the midst of two migrations, here in the central valley. We sit under the “Pacific Flyway,” which routes waterfowl and wading birds from the Alaskan tundra to winter grounds in California and Mexico. I can hear the squeaking of flocks of ducks and the rusty-windmill clatter of sandhill cranes when I walk the dog at night. During the day, I’m mesmerized by these flocks. Hundreds of birds, in long, strung-out, ever-shifting lines, they move into sight from the northern horizon and fade from view in the south. Silhouetted against the overcast sky, they look like strands of spider silk drifting in the wind.

There’s another migration going on right now, a migration we can feel. During my class’s midterm on Wednesday, a normally quiet student sitting in the front row became agitated. She eventually started shaking her hand to remove something, and when I went to look, she was dealing with a teeny spider and a very long length of silk. I gathered up the millimeter-sized spider (and the meter of silk it made) and took it outside. When I looked up at the sky, I could see clots and bunches of spider silk drifting in the breeze, gyrating like dancers in a stately adagio. Some were several meters long, and some were shorter but clumped and clotted. They tumbled and shifted lazily as they rode the wind north. It’s “ballooning” season here in the Central Valley, and millions of baby spiders are dispersing, riding strands of silk wherever the wind will take them.

Shifting and tumbling through the sky, both spider silk and strings of migrating birds visually remind me of that DNA tumbling around in a test tube long ago. But having made biology my study, I feel like I am actually seeing DNA drifting through the skies. Watching spiders drift along like aerial plankton, I am seeing bundles of genes venturing northwards, trusting chance to lead them to new environments. Most of these bundles of genes will perish, meeting fates even worse than exam-taking undergrads, but some will discover a new and friendly place, and these airborne bundles of genes will thrive and produce thousands more spiders. The strings of birds are compelled southwards by their own genes—genes that are using those birds to take them to a place with lots of food, where those genes prepare to reproduce again. The birds’ migratory behavior is written in these genes, edited and revised by millions of years of evolution. As I watch an awkward echelon of sandhill cranes fading in the south above drifts of gossamer, I hope these genes fill our skies for millions of years to come.

Friday Flora

Say some slick huckster oozes onto the late-night TV screen and spins you a deal too good to be true. A wonder of a machine! Solar powered! It actually removes greenhouse gases from the air! It's so green, it's actually green! You just open the fuel tank, put in a few simple salts (nothing you couldn’t put in your own food), and you put in water—yes, ladies and gentlemen, pure water!—and this miracle of a machine will set to work. No toxic chemicals, no hazardous wastes, this marvel of modern engineering will spin out perfumes to bewitch the senses and dyes to dazzle the eye. This machine will do all that—and more! It will actually make copies of itself—so if you like the results (and I think you will!), you can give this machine to your friends absolutely for free! No royalties, no copyrights, no legalities. Just give it away!

You would be justified in being somewhat skeptical of the huckster selling this product. Unless the huckster was trying to sell Sophronitella coernua.

Wednesday, November 10, 2010

A fun way to spend Halloween. Well, more fun than handing out candy at any rate.

The Real Doctor and I went to see a lecture/demonstration by Alfred Brendel on the last night of October. Brendel no longer gives concerts; his fingers no longer have the agility or stamina needed to live up to his standards. However, his mind is still sharp and overflowing with wit and scholarship, so he gives lectures punctuated by short musical excerpts. The subject of this lecture was humor in music.

It’s good practice in argument, as in war, to dictate the field of action to suit your own strengths. Brendel did this. Although he has an extensive recorded repertoire, from Bach to Schoenberg and beyond, he has made his name as a cerebral master of the Viennese classics, Mozart, Haydn, Beethoven, and Schubert. So, he chose to define humor in such a way that it can only really be found in the high Classical style (and perhaps Ligeti).

