Sunday, February 27, 2011

As yet unnamed

(Shhhhhhhhhhhh!!!!!! Be very, very quiet)
(There--do you see it sticking out there?)
Hmphthgphgnthfthffrrwhawhaheywhat what are you doing with that camera?!?
Oh the shame of being caught with your tongue hanging out!

Friday, February 25, 2011

Friday Flora no make that Fungus

Helvella lacunosa.
It makes me genuinely happy to see this fungus. Seeing Helvella lacunosa gives me the same feeling I get from seeing an interesting friend whom I haven't seen in a very long time. This is appropriate; H. lacunosa is interesting (I mean, just look at it!) and friendly (it's allegedly edible, though I am not going to try it without having a real mushroom person identify it). It is also, inevitably, something I haven't seen in a while. Around here, I know of exactly one place that it grows: right along the bike trail, in a patch a few dozen meters long.
It only sends up mushrooms after very heavy rains, even then it's not too reliable. We've lived in Sacramento for more than a decade, and I've seen it four times. It's too lovely to part with, so here's a couple more pictures:
(We got a couple of stares from passing bicyclists--I was down on my hands and knees by the side of the trail in full cycling duds, which I am sure was confusing to most people. I wonder what percent of the people who passed by had any clue about the lovely things they were missing.)
The mushrooms are already deliquescing, and today's pounding rain won't help them. I wonder, with a little sadness, when I'll see them again.

Wednesday, February 23, 2011

Overheard in Mic105 Lab

"Grow, you motherf****rs!"
"Uh, they reproduce asexually, you know."

Caulobacter Crazy (Anti-) Glue

There are few things as annoying as out-of-control glue. Klister is one example—it gets everywhere. In violin-building, I use hide glue which is difficult to control for another reason: it is only sticky for a few minutes, which gives you very little time to get your work done. Ideally, glue should only stick when and where you want it.

The wonderful glue used by Caulobacter is amazing not only for its strength, but as we’ve recently found, it can actually be turned off pretty simply. This surprising discovery suggests that Caulobacter may have a more complicated social life than previously thought.

To begin with, I have to show you the canonical Caulobacter picture, from the lab of Yves Brun:

This is a picture that, for a while, seemed to be featured in every single paper and talk on the organism. It shows the “life cycle” of Caulobacter: it starts out (on the left) as a freely-swimming single cell. If it swims to a nice place, it sheds its flagellum, and grows that famous stalk and holdfast. Once anchored, it grows and divides, giving birth to a new free-swimming cell. Only the anchored cells divide, and once they’ve anchored, they never move again. So, as long as there is sufficient food, they’ll crank out swimming cells; when conditions turn bad, they are doomed.

Caulobacter, like a lot of bacteria, will form fairly dense growths of cells on a surface—a so-called biofilm. All the cells in a Caulobacter biofilm are growing on stalks, anchored by that marvelous glue—I can picture wandering through such a film, like wandering through a forest of oddly shaped trees that occasionally give birth to flagellated blobs. If conditions are good in this biofilm forest, then it’s advantageous for the newly-hatched Caulobacter swimmers to immediately stop swimming, grow a holdfast, and settle right in place—and so they do. The Caulobacter doesn’t fall far from the tree--sometimes they even cling to each other.

However, if times are tough, all the food has been used up and there are predators around, the existing Caulobacter might wish to urge their offspring to move on a bit before they settle down. A group of researchers, led by Yves Brun, found that this is exactly what happens: distressed Caulobacter biofilms produce something that essentially keeps Caulobacter glue from sticking.

There are several examples of Bacterial cells communicating with members of the same species using a variety of small molecules, so Brun set to work to figure out what Caulobacter used. Surprisingly, the molecule that inactivates Caulobacter glue is Caulobacter DNA. Brun found that a lot of cells in a stressed-out biofilm die, and shed their DNA into the area—and this DNA specifically interacts with the newly-formed holdfast of a former swimming cell, and completely turns off the glue.

Brun was commendably thorough in trying to prove that this was really happening. Unlike other known chemical signals used by Bacteria, the DNA didn’t trigger any changes in gene expression—so it wasn’t the case that the DNA stopped production of the glue: it inactivated the glue that was already there. His group purified large quantities of Caulobacter holdfasts, and found that the DNA only attached to the sticky end of the holdfast. The DNA didn’t interact with any other part of the cell. So, it seemed that the DNA from dead Caulobacter cells was a very specific “anti-glue.”

