Thursday, December 30, 2010

Friday Flora

From my Mom's garden, which is better than yours:

Orbea variegata (formerly Stapelia variegata), about 10cm across. Part of the milkweed family, would you believe.

Wednesday, December 29, 2010

Encroaching decrepitude

At the prompting of the Real Doctor, I have gotten some glasses. Not just glasses, fogey glasses: bifocals.
The Real Doctor has always been bothered by the near-perfectness of my vision. However, reading too many student essays by timid frosh who write about like this for a whole page made reading glasses advisable. A thorough eye exam showed that my lenses were no longer perfect (an observation supported by my noticing that stars were no longer points, but, well, sort of star-shaped). So, glasses. And I gotta say, they make a difference. Reading is easier. Stars are a lot more finely resolved.

It's also been noted that I look more professorial.

Monday, December 27, 2010

Monday Musical Offering

I haven't had much time to practice, mainly because I've spent most of my time last week skiing--a week at the excellent Sovereign Lake Nordic Center near Vernon, British Columbia, plus a fine day at Royal Gorge here in California. So, some appropriately wintry music I played last year and some pictures to go with it.

Friday, December 24, 2010

The Microwunderkammer pledge

We spent most of the day traveling home from Vernon, British Columbia, a trip that involved a very hurried stop in Seattle. Our sojourn in SeaTac provided me with an observation about my fellow citizens that leads to the following pledge:

No posting on this blog, Microwunderkammer, will ever be typed or texted while using a urinal.

Friday Flora Frosty Flower Edition

Pretty crystals--Sovereign Lake Ski Club, Canada.

Monday, December 20, 2010

Monday Musical Offering

I don't have anything to offer, and I don't usually put other people's music here, but this needs greater fame than it has. You can hear some samples at Amazon, and they are well worth it.

Saturday, December 18, 2010

Well, we liked it

A couple of weekends ago we went to see a rather remarkable concert--the German violinist Christian Tetzlaff playing the entire Bach Sonatas and Partitas for solo violin. I don't really have standing to offer trenchant criticism of the concert--I'm not really a violinist, and I'm not that familiar with the score. So, I used the concert as an opportunity to learn the music--follow along with the score in hand, see and hear the architecture of the music. Unsurprisingly, I'm convinced that the Sonatas and Partitas are really good stuff.

I can talk a little about the performance--Tetzlaff clearly can do whatever he wants on the violin, and some of what he did that night was really magnificent. He communicated the music clearly, and with enough freedom that it became personal. I particularly enjoyed his slower movements. I did take issue with some of the faster movements, especially the Gigues with which the suites end. These are supposed to be fast, but they are dances and should maintain their distinctive triple beat. However, Tetzlaff played them really really fast--so fast that they pretty nearly lost their beat, and just became a rapid-fire string of notes. However, on the whole, I really enjoyed the concert.

There were people there who did have standing to be critics; seated behind us was an older woman who also had the score with her. She worked as a violin teacher, and she said of his faster movements that "that's not the way I learned it. Perhaps he had a plane to catch."

Friday, December 17, 2010

Friday Flora--teeny tiny edition

Haraella retrocallaso cute! It opened up a bit further, but never got all that big.

Thursday, December 16, 2010

Buddy Breathing

We all need to breathe. This is true for us humans, and it’s true for most microbes. However, many microbes have different approaches to breathing. A new discovery from Derek Lovley at University of Massachusetts reveals surprising flexibility in microbial respiration—and how a couple of bacteria can cooperate and evolve to meet a challenge to their survival.


When we breathe, we’re consuming oxygen; we need this oxygen to oxidize our food, which is mostly carbon and hydrogen (think “carbohydrates”). We often think of oxidation as simply “reaction with oxygen”. After all, we are taking the carbon and hydrogen we eat and making it into carbon dioxide and di-hydrogen oxide (or water, for the less nerdy). However, there is a more precise definition of oxidation that appeals to chemists and microbiologists. Oxidation is the loss of electrons by an atom; since the electrons have to go somewhere, they are accepted by another atom, which we say is getting reduced.


When we respire (which is why we breathe), we are taking electrons away from the carbon and hydrogen in our food, and giving those electrons to oxygen. We get energy from this process, which we use to make the ATP that powers the cell. But Bacteria and Archaea have figured out how to take electrons from carbon and hydrogen and give them to atoms other than oxygen: sulfur, iron, arsenic, and all manner of other atoms. They don’t necessarily get as much energy out of these processes, but it’s better than dying if no oxygen is available.


One example of this type of anaerobic (no-oxygen) respiration is seen in the Bacterium Geobacter metalloreducens, which, as its name suggests, reduces metals. When it respires, it “eats” ethanol, taking away its electrons, and “breathes” metals such as iron, giving them electrons and producing rust. Another example of this type of respiration is found in the related bacterium Geobacter sulfurreducens. It can’t eat ethanol, but it can eat hydrogen. It can’t “breathe” oxygen or iron, but it can give electrons to sulfur (as the name suggests) or the compound fumarate.


Whether or not oxygen is used for respiration, the basic outline of the process is the same: electrons are plucked off of the food, and go through a series of intermediate carrier molecules before they end up at the terminal electron acceptor. The whole process takes place in the cell membrane: the electrons on their carriers never leave the cell until they are handed to the terminal electron acceptor. As the electron is passed from carrier to carrier, it releases energy, which is used to make ATP.


The outline of this process is the same for us, and for Geobacter metalloreducens and for its cousin sulfurreducens. However, metalloreducens and sulfurreducens are specialized for particular combinations of food and electron acceptor: metalloreducens likes ethanol and iron, while sulfurreducens likes hydrogen and fumarate.


But what happens if you put these two organisms in an environment with food for only one, and an electron acceptor for only the other—ethanol and fumarate? It would seem that metalloreducens could take electrons from ethanol, but not get rid of them, while sulfurreducens could give electrons to fumarate—if only it could obtain some electrons from somewhere!


Fortunately, these two different types of cells can cooperate. Geobacter metalloreducens can get rid of electrons from ethanol—it just won’t get much energy out of the deal. Water, it turns out, is mainly H2O, but always has some OH- and some H+; metalloreducens can give those electrons from oxidizing ethanol to H+, making hydrogen gas. This works out nicely, since sulfurreducens can “eat” the hydrogen, and give the electrons to fumarate. So, even though each member of the partnership only gets half as much energy, it’s better than getting no energy at all.


This type of collaboration is called “syntrophy,” and it’s actually fairly common in the microbial world. One organism respires, producing hydrogen; the next organism respires, “eating” that hydrogen. Each organism has a complete respiratory system, but the two respiratory systems are dependent upon each other. Syntrophy occurs in your own personal digestive system, in which one organism makes hydrogen, giving electrons to another organism, which uses them to make the methane that makes our farts flammable. Up till now, when syntrophy has been studied, it has always involved hydrogen as the electron carrier. However, Lovley’s group introduced an interesting complication to this process.


Lovley’s group mutated sulfurreducens so that it absolutely can’t eat hydrogen. They then started the experiment again, giving a mixture of metalloreducens and sulfurreducens nothing but ethanol to eat and nothing but fumarate to breathe. Given that the options for these populations of cells were (a) evolve or (b) die, it’s unsurprising that option (a) was chosen.


What was surprising was the way that evolution worked. Rather than jury-rigging a way for sulfurreducens to eat hydrogen, evolution chose a method that involved the direct transfer of electrons from metalloreducens to sulfurreducens. I mentioned that when a cell respires, the electron gets shuttled from one carrier molecule to another as it moves from the “food” to the electron acceptor. These carrier molecules stay in the cell membrane, and respiration happens strictly within the confines of the cell.


What Lovley found was a mutant form of sulfurreducens that produced electron carriers that could be exported to cells of metalloreducens, pick up electrons, and then shuttle back to sulfurreducens. The sulfurreducens cell had to make filaments for these carriers to travel along, and had to grow next to metalloreducens—but one part of respiration was happening in one cell, and the other part of respiration was happening in another cell. This is syntrophy, but without using hydrogen to transfer the electrons. Electrons were flowing directly from one cell to the other.


Being thorough, Lovley’s group made sure that they were seeing electrons moving directly between the two cells. They checked to see if hydrogen was being exchanged—it wasn’t. They found the genes in sulfurreducens that had mutated to allow this to happen, and deleted them—and growth stopped. They looked for electrical current between cells—and found up to four microamperes of electron flow. They looked at the cells using various forms of microscopy, and found that they grow in close contact…

(this is a clump of cells, with metalloreducens stained green and sulfurreducens stained red. They can't grow separately, like the cells in a normal syntrophic relationship.)


…and they used the much higher magnification of electron microscopy to show that sulfurreducens made a web of filaments that connected it to metalloreducens cells, and that electron carriers (visible as dark spots) could move along those filaments:

This has never been seen before—respiration has always been contained within one cell. But now, we know that the process of respiration can be completely shared between two cells, a sort of bacterial “buddy breathing.” One cell oxidizes food (metalloreducens taking electrons from ethanol) and the other reduces an electron acceptor (sulfurreducens giving electrons to fumarate). This kind of metabolic sharing allows both cells to survive in an environment that could not sustain each individual, and so gives life the ability to exploit ever more of the earth’s environment. It’s also a nice example of life’s seemingly endless creativity—what Daniel Koshland calls “improvisation”—using mutation and selection to try out novel solutions to novel problems.


Zarath M. Summers, Heather E. Fogarty, Ching Leang, Ashley E. Franks, Nikhil S. Malvankar, and Derek R. Lovley (2010). Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria. Science 330: 1413-1415.


Koshland, Daniel (2002). The Seven Pillars of Life. Science 295:2215-6.


Tuesday, December 14, 2010

Twitchy

The most common image that people have of how bacteria move is of a little bug swimming along using its flagella. So busy!

video

But the bacteria have other means of getting around—one of the more amusing ways of moving is called “twitching motility.” Cells that move by twitching motility don’t have a flagellum. Instead, they produce a thing called a "pilus." This is kind of like the telescoping radio antenna you see on a car: it’s a thin shaft of protein that can extend from the cell, then retract back--here's Pseudomonas pulling in some pili:

video

The end of the pilus has a sticky protein on it, so to continue our metaphor, the pilus is like a telescoping antenna with a blob of crazy glue on the end. A twitching cell extends its pilus, sticks it to something, then draws it back in. Here's Pseudomonas grabbing onto a hair, then pulling itself along:

video

Rather than smoothly swimming, the motion is herky-jerky. Or, twitching. So, it's called twitching motility!


This is how I’ve always pictured twitching motility: a cell lying down, and moving in a linear motion. But, what if the cell is standing on end? If it just made one pilus, it would pogo up and down. But if it made a few pili, it would sort of stagger—go up, then go down a little off to one side; go up, then go down a little off in another direction, depending on how poorly synchronized the pili were. A twitching cell standing on end would “walk,” but it would be a drunkard’s walk.


It turns out that there are situations where a drunkard’s walk is actually very useful. An army of drunkards, all starting at the same place, will effectively “explore” every nook and cranny of an area. If the “drunkards” are twitching bacteria, standing on end, then a population of bacteria can effectively, if blindly, explore every bit of an area, and if there’s a particularly good place to set up shop, at least one individual bacterium is bound to find it (panel A).

In contrast, the bacteria who are “lying down” and moving by twitching motility will travel farther, but won’t cover an area as thoroughly (panel B).

This isn’t just an amusing vision of staggering bacteria—a set of experiments led by Gerard C. L. Wong showed that certain types of bacteria actually use this method to effectively explore an area. Using microscopes rigged with cameras and computers, he was able to track individual bacteria; he found that the “staggerers” were much better at covering an area than the twitchers who were lying down, or those lacking pili altogether.


The bacteria that lacked the ability to make pili never really explored their environment, so they ended up crowded—a situation that makes it hard for them to get the food they need.

Bacteria that could make pili and walk around after dividing were nicely spaced out, with plenty of elbow room—and access to food.

The need to get up and explore seems to be built in to the bacterial program: Wong’s group watched hundreds of individual bacteria divide, and most often division resulted in one cell that was lying down and another cell that was “standing,” ready to get up on its pili and stagger around. If things were just due to chance, you'd expect far more freshly divided bacteria to be lying down--not the most efficient way to disperse. It seems that roving is in the genes.


This is not an earth-shattering discovery. However it does provide some insight into how bacteria explore and exploit their environment, and how wanderlust seems to be genetically programmed. It also provides the amusing mental image of a cell, twitching and staggering around like a Dickensian drunkard looking for a place to sleep it off.


Maxsim L. Gibiansky, Jacinta C. Conrad, Fan Jin, Vernita D. Gordon, Dominick A. Motto, Margie A. Mathewson, Wiktor G. Stopka, Daria C. Zelasko, Joshua D. Shrout, Gerard C. L. Wong (2010) Bacteria Use Type IV Pili to Walk Upright and Detach from Surfaces
. Science 330:197.

The movies are from Howard Berg's lab's excellent website.

Alea jacta est!

The grades are finally handed in. There's one incomplete (a guy got a concussion the day before the exam), and there's always some who are dissatisfied with their grades...so I'm not truly thoroughly completely absolutely done. But, I'm done.

Now, time to write the letters of recommendation.

Wednesday, December 8, 2010

"Will they re-write the textbooks?"

This was the question from one of my students, about the whole Arsenic-using microbe thing. The answer is "no." I didn't really think so on a casual read of the paper, and a bit more thorough read makes me even less sanguine.

The authors really needed to do a bit more chemistry--as they noted, the cells still contain phosphorus, and some patient calculations (by people who weren't busy with the final week of the quarter) suggested that the amount of phosphorus is enough to sustain a somewhat unhappy cell. Indeed, that's the most vexing thing--even after many generations of passage, there was still phosphorus in all the cells, leaving a lingering doubt throughout the whole project. More rigorous chemistry procedures are required. It's necessary to do the hard work to make really phosphorus free media, and really really purify the DNA and small-molecule fractions so there's no chance of random cellular arsenic contaminating an otherwise normal sample. So, there's stuff to be cleaned up, and it can and should be cleaned up. I think that the authors' claim is still possible, but more proof is necessary.

It's been interesting to see how various blogs have treated the story--generally, not nicely (see here, here, and here for a few, including John Roth and Jonathan Eisen here at Davis). Part of the issue has been the lack of necessary rigor. But I think people have been especially eager to hit this story because of how it was presented: this was the classic case of science by press release, with a one-week-long drum roll leading to the reveal. That's just asking for it. While newspapers love science by press release (it saves thinking), most bloggers (who are more scientist than journo) hate hate HATE science by press release.

UPDATE--14 December. I just spent the weekend at the West Coast Bacterial Physiologists Annual Meeting. This was not mentioned once--an index of how much regard it has gotten.

Monday, December 6, 2010

Monday Musical Offering better late than never edition

I bought the score back in July, got distracted by some other parts of the book, learned the piece, and then put off recording it for a month. Finally, here it is: Beethoven's "Andante Favori." Not my best recording, but at least it's done. Enjoy!

Friday, December 3, 2010

Friday Flora Frakking Fall edition

Too many leaves.




I marvel at deciduous trees. So much carbon wasted every year.

OMG! ARSENIC EATING MICROBES!!1!

It’s quite a roll-out: first, NASA’s astrobiology program announces a very important press conference coming in one week. There is all kinds of speculation, some of it quite fervid. Finally, the news. No Martians, no radio signals from Tau Centauri. Instead, a more mundane headline in the NY Times says “Microbe Finds Arsenic Tasty; Redefines Life.”

The actual science is interesting, though it doesn’t quite live up to the hype (surprise!). While the the hype is about “redefining life” and “stretching the possibilities for extra-terrestrial life,” the real interest lies in a demonstration of the power of selection and what down-to-earth microbes can do.


Here on earth, microbes (and humans, and every other living thing) have to grow—they take in atoms from their environment and convert that “dead” matter into a part of a cell. Every living thing uses pretty much the same ingredients: Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus, with a sprinkle of other elements Why only those particular elements? Carbon is neat, but could it be substituted with an element from the same column on the periodic table, such as Silicon? No. Even though it shares some characteristics with carbon, it just doesn’t have the same wonderful reactive repertoire.


This has not stopped speculation about the other ingredients found in a cell; Felisa Wolfe-Simon at the NASA Astrobiology Institute and her coworkers wondered if the phosphorus found in the cell could be replaced with a similar atom on the periodic table. However, the element most similar to phosphorus on the periodic table is Arsenic.


As the headline suggests, Wolfe-Simon found—or more correctly, evolved—a microbe that can almost completely replace its phosphorus with arsenic. In this cell, arsenic behaves similarly enough to phosphorus that it grows reasonably well. However, despite the headlines, very little adjustment need be made to the definition of life. Some definitions of life hold that “life is mainly made of the elements Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus.” So, that can be revised to read “…and Phosphorus (or Arsenic).” Ho hum.


The most interesting thing about this report was its application of selection. Natural selection is one of the driving forces behind evolution—from a varied initial population, the environment selects those individuals who are best able to survive and reproduce, and allows them to do so. The rest don’t make it. It’s very simple, but amazingly powerful. You can do this in the laboratory: start with a varied initial population, select only those individuals who have a certain trait (say, the ability to survive exposure to Arsenic), and allow only them to reproduce; the rest die.


As my mentors taught me, “you get what you select for.” If you start with a very large and very varied population, and slowly ratchet up the selection pressure, you can select for, and evolve, almost anything. In fact, something very similar to this recent study was accomplished over a decade ago, using slightly cleverer techniques.


A biology textbook might refine the above definition of life by mentioning proteins, and how they are all made of the same 20 amino acids, just in different arrangements. There is a genetic code, in which each of the 20 amino acids is specified by three nucleotides strung together in DNA. There are four different nucleotides (called A, G, C, and T), so there are 64 possible three-nucleotide combinations. 61 of these specify the 20 amino acids (there is obviously some redundancy), and three specify the end of a protein. You probably saw this table back in high school:

Starting in the 1980s, researchers (most notably Peter Schultz) tried to redefine life: they wanted to make proteins that had different, new, non-biological amino acids in them. To do this, they had to somehow persuade the cells to change the way they decoded their genetic information. Essentially, they had to convince a cell that “UAG” no longer should be decoded as “stop”, but rather as the bizarre new amino acid Propargyloxyphenylalanine. The cell, you might imagine, required some strong persuasion—and this is where selection came in.


Schultz’s group cleverly placed a gene in the cell for chloramphenicol resistance—if this gene were properly expressed, the cell could survive exposure to the antibiotic chloramphenicol. However, this gene was modified: it could only be properly expressed if “UAG” were translated as Propargyloxyphenylalanine. If UAG were used normally, as “stop”, the cell would stop making the protein, and die. That’s selection for you—and it allowed Schultz to find the very rare cell that had mutated so that it could pull of this trick. All he had to do was look for cells that survived chloramphenicol exposure.


Schultz used selection again to make sure hat he had succeeded; there was, after all, the possibility that the cell sometimes translated UAG as Propargyloxyphenylalanine, and sometimes translated UAG as some other amino acid. So, he cleverly placed another gene in the cell that encoded a weird protein called “barnase.” If the cell makes even a little bit of barnase, the barnase will kill the cell. The gene that Schultz used also had a UAG in it, but in this case, functional barnase would only be produced if UAG were translated as anything but Propargyloxyphenylalanine. Again, selection allowed Schultz to find the very rare cell that only translated UAG as Propargyloxyphenylalanine—selection killed every other cell. Again, all he had to do was look for the surviving cells.


So, you get what you select for—no matter how rare or absurd. Using the power of selection, Schultz and others have evolved cells that use more than 70 different, completely non-biological amino acids in their proteins—a pretty thorough redefinition of this aspect of life. How does this relate to the Arsenic story? Selection. Wolfe-Simon selected for the ability to use Arsenic in place of phosphorus, and you get what you select for.


She started with microbes that were already pretty tolerant of arsenic. They are not from a very unusual family—they are proteobacteria, a family name as bland among bacteria as “Smith” among Americans. However, these had been recovered from Mono Lake in California, an environment with unusually high concentrations of arsenic. In the lab, the cells were grown with increasing amounts of arsenic and decreasing amounts of phosphorus. These conditions selected for the ability to replace phosphorus with arsenic, so cells that could do this would grow and reproduce. Those cells that could not (and these were the vast majority) simply died. The selection was made harsher and harsher, so that eventually cells were growing in as close to phosphorus-free conditions as could be managed. Selection found the rare cells that learned to use arsenic, and all Wolf-Simon had to do was look for the survivors. Over the course of just a few generations, Wolfe-Simon forced the evolution of an Arsenic-using bacterium (figure C).

This is a rather extraordinary claim, and as Carl Sagan noted, extraordinary claims require extraordinary evidence. So, the bulk of Wolf-Simon’s report consists of proofs that these cells are chock-full of arsenic and very low in phosphorus. It’s bizarre—virtually everything that is usually has phosphorus has arsenic. So DNA and RNA have a sugar-arsenate backbone; ATP is now Adenosine tri-Arsenate; NADH has Arsenate rather than phosphate; the membrane phospholipids are now arseno-lipids, and so on. There’s a hint of phosphorus left. (One thing that needs to be cleared up is just how much phosphorus there is left, and where it is.) These cells (figure C) are strikingly different in aspect from their immediate “wild” ancestors (figure D). The Arsenic-incorporating cells are larger and somewhat irregularly shaped. A cross-section electron micrograph shows that much of their volume is made up of storage vacuoles absent in their ancestors (figure E; note that the magnification is five times greater). These may be for storing excess arsenic, or protecting some cellular machinery from arsenic. These are not exceptionally happy cells, though: it takes them almost two days to grow and divide. One can almost hear them sighing with relief when the arsenic is taken away and replaced with phosphorus; their growth rate almost doubles.


Like any good study, this one raises lots of new (and previously undreamt-of) questions. The ancestors of these cells were isolated from an arsenic-rich environment—so, how much arsenic (if any) is there incorporated into these cells in the wild? How much actual genetic difference is there between the laboratory-grown cells and wild cells? Could one evolve arsenic-using cells from other cells in the same environment, or even cells from other environments? The cells grown on arsenic are clearly sick—could they evolve to actually prefer arsenic to phosphorus? These are all questions that would really help us understand life on earth.


I don’t think this has the hyped impact on astrobiology. For one thing, NASA’s own definition of life scrupulously avoids mentioning specific elements as being necessary for life. Furthermore, arsenic is a much less common element in the universe than phosphorus. However, this is a really neat finding, the result of clever work, and it gives us fresh opportunity to marvel at what life can do.


Liu, Chang. C, and Peter G. Schultz. (2010). Adding New Chemistry to the Genetic Code. Annual Review of Biochemistry 79: 413-44.


Felisa Wolfe-Simon, Felisa, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies, Ariel D. Anbar, and Ronald S. Oremland (2010). A Bacterium that can Grow by Using Arsenic Instead of Phosphorus. Published on-line ahead of print: Science DOI: 10.1126/science.1197258.


We’ll leave the last word to XKCD: (click to get the punch-line.)

Wednesday, December 1, 2010

The problem is that truth is boring

I had a phone conversation with a parent the other day. He was concerned about vaccination for his daughter, and had questions about safety and long-term effects of vaccines. The nature of his questions--which were the well-intentioned questions of a concerned parent--reflected the ways that different types of information get around. It's like Mark Twain is alleged to have said, a lie travels halfway around the world while the truth is still getting its shoes on.

The questions the parent had were familiar to anyone who has paid attention to the vaccine "controversy." Is there a link between vaccines and autism? Is the mercury in vaccines going to cause brain damage? Is the aluminum in vaccines going to cause problems? There are so many vaccines--won't the immune system get tired out? Isn't the flu vaccine ineffective? Was the whole response to H1N1 completely overblown?

The answer to all of these questions is no. The undying persistence of these questions is really frustrating, and shows the sort of asymmetrical warfare that goes on between reality and wishful thinking. All you have to do is mention some poorly-supported hypothesis once, and it is established. If it appeals to people's fears or prejudices, then it is solidly rooted. The problem, though, is that the truth is boring. It can take a long explanation with lots of evidence and patient demonstration to prove the obvious--and even then, there has been some research showing that people still assign greater trust to the thing that they heard first, even if they've been shown solid evidence to the contrary.

So I tried to be patient and tactful with the concerned parent. I pointed out the origin of each of the rumors, how they were generally based on very incomplete and biased information. How, if you directly tested the question, the problem just disappeared. How the immune system can generate a virtually infinite number of immunities. How, due to poor sampling and a knowledge of history, H1N1 was initially terrifying to epidemiologists. How there's a whooping cough epidemic going on in California, and how it is totally unnecessary. How, if you were concerned about risk, you'd avoid McDonalds and driving. But I don't know if the concerned parent will vaccinate. Too often, if reality doesn't conform to bias, bias wins.

This pattern goes on too often. Just about any popular "debate" about science follows this pattern--evolution, climate change, vaccination, you name it. Rumor blurts something out, and refuting it takes patient work with lots of footnotes.

The day after my conversation, this cartoon appeared on the web, from the often amusing SMBC:

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 forward...open 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

Saturday, October 30, 2010

Jeremy Denk recital

After a couple of years’ worth of anticipation, I finally got to see Jeremy Denk in a solo recital last weekend. The Real Doctor and I have seen him a couple of times in his capacity as accompanist to Joshua Bell, and both times I was really impressed. The star of the show was the violinist, of course. But going to a Joshua Bell recital and being impressed by the pianist is like being dazzled by the moon on a sunny day. From the first, Denk’s playing made me want to see him solo. Reading his excellent blog only made me want to see him the more.


Finally, Denk has made a recital appearance in Berkeley. Unfortunately, the Real Doctor couldn’t make it—she was in Michigan—so I went with my piano technician, who is a pretty brilliant pianist and a composer to boot. The advertised program was intimidating: the Ligeti Etudes (nearly an hour of avant-garde puzzles and brain-games, conveyed through finger-breaking keyboard pyrotechnics) and the Bach “Goldberg Variations” (same, only read “Baroque” for “avant-garde”). It was almost a relief that there was an announced program change. Book two of the Etudes would be replaced by the meaty (but less mental) “Dante Sonata” by Liszt.

The Ligeti Etudes are avant-garde music that you can love. They are not easy listening, minimalism or neoromanticism; these are mid-century Mitteleuropean modernism. Nonetheless, they give even the first-time listener enough to hold onto that one can follow through each piece—in some places, there are even things reminiscent of melodies. Most of the etudes are clearly about one thing—relentless upward scales, an overall downward motion, a constant, pushing eccentric rhythm. They tend not to be massively written, and in some the texture becomes transparent to the point of nothingness. However, these are not “pink bonbons stuffed with snow” (as Debussy described the music of Grieg). These etudes are precise, spiky, but strangely elegant blooming cactuses. Denk delivered these bristling packages cleanly, highlighting the hooks that rescue the first-time listener. His touch was sure, and he found an astonishing number of shades of “piano” in the quietest passages. I came away from the performance hoping that at least half of what we heard become standards in the repertoire.

Announcing the Liszt from the stage, Denk highlighted the parallels between the diabolical theme in the “Dante” sonata and the descending motif in the last etude; this was perhaps a stretch, but no matter. Despite the title (“Fantasy-Sonata after a Reading of Dante”) it’s not the deepest stuff that Liszt ever wrote. It’s programmatic to the point that it requires little imagination, and chockablock with Lisztian pianism. After the rigors of Ligeti, listening to the Liszt was like reading a satisfyingly pulpy piece of genre fiction after plowing through imagist poetry. However, it was not really Denk’s strong suit. It was not badly played, but nor was it especially memorable. For example, things could get muddy in the sections of greatest turmoil. However, it must be said that the quieter sections of “Heaven” showed some absolutely lovely playing and tone.

It’s audacious to program the Goldberg Variations in a recital. According to legend, the piece was designed to put its insomniac dedicatee to sleep. It’s a very long piece, and also a substantial mental challenge. Every third variation is a canon, each on a different interval. Sometimes the canons are inverted, sometimes they are dilated, or augmented—Bach plays every trick he can. The ending is a double quodlibet, in which two different tunes are superimposed over the ground of the theme. The paths of least resistance are to turn the piece into a dry exercise, or treat it with so much solemnity that it really does work as a soporific. Given Denk’s intellectual bent, I almost expected this.

However, Denk also has a wickedly sharp sense of humor. His was a very fleet Goldberg Variations. Some of the spaces between contrasting variations were pressed a little, as if to keep the listener off-balance; sometimes repeats were omitted to keep proceedings moving right along. The playing was always transparent and articulated, and when solemnity was called for, it was delivered. On the whole, though, the Bach who wrote Denk’s version of the Goldberg Variations was a keen wit who was not above pointing out that he was a keen wit—when the quodlibet rolled around, the two rather earthy folksongs were really punched out. Denk’s Goldberg Variations will stay in my memory as one of my favorite perfomances of this piece, but reflecting on it the next day, I felt almost as though I had heard the Goldberg Variations written by the smart, sardonically funny Beethoven who wrote the Diabelli Variations.

It’s nice when things live up to the anticipation. This wasn’t the greatest concert ever, and Denk’s mannerisms can be a bit distracting. But, as expected, the recital was stimulating and rewarding. So, now I am anticipating the next time this pianist comes out west. And, I am hoping he plays some Beethoven, maybe the Diabelli Variations.