Friday, September 30, 2011
It was a long day of hiking, but well worth it. As you go up in elevation, you go botanically back through the calendar. As we had lots of snow this year--and there were still big patches of snow at the higher elevations--up at the passes it was still early spring. So, going up and down I got to see a year's worth of flowers in one long day. Quite a treat.
Here's some early spring, blooming at around 2750 meters in late September:
A shooting star, one of my all-time favorite plants. I'm more accustomed to seeing this in March!
Marsh Marigold, Caltha leptosepala. I'd never seen this blooming before, but it was lovely.
Dwarf Willows--I'm always amused to see willow trees (probably older than me) that are only two inches tall. They were blooming, but they had better hurry up--the weather forecast calls for snow in a few days. A spectacularly short growing season.
Wednesday, September 28, 2011
There was a bit of news last week that generated headlines such as “Gamers Solve Problem that Stumped Scientists.” As always with science by press release, the reality is cool but not that cool.
The “Protein Folding Problem” is one of the most damnable problems facing biology. It would really be nice to reliably predict protein structures. Knowing the structure of a protein allows us to understand how the protein works, so we can do useful things like design effective drugs. However, precisely determining the 3-D structure of a protein is extremely time-consuming, fiddly work that has a low probability of success. So, there’s a lot of interest in using computers to predict the 3-D structure of a protein.
The problem is this: genes encode proteins, and we can easily “read” a gene to predict the linear sequence of amino acids in a protein. However, a linear sequence of amino acids is useless: it must fold on itself in an often-incredibly complicated structure to make a functional protein. Starting with a linear sequence—basically a string—there’s a nearly infinite number of three-dimensional structures that are possible. Some possible shapes can be eliminated, since certain amino acids in the string don’t want to be near each other or near water. Some other possible shapes are more likely, since certain amino acids in the string want to be near each other, or near water.
In principle, those simple rules should make it possible to predict how a linear sequence of amino acids will fold to make a protein. However, a typical protein is made of several hundred amino acids. So, while computers are OK at predicting structures of very short fragments of proteins, predicting the structure of a protein requires more power. Lots of power—the number of possible ways a typical protein can fold far exceeds the number of possible moves in a game of chess (about 1046), so IBM built a successor to the chess-playing “Deep Blue” supercomputer and called it “Blue Gene,” intending it to work on this problem. Blue Gene has been among the most powerful supercomputers for several years, but it still is far from efficient at predicting protein structures
A somewhat more effective approach to “the protein problem” has been to use distributed computing—borrowing time on hundreds or thousands of networked PCs when their owners are not using them. SETI@home, which screens huge amounts of radio telescope data for potential signals of extraterrestrial life, is a famous example of this. Biochemists have Rosetta@home, which uses the same approach to predict protein structure. This venture has actually produced some predictions which jibed pretty well with the actual structures. But Rosetta is still limited; being a computer program, it relies on brute force and wastes resources looking at possibilities that are “stupid.”
One way to get around this problem is to borrow from humans something that computers lack: intuition. This has been the approach of the creators of “Foldit,” a program that turns the protein folding problem into a game. Players are given a snippet of a protein, and (not needing to understand anything about Van der Waals forces or acid-base interactions), jiggle it around until it reaches a very stable conformation—which corresponds to a high score. As the authors of the paper that made the headlines say, this program uses the power of games…
“to channel human intuition and three-dimensional pattern-matching skills to solve challenging scientific problems. Although much attention has recently been given to the potential of crowdsourcing and game playing, this is the first instance that we are aware of in which online gamers solved a longstanding scientific problem. These results indicate the potential for integrating video games into the real-world scientific process: the ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.”
So what did the gamers actually do? They started with a bunch of predicted structures for one protein, generated by Rosetta@home, and tweaked them. Once the actual protein structures were experimentally determined (again, a terribly painful and difficult task), the gamers’ predictions were noticeably better than Rosetta’s. Here’s a picture comparing their results with the actual structure—the linear string of amino acids is sometimes presented as a flat ribbon, sometimes as a noodle; it can curl up like a telephone cord, or lie flat in a sheet, but this picture shows one string.
