Saturday, December 31, 2011

Buried treasure

Aesop tells a fable about a father who, on his deathbed, tells his sons that there's gold buried in his vineyard. Clever dad is speaking in metaphor: the brothers so vigorously turn over the soil that the vines are well cultivated and produce richly, giving the brothers the gold they sought.

This has not yet happened on our property. However, the blackberry bramble removal project has stumbled on riches. The other day, the tractor driver was cruising along, merrily rendering vines into mulch, when the brush hog gave a mighty WHACKCLANG! and stalled. When he stopped to see what it was...well, this happened about 3:00, and let's look at the police report from the Roseburg News-Review:

Although the impact managed to stall the tractor and dented a blade on the brush hog, the jewelry safe was the clear loser in the conflict. It was chopped into three large pieces and a myriad of shrapnel. It was only with the help of a metal detector that anything was recovered. The tractor driver, who was formerly a deputy with the sheriff's, reckons that the safe was stolen, and the thieves tried to get rid of the evidence by dumping it in a bramble when they discovered they couldn't open it.

As yet, our property has not yielded any gold, real or metaphorical--we've been spending lavishly on it, and we can't keep the small amount of recovered jewelry from this incident, either. However, despite of the aches and pains I've gotten from trying to restore the place, it has yielded some good feelings, and hopefully will continue to do so.

That was the year that was

I like boredom, I really do. Slow and steady, that's the deal--no excitement, no radical changes, just incremental growth. My dislike of suspense is such that I routinely read half of a novel, then skip ahead and read the ending, then finish the book. "Xtreme" is not for me; if you catch me shredding, it is less likely to be on a gnarly downhill than with a cheese grater. That said, 2011 provided me with about as much excitement as I can stand. At the beginning of this year, I had only a small serving of anxiety about just how much and what I would be teaching. As the year ends, I have a have a whole buffet of stuff I'm not sure about, ranging from my parents' health to just what my identity is now that I'm not lecturing to undergrads.

Anyway, let's hope for a new year without unpleasant surprises, and full of gradual, incremental learning. And of course, peace, prosperity, and happiness for all.

Saturday, December 24, 2011

Flora, explained

Here's another, more revealing photo of Friday's thing:

Our Friday Flora was Rubus discolor, the oh-so-invasive Himalayan Blackberry. Like much of Oregon, we have a blackberry problem. You can make a dent in it with hand tools, but this is a literal pain. If you want to do more damage to the plant than the plant does to you, you need power tools. A Kubota tractor with a Brush Hog will do the trick, but it leaves you with piles of brambles. This being out in the country, you don't put your clippings in the green bin on Tuesday. You burn them.
So goes life. Carbon dioxide and water gets sucked out of the atmosphere and is trapped in a bramble for ten or twenty years; we come along and set it free again. I wonder how long it will remain free.

Friday, December 23, 2011

Friday Flora

(There will be an explanation, anon.)

Sunday, December 18, 2011

The farm: Before

Here's a panorama of our new place (click on it to make it bigger):
(The breaks in the pan are from moving slightly while I rotated). Going left to right, there's the house. From about 1/4 to 1/2 way across the pan, there's some power lines; these parallel Hwy. 138, and the eastern edge of the property. From about 1/2 way to about 2/3 of the way across the pan, there's a row of oaks; these are the western edge of the property. The house and barn at 2/3 of the way across the pan are our neighbors; the rest of the pan goes along the northern edge of the lot, which includes the oak forest (and the eponymous Oak Creek) but not the hillside.

Here's a view of the house, "before."
Things have been very, very busy this last couple of weeks, and things already look quite different. This can serve as a benchmark.

Tuesday, December 6, 2011

Back from LA/So it begins...

I'm finally back from La-la land; more about the situation there later. Someday I will manage the drive from LA to Roseburg in a leisurely manner. Maybe I'll take some detour along the way--see some of the Tehachapi mountains or the coast range, see the sundial bridge in Redding, visit Castle Crags or Shasta or the Klamath or Rogue River or get some culture in Ashland. But for now, the pattern is A to B, ASAP.

The urgency this time had to do with our new house, which I hadn't seen in a long time. I had to be brought up to date on all the things the Real Doctor had done in my absence, so I could tell the various contractors what to do. Of course, the Real Doctor also had to show me what I had to do.