Humor can be found in music where we see foiled harmonic expectations, pratfalls where expertise fails, the simulation of laughter, inappropriate or contradictory expressions, and the like. The bottom line is that, by his definition, humor basically requires expectations—expectations that can be created by the relatively structured nature of the Classical style. (Though I’m not sure Brendel would approve, this is exactly what PDQ Bach and Victor Borge take advantage of.) Having set up his argument, Brendel easily carried it off, dismissing any opposition. When Schumann writes a piece with the marking “mit humor,” the piece itself is not funny, it’s pervaded by a humorous mood. When Bartok lampoons Shostakovich in the Concerto for Orchestra, it’s not humorous, it’s grotesque. Scherzos—“jokes”—from Chopin to Rachmaninoff? Not really funny funny, again, more grotesque. Bach? Not funny at all.

You might imagine that an evening watching an elderly German guy dissect and analyze humor would be deadly. It was actually quite entertaining. Though he’s not as strong at the piano as he used to be, Brendel illustrated his rather narrow argument with excellent examples. The humor in a Haydn sonata was intensified when Brendel played the same piece drained of all humor by hewing to expectations. A riotous Beethoven Bagatelle that incongruously juxtaposes a jaunty mood with a minor key was made funnier when Brendel played it in the major, turning it into an icky puddle of sap. Beethoven (who is for my money the funniest composer out there) received the most attention, especially the Diabelli variations. Interestingly, for Brendel, Mozart and Schubert are pretty much without humor. Their music is so concerned with beauty and singing that humor just didn’t seem to interest them.

There was an element of gentle polemic to the evening as well. Brendel is intellectual, but he is also a vigorous advocate of humor. Why, he wondered, is coughing permitted in concert halls, but laughing banned? Why do some players do their best to suppress humor? He concluded, somewhat sadly, that some people just don’t get it. It’s like being color blind. It’s not their fault.

In his role as humor advocate, Brendel does come across differently from Brendel as concert artist. He satirized the humorless Haydn player by sitting at the piano and charging right into a witty sonata movement—then playing it as it should be played: sitting at the piano, pausing to arch one eyebrow above his glasses at the audience, and then launching into the joke. On the whole, he was much more facially involved than I had ever seen him, emphasizing jokes and contrasts with a degree of mugging that I found surprising. So, although he had a sound intellectual argument as the foundation of the evening, Brendel left me with another question.

Music is about communication by sound, and the role of the performer is to communicate the sounds the composer specified (plus some of his or her own interpretation) to the listener. There definitely is humor in music; I can listen to a recording of the Diabelli Variations or Bagatelles in a dark room and still get a laugh. But when we are dealing with humor—or pathos, or whatever emotion is needed—how much of the performer’s job is visual? And, did Brendel’s face answer this question in a way that his intellect would approve of?

Monday, November 8, 2010

The supposed future of higher ed, other views

From another blog that has connections to Davis, more on the NY Times article about online teaching and its dubious effectiveness but its undisputed cheapness. "Not really sure what to make of this..."

Friday, November 5, 2010

The supposed future of higher ed

A couple of days ago I got a bulk email from the Provost's office, excitedly announcing the launch of "a systemwide Project to evaluate the potential application and effectiveness of online instruction in UC’s undergraduate curriculum." The project is supposed to
evaluate the applicability and effectiveness of online instruction in delivering a UC-quality undergraduate education. Letters of intent (LOI) are sought in particular from faculty who are passionate about teaching and learning, and who are curious about the roles technology may play in support.

In their LOI faculty will identify the undergraduate course or courses they would like to develop as part of the Project and provide some additional information, e.g. about themselves and their approach to determining content scope and learning objectives. In this request, online refers to courses that are largely or wholly online.

In the planning phase, selected faculty will bring their creativity and their expertise as subject specialists and as teachers to bear in thinking about the online learning environment and the course design principles that will be used for the Project. They will also advise in the development of an evaluation framework to assess the Project’s progress and the efficacy of online instruction in UC’s undergraduate curricula.
This morning there's an article in the NY Times about how many undergrads are getting their coursework entirely online. Despite the breathless excitement about online ed that the UC is trying to whip up, the real driving force is the what the Times article discusses: money. There just isn't enough money to teach all the students. So, rather than teaching them, the University has them watch a video.