The red ribbons represent the predictions of Rosetta; the yellow represent the predictions of the gamers; and the blue is the real structure of the protein. All three are superimposed. In almost all parts of the protein, the yellow, gamers’ structure is closer to the real, blue structure than the red, Rosetta structure. Bravo gamers! However, it is worth noting that the gamers started from structural predictions by Rosetta, and there are still places where neither Rosetta nor the gamers predicted reality very well.
This result leaves the protein structure problem in an interesting place. On the one hand, progress could be made by using more of that intangible, unquantifiable whatzit, human intuition. However, this is not intellectually satisfying; it would be nice to say that we really understood the rules of protein folding—and if we could understand them, we could teach these rules to a sufficiently powerful computer. After all, a computer has no intuition, but then again, nor does a string of amino acids, which just follows the rules of physical law. So, clearly, we need bigger more powerful computers which can more closely simulate reality.
This seemed like an insurmountable challenge—only so many people will join with a distributed network such as Rosetta@home, and machines much bigger than Blue Gene are prohibitively expensive. However, Felix Balatro and his coworkers at Miskatonic University and in the Ukraine arrived at a devious solution to the problem. In a series of stunning papers starting in the December 2011 issue of the (admittedly rather obscure) Ukrainskii Zhurnal Tsilkovita Durnitsya , Balatro predicted the structure of a half-dozen difficult proteins with unprecedented accuracy.
These results were not widely reported in the popular news, but they raised a lot of questions in academia. After all, Miskatonic was not known as a computer science powerhouse, and the Ukrainian group seemed suspiciously difficult to contact for discussion about methods. Nonetheless, the results kept coming in the early part of 2012, and the predictions only gained in sophistication. In fact, one of the predictions was actually used to develop an anti-retroviral drug.
The curtain was finally lifted on the mystery by the German weekly der Zwiebel. The elusive Ukrainians were a front group for an organized crime syndicate that rented out time on the botnet of more than seven million computers infected with the “Conficker” worm. Balatro realized that this botnet was by far the world’s largest distributed computing network, and that its masters—although very punctilious about their payment schedule—were essentially in the business of renting computing power. Granted, nearly all of their other customers were criminals, and the power was typically used for card-hacking and DDOS attacks, but the rates were very cheap and the programmers very clever. Balatro arrived at the conclusion that this was the best way he could use his insubstantial research funding.
This disclosure left the scientific community, and society as a whole, in a quandary. Some demanded that Balatro’s papers should be retracted—but they couldn’t say exactly why, since the results were valid and there were no obvious conflicts of interest. Some prosecutors wanted to bring suit—but there really weren’t any injured parties, and no US laws were broken. An intriguing new avenue for drug design had been suggested by some of his results—but would such a drug be ethically tainted?
Although the scientific worth of Balatro’s results remains unchallenged, the ethical clouds surrounding the results continue to gather. An anonymous whistleblower recently revealed to der Zwiebel that DARPA actually considered and partially developed a worm that would allow it to run simulations of atomic weapon tests at low cost. Balatro himself provides the most recent puzzle; he was unexpectedly absent for the first day of his own class in the summer 2012 session at Miskatonic University, and the university administration has not been able to get in contact with him for over a month. There is concern that the Ukrainians did not appreciate the attention he drew to them, or worse—that he failed to make a payment.
Allen, F., et al (2001). Blue Gene: A vision for protein science using a petaflop supercomputer. IBM Systems Journal 40: 310-327.
Firas Khatib, Frank DiMaio, Foldit Contenders Group, Foldit Void Crushers Group,
Seth Cooper, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, Iva Pichova, James Thompson, Zoran Popović, Mariusz Jaskolski, David Baker (2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology. Published online 18 September 2011; doi:10.1038/nsmb.2119.
Balatro, Felix, and Українська асоціація обманщики (2012). You shouldn’t believe everything you read. український журнал цілковита дурниця 22: 18-41.
Balatro, Felix, and Українська асоціація обманщики (2012). It’s probably a good idea to run these author names through Google translate. український журнал цілковита дурниця 22: 138-141.