So (having told various electricians and roofers what to do, as if I knew what was going on) I've labored the last two days on fencing. The existing fence was in terrible shape--rotten posts, tangled and fallen wires, overgrown, etc. It needed to be removed and replaced. The Real Doctor, aided by a couple of local youths, got a start on the project. I spent yesterday with one of the same locals getting the bulk of it done. This involved unclipping the heavy galvanized wire from the fence posts--or pulling it out of the ground where it had fallen and been trampled--or untangling it from a blackberry bramble--and coiling it up. Of course, any kinks or snarls meant that it wouldn't pull onto the coil, so we had to hike along the fence line to find and solve the problem and begin again.

(I'd like to make a brief aside here to sing the praises of fencing pliers. They are a great tool, and I hope whoever invented them was richly rewarded. If nothing else, their inventor has earned a lot of gratitude.)

The property's about a third of a mile long, and the fences have four or five courses of wire, and the wire has a lot of kinks, so it makes for a lot of walking and a lot of wire. This pile, shown here with the reel, is just from one short section of fence.
To take down a fence, you first have to find it. Unfortunately, we have a blackberry problem that's visible from space. So, a big chunk of yesterday and today was spent on just one section of fence that was swallowed by a bramble. Here's local youth George with some of his handiwork, just before we started to remove the wires. The fence disappears into that tunnel, which we had to carve into the mound of blackberries.
Two days of this and we're knackered and scratched like we've been wrasslin' cats. Tomorrow, we bring in the power tools and remove the fence posts.

Friday, December 2, 2011

Friday Flora


From my Mom's garden (which is better than yours), where these things grow like weeds. My Mom calls them afternoon flower, because that's when they bloom, and they're sold as tiger's jaws. Makes sense. The scientific name is Mesembryanthemum tigrina, which means mid-day blooming tiger.

Wednesday, November 30, 2011

Home is where the...well, where is it exactly?

I’m back in La-La Land, both in the Los Angeles sense of the term, and in the sense of living with the craziness of Alzheimer’s disease.

My parents live in Pacific Palisades, a coastal suburb of LA name-checked by the Beach Boys in “Surfin USA” (though more for the scansion than the waves). They moved here before I was born and they still live in the same house. In 1967, the town was welcoming to the modest means of a new assistant professor. Now, in the language of the moment, the average resident of the Palisades is closer to being “the 1%” than part of “the 99%”. With my every visit, the town I knew is further buried under hyper-architectonic mansions crammed onto the lots formerly occupied by bungalows. Upscale boutiques occupy storefronts that used to sell useful stuff.

The population of the town has changed too, both with generational turnover and with the influx of new money. I’ll admit it makes for good people-watching. Some sightings from the last week:

--three very, very white teenagers filming themselves doing a rap video with some very, very expensive camera equipment

--a guy bringing his ‘cello and music stand down to the beach to play, perhaps for the amusement of the fishes

--a rather ample man and woman doing a wedding photo shoot down at the beach, right next to a woman taking photos of her daughter all bundled up for Christmas cards. After they left, a crew came in and filmed a TV commercial.

--a terribly elegant woman jogging with her two terribly elegant afghan hounds; everything was progressing elegantly until the dogs spotted a squirrel…

--a guy who walks his pug every morning, moving very slowly and never once looking up from his texting

--tides of students to and from the high school across the street (Alma mater!), illustrating the toxic combination of teenage peer pressure, teenage lack of judgment, and too much parental money

--a vegan activist who adopts two turkeys before every Thanksgiving, and gives them the run of her front yard until after Christmas, when they go to an animal rescue farm.

Also, since this is Los Angeles and who you are is what you drive, the car-watching is also great. It’s difficult to drive in West LA without encountering automotive ostentation. Two weeks ago, while I was walking to the grocery store, I was almost hit by a car that (seriously!) cost more than my house. The driver certainly had money, but was apparently void of driving skill. At the store, there was a perfectly-restored 1950's Messerschmitt "bubble car" in the lot:

The Palisades offers an endless variety of such cars, expressing a wide range of character traits: no brains and lots of money, an abundance of ego and money, masculine insecurity and money, a love of antiques and money, eccentricity and money, too much testosterone and money, and so on. [update 1 Dec; a desire for eco-chic and money--while on a walk last night, I saw a Chevy Volt, and this is where I saw my first Tesla.]