I really can't generate any enthusiasm about this online ed, and it's not just because it would make me redundant. There was an additional article in the Times that elicited a "well, duh!" response. It reported a study that--surprise!--showed that students who did everything on line didn't learn as well, and scored a full letter grade lower than their peers, even those who had sat in a lecture hall with 499 other students.

Wednesday, November 3, 2010

A real hunger artist

There was an article in yesterday's Science section of the NY Times about how biological systems often function at or near the theoretical limits of physics. The photoreceptors in our eyes, for instance, can be triggered by a single photon--and you can't have less light than a photon.

Evolution has produced some amazing systems, which is not too surprising; selection is relentless, and if you give it a few billion years to work, it can do wonders. But evolution is a terribly messy way to get improvement, and there are LOTS of examples of evolution producing wretchedly imperfect systems--things that are so bad that when I tell students about them, they ask how something so inefficient could possibly exist. The bottom line is that they work, and they are about as good as can be gotten by improving a jury-rigged prototype. Knees and backs are all-too-familiar examples of this, but our eyes, with those wonderful photoreceptors, are another.

Our photoreceptors can be triggered by one photon; however, the overall design of our eyes is idiotic. The photoreceptors are upside-down, so the photon has to make it through a layer of support cells before it can hit a photoreceptor. Our lens is prone to clouding over, and the Real Doctor can tell you about all the other problems an eye is prone to. Suffice to say, it is not at the maximum efficiency permitted by physical law.

Coincidentally, I spent a chunk of the day reading about a type of photosynthetic bacterium called Chlorobium. It uses light for energy--it is completely unable to use anything else. A group of researchers from Munich, led by Jorg Overmann, found Chlorobium growing over 100 meters under the surface of the Black Sea. The light intensity--well, intensity is the wrong word for such inky darkness. The irradiance can be measured in the number of photons moving through a square meter every second--at that depth it's about 100,000,000,000,000 photons per second. That seems like a lot of photons, but it's important to note that a single Chlorobium cell is not a square meter across! It's a generous estimate to say that a single Chlorobium cell has about a square micrometer of surface area. A meter is 1,000,000 micrometers, so a square meter is 1,000,000,000,000 square micrometers. So, the average Chlorobium cell at that depth is getting by on 100 photons per second.

That's a meager diet. Despite the vaunted efficiency of biological systems, chlorophyll is not so good. Only about 10% of the light's energy actually gets used by the cell (which isn't so different from the efficiency of a standard electrical solar cell). This energy has to be used to do everything a cell must do to live: make DNA, make ATP, make protein, make more of the cell, etc. Considering that mere existence requires the constant input of energy (for instance, to repair DNA damage from random radiation and repair protein damage from oxidation), it's amazing that anything is left over for growth. And truly, very little is left over for growth. Making one cell requires, by a back-of-the-envelope calculation, the energy from well over 100,000,000,000 molecules of ATP; at maximum efficiency, these cells can make slightly more than three molecules of ATP per second.

These cells are on the very ragged edge of life, growing so slowly that they barely outrun entropy. The goal of every living thing, it's been said, is to make two living things; Overmann's group calculated that it takes these cells about 26 years to do that.

Life has evolved out to the outer boundaries of what is physically possible. A photoreceptor that can detect a single photon is neat, but I think a cell that can survive and grow on a hundred photons per second is even more impressive.

Marschall, E., Jogler, M., Henssge, U., and Overmann, J. (2010) Large-scale distribution and activity patterns of an extremely low-light-adapted population of green sulfur

bacteria in the Black Sea. Environmental Microbiology 12 (5) 1348-1362.

BioNumbers database