Here’s the really weird bit: only Caulobacter DNA was effective as an anti-glue. They tried DNA from other organisms; they tried DNA from distant and near relatives of Caulobacter—and only Caulobacter DNA was effective as an anti-glue! Some close relatives’ DNA could slightly reduce the glue’s effectiveness—but not as effectively as Caulobacter.

This is a real puzzle, and as yet there’s no satisfactory explanation. This is a glue that can stick to glass, plastic, rock, metal, you name it. Brun’s group tried DNA with the same overall chemical composition—the same percentage of G:C bases as Caulobacter—and got nothing. They searched the Caulobacter genome for distinctive genes or motifs—and got nothing. They looked for Caulobacter proteins or other small molecules contaminating their DNA—and got nothing. There is something yet to be found about Caulobacter DNA that does this.

There is something interesting in the fact that this signal that says “Warning! Go Away!” comes from dead cells.

We could look upon this as being a perfectly sensible system for free-swimming cells to avoid settling down where conditions are bad. The presence of loose Caulobacter DNA is a sure sign that Caulobacter cells have been there, and died. So, from the swimming cell’s point of view, it is not the place to settle down.

However, there is a growing number of researchers who look upon Bacteria as being social organisms—organisms that will not just communicate with each other, but also lay down their lives for others of the same species. So, these researchers say, look at it from the point of view of the stalked cell in the biofilm. You’re producing swimmer cells, each of which has 100% of your DNA. If conditions are bad, it would be worth your life to urge your offspring to get away. From this point of view, cells can actually commit suicide just to send that message.

This debate is as yet unresolved, and this recent finding about glue and antiglue doesn’t answer it one way or the other. However, it makes the amazing glue of Caulobacter seem even more amazing, and forces us to re-write the advertising copy: “Sticks like crazy to EVERYTHING!!!*”

(*except certain DNA sequences. We don’t know why.)

Berne, Cecile, David T. Kysela, and Yves V. Brun (2010). A Bacterial Extracellular DNA Inhibits Settling of Microbial Progeny Cells Within a Biofilm. Molecular Microbiology 77(4), 815-829.

deep geopolitical metaphysical thought

I can't help but wonder if there's some parallel universe in which the supreme court acted with intellectual consistency in Bush v. Gore; and in this parallel universe, Saddam Hussein has watched what happened in Egypt and Libya and Tunisia and Bahrain, and is just now delivering a rambling, hour-long speech in which he vows to fight on; and meanwhile, his soldiers have decided that they are tired of shooting their fellow-countrymen.

Tuesday, February 22, 2011

Monday (no, Tuesday) Musical Offering (no, review)

We didn’t go to Berkeley just to look at amusing restaurant signage; we went to see the young British pianist Paul Lewis in a recital.

The way it seems to happen is like this: a young pianist emerges, bursting with promise. He or she wins a competition or two, or attracts the mentorship of a universally respected elder, or releases a breathlessly-reviewed CD. Then, there’s a year or so of making concert appearances. A very few go on to super-stardom (whether earned—like Leif Ove Andsnes—or not—like Lang Lang). Most don’t quite live up to the breathless hype, but do establish themselves as very respectable figures. Some, you just wonder whatever happened to them (Dmitri Sgouros, anyone?). So I always wonder what I’m going to get when I go to such a recital.

Paul Lewis is youngish, and has released a critically-loved complete set of the Beethoven Piano Sonatas. He’s studied with no less than Alfred Brendel, who famously doesn’t take many students. And now, he’s on tour, and (based on an impressive recording of Beethoven I heard on the radio, and a nice recording of some Schubert Sonatas) I wanted to see if he was all that. He is—as far as I can tell, which is not very far.

The program on Sunday included two Schubert Sonatas (a minor and D major) and the three piano pieces, from just before Schubert’s death. There is no doubt that this is well within Lewis’ comfort zone, and he played everything beautifully. Schubert is sometimes portrayed as an heir to Beethoven’s tradition, but the spirit behind the Schubert piano sonatas is (to me, at least) fundamentally different from the spirit behind the Beethoven sonatas. Beethoven’s works (with the exception of the “Hammerklavier”) strike me as being intensely personal chamber music—very much solo piano pieces, unimaginable recast as quartets or symphonies. Schubert, however, was writing symphonic works that happened to be playable on a piano. The music is no less touching or profound, but it is less personal. That sounds bad, but I could just as honestly say that it is “more pure”.

Lewis handles the technical and aesthetic demands of this music very well. He presented the orchestral effects convincingly: with too much clarity, they become annoying detail, and with too much distance, they lose their form. I was impressed by his ability to minutely control the volume of his accompaniments; the ability to shape these informed every phrase. I could readily hear these pieces in their symphonic form. It is easy for these pieces to sound much too long (for example, when I play them), but Lewis’ command of the architecture of these pieces made them seem all-to brief.

I am most familiar with the Three Piano Pieces, having played them myself. These are aptly named; they are less symphonic, more personal than the Sonatas. Knowing that a piece was among the last things that a composer wrote invariably makes you think differently about it—it must be especially poignant and elegiac. However, the Piano Pieces are especially poignant and elegiac because Schubert was on form when he wrote them. Lewis played them with personality (though perhaps slightly less than is possible, within the bounds of good taste).

Overall, I was rather liked Lewis’ playing. His subtlety of shading was very pleasing. Although the nature of the Sonatas is symphonic, he played with a pleasing elasticity of tempo that would be impossible but for the best orchestras. He did not have a hugely powerful sound, but it was certainly good for Hertz Hall. There was some imprecision in the release of the damper pedal, but this was probably more the fault of the technician than the pianist. The lasting memory is of Schubert, played with consummate musicianship.

Note that the memory is not of brilliant pianism, nor is it of a forceful personality. The program—and all I know of Lewis—is narrowly constrained to Vienna, between 1785 and 1830. Though there is absorbing depth enough in this repertoire, there is much more to pianism than the Viennese classics. Can he play Scarlatti? Bach? Schumann? Chopin? Rachmaninoff? Shostakovich? Lewis has recorded a disc of Liszt, and in this, he may be following his teacher Brendel. So, I don’t know if Paul Lewis is the next great pianist, or even the next Alfred Brendel (whose repertoire went from Bach to Schoenberg, though he’s most famous for those Viennese classics and Liszt). He sure can play Schubert, though.

(I did get his autograph, and an admonition.)

Monday, February 21, 2011


A Soviet-era joke shows the twin bogeymen of the paranoid Russian mind:
Q: How does the wise Soviet diner prepare for the cuisine of the future?
A: Learn to eat matzo with chopsticks.
Yesterday, driving through the People's Republic of Berkeley, I saw a sign that probably would trigger a panic in the modern, paranoid Right-wing mind:


Saturday, February 19, 2011

Those were the days...

Any well-established university science department has its elders, venerated as much for their scientific achievements as for their embodiment of a physical connection to the departed giants of the field. One of our microbiology department's elders is John Ingraham. He's rightly celebrated for his discoveries (do you like wine with a controlled malo-lactic fermentation? Thank John), and when you look at him you see a lineage that goes to C. B. van Niel and then to Kluyver and then to Beijerinck.

I was reading an autobiographical sketch John wrote for the 1991 Annual Review of Microbiology (1991--twenty years ago he was already an eminence grise), and came upon this nugget about working at UC Davis:
It seems almost dream-like to recall the cordial relations between state government, university administration, faculty and students, the emotion-choked Chancellor at retirement responding to the standing faculty’s applause with, “Only at Davis.” Phone calls to administration, support staff and other faculty were almost always greeted with, “What can I do to help?” The governor and members of the legislature (almost all UC graduates) were proud of their excellent educational system from kindergarten through graduate school. The governor always attended picnic day (Davis’ annual campus/community joint celebration) to ride in the lead car of the parade and greet all comers. But Governor Pat Brown was the last to do so. With the coming of the 1960s, Vietnam, and Ronald Reagan’s governorship, university/state government relations soured.
I think if Mark Yudof were in the lead car at Picnic Day, he'd get tomatoes thrown at him. If the governor were in the lead car, the tomatoes would still be in the can.

Ingraham, John L. (1991). Learning to Fly Fish. Annual Review of Microbiology 55, 1-9.

Friday, February 18, 2011

Nice to know I'm doing it right

There was a midterm today, followed immediately by lab. One of the brighter students in the lab was just sitting at his bench for a bit, looking brain-weary. After a while, he shook his head as if clearing his thoughts, and exclaimed, "Whew! That was tiring! I'm not used to midterms where I gotta think!"

Thursday, February 17, 2011

The most beautiful Caulobacter yet

Lab is getting really busy--and satisfying. The goal of the lab is enrichment and isolation: the students start with mud or soil or gutter water, and using selective media and growth conditions that favor certain organisms, they isolate pure cultures of specific types of microbes. A maxim of environmental microbiology states that "Everything is everywhere." That is, you can take any sample, and you can isolate any type from it. So, from the same sample, the students isolate Bacilli, Streptomyces, Purple Bacteria, Cyanobacteria, Prosthecate Bacteria, Fermenters, and so on.

The first five weeks of this are frustrating for the impatient. Stuff has to grow, and many things grow slowly. But now, after seven weeks, we get the payoff: students sit down, twiddle with their microscopes, and spontaneously get up and dance a happy dance. It's the dance of somebody who finally has a beautiful pure culture of Caulobacter: Isn't that just beautiful? More on Caulobacter later.

Monday, February 14, 2011

Monday Musical Offering Movie Minimalism Edition

Sorry, still no performances from me. Hopefully there will be some soon. Part of the reason is time away from the piano: we spent the last four days at Squaw Valley, where the Real Doctor was attending a conference. (Some skiing was done, too.) Of course, being a Real Doctor conference, the sessions were held at a Swanky Hotel, with its own take on Swanky Hotel Lobby decor that announced its location in the wilds of the Sierra Nevada. That is, pretty much the same as any other, with perhaps a few more Craftsman/Frank Lloyd Wright touches, and two enormous granite boulders in the lobby.

Our last sojourn in realm of swanky hotel lobbies (and a visit to the Art Institute of Chicago) inspired a rant on minimalism--so, it's completely appropriate that, while waiting in the swanky lobby and checking out the amusing Opera Chic blog, I found this amusing take on one of the seminal pieces of modern musical minimalism: Steve Reich's "Clapping Music":

I'll insist (again) that this is really music--it's polyrhythmy, rather than polyphony, like a Bach two-part invention only playing with pulse rather than pitch. This video makes it a bit clearer...

Now, go back and watch Lee Marvin and Angie Dickinson again. Pretty slick.

Friday, February 11, 2011

Friday Flora

Orbea variegata, clone from my Mom's garden. We got it to bloom under our plant lights.

I learned the name of this plant as "Stapelia variegata," and so it was named by Linnaeus himself. However, the powers that be decided that it wasn't really part of the genus Stapelia--no other member had that pronounced annulus, while that was the defining feature of the Orbea. So, it was reclassified. It's like finding out that a childhood friend has changed his name.
A close-up allows you to see the essential milkweed-ness of the flower.

Wednesday, February 9, 2011

Today's lesson

Axiom: Always wear clean underwear. You don't want to be embarrassed if you're in a traffic accident and the paramedics have to peel you off the pavement.

Corrolary: Always keep your back yard tidy and don't leave your underwear on the clothesline. You don't want to be embarrassed if there's an armed robbery down the street and the police have to look there for the suspect.

As far as I know, he's still at large. He was not in the chicken coop.

Tuesday, February 8, 2011

As yet unnamed

Rejected names:
Rommelpot (Medieval folk instrument, makes rumbling noise)
Feathers McGraw
umuD (a "mutator" gene)
dinB (another "mutator" gene)

So far, all these names have been rejected by the Real Doctor. I'm the first to admit that I don't have the most normal history for naming beasts--I or my family have had "Nothing" the kangaroo rat, "Stupid" the Carolina anole, "Fuzzybutt Turdflinger" the chinchilla, and Opal (named after a famous mutant). If you have suggestions, please comment.

Monday, February 7, 2011

Monday Musical Offering Flat Pack Edition

Not my own, obviously, but appropriate. We went to IKEA over the weekend. Fascinating place--excellently thought out, wonderfully efficient, well staffed, exceedingly good design, kind of marginal components. We now have additional closet space and an urge to name every stick of furniture in the house with a quaint, vaguely nordic-sounding name. I'm sitting on Faldbo the chair, at Hojmska the table, beside Humsu the bookshelf and Grypaar the music stand! It's like I'm surrounded by sophisticated and worldly friends.

Anyway, our experience was better than this:

Sunday, February 6, 2011


I mentioned that it hasn't snowed in a while. This is not exactly correct--as this photo of a light dusting shows.

It's just the horribly wrong kind of snow*. Large flocks of crows gather in the trees surrounding the West parking garage every evening, cawing and pooping--it's right about when people are heading home, and you can hear something like a squishy rain. The condensation from the thick fog in the morning makes the guano into a kind of slurry, and it smells worse than a seabird rookery I once visited.

It has also drawn the attention of the powers that be. I received this bulk email this week from the Bio department administration:

At this morning’s recharge group meeting, the presenters were from Grounds Maintenance. I asked about the crow situation surrounding the West Entry Parking Structure, parking lots 40 and 41, etc. They were not encouraging, saying that crows are very smart (for birds) and figure out quickly that when predator sounds are played in the area no birds are being killed so there must not be a real threat. They are going to attempt the predator sound approach starting approximately next week to see if they can get any improvement. Unfortunately they say the birds will likely just move over a few trees, then return later.

Bob Segar (campus planning) was giving their presentation, and stated that his office’s first priority is campus visitors: making a good impression on them when they arrive so they will want to come back. I told him he better hope they aren’t parking in our area, or they will never return! I also stressed that the current situation is both a health and safety hazard.

Bottom line: continue to wear a coat with a hood or use an umbrella to protect your head and clothes, wear shoes with traction, and have paper towels handy to use on the hand rails!
*I don't think that even the Wax Curmudgeon would know how to wax for it!

Saturday, February 5, 2011

Sage skiing advice

A fine day of skiing. We all—Rad, the Real Doctor, and I—felt a bit like we were playing hooky, but on the other hand, sometimes you just gotta go. Especially after a week like the last, and especially if it seems like the snow is all about to go away because it’s been so warm. The warm conditions demand klister, and klister demands attention.

The Wax Curmudgeon is full of sage advice on how to deal with the challenge of wet, three-week old snow. So of course, I asked how he prepared for the day’s snow, and received an earful: “Avoid Swix klisters above KR40. I just haven’t gotten them to work. Now, Toko makes a silver klister—mind you, not Swix silver, which is entirely different—that they sell as a base layer, but that I use as a kick wax when the snow is old like this, but not really wet. With it wet like this, you want to try Start klister. They sell it as “OU” or “OY” or something, but I just grab the red box or the yellow box. That could work today, but it’s kind of a dry wind. Rode makes a klister they call “Gialla” that’s good for really wet snow like this, but only if it’s warmer. I saw G______ from Truckee put a base of Toko silver, with a layer of Star—not Start, Star—fluoro klister, and he could get grip on snow that was submerged in a puddle of meltwater, so if you feel like blending klisters, that would work. Right now I’m trying out a klister by a Canadian company—it’s outrageously expensive, $40 a tube, but it’s supposed to go all the way from plus 2 to plus 20. I tried it at 13 degrees and it was useless. I thought I would give it one more try, and today it seems to be working. What are you on?”

“Um, Swix KR70, stuff that was left on my skis from two weeks ago. It sorta works.”

Using klister necessitates removing klister. Which leads to V.’s comment, related by somebody who might be a cousin of the Wax Curmudgeon:

…when you set about trying to remove the klister from your skis, take a thin sheet of papery paper towel and stick it firmly to the klister on the bottom of your ski, ripping off any extra paper that overhangs the ski, then get yourself a sharp scraper, maybe even metal, but in any case, thin, and sharp, and begin scraping off the paper-toweled klister, et voila, eh? Normally klister when you try to scrape it will first begin to roll up, and then, suddenly, right before you were going to stop and wipe and reset, whammo, reverso-gobster, impossible to get off! Do not at this point get frustrated and swear and cuss and sweat and try to wipe off the klister by rubbing the whole ski up and down the front of your shirt and your face, no-non little grasshopper, with ze powerful and sleek paper towel method, klister comes off cleanly, and it is bound and corralled by the paper towel, so you can toss it away, knowing that you have captured all the klister in the paper towel and also not gotten boogers all over oneself nor anyone else! Hoo hah! ya hey dere, den...

So I tried this, and it worked, mostly. There was one big problem, and one lesson learned. When you have successfully removed the icky sticky klister from the ski, and a good blob of it is on your hand, do not swat the mosquito that just landed on your face…

Friday, February 4, 2011

Friday Flora--stinking up the place

After last week's tease, the grand opening...

Stapelia (I lost the tag that had the species name--it's from my Mom's garden, which is better than yours). Since I was a sprout, I've had a thing about the Stapeliads. They're a group within the milkweed (Asclepiads) that produce succulent stems and five-petaled flowers that tend to be fly-pollinated. As such, they have evolved to attract flies--they smell like poop or rotting meat, and the flowers have the look of a morsel of carrion--down to the hair you can see fringing this flower. This one's pretty small, only a couple of cm across, but it can be smelt at arm's length. My Mom has one, "Piranthus foetidus" which has a tiny flower but you can smell it from several meters away.

So, now another tease:
Kind of a busy week, so not able to post much. Hopefully more next week.