This town, Pacific Palisades is—in one sense of the word—home. I grew up with a positively un-American level of stability: we never moved, and my parents have avoided divorce for more than 50 years. This house with its termite-riddled roof and Edenic garden--the walk down the canyon to Will Rogers State Beach--the walk up the canyon into the Santa Monica Mountains: these have all been a rock to me and my family. I was walking on the beach during an hour off of my parent-sitting duties, when I was struck by the sobering thought that in a year’s time, if everything goes as I hope it will, this rock will be gone.

The day-to-day task of providing care for my father (and mother) has really made their health the focus of my thinking about them. From this narrow point of view, I really want them to move out of their house. I feel that my father needs more specialized care than can be provided at home, and that my mother would do well to be closer to me or one of my brothers. So, I’ve been hoping that I can persuade them to move to Roseburg. In focusing so hard on this issue, I’d practically ignored—until that walk on the beach—that this would mean erasing “home.”

Well, as has been noted, you can’t go home again, and has also been noted, attachment to the material world only leads to grief. I’m pretty sure the Santa Monica Mountains will outlast Los Angeles, and despite its charms, Will Rogers State Beach can’t hold a candle to the Oregon shore. I dislike Los Angeles proper. This house is not really good for an older couple—it’s got a severe termite problem, the balcony overlooking the canyon is listing, and it’s nearly impossible to keep warm. The only real tie I have to this place is a work of art that is literally rooted to the spot—my mother’s garden, which (as has also been noted) is better than yours. While it’s not as bad as the historic eviction from Eden, saying goodbye to this garden is the only thing that would sadden me about saying goodbye to this “home.” Without it, I find myself wondering if I’ll ever bother to visit Los Angeles.


It's with wistfulness that we note the passing of Vasily Alexeyev, "the strongest man in the world." Alexeyev was a Soviet-era Russian weightlifter, and handily won gold medals in the 1972 and 1976 Olympic Games. He could pick up and put down a staggering amount of weight.
In 1972 I was five years old, and I thought it was the best thing in the world that a guy with a name like Alex was on TV, being celebrated as the champion of strength and power. Apparently, though I don't remember it well, I'd go around the house hoisting objects above my head and claiming to be Alexeyev, champion of the world.

This is not a situation well tolerated by a five-year-old's elder brothers. It won't do for the youngest to be the champ. For the two elder brothers, it's far better to have the youngest to be the loser, in third place, and even better for him to have a funny name. In this photo from '72, the guy on the right is the bronze medalist, the East German Gerd Bonk.
Every time I Alexeyev-ed, I was Bonk-ed with greater vigor. This went on till Bonk became my nickname, and I still answer to it. So, today I am obliged to pick something heavy up and grunt as I hold it over my head in honor of my late, almost namesake. As for Gerd, he's still alive, though apparently not doing well. His body is a wreck, debris from the East German penchant for chemically-enhanced athleticism.

Tuesday, November 15, 2011

The alea est even more jacta

Escrow has closed, and papers have been filed. The Real Doctor and I have bought the farm!

In other news, the Real Doctor has signed us up to get a half-dozen Nigerian Dwarf goats in spring of 2012.

Monday, November 14, 2011

Monday Musical Offering Grad School Flashback Edition

Not by me, but about me almost 20 years ago. Of course, when I was in grad school we had to do PCR on horrible machines, and developed our westerns by sloshing X-ray film in tanks of developer in a darkroom. And with one significant exception, there were no cute chicks singing my praises.

Sunday, November 13, 2011

alea jacta est

While we appear to be in Roseburg, we are actually in the magical land of Escrow. Thursday we saw the movement of a shockingly large amount of money. Friday, instead of watching the Veterans' Day parade, we entertained a parade of engineers, surveyors, architects, electricians, painters, and other contractors. The whole time I had a vision in my head of the numbers on an old-fashioned gas pump spiraling ever upward, and that lovely ding, ding, ding they made. Yesterday we drove up to Eugene to look at appliances (ding! ding!).

The state of shock that we are in is not unexpected, nor is it un-hoped-for. We made our first moves on this property in April, when we waved a large pile of cash at the bank involved. It's nice to finally be in escrow, and get started on this project.

Wednesday, November 9, 2011

Back Home, for now.

I am back at home, after a sojourn in the bizarre land of Alzheimer’s disease. My visit there was intended to be short, but grew longer and longer. It was only curtailed by some rather urgent home business, and even now I am thinking that I’ll need to go back sooner rather than later.