Balatro, Felix, and Українська асоціація обманщики (2012). Miskatonic University may ring a bell for sci-fi fans. український журнал цілковита дурниця 23: 77-91.
Tuesday, September 27, 2011
There's still geological drama today, though, and lots of sentients to see it and measure it. While in camp, I finally got around to reading some of the scientific reports about what is now called the Tohoku-Oki Earthquake of March this year, and about the Maule Earthquake in Chile in 2010. Both of these megaquakes were extremely well measured, thanks to GPS sensors, and produced reams of data--data that could be distilled into a couple of pictures that can give you nightmares (as if the videos and photos of the quake and tsunami didn't do it). This one just made me gape:
You definitely need to click on that and blow it up. Ideally, you should blow it up so that it's about the size of a football field. See those black arrows on the picture of Japan? You should blow up this picture so that they are 24 meters long. Each arrow represents a report on the horizontal movement of a fixed GPS station during the recent megaquakes. It's a useful exercise to simply pace out 24 meters, just to see how big a distance it is. When you think in terms of a region moving that far, it's damn big.
That scary picture is from a review article; the primary sources have scary pictures of their own. Here's one from the report on the Chilean megaquake, measured at M8.8.
This figure is, like many figures from the primary literature, so information-dense as to be difficult to grasp. It records many things (movement of the GPS stations, regions of slip from almost a dozen previous earthquakes, etc), but for me the trippiest is the squiggles off to the left. These record not just the final displacement of the GPS stations (the red arrows), but the route they took to get there over the course of three minutes (the trail of dots that connects the beginning and the end of the arrow). I don't know what would be worse--to be in Constitucion and go 15 meters in one direction, or to be in San Javier (SJAV) and three minutes wandering all over. Another figure from the same paper shows vertical displacements; the station at Concepcion (CONZ) actually rose almost two meters.
The figures from the paper about the M9.0 Tohoku-Oki megaquake are even worse, largely because the data is better. All of the sensors used in the Chilean earthquake were on land, and thus pretty far from the actual subduction trench where all the action occurred (it's the black line on that picture). The Japanese had GPS sensors on the ocean floor, right near the subduction zone.
(This last sentence shouldn't make sense--GPS systems require an unobstructed "view" of a satellite to work, so a sensor on the sea floor shouldn't be able to communicate with a GPS satellite. However, by putting a lot of acoustic sensors on the sea floor, a ship or buoy can triangulate to figure out its exact relationship to the sensors, and then communicate with a GPS satellite to figure out its precise location. Here's a figure from the Japanese paper to illustrate:
So, here's the data they recorded, and if doesn't make your hair curl, something is dead in your soul:
So, bits of Japan lurched eastward 24 meters and rose by three meters. I'm trying to picture the place where I'm sitting doing that, and I confess that I am utterly failing in my efforts--let's see, I think it would place me on the roof of my neighbor's neighbor's house.
This is plenty scary on its own--but here I am in Oregon, and the subduction zone off our coast is due for precisely this kind of megaquake. We're always cautioned the geographically separated earthquakes that occur close together in time are not connected. However, these megaquakes seem to be a different thing, and there's some opinion that they megaquakes around the Pacific rim may cluster--there was a bunch of them back in the early 1960's (Chile, Alaska, Kamchatka/Kuril islands) and now we may be seeing another bunch. I live well inland, but when I do go out to the Oregon coast, I take care to notice all the signs for tsunami evacuation routes. I appreciate geological drama, but its toll on human life overwhelms me. I prefer to view such drama with the remove of a scientific paper, or (as with the Sierras) at the distance of a hundred million years. It's scary enough for me.
Heki, Kosuke (2011). A Tale of Two Earthquakes. Science 322: 1390-1391.
