Saturday, July 31, 2010
You may have met him,--did you not,
His notice sudden is.
The grass divides as with a comb,
A spotted shaft is seen;
And then it closes at your feet
And opens further on.
He likes a boggy acre,
A floor too cool for corn.
Yet when a child, and barefoot,
I more than once, at morn,
Have passed, I thought, a whip-lash
Unbraiding in the sun,--
When, stooping to secure it,
It wrinkled, and was gone.
Several of nature's people
I know, and they know me;
I feel for them a transport
But never met this fellow,
Attended or alone,
Without a tighter breathing,
And zero at the bone.
We met a narrow fellow today while out for a ride on the bike trail. He--snakes are stereotypically masculine, as spiders are feminine--was a really large Pacific rattlesnake crossing the trail. D. thought he was over a meter, I thought somewhat less, though in the way of snakes and memory, he now seems more like four feet. This was a snake that had been having a good year. He had recently shed his skin, and his scales had a beautiful gloss to them. His diamond-patterned body had tinges of yellow, chestnut, olive, and maroon, and his rattle was at least seven segments. Folk traditions speak of snakes mesmerizing their prey, and his progress through the grass was mesmerizing. Snakes sometimes blunder; I’ve seen garter snakes stumbling, which they are clumsy enough to do even without legs. But for this snake, there was no frantic zigzagging or blundering along. He just moved as if he was water being poured through a channel in the weeds. Every so often, on viewing a particularly graceful dancer or skier, I've been seized by desire--not for the person, but for the ability to move like them. I felt the same way for this snake.
Thursday, July 29, 2010
Yesterday was the last lecture for my introductory biology class. I finished the day’s instruction (the topic was Eukaryotic cells), and because time was short I finished with a very short exhortation. Nothing near as eloquent as Darwin’s “Tangled bank”, but a short reminder about why biology is so rewarding to study and how they hopefully now have a foundation for their further explorations. The lecture ended, and the class applauded.
This is a curious tradition. It’s odd enough in the concert hall. The conductor Leopold Stokowski (the guy who shakes Mickey Mouse’s hand in “Fantasia”) once chided an audience for applauding between movements: “I have been considering this matter of applause, a relic from the Dark Ages, a survival of customs at some rite or ceremonial dance in primitive times… When you see a beautiful painting you do not applaud. When you stand before a statue, whether you like it or not, you neither applaud nor hiss.” Applause seems even more out of place in the lecture hall. I’ve seen it here at Davis in all the classes I’ve taught, but I don’t recall ever seeing it anywhere else in any of my university experience. Despite the incongruity, I appreciate it. Who doesn’t appreciate some sort of acknowledgement, no matter how pro forma, and I'm certainly not getting that much love from my employer. But it reminds me of how much what I do as a teacher is performance. As a lecturer I cultivate performance skill as well as my knowledge of the subject. When the class ends with applause, I feel that the students are honoring something secondary—the performance aspect of my work—rather than the primary aspect, the learning. I’d happily take stony silence at the end of the lecture in exchange for a class in which every student scored 100% on the final.
This being summer session, an entire quarter has been wedged into five weeks. Quarters are short enough that they feel rushed, so a five week quarter is just absurd. This frenzy of living life at double speed has inevitably affected my ability to do anything else. The garden is run to weeds, I have touched neither the violin that I am building nor the one that I play, and I haven’t seriously played the piano in weeks. Naturally, there’s been less activity here in the wunderkammer. However, things should soon improve all over.
Monday, July 26, 2010
If you click on the picture, you'll see the chicks.
We had human visitors too--the parents blew through for a short stay. I've essentially neglected all housekeeping for the last four weeks due to the demands of summer session. So, I spent all Saturday atoning for my sins of omission. Adding to the fun: grading 115 midterms. More fun: one of my TAs and the grader have been sick the last week. I don't feel well-rested, and unsurprisingly, there's no Monday Musical Offering.