During that month, it struck me how normal things became. Anything, no matter how demented, can become normal, if it just lasts long enough and excludes all else, and that is the way of Alzheimer’s dementia. It becomes normal to wake up every night at midnight, and 2:00, and 4:00, and maybe at 5:30 as well to respond to whatever loudly expressed needs arise. It becomes normal to have to remind a man who used to have a too-hearty appetite what to do with toast and coffee. It becomes normal to have to reassure a man who used to be a professor that the people in the TV set aren’t in the next room and won’t be needing a place to stay for the night. Normal also includes attempting to shave one’s sweater, using a toothbrush on a bar of soap, and waking up in bed wearing one’s shoes.

Living with such a definition of normal is exhausting, and it’s well beyond the abilities of a single person to provide care for such an individual for an extended period of time. (I predicted I wouldn’t last a month. I did, but the Real Doctor says I look like heck.) However, the problem is that the definition of normal changes so incrementally and imperceptibly—especially if one’s senses are dulled by a lack of sleep. Because the metaphor lacks a factual basis, I hesitate to bring up the image of a frog in a steadily warming pot of water, but it fits here.

A major point of my visit to the parental homestead was to convince my mother, who is acting as my father’s sole caregiver, that the “normal” she was experiencing was (like boiling water for a frog) detrimental to her health. I did not succeed in this. I think I may have brought it to her attention that the water was unusually warm, a fact of which she was previously unaware. However, the current trajectory, one that has been followed by all too many families in the same situation, is a self-reinforcing decline. The patient suffers because the caregiver can’t keep up, and so he becomes even more taxing; the caregiver, faced with ever more work, tires all the more, and fails to provide adequate care—and so on to an ugly end. Through it all, my mother insists that everything is normal.

Several million people have Alzheimer’s disease. Many more millions of family members have their lives warped by it. There’s nothing that I can add, either in terms of data or eloquence, that hasn’t been covered before. But, a tragedy is a tragedy no matter how many times it is played.


Just now, as I finished that last paragraph, I got a desperate phone call from my Mom—my Dad behaving oddly, and she in a panic because she can’t find his wallet and she’s convinced somebody stole it. I will have to return, sooner than I’d planned. My hope is that she will realize how things are—that the water has gotten too damn hot, and she needs to get out now.


I feel obligated to note that the original point of this blog--to talk about stuff like microbiology and music and gardening and such--remains. However, for the last month I have been consumed by being a caregiver essentially 24 hours a day. I think I played the piano for a total of two hours, and the small amount of reading I did was not focused enough to digest a journal article. Things will remain this way for at least a couple more weeks. I hope that we'll be able to return to the usual menu of Monday Musical Offerings and Friday Flora and interesting microbiology in the not-too-distant future.

Monday, October 24, 2011

Because, apparently, not enough had gone wrong today

This happened in the oven, early enough in the process that a bunch of kugel batter glorped through the crack, onto the oven floor, and burned, producing voluminous smoke.

Saturday, October 22, 2011

Friday Flora (better late than never)

Okay, so it's very late Friday. Things have been a bit crazy here, but there's still my Mom's garden. Remember the "naked lady" from a few weeks back? Well, that was from our garden. Of course, my Mom's garden is better--here's a couple of the naked lady's relatives, native to South Africa:
Nerine humilis
Nerine falcata

Friday, October 14, 2011

Life With Father

My parents are old. I feel a little awkward using the word “old,” as it seems to have picked up some baggage during its life, but my folks are north of 75. My mom is OK , but my dad is quite infirm: a spinal fusion screwed up his posture, necessitating the later replacement of two knees and one hip. What joints are not metal are arthritic, and they all hurt. Prostate surgery has left him incontinent, and Alzheimer’s has robbed his mind. He’s like a ship, proud in my memory, but whose hull is rotting, engines are almost dead and whose captain has fled.

Anyway, I’m with my folks for a few weeks. I am mainly here to take care of my dad for a while, so my mom and her brother can attend a college hiking club reunion. My mom has been, by her own insistence, my dad’s sole caregiver as his condition has worsened over the last decade. It’s my reckoning, as well as that of my brothers, her brother, her doctor, and several family friends, that this is killing her. The fatigue and stress of being a caregiver is eroding her mental and physical capabilities. Nonetheless, she remains adamant that this is what she wants. I am giving her a few days respite—the first she’s ever really allowed herself—to attend the reunion, and my hope is that it will clear her head somewhat, and allow her to realize that she needs assistance. In the meantime, I am developing a better appreciation of what life with Alzheimer’s is like. I have been my dad’s caregiver for less than a week, and if I were in my mother’s position, I wouldn’t last a month.