C. Vigny, A. Socquet, S. Peyrat, J.-C. Ruegg, M. Métois, R. Madariaga, S. Morvan, M. Lancieri, R. Lacassin, J. Campos, D. Carrizo, M. Bejar-Pizarro, S. Barrientos, R. Armijo, C. Aranda, M.-C. Valderas-Bermejo, I. Ortega, F. Bondoux, S. Baize, H. Lyon-Caen, A. Pavez, J. P. Vilotte, M. Bevis, B. Brooks, R. Smalley, H. Parra, J.-C. Baez, M. Blanco, S. Cimbaro, E. Kendrick (2011). The 2010 Mw 8.8 Maule Megathrust Earthquake of Central Chile, Monitored by GPS. Science 322: 1417-1421.
Sato, Mariko, and Tadashi Ishikawa, Naoto Ujihara, Shigeru Yoshida, Masayuki Fujita, Masashi Mochizuki,Akira Asada (2011). Displacement Above the Hypocenter of the 2011 Tohoku-Oki Earthquake. Science 332: 1395.
I've been away from the web for a few days, in the presence of this:
Without fail, any time I am out camping, I find this lyric running uninvited through my head--it's by "Banjo" Patterson, the Australian poet, from his ballad "Clancy of the Overflow," in which he rather romantically imagines the life of the outdoorsman:
...And the bush has friends to meet him
And their kindly voices greet him
An the murmur of the breezes and the river on its bars.
And he sees the vision splendid
Of the sunlit plains extended
And at night the wondrous glory of the everlasting stars.
So, combined with the wind blowing through the trees, here's the music for the last few days:
Thursday, September 22, 2011
Normally I wouldn't bother to read such a review, but for the fact that I got to see some of the filming of this entertainment. The last time I visited my parents, we went for a hike at Will Rogers State Park. Old Will was quite a horseman, quite wealthy, and so his estate (now the state park) has a polo field. Apparently the Will Rogers polo field is more convenient for filming than one in the Hamptons, so the place was swarming with the film crew, real polo players and ponies hired for the show, and a passel of extras. But how to make it look like the Hamptons, and not Southern California? Just label everything "Hamptons" with a sign fresh out of the laserjet (click on the picture to enlarge).
Never you mind those eucalyptus trees! Now, all that's needed for total Hampton-ness is some Hampton-y looking people. A cattle call and a quick visit to wardrobe produced this tony crowd:
(Not the best photo, but it was very much the rich-east-coast stereotype (except for being, overall, several skin shades less white). Oh, and do make sure that the Porsche and Land-Rover stay in the picture!)
Finally, the polo. They had to make the polo grounds look like they'd been used. Rather than actually waste time playing polo (which I'm sure the real players would not have minded being paid for), they had this guy drive all over the field, randomly flinging clods of turf around.
At this point, I started wondering just how many minutes of screen time this was going to amount to, how much it was costing--and just how much it would be worth. Oh, and make sure the Mercedes stays in the picture.
Finally, some polo! First the leading man has to get his polo jersey sweat-stained--easy, he lifts his arm and the make-up lady spritzes them with a spray bottle. Then, it's up into the saddle of his doughty steed, already poised in front of the camera:
Well, that was worth it. If anyone out there who reads this actually sees this moment on TV, let me know. I'm curious as to whether it was worth the efforts of everybody at the shoot. We found it diverting, but it was free.
Tuesday, September 20, 2011
Rather than further traumatizing this sensitive soul, the Real Doctor and I felt he would benefit from the more stable environment of a friend's house. Then, when things had died down somewhat, we could reclaim him. Well...he kind of glued himself onto those friends, and manifested no interest in rejoining us. We miss the beastie, but he evinces no nostalgia:
The Real Doctor suggests that we may have alienated Unnamed Cat because we never named him. Well, his new name is "Mr." Besides, I think Unnamed Cat is a fine name, and consistent with pet names in my family.
When I was a tyke of three or four years' age, we had a pet kangaroo rat. My memories of the creature are hazy at best, but I think he was a leftover from one of my dad's colleague's research projects (kangaroo rats have some crazy physiology to conserve water). I don't know if I ever saw the critter--kangaroo rats are exclusively nocturnal and I was pretty heavily diurnal at the time. His home (if I recall correctly) was a small brown glass jar inside a large glass carboy, all situated above toddler-eye level, so I couldn't even really see him sleeping. Such an enigma! When my parents had some guests over, one of them asked my brother what the critter's name was. The beast was enough of a non-presence that he had never been given a name, so my brother replied with complete honesty "nothing." That statement of fact became the animal's name, Nothing.
The Real Doctor feels that "Nothing" is not a proper name for an animal, and the names of my family's subsequent pets (e.g. "Stupid" the Carolina Anole, "Fuzzybutt Turdflinger" the chinchilla) also met with her disapproval, as did my suggestions for Unnamed Cat. I have to say, though, that I feel somewhat vindicated by our ex-cat's new name, as well as the name of a pig that we saw at the Douglas County fair a few weeks ago. Bear in mind that this pig was some kid's pride and joy, and did well in competition:
Monday, September 19, 2011
This piece has some little bits that are just difficult for fingers to do--play legato with your fourth and fifth fingers while playing staccato with the first and second, and so on. It's definitely a good etude. It's also pretty amusing music--I like the bit just before the ending where he crawls up the keyboard in a desperate search for a home key, and then just gives up and starts the finale.
Friday, September 16, 2011
Tuesday, September 13, 2011
Since then, biking has been many things: a way to get from California to Wisconsin, a way to learn about an area, a way to make friends, a way to blow off stress and keep in some sort of shape. It was how I met and got to know the Real Doctor. Our wedding invitation has a picture of us on a tandem, and we rode away from the wedding on the same bike.
The last few years, however, haven't been so great for biking. Sacramento has the American River Bike Trail, which is wonderful, but if you don't want to drive to ride your bike, that's about it. So, biking became exceedingly flat and one-dimensional. Sacramento is very sprawly, so although we made friends through the excellent bike club, we rarely interacted with them outside of rides--an evening dinner would mean a 45-minute drive each way. We gradually lost interest in waking up at 6:00 on a Saturday and driving an hour to get to the start of the club ride, and biking lost a lot of appeal. In the last two years, I don't think we've ridden a ride longer than fifty miles with more than a couple hundred feet of climbing--the most you can do on the bike trail. This year, the stress of moving and teaching a class of 300 frosh and aging parents and more kept me off the bike entirely from about May onwards.
So now we are Roseburg, an excellent town for biking. Good roads, good terrain, a nice club, and we're trying to get back in shape. Our first ride, in mid July, was awful beyond words. It was about the same length as my high school classmate's mind-blowing ride, and about as flat as possible in this neck of the woods. We were slow. We went up gentle rises in our lowest granny gear. That evening and all the next day I was walking around like an arthritic cripple, with shuffling step and plenty of groaning.
Riding has gotten better, though. We've started to explore new terrain, and for the first time in over a decade I am having the wonderful feeling of discovery you get from riding up an unknown road for the first time. There are hills that forced us into the lowest granny gear a few weeks ago that we now sail over in the middle ring. Last weekend, despite much trepidation, we did the 60-mile Cycle Umpqua Vineyard Tour. It went very well--we finished in good time and with legs that felt pretty good. We actually ended up dropping our original pacesetters, a bunch of FOGs* from Grant's Pass. I formerly regarded metric centuries as a cop-out. However, I'm pretty darn pleased. Hopefully we'll be able to keep this up through the snotty season.
(The Real Doctor (shadow on the right) takes a picture as we ride through scenic Garden Valley, a few miles out of Roseburg)
*FOG = Fast Old Guy; there are usually lots of these at centuries.
Monday, September 12, 2011
With all the sturm und drang of moving, etc, my piano practice pretty much stopped. I had Beethoven's Tempest Sonata ready to record back in May, but then my piano got packed up. It's now in storage, waiting until we move out of our rental. I didn't get to practice at all for about two months in there, and the Real Doctor realized I was going crazy--so she prescribed a temporary piano. The Rx here is a 1970's Kawai K-15, which is actually a rather good piano for its size and price.
My right hand has become somewhat fragile in the last few years, so rather jump right in with the Prokofieff and Medtner that I was working on before the hiatus, I've started up with a set of left-hand etudes by Saint-Saens and some nice-but-less-stressful stuff by...well, I'll keep you in suspense. There's a lot of left-hand-alone stuff that I think is better music than these etudes. However, these are among the best that I've played as technical studies, and the music is definitely not bad. It's interesting to see a guy as traditionally rooted as Saint-Saens edging towards atonality in some of the pieces.
Friday, September 9, 2011
Be glad it's only a few cm tall--it's a carnivore. If gnat brains had room for dreams, then this would fill them with nightmares. The leaves are covered with glands secreting an attractive adhesive. The trapped insects die, yielding their nutrients to the hungry plant. An interesting way to cope with nutritional stress.
Thursday, September 8, 2011
The other reason I gravitated towards education rather than research is that I want an educated society. There's so much in this modern world where even a smidge of education--let alone acknowledgement of reality--is useful, that I feel an obligation to work towards that end.
I can take this latter motivation personally. When I see something that militates against understanding--say, a presidential debate for a party that boasts the support of approximately half of the nation, in which the default position is either a flat-out rejection of science or at best mealy-mouthed equivocation*--I take it as a personal affront. When a big chunk of society does it, I can feel a bit rejected. So I'm in a bit of funk today, and wondering just how much worse it will get.
There's this odd recreation called fantasy football. As I understand it, you get to put together an imaginary team of real players and let it compete against other imaginary teams. I think we need to have all of these political aspirants who don't want to engage with reality and let them play fantasy politics. They can all be the fantasy president of their fantasy countries, and make all the fantasy decisions they like--and leave reality to those who care deal with it. Feh.
*Yes, I know there's one exception, but few people give him any chance at success.
Tuesday, September 6, 2011
Trying to take a decent picture of Crater Lake is like trying to take a decent picture of Beethoven's ninth symphony. The color of blue is unique, and there's plenty of visual beauty around. But (for me) the lasting impact of Crater Lake is not an image, but how it makes me feel, thinking about the forces and events that created this sight.
We also went the other direction to check out the Oregon Coast. Cape Blanco is the westernmost* point in the continental U.S., and home to a classic lighthouse.
(Click on the picture to get the full effect.) The place has as much drama as Crater Lake--it's either rainy and windy, impenetrably foggy and windy, or sunny and very windy. The lighthouse is one of the few that the USCG will allow civilians to enter. The real attraction on the tour is the Fresnel lens, a work of functional art built in the '30's in Paris. It's huge, over 2 m tall, and mesmerizingly beautiful.
And what do you know, it works--here's the view from Agate Beach in Port Orford, ten miles away. Click on the picture and you can see the wink of the light:
I have to say, there's plenty of Sturm und Drang in the landscape here.
It was good to act like a tourist, since I don't really feel like a native in this landscape yet. I am still learning the plot.
Every landscape has a story. I've always told my students that the life we see today is just one still from a motion picture
Landscapes are the same way. In most of the places I've lived, the plot has been easy to follow. The Sierras are like Wagnerian Opera, with ice giants and godly forces. Wisconsin and Sacramento are like a minimalist opera, with little movement but the steady back and forth of erosion and flood deposition. The Bay Area is like a disaster flick, mostly boring but with predictable, violent events. But Roseburg? The plot here leaves me confused and disoriented.
It's like three completely different movies showing on the same screen at the same time. On the west edge of town, we have coast range geology, with sedimentary mudstones and pillow basalts folded into a complex mess. On the east side, we have the flood basalts and ash deposits of the Cascades. And butting into the south of town is the mysterious, ancient mess of the Klamath mountains. They used to be attached to the Sierras, but 100 million years ago decided to up and move themselves 80 miles away. If you get to a high enough vantage point to see a big area, no single plot emerges. There are valleys and ridges running every which way, and all sorts of different rocks. It's a mess, and I'm still disoriented. So, I should get out and be the tourist more--drive around with my Roadside Geology of Oregon, maybe take a float down the Umpqua river. It can be hard to follow the opera without the libretto.
*There's a place in Washington that makes the same claim; however, except at very low tides, it is an island and not part of the mainland.