Thursday, March 31, 2011

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, March 28, 2011

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.

Sunday, March 27, 2011

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.

Saturday, March 26, 2011

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, March 25, 2011

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.)

Thursday, March 24, 2011

Oozing along with Beggiatoa (part II)

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

video

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:

video

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.

video

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.)

Wednesday, March 23, 2011

Oozing along with Beggiatoa (part I)


This beauty is from some mud I looked at in the recently-finished microbial diversity lab.
video
It's Beggiatoa (Bedgy-a-toe-uh, “Bedgy” to its friends), a pretty common resident of the top layer of muddy sediments; it likes a little oxygen, but not very much. Bedgy oozes up and down in the sediments, between oxygen-rich water and anoxic mud to get oxygen levels juuuuuust right.


Bedgy is easy to find, as common as mud, and absolutely hypnotic. Here’s another specimen under higher magnification, looking like a jeweled necklace. I sat and watched this string of cells oozing by for a few minutes minutes, and I never saw the beginning or end of it. You MUST watch it full-screen.


video


Your high-school biology textbook probably had a general equation for photosynthesis that went like so:


H2O + CO2 --> C6H12O6 + O2


The atoms in water and carbon dioxide are rearranged to produce glucose and oxygen. This takes a lot of energy, and the energy comes from light.


Bedgy is an important bacterium in the history of science. It was the first organism that was observed to perform “chemosynthesis,” rather than photosynthesis. If you look at the periodic table, you’ll see that Sulfur is in the same column as Oxygen, and that Sulfur behaves chemically in some of the same ways as Oxygen. What’s kind of neat is that Bedgy does this:


H2S + CO2 --> C6H12O6 + S (and some SO4)


A difference between Oxygen and Sulfur is that Oxygen is soluble—it dissolves in water, and floats away in our atmosphere when it’s made by photosynthesis. However, the sulfur that Bedgy produces isn’t soluble—so it forms little semi-solid pellets, and that’s what those little yellow dots are. And unlike photosynthesis, the energy for what Bedgy is doing comes from respiration, not light—so, “chemosynthesis,” not photosynthesis. That same high-school biology textbook with the equation about photosynthesis also says that all life ultimately depends upon energy from the sun; Bedgy is there, oozing along and proving them wrong.


When one of my students looked through the 'scope and saw this, the reaction was "WOW!" followed immediately by "Wait--how does it do that?"


Stay tuned.

Monday, March 21, 2011

Monday Musical Offering

It's been rather a drought lately for music here. A combination of a new class and four-days-a-week lab has had awful effects on my practicing time. However, the quarter is all over but the grading, so here's some very sunny Bach to celebrate.


Bach made a bunch of transcriptions of Vivaldi violin concertos for keyboard. Then, he decided to write his own. In some ways it's an odd piece--it's very clearly written from the start as a keyboard piece, not a transcription of some preexisting violin concerto. But, for me, the only way to really play this piece properly is to pretend that I'm playing the violin.

Sunday, March 20, 2011

The merit of our forefathers...

The Real Doctor called me during the last day of Mic105 lab, a week ago. She was rather excited; calling from her car’s phone, which always muddies the reception, I gathered that I should call in to NPR’s Talk of the Nation Science Friday immediately. They were talking about a subject of personal relevance and expertise, so it would be good for me to contribute. It took a moment to find the number, and by the time I did it was 12:59:50—too late.


The subject was the origin of the word “clone.” This is a word which was dragged out of the Greek and attached to the meaning of “a group of plants that are propagated by the use of any form of vegetative parts such as bulbs, tubers, cuttings, grafts, buds, etc., and which are simply parts of the same individual seedling.” The person responsible for this appropriation, proposed in the October 16 1903 issue of Science, was Dr. Herbert John Webber, of the Department of Agriculture Plant Breeding Laboratory. What gave it personal relevance was that Dr. Webber was my great-grandfather.


I never met H.J. Webber, though I have an eighth of his genes. My grandfather, Dr. John Milton Webber, was also an academic horticulturalist. My mom, as has been noted, has a better garden than you and a groaning bookshelf of horticultural tomes. And then there’s me, also toiling in the vineyards of science. This brings up another term from the same 1903 paper—“transmitting power.” This is “the faculty which an individual organism has of transmitting its individual peculiarities to its progeny.” Although the word “clone” stuck—and has broadened its meaning far beyond what my great grandfather could imagine in 1903—“transmitting power” fell by the wayside, replaced in some ways by “penetrance.” However you describe it, H.J.’s biologist/academic genes had transmitting power or penetrance.

Occasionally, a name on the roster really jumps out at you. The name was “Leidy,” which in a Microbial Diversity class roster sticks out like “Saint-Saens” in a music appreciation class roster. I queried the student, and sure enough, he’s a descendant of the brother of Joseph Leidy, the pioneering American doctor / anatomist / paleontologist / microbiologist / microscopist / parasitologist. (his biography is subtitled “The Last Man who Knew Everything.”) If you want to know about amoebas, or if you just want to look at some absolutely ravishing hand-drawn illustrations by a brilliant microscopist, check out his “Fresh-water Rhizopods of North America,” available in its entirety online. So, now I can say that I’ve schooled Leidy on microbiology.

Saturday, March 19, 2011

As yet unnamed comments on rainy days

So, as yet unnamed, how do you feel about the first day of spring break being a bleak and rainy day?

Indeed.

Friday, March 18, 2011

Friday Flora





Hey Moomintroll, what kind of flower do we have this week?
Again? Yes, because that's what's blooming now. It's Dendrobium rigidum, a native of Australian mangrove swamps and Sacramento plant stands. Weird little thing.
The planter is inelegant, but works very well at keeping them happy. It could be worse; some growers find that their orchids grow very nicely on a bed of styrofoam.

Sunday, March 13, 2011

Yefim Bronfman, piano recital

It’s kind of unfair to go to a concert—like last night’s piano recital by Yefim Bronfman—with a lot of preconceptions. Sometimes, those preconceptions are served up so powerfully that it is hard to shake them: just try to get the following passage by Philip Roth out of your head:

Then Bronfman appears. Bronfman the brontosaur! Mr. Fortissimo. Enter Bronfman to play Prokofiev at such a pace and with such bravado as to knock my morbidity clear out of the ring. He is conspicuously massive through the upper torso, a force of nature camouflaged in a sweatshirt, somebody who has strolled into the Music Shed out of a circus where is the strongman and who takes on the piano as a ridiculous challenge to the gargantuan strength he revels in. Yefim Bronfman looks less like the person who is going to play the piano than like the guy who should be moving it. I had never before seen anybody go at a piano like this sturdy little barrel of an unshaven Russian Jew. When he's finished, I thought, they'll have to throw the thing out. He crushes it. He doesn't let that piano conceal a thing. Whatever's in there is going to come out, and come out with its hands in the air. And when it does, everything there out in the open, the last of the last pulsation, he himself gets up and goes, leaving behind him our redemption. With a jaunty wave, he is suddenly gone, and though he takes all his fire off with him like no less a force than Prometheus, our own lives now seem inextinguishable. Nobody is dying, nobody - not if Bronfman has anything to say about it.

So, even though I’ve heard plenty of recordings of Bronfman as a sensitive chamber musician and playing delicate miniatures by Tchaikovsky, I still had this image of him as a piano-crushing force of nature. Well, Mr. Bronfman is a piano-crushing force of nature and a refined, romantically tinged miniaturist. That is to say, he’s a really good, well-rounded pianist.

The concert started almost abruptly with one of the late Haydn sonatas: Bronfman strode out, sat down and played, pretty much as one brusque motion. His Haydn was elegant, and certainly more romantically colored than Paul Lewis’ view of the classics. The playing was elegantly relaxed but not indulgent. This was followed by more Germanic jest, Schumann’s lumpy, amorphous Humoresque. This is written as a single ½ hour piece, but it jumps distractedly from thought to thought. Sometimes Schumann makes this work, as in the Papillons, but it’s hard to make the Humoresque sound like a unified whole. Bronfman presented the fragments eloquently, vividly illustrating humor and fancy and romance bubbling out of the depths of Schumann’s subconscious. Schumann’s fancy allowed Bronfman to alternate between lyrical poet and piano-crusher (and there were a few points where I really was worried about the piano: he’s a big, barrel-chested guy, needing a special riser for his bench, and he actually makes a Steinway D look kind of small.) However, whether it is Bronfman’s or Schumann’s fault, the piece as a whole didn’t quite add up.

The second half of the program was the Chopin Etudes Op. 10, one of the cornerstones of the piano repertoire. These give the pianist endless variety, and again gave Bronfman the opportunity for poetry and pyrotechnics. His poetry was of an interesting sort. He seemed to have a certain detachment, as if he was presenting the music with as little of his personal intervention as possible. In most cases (for example, Op. 10 No. 2 and 5), there is enough poetry built in that his approach pays off handsomely. I was left feeling that I’d heard a pretty pure distillate of Chopin. This approach also worked in the first two movements of the Haydn, most of the Schumann, and in one his encores, a perfect rendition of Schumann’s Arabesque.

However, there were occasions that left me wishing that Bronfman would put more of himself into the music. It would be less pure, yes, but more personal. His restraint from injecting himself into the music was noticeable in the last movement of the Haydn, in which he seemed to be reading Haydn’s jokes rather than telling them. A strong infusion of personality may have also served to unify the scattered elements of the Schumann Humoresque. It must be noted that this is a minor fault in an approach that is generally sound.

Bronfman’s pyrotechnics are of the highest order. The dazzlers in the Chopin set dazzled, just as they should, with Bronfman’s technique steamrolling these peaks of the repertoire into a level highway. He played the final “Revolutionary” Etude faster and more powerfully than I’ve ever heard it, and it sounded like he was showing some restraint. Restraint was discarded for the last encore: Bronfman finally engaged his top gears in a Liszt transcription of one of the Paganini caprices. Most of the Paganini caprices are pretty much void of musical depth: they are pure showing-off, a single catchy “hook” presented with lots of 10ths and double-stops and ricochets. Liszt was perfectly capable of doing the same thing on the piano, and when he transcribed Paganini, the result was a synergy of musical vacuity and pyrotechnics. Taken as such, it was enjoyably brainless fun that left me with an earworm that lasted the rest of the evening.

So, Bronfman the brontosaur? Life-affirming force of nature? Well, yes, but—a very poetic, sensitive brontosaur, capable of the greatest restraint and delicacy. I’ll leave Philip Roth to figure out how to put that into a nice image.

Friday, March 11, 2011

Friday Flora

Hey Moomintroll, what sort of flower do we have this week?
Well, that clears that up. Here's this week's gem:
Promenaea "Limelight" x Crawshayana "Springtime"

Thursday, March 10, 2011

"No special skills are needed"

"Anyone with a basic knowledge can teach introductory biology. No special skills are needed. In the eyes of these people, a postdoc could do it, a grad student could do it. Heck, even [National Academy member who won't be named] could do it."

I was talking with M______, the department's vice-chair for teaching, about instructors for introductory biology in the Fall quarter of next year. M_______'s situation is not happy. The upper echelons of the university administration are preventing her from using lecturers, who have done the majority of intro bio teaching. M______ summarized their rationale, above. "Why," these administrators wonder, "should we be throwing away money on lecturers when we have these faculty who don't teach enough, and grad students who need to work for their keep?"

I make a point of watching other professors at work--it's a way for me to learn what to do better (and what to avoid). Last week I watched K____ delivering a lecture on energetics to an audience of almost 500 students. She made no stunning revelations about what is (truthfully) pretty simple material. However, she showed amazing skill in presenting material in an interactive and engaging and effective manner. Everything in her presentation was engineered to compel students to stay awake and engaged with the material. This kind of lecture is not the fruit of some natural gift; it is the result of careful study and LOTS of work. Having worked with K_____'s students in other classes, I know that she's effective.

I also watched J___ giving a lecture to a similar audience. J___ is the rare researcher who gives a rat's ass about teaching. He has been heroic about reforming the introductory bio classes in the face of unbelievably intense opposition. He's a brilliant geneticist and a deep thinker. He's not a bad lecturer, either--but he's not in the same league as K____. He is not quite as skilled as she, because he has not focused on teaching with the same intensity as K____ . The intensely curious and highly motivated would thrive in his class, but those adjectives don't describe most of the 500 students in the hall. As I watched, I saw plenty of students texting, watching videos, browsing the web, doing homework for other classes, and so on.

Next year, I probably won't be at the University; K____'s contract has been "non-renewed" as part of the purge of lecturers, and J___ is retiring soon. However, like any year, there will be a few thousand students needing introductory biology--a class that every other class in their majors will build on. But the administration is serene. They'll find someone to give all these students a sound foundation in the sciences. After all, no special skills are needed to teach introductory biology.

Tuesday, March 8, 2011

Someone needs to walk a mile in somebody else's shoes...

So I ask my brother the high school teacher how it feels to be the latest supervillain, hell-bent on the destruction of all that is good and fiscally responsible. The next day the New York Times ran this article, "Teachers Wonder, Why the Scorn?" about how Wisconsin teachers are coping with this very question.

The letters come in. Most are sensible. One, authored by Richard Frauenglass, comes from the planet Fox-Teabag. I quote it in full, because it is so unmoored from reality.

It is a mystery why teachers fail to understand the public perception. They do not work a full day, they have significant time off during the day, they have extensive vacation time, they can be granted tenure and they have a retirement benefits package that is the envy of all except top corporate executives. Any additional activity, like being a coach, club leader or adviser, is generally compensated.

Now don’t get me wrong. The uniformed unions also have overreaching benefits that need renegotiation. But it is the teachers with whom the public has the greatest contact and who regularly whine about how poorly treated they are and demand raises from struggling taxpayers on whose shoulders their compensation falls.

It is high time they wake up and begin to understand that they do not exist in a vacuum and that their ivory towers need a dose of reality.



Wow. Just, wow. It takes your breath away. There is some temptation to find the author's phone number, and have brother M. call him in the morning when he starts, and at night when he's done with the day's work. Better yet, brother M's suggestion that he actually try teaching for just one day. M's prediction is that Mr. Frauenglass would by crying by 10:00 AM and face-down and comatose by 1:00 PM.

And don't even get me started on how the University insists that teaching a class of 300 frosh is a "half-time position."

Science-speak gem of the day

Science writing occasionally barfs up pithy nuggets, worthy of Basho or Rumsfeld:

"An unexpected residual excess of teleological thinking has influenced the evolution of biological sciences during the last few decades."

J. F. Linares, I. Gustafsson, F. Baquero, and J. L. Martinez (2006). Antibiotics as intermicrobial signaling agents instead of weapons. Proc. Natl. Acad. Sci. USA 103:51, 19484-19489.

Sunday, March 6, 2011

There was a ski race. It was Great

Today was the annual Great Ski Race--30 km from Lake Tahoe to Truckee. 12 km of up, up, up, up; 10 km of down, down, down; 7.9 km of rolling flat; 100 m of terrifying downhill. This is always a fun ski--it's kind of a ski equivalent of Bay to Breakers. This year there was a bevy of skiing leprechauns, the skiing Playboy bunnies, the leisure-suit guy, and other colorful characters (I've met a guy who did it with a friend on tandem skis). I'm afraid I wasn't much for costume this year:

(I guess that guy behind me was dressed as the devil.)

Anyway, conditions were better than I had feared--the forecast was for rain, but fortunately all the precipitation was in the form of snow. My technique was pretty good, thanks to the trip to Canada. However, I am just not in great shape this year--the guys in the first wave (shown here at the start) finished in an hour and a half; I rolled in an hour later.
Out of about 800 skiers, I was again smack in the middle of the pack. My time was ten minutes slower than the last time, but the wet snow slowed everybody down--the winning time was also ten minutes slower than in previous years. Anyway, I finished, I didn't bonk, I didn't biff on the final hill, and I had a fine day of skiing. I'll count it as a win.

Friday, March 4, 2011

Friday Flora


Masdevallia hybrid "Pretty Pink." From Santa Barbara Orchid Estates. The flower is not huge, maybe three or four cm from tip to tip. This is kind of an old photo, but the same plant is blooming like crazy right now--I'm just too lazy to try to take a nice photo.

Nice to know I'm doing it right

(Shouted, as a chorus in perfect unison, by a car-full of college students who stopped at an intersection, watching me rollerski along M street):

"DUDE! THAT IS F***ING AWESOME"

Wednesday, March 2, 2011

Bold Traveler

One of my favorite television series is Life on Earth, produced by David Attenborough. Every episode seemed to feature him walking across one of the Dry Valleys of Antarctica, or the Atacama desert, or an iceberg, or solfatara. After noting how hostile the area was, Attenborough would turn over a rock and point at a green smudge or a tiny insect, and in his plummy British accent say “And yet…even here...in this harsh environment, life persists!” For champions of endurance, though, Attenborough should have pointed to microbes. As a harsh environment, it’s hard to beat hot rocks nearly three kilometers underground—but microbial life doesn’t just persist there, it seems to thrive.

Interest in life deep beneath the Earth’s surface has been growing in recent years. There was considerable surprise when deep-drilling projects in the 1980’s revealed that oceanic basalts held diverse communities of Bacteria and Archaea. Because of the way these basalts form, we could figure out how old they were. Amazingly, rock that had been buried for millions of years carried millions and sometimes billions of microbial cells. Microscopic analysis using dyes that only stain living cells showed that the majority of these cells were alive, although living veeeery slowly. These observations stimulated further questions—in fact, the two basic questions asked by all environmental microbiologists: who are these guys, and what are they doing?

“Who is there” is easily answered in this day and age by DNA sequencing. Since Bacteria and Archaea are generally identified on the basis of ribosomal RNA sequence, DNA was extracted from these rock samples and probed for the genes encoding ribosomal RNA. These genes could be sequenced and the results would show “who” lived in young (only tens of thousands of years old) oceanic basalts. The answer is somewhat surprising. The Archaea generally have a reputation as “extremophiles,” capable of living in the harshest environments. They also are about half of the organisms found in the deepest oceans. However, in young oceanic basalts, they are only 10% of a surprisingly diverse population. In fact, there seems to be twice the diversity of bacterial species in the young basalts than in the surrounding seawater.

Probing of older basalts showed that as the environment got harsher, diversity decreased. Drilling 1600 meters beneath the ocean floor (into rocks that were deposited over 100 million years ago), researchers found an environment with temperatures ranging from 60 to 90 degrees Celsius, but with a million cells per gram of rock. These cells were definitely alive. However, unlike the younger basalts, the diversity of life sustained by these deep rocks was very low. Generally, only a few types were found, and they were evenly divided between anaerobic Bacteria and methanogenic Archaea. So there seemed to be a trend: deeper and older meant fewer cells and less diversity.

The current record for human curiosity in this subject was established in 2008. In this case, curiosity was helped by greed, as the scientists gained access to a South African gold mine and sampled the water percolating through porous rocks 2,800 meters below the surface of the earth. Conditions there are beastly—a temperature of 60°C (140°F—give a thought to the humans who work there!). Worse, there’s very little energy available. We humans get energy by burning carbon compounds in oxygen; the bacteria living in ocean sediments get energy by burning carbon compounds in sulfates. But in these deep rocks, it seems at first glance that there’s nothing to burn.

“And yet, even here in this harsh environment, life persists!” Not much life, though, and no diversity. The researchers didn’t actually observe any cells—they simply collected DNA. Although this DNA was somewhat similar to that of known types of bacteria, it was unique—enough so that the researchers postulated that it belong to a previously unknown organism, which they named Desulforudis audaxviator. Amazingly, there is no diversity in this environment. They sampled half a million pieces of DNA from this environment, and 99.96% of it came from D. audaxviator. They found essentially no other DNA in their samples. It appears that D. audaxviator—it means “bold traveler”—lives alone in the rocky depths.

We are used to a “web of life,” with organisms interconnected by chemistry and energy: up here, the plants take light and carbon dioxide to make glucose, while we eat the plants to make carbon dioxide, and so on. There are similar cycles for nitrogen, sulfur and other elements, and ultimately, all of these cycles are powered by energy from the sun. Bold traveler lives by itself, depending on no one and feeding no one, a situation unique in my experience in biology. The researchers’ analysis of Bold traveler’s genes show how it can be a one-species ecosystem. It’s able to take in carbon dioxide and make sugar (instead of photosynthesis, it uses chemosynthesis, a light-independent process). It can also “burn” that sugar, using sulfate instead of oxygen, and get energy. It can fix nitrogen, the same way that the bacteria that live in bean plants do. It contains all the element cycles in itself.

If a solo ecosystem is surprising, the energy that probably powers this ecosystem is amazing. We can tell by its genes that Bold traveler burns its fuel using sulfate in place of oxygen—it has the genes for it. But what is less clear is the nature of the fuel it uses. The fuel may be sugar, but there’s very little of that available in the deep rocks. Its genes suggest that Bold traveler burns hydrogen as its fuel. You might reasonably expect hydrogen to be rare in these rocks—it’s a light gas, and would want to be up in the air. But there is water in these rocks, and there is another critical thing: energy.

You may have seen an apparatus that uses electricity to break water into its constituents: electrodes are dipped into water, and a fairly powerful voltage results in oxygen coming off of one electrode, hydrogen off the other. There are no electrodes in the rocks deep underground, but there is energy: the radioactive decay of elements such as thorium and uranium is able to pry hydrogen away from oxygen. Although we don’t know this for sure, we can calculate that the amount of radioactivity present in these rocks is sufficient to keep cells such as Bold traveler alive. So, our best guess is that Bold traveler is, indirectly, nuclear powered: radioactive decay produces hydrogen from water, and Bold traveler burns that hydrogen using sulfate in the rocks it lives in. Unlike just about every other organism we’ve ever seen, Bold traveler is completely independent of the sun.

This all sounds freaky, and for one trained in the biology of “normal” organisms, rather suspect. But what is normal? If normal is what the majority does, that Bold traveler may be normal, and we are the freaks. All the life we are used to—all the birds and trees and people and whales, all the microbes that live in the soil and oceans—are just the thinnest of films on the surface of the earth. The biosphere we know is at best a few meters thick on a globe twelve and a half million meters across. Sure, the life we know may grow to great densities in this environment, but it is a tiny environment. Now consider bold traveler and its fellows: their environment is poor, but thousands of times larger than ours. A simple calculation shows that the majority of microbial life--perhaps the majority of all life--persists in this harsh environment. It's enough to make me envision a microbial Attenborough, trudging through a lush rainforest or fertile farmland, saying "...and yet, even in this harsh environment, life persists!"


By the way, that name—D. audaxviator—is kind of a joke. It refers to Jules Vernes Journey to the Center of the Earth. The heroes of the story are guided by instructions, in Latin, addressed to the “bold traveler”, or audax viator.

Dylan Chivian et al. (2008). Environmental Genomics Reveals a Single-Species Ecosystem Deep Within the Earth. Science 322: 275-278.

Erwin Roussel et al. (2008). Extending the Sub-Sea-Floor Biosphere. Science 320: 1046.

Cara M. Santelli et al (2008). Abundance and Diversity of Microbial Life in Ocean Crust. Nature 453: 653-657.

"Good work. I'll probably kill you tomorrow."

There’s a passage in William Goldman’s excellent novel “The Princess Bride” in which the hero’s ship is captured by the Dread Pirate Roberts. All aboard are killed except for our hero; he is kept alive for one day, forced to work. At the end of the day, the Dread Pirate Roberts tells our hero that he did a good job, and he’ll probably be killed tomorrow. The next day, our hero is put to work again, and at the end of the day, the Dread Pirate Roberts says “You did very well today. I’ll probably kill you tomorrow.” This goes on, Scheherezade-like, until our hero becomes the Dread Pirate Roberts’ apprentice and successor.


Despite it's being a fantasy about pirates and swordfights and the like, this is actually a reasonable approximation of life as a lecturer as I know it. There are two types of lecturers here, a “Lecturer with Job Security” (that’s the actual title) and a “Lecturer.” The lecturer with Job Security can only be terminated with a year’s notice. I am not one of those; I am a lecturer.


Towards the end of every quarter, I have a talk with M_______, the department vice-chair in charge of teaching. Every time, she says the same thing. “You’re doing a good job. We probably won’t hire you next quarter.” There’s some difficulty getting money, or not enough students have enrolled, or the dean wants so-and-so to actually teach, or the University has decided that it hates non-faculty lecturers—whatever. Sometimes this actually happens, and I don’t have a job for three months.


When I talked with M________ earlier this quarter, I was told the same thing. I’m doing a good job; I almost certainly won’t be hired next quarter.


Apparently, the Powers That Be (that is, those even higher in the administration than the Dean) have decided to get more Frosh through Bis2A—like, a lot more Frosh. So, these powers opened up a pot of money, opened up a giant lecture hall, and opened up registration. So, a reprieve: I will be teaching next quarter (that’s just three weeks away), and I’ll have a class of two or three hundred freshlings to deal with. I am starting to get anxious about this—but on the whole, it’s better than the alternative. I wouldn’t say I feel like Westley, the hero of The Princess Bride—but I do feel relieved.