Though I titled this “Life with Father,” this really is life with Alzheimer’s. Aside from the very faintest glimmer of rascality there is none of my dad left that I can detect. His personhood has been replaced by the stereotypical attributes of Alzheimer’s.

There are patterns that occur every day. He wakes up after 9:00. My mom usually wakens him, but I am choosing not to do so—sleep is good, and I have no doubt that he is happier in sleep than awake. The day starts with a trip to the loo: it takes about twenty or twenty-five minutes for him to walk down the hall, then another few minutes of argument to convince him that he should really sit on the toilet. Over more or less continuous objections, his diaper is changed and clothing is put on, hands are washed, and face is shaved. It takes another ten minutes to walk from the bathroom to the breakfast table.

“Walking” (as my father does it) requires a walker and vast reserves of patience. As noted, his ship’s motors are no good and the captain has abdicated, so each step requires a minute (mostly due to severe arthritic pain; my mom believes that use of any sort of painkiller, from aspirin to heroin, is a sign of moral weakness), and after each step he needs to be reminded to take another in a particular direction. The soundtrack for one step of such a walk sounds like this:

“Keep moving,”

“What about the…(waves hands at a countertop in a vague manner)…?

“Over here. How about another step?”

“Allright.” (doesn’t take a step; looks behind himself)

“You have to take a step now.”

“Are those people behind us going to…(waves hands as if counting people in a crowd)…?”

“Take a step. Keep moving. This way, please.”

“we just…three…need to keep three channels open.” (rocks back and forth, winces in evident agony, lurches forward)


The day continues; after breakfast, my dad typically dozes at the table until about noon. Then, it’s time for another trip to the loo, and lunch. Per doctor’s orders, I try to get him out of the house for a short walk after lunch. After that, another trip to the loo, and a nap (or at least a period of reduced consciousness).

A reliable part of the daily schedule is “sundowning.” Around 4:00, the crankiness and anxiety start—constant questions about what’s going on, who is present, why somebody is trying to swindle us, whether there will be enough room for all the people who are here, and so on. This lasts through dinner, until about 8:00. It’s four hours of nonstop angry anxiety, and it’s nearly impossible to get anything done while it’s going on. It’s somewhat like dealing with the world’s crankiest two-year-old, but society doesn’t demand that we honor and respect two-year-olds. Eventually, things calm down, and the process of easing into bed (which takes about 45 minutes) can finish up by 10:00.

This daily schedule is a rough guide; Alzheimer’s disease guarantees that every day is uniquely annoying.

Yesterday, my dad had contrived to remove his diaper during the night, soaking the bed. The sundowning was particularly agitated, but more anxious than angry. Every two minutes would bring a nervous question about whether there was enough room for all the people in the bathroom to get through the door (I’m not sure, but I think he may have thought that the figures on the television were real people in the next room).

The day before was characterized by obstreperousness. My dad needed to go to the bathroom, but wouldn’t get up to do it; after getting up, he wouldn’t walk; after walking, he wouldn’t enter the bathroom; after entering the bathroom, he wouldn’t take of his trousers; he wouldn’t sit on the toilet, wouldn’t wash his hands, and so on. Everything was a struggle. It takes huge reserves of patience to deal with this, and not a little bit of creativity to persuade my dad that he really wants to do what he should do. My mother is one of the most patient souls on the planet, and I am not surprised that I have seen her utterly lose it with my dad under these circumstances.

The day before that was dominated by paranoia. We went out for a walk around 4:00—sundowning time—and by the end of the walk he was convinced he’d been swindled. When we got home, he was sure that everything was fake and that his stuff had been stolen. He was alarmed that he’d have to pay for his dinner, and that he’d have to pay to get home, and that he had no money because it was all stolen.

There’s been some debate recently about the value of screening for prostate cancer. On the one hand, a PSA test does reveal the presence of a lethal cancer that can be treated. On the other hand, the treatment has a high probability of unpleasant side effects—such as my dad’s incontinence—and the cancer usually moves so slowly that it kills the very old. The Real Doctor tells me that medicos call pneumonia the “old man’s friend,” since it brings a relatively rapid death to a frail body tired of life; prostate cancer may be looked at the same way. There is no really good way to die. I have to say, though, that Alzheimer’s disease is teaching me that there are really bad ways to live.