Wednesday, July 21, 2010
updated 23 July--There are reports that fuzzy turkey chicks are definitely citizens of the land of cute when they are back-lit by morning sun as they stumble across the bike trail.
Monday, July 19, 2010
I am slowly working my way through them all, so stay tuned!
Saturday, July 17, 2010
As Ricky Lee Jones’ kid-inspired lyrics suggest, fairness is at least partly a learned quality. A young child doesn’t get fairness at all, and views of fairness change as children mature. I was amused to read a paper by a group of Norwegian economists who were trying to quantify this process.
A classic tool for looking at fairness in human interactions is “The Dictator Game.” The economist/sociologist/researcher gets two people, and gives one of them, the “dictator,” a sum of money. The dictator is then asked to divide up the money as he or she sees fit. Purely selfish people will keep it all, but (reassuringly) purely selfish people are rare. Most dictators give the other test subject some of the money. This is true across cultures and across ages.
But life is rarely as simple as the dictator game. Wealth is, alas, all too rarely bestowed by a rich uncle; it must be earned. But life is capricious—some have wealth due to luck, whether due to a rich uncle or a happy accident. And further complicating things, not everybody needs the same things, so a gift to some is worth far more than a gift to others—a factor the economists call “efficiency”. How does a person’s idea of fairness account for these factors of effort, luck, and efficiency? The Norwegians found that for most people, views of fairness change with age.
The Norwegians modified the dictator game so that the dictator divvied up wealth that was “earned,” in this case by the dictator and the partner sorting numbers on a computer screen for a while. Both dictator and partner were perfectly free to play video games, but most everybody “worked.” The researchers then modified the game—at random, one of the subjects of the game would be compensated for their “work” at a vastly higher rate. Since this was due to chance, the idea was that this would model “luck.” And finally, they modified the game by telling the dictator that every cent he or she kept would be worth one cent, but every cent he or she gave to the partner would be doubled, trebled, or quadrupled. It would be most “efficient,” and result in maximum benefit to society, for the dictator to give everything to the partner.
The Norwegians found that younger kids have, on average, a simple notion of fairness which they called “egalitarianism.” Regardless of effort, luck, or efficiency, the dictator divided things 50-50. As children aged, up to the end of high school, things changed. They steadily became more “meritocratic,” with dictators assigning wealth according to effort. Additionally, children paid more attention to efficiency, but this was a late development. Interestingly, boys (on average) discovered efficiency by age 13, while it took longer for it to be a factor for girls.
It’s not too surprising that most peoples’ views of fairness change as they grow up. A meritocratic view of fairness, accounting for efficiency, requires a certain level of cognitive development. But, as the authors note, this development must be in part driven by society. This study was not done in the United State, the world’s leading light of market-driven capitalism. This study was done in Norway, which is one of those awful European hell-holes that the champions of the invisible hand warn us about, and the toxin of Euro-socialism can’t help but warp impressionable young minds.
However, there is something here for the free-marketers. Besides the egalitarianism and the meritocracy, there is a third view of fairness manifested in this study. The authors call it “libertarianism, which justifies all inequalities in earnings.” Libertarian dictators give themselves all the wealth that is to be distributed. It appears, according to this study, that about a third of children are born libertarians, and since that number remains constant, it appears that the libertarians never grow up.
Having interacted with a few libertarians, this is also not surprising.
Ingvild Almas, Alexander W. Cappelen, Erik O. Sorensen, and Bertil Tungodden (2010). Fairness and the Development of Inequality Acceptance. Science 328, pp. 1176 - 1178.
Friday, July 16, 2010
Tuesday, July 13, 2010
It was observed that the Core Mission of the University of California is to pay lip service to education.
Meanwhile, over at the Cal State University, things are little better. Back in May, I was supposed to know something about employment for the coming year. The deadline passed, and even then they only knew about the fall. I recently asked about the spring semester, and thanks to California's annual budget gyrations, they won't be able to tell me anything until November.
In addition to the trillions of bacteria in our gut, there are other residents of our intestines that we have evolved with—the myriad types of worms that parasitize us. Given the deservedly bad reputation of whipworm, ringworm, tapeworm, schistosomes, and their helminthic ilk, it comes as a surprise that the last ten years of research indicate that these worms can actually do us some good.
Our immune systems evolved in a world of worms; the worms evolved in the world of our immune system. For a worm to survive in our gut it has to somehow survive the assault of our immune system, and so evolution has favored those worms that have figured out how to tame an immune response. For us to have survived with such parasites, our immune system evolved with the assumption that it’s being restrained. If, with modern hygiene, the reins are off the immune system, it can run wild. So, we in the modern western world are far more likely to have allergic reactions and autoimmune disorders. If you can stomach it, you can now effectively treat your allergies not with antihistamines, but with intestinal worms purified from other peoples’ poop.
So far, most of the research on the interaction between human and worm has focused on the human half of the equation—exactly what immune cells are being stimulated and suppressed by the worms. People are now trying to understand the worms’ point of view.
Worms infect our guts, and use the nutrients that they steal from us to produce millions of eggs, which we spread by defecating. These eggs can infect another human when the eggs are eaten; it's polite to say that it’s oral-fecal contamination, but really it’s just getting stuff in your mouth that has some s#!t on it. The eggs don’t want to hatch until they are in the human gut, but what I find surprising is that the eggs do not recognize the human gut. The way they know that they’re in a human is by recognizing the bacteria that live in our gut. It's only when they see the right bacteria that they hatch (here's the movie):
A group of researchers at the University of Manchester studies whipworm, and tried hatching whipworm eggs in vitro. Initially, they found that the eggs hatched only if there was some material from the host animal’s gut present. Using a microscope, they found that the ends of the eggs that were ready to hatch were covered in bacteria (here treated so that they glow green).
Some further experimentation showed that most of the inhabitants of the animal gut worked to trigger egg hatching, and that direct contact between the egg and the bacteria was absolutely necessary for hatching. But what is the nature of the interaction between bacteria and egg? Intestinal Bacteria produce a variety of protein structures that allow them to stick to their hosts’ cells. The “fimbriae,” or fringes, are little filaments of protein with extra-sticky proteins at their ends:
Bacterial cells that couldn’t make fimbriae, or those that had their fimbriae covered up, were both incapable of triggering egg hatching. So, that’s the bacterial side of the interaction; the worm’s egg side remains a little hazy, but the researchers guess that there is a receptor on the egg that is triggered by the fimbrial protein.
One cool aspect of this study is that they were able to show that this relationship has real-world significance. The researchers used mice, and treated them with strong antibiotics to remove most of the bacteria from their guts. After two days of this treatment, the mice were infected with whipworm eggs. After 18 days, they had about a third as many intestinal parasites as their siblings who had not been given antibiotics. That’s the good news; the bad news is that they have a rather extreme immune response to the worms, probably on account of not having enough bacteria in their guts. And of course, if worms do become established, they further regulate the immune system.
Hygiene is good—nobody argues for a return to the bad old days, in which pretty much everybody had multiple infections and suffered the harm they caused. But allergies and autoimmune diseases are bad. Hopefully, we will eventually understand the complicated evolutionary ménage a trois of ourselves, our bacteria, and our worms, and we can reach an equilibrium without worms or dust allergies.
K. S. Hayes, A. J. Bancroft, M. Goldrick, C. Portsmouth, I. S. Roberts, and R. K. Grencis (2010). Exploitation of the Intestinal Microflora by the Parasitic Nematode Trichuris muris. Science 328:1391-1394.
Picture of Fimbriae from Brock Biology of Microorganisms
Monday, July 12, 2010
I've heard there are other good videos available on the web.
Sunday, July 11, 2010
However, I hate midterm writing more than I like it. It reminds me of the inadequacies and impersonality of education in this setting. So far, this class has met for the equivalent of 14 class hours, and the students have read a great deal outside of class. In a one-hour midterm, it's possible for the students to answer maybe twenty to thirty multiple choice questions, plus a handful of short answer questions. I am pretty sure that I've taught my students more than thirty-five discreet concepts. So, at some level, such midterms are not the most meaningful indicator of how a student is doing.
It's not that difficult to figure out a better evaluation mechanism--sit down with the student, ask them to explain each concept, unprompted, with regard to some specific example. (Of course, I would do this after using my jet-pack to fly to work from my private tropical island.)
I got to participate in a few oral exams for graduating seniors in a previous job, and I found that they actually could reveal a lot about the student. The closest I get with my students is asking them to write a short paragraph--but five sentences is rarely enough to reveal a scholastic personality, and after grading a hundred and thirty of those, I don't feel like I know anybody particularly well. And now, I find, that the oral exam isn't even part of the doctoral thesis defense here.
I sometimes consider giving my students the option of having their grade in the class based on an oral exam or a long-form essay. I wonder if any students would choose such an option; I wonder what percent of all students would pass. I would guess that such a policy would make me even more unpopular than I am now.
Saturday, July 10, 2010
Friday, July 9, 2010
Thursday, July 8, 2010
I’m teaching introductory biology this summer. This is the first college biology class for these students. I don’t really know who has a worse time—the complete newbies, or the whizzes who aced the A.P. biology exam.
The newbies remind me of the fourth child in the Passover Seder—the one who doesn’t know how to ask. I’ll ask the class a question that they have a few minutes to work on, for instance drawing a picture of how two processes interact. When I walk around the room to see how people are doing, some people are busy, copying something that they remember seeing, but the newbies just sit, looking blankly at the question on the board. If I ask them about it, they’ll say “I…I…I don’t even know where to start.”
I’ll ask, “do you know [fact from previous lecture]?”
“Do you know [other fact from previous lecture]?”
“How about [this thing which I just mentioned five minutes ago]. Does it have any connection with the other two things?”
In some cases, they get it; it's just that they've never been required to make connections between things. In other cases, further questioning reveals that they didn’t really know those facts from previous lectures.
The A.P. whizzes provide their own set of challenges. The A.P. exam is a clearly defined thing; it’s very challenging with lots of facts and covering a huge range of subjects. However, A.P. biology teaches the biology that is in most college biology textbooks—a biology that doggedly insists that the only living things on earth are corn, humans, and one type of bacterium that, remarkably, does not have any metabolism. Or, as a high school principal said when contrasting the A.P. exam with the International Baccalaureate program,
“A.P. is great for content-based traditional learning,” he said. “It’s great for kids who like to memorize.”
So, I’ll ask the A.P. whiz about something that is not corn or human—say, the bugs that make marsh gas. These organisms respire without using oxygen. This is not what corn or humans do, so it’s not part of their credo. The exchange gets circular. I’ll ask,
“Is this respiration?”
“No, there’s no oxygen.”
“But, does it have [a long list of characteristics, all of which define respiration]?
“So, is this respiration?
“No, it’s fermentation. There’s no oxygen.”
So, I’ll go through it again, step by step, leading inexorably to the conclusion that it is respiration.
“But…but…what about oxygen? What do they do for oxygen?”
These students are smart and have prodigious memories. But, they have a dogmatic world-view that reminds me of especially dogmatic religious folks. A friend of mine once visited some pious Christian in-laws in Georgia. She talked with their son, and for some reason the subject of Judaism came up. The son was curious, so she explained about Moses and the commandments and the Torah. She told about the Sabbath and Passover and Yom Kippur. He seemed to get the general idea, but he was completely stumped by nagging concern—“But..but...what about Jesus? What do they do for Jesus?”
Wednesday, July 7, 2010
So, I was a consumer with a need. No local brick-and-mortar store has any Vienna Urtext editions; if I wanted to buy a copy of this score, I could order one from the publisher, in Vienna, and pay an arm and a leg for it--and without an arm and a leg, I couldn't very well play it.
So here's the miracle of the internet. Somewhere in deepest darkest England, there is a used book merchant who had a used copy of the score for cheap. Amazon connected me, the consumer with a need, and the bookseller with some goods, eight time zones away. Five days later, the book is in my hot little hands. That is incredible market efficiency. Given the microscopic niche size of the market and the distances and times involved, it practically does merit the word "miracle." Essentially, in this economy, neither distance nor market size count for anything. Such a thing couldn't have happened ten years ago. Given the inexorable rise in fuel prices (and thus transport), it may not be possible in another ten or twenty years. But I'll enjoy it while I can, and hopefully sometime soon the Monday Musical Offering will be the Andante Favori.
Tuesday, July 6, 2010
It’s kind of annoying how some things get hyped. There is no clear relationship between scientific significance and press. There is a weak correlation between “coolness” and press, witness the excited newspaper articles about the fossil giant predatory sperm whale with thirty-centimeter-long teeth. That is cool, so the press is justified. But there was another fossil find this week, published in the same issue of Nature, that some undue hype.
The hype was about “the oldest multicellular organism” or “2 billion year old multicellular life.” This would be interesting—there’s good fossil evidence of organized multicellular organisms going back about 600 million years. These fossils, the “Ediacaran fauna,” are mysterious. Unlike their geological successors in the Cambrian, at 500 million years, the Ediacaran biota don’t resemble any modern organisms. There are very few believable fossils of real, organized multicellular life before the Ediacaran—so the press blurbs about two billion-year-old multicellular organisms made me suspicious.
The discovery of these fossils in Gabon is interesting, but doesn’t quite justify the hype. The reason has to do with the definition of “multicellularity.” We are multicellular. Each of us is a colony of genetically identical cells that have specialized for particular tasks. The Ediacaran fauna were multicellular. There are recognizably differently shaped organs and appendages in each of the different fossil types. Even Fuligo, which spends some of its life as a giant multi-nucleate cell, is multicellular. At the critical point in its life cycle, it differentiates into individual cells with different shapes, dedicated to different tasks. The achievement of this sort of multicellularity is an evolutionary milestone; it asks individual cells to form a cooperative, and the majority of these cells will die without leaving any offspring. For us, really, only our sperm and ova will have any direct descendants a hundred years hence.
But where do we draw the line on multicellularity? There are plenty of Bacteria, and some Archaea, that achieve something like multicellularity. Some types of Cyanobacteria—pond-scum—form long chains of cells where every 10th cell or so is different, both metabolically and morphologically. These specialized cells, like most of the cells in our body, have sacrificed their own chances for reproduction for the "common good". This sort of multicellularity has been invented over a dozen times in the Bacterial and Archaeal world, and challenges the traditional view of multicellularity as being an exclusively Eukaryotic invention.
But to some biologists, even the biofilms that make the rocks in a stream slippery can be thought of as multicellular entities. A biofilm has many different types of cells embedded in a matrix of slime like raisins in a loaf of pannettone. The different types of cells in the biofilm, which may be of completely different species, all have different and specialized roles in the biofilm. However, a critical difference between biofilms and the other types of multicellularity is that there is no organization, no distinctive organs. A biofilm is just a layer of scunge that can get bigger and bigger without pattern.
This brings us to the Gabon fossils. They are big, a couple of centimeters across, so they are definitely multicellular. They have some distinctive shapes—ruffled edges, and a thicker blob in the center. Because of the taphonomy (I love saying that word, it just rolls off the tongue. It just means how the process of fossilizing replaced biological material with minerals, in this case pyrite) of these specimens, it is impossible to resolve individual cells. The researchers do a good job of establishing that they are really fossils of formerly living things, and not just some geological trick (they examined the carbon composition of the fossils; carbon that has been part of life has a different isotopic composition than carbon from, say, a volcano). They are also able to precisely date these fossils to 2.1 billion years ago, since they are in the vicinity of the well-studied Oklo formation (a natural nuclear reactor—very cool). They even make a case, though far from iron-clad, that the fossils are those of Eukaryotes (the same Oklo formation has some fossilized carbon compounds that only Eukaryotes can make—but these fossils are only near Oklo, not in it). So the fossils are big, old, eukaryotic—but are they multicellular like us, or multicellular like a biofilm?
The researchers, unlike the press managers, are conservative in their interpretation. They point out that the feature of these fossils that look like distinct organs—the fringes at the edge, the blob in the middle—can be achieved by modern bacterial cells grown in the unusual conditions of the laboratory. These modern cells don’t normally have a tendency towards multicellularity, but they do have mechanisms for communicating with each other and regulating their growth in response to neighboring cells. Some of these patterns are quite striking:
While these patterns are not the result of multicellularity with specialization, their production does require a well-evolved mechanism for signaling and responding between cells. Seeing such patterns in the Gabon fossils does at least indicate that life had evolved some form of social interactions by this time.
So, we have NOT discovered the fossils of our great-great-diddly-great grandparents. I want to find the publicists and press people who ginned this up, and slap them. But I’d also like to find the authors of this paper, and complement them on their admirable restraint. They conclude that they have found good evidence of colony-forming organisms that are very, very, very old, and that they had evolved some methods for interacting with their neighbors similar to those used by modern organisms. They note that the fossils have a shape that hasn’t been seen preserved before, that they are the oldest fossils of colonial organisms, and that they might be eukaryotic. And while that lacks the bite of a whale with thirty-centimeter-long teeth, it’s still really cool. To me.
Abderrazak El Albani, Stefan Bengtson, Donald E. Canfield, Andrey Bekker, Roberto Macchiarell, Arnaud Mazurier, Emma U. Hammarlund, Philippe Boulvais, Jean-Jacques Dupuy, Claude Fontaine, Franz T. Fursich, Francois Gauthier-Lafaye, Philippe Janvier, Emmanuelle Javaux, Frantz Ossa Ossa, Anne-Catherine Pierson-Wickmann, Armelle Riboulleau, Paul Sardini, Daniel Vachard, Martin Whitehouse & Alain Meunier (2010). "Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago." Nature 466: 100-104.
Eshel Ben-Jacob, Inon Cohen, and David L. Gutnick (1998). COOPERATIVE ORGANIZATION OF BACTERIAL COLONIES: From Genotype to Morphotype. Annual Review of Microbiology 52:779–806.
Monday, July 5, 2010
D. is not well known as a composer of piano music--there's a piano concerto that's never played, the Humoresques (despite the annoying popularity of the violin version of one of these, they were originally written for piano), a couple of other collections of short pieces, a few variations. When you do hear Dvorak on the piano, it's typically the Slavonic Dances, which are so fun to play. The humoresques sound so Dvorak-y, good-natured, slightly folksy and lyrical. Playing them, you can hear bits of the "American" quartet and snippets of his other music. Playing them also gives a clue as to their obscurity; Dvorak was a violist, and occasionally the piano writing is just downright awkward.
One last note about the music; there is a Dover edition out there of these pieces, but it's poorly edited and has some questionable stuff in it. Much better to get the edition available on the IMSLP website.
Friday, July 2, 2010
Scarlet Sticky Monkeyflower.
One of life's great pleasures is tickling monkeyflower stigmas. You can see an example pretty well in the flower on the left, like white lips just under the top petals. An insect carrying pollen and landing on the flower will brush up against the lips before visiting the back of the flower. The insect could, while backing out of the flower, put pollen from the same flower back on the stigma. This self-pollination is undesirable, so as soon as the lips are tickled by the landing insect--or a human with a leaf of grass--the lips close tightly shut. Personally, I find this endlessly amusing. Perhaps it is not as good as trigger-plant (go to 1:25) or dogberry or mimosa, but it will suffice.