Friday Flora

My Mom's garden is better than yours. It's better than mine. She doesn't hesitate to rub it in. I get all excited when I get this:
From Microwunderkammer
She is completely blasé when she gets this:

Stapelia scitula, a real stinker of a plant.

Tuesday, October 4, 2011

Getting everything wet...

Well, today the Real Doctor and I started out for a ride even though it was raining at the time. Yay good rain gear and fenders!

(Boo, however, to jagged 5mm spikes of metal that give you a flat tire that you have to change in the rain, getting quite chilled in the process.)

Monday, October 3, 2011

Getting our feet wet

You can test your courage by deliberately entering into a challenging situation--or, you can have it tested for you by entering an innocuous situation that turns challenging. Yesterday, we were kind of reluctant to try the former. Today, we ended up with the latter--it was fine when we started our ride, but it soon started raining. I was glad to find that the raingear and fenders worked just as advertised, and heck--having gotten my feet wet both metaphorically and literally, I might even opt to start a ride in the rain.

I forgot to mention one thing about Eugene, Oregon, where we did our shopping for bike fittings. It is a town that is so cycling-oriented that I feel noticeably guilty about getting around by car. I almost want to wear a sign on my shirt saying
"I'm only going by car because I came from 70 miles away and I'm not strong enough to ride here and back in one day and besides the car is a Prius so cut me some slack OK?"
The feeling is reminiscent of what I felt as an American traveling in France in 2003.

Sunday, October 2, 2011

Discretion is the better part of valor

The seasons just changed here. Thursday was fine and sunny and warm--almost hot. Friday we looked out and saw a wall of clouds coming in from the west, and since then it's been overcast and cool and wet, alternating between drizzling and looking like it's gonna drizzle any second now.

Yesterday, acknowledging that a decade in Sacramento had made us soft, we went out and purchased some new rain gear that's supposed to breathe well while you're riding a bike. Today, I installed fenders on a couple of bikes.

I usually hate installing fenders--it seems that most fenders that are sold fit perfectly on some Platonic ideal of "bicycle," but simply don't work on a real bike. The fenders get bent in storage and only fit pretzel-shaped wheels, or don't attach to metric-threaded braze-ons, or occupy exactly the same space as the brakes (which would you rather have--brakes or fenders? Choose wisely). So, it took an hour and a half to drill the rivets out of the new fenders, bend a new piece of sheet aluminum, bolt it on, trim away several cm of the fender, bend the fender stays, zip-tie things down--and gouge out a chunk of my left 2nd finger--before I had functional fenders for my recumbent. The tandem was much easier. The Bike Friday people are engineers, and their stuff is perfectly set up. So, twenty minutes and everything is done.

New fenders, new rain gear, we girded up our loins, we screwed our courage to the sticking-place, we looked at the weather radar, we looked out the window...and decided to give it a miss. We will have other opportunities to ride in the rain, I'm sure.

Friday, September 30, 2011

Friday Flora High Sierra edition

Last weekend, as noted, I was in the Carson Pass area, south of Lake Tahoe, with brother M. and about 20 of his high school students. Before they arrived, I went on a kind of longish day-hike: start at Woods Lake, where we camped, go up to Round Top Lake, over the pass and down to Fourth of July Lake, down to Summit City Creek, then up and over a couple of passes back to Winnemucca Lake, and finally back down to Woods Lake.

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

Proteins, Puzzles, and Perjury

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

Scary geology

I spent the weekend in an area that proclaimed geological drama. The mountains in whose shadow we camped were basaltic, the product of long-ago volcanic events. However, these mountains were elevated and pushed up and out of the way by a granitic intrusion, making them into "roof pendants." We camped upon the granite. It must have been something to see happen, though I'm not sure any sentient witnesses were present 150 million years ago.

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.

Monday Musical Offering, sort of

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

I thirst for REVENGE!!! (and a pony, please)

Looking through the entertainment section of the Gray Lady (something that sounds far more scandalous than it actually is), I see that a wonderful new miniseries is going to rear its head on the networks. "Revenge," a tale of...revenge apparently, involving various high-society and filthy rich and snobby types traipsing around the Hamptons and getting what is coming to them. I glanced at the review and an online preview (I won't provide the link, as a gesture of my respect for you), and Gott in Himmel it looks unwatchable.

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

The Saga of Unnamed Cat

It's time for an update on a former pet. After making a brief splash in our life (and in these pages), Unnamed Cat moved on to a better place. The few weeks prior to our move from Sacramento were hectic, and not conducive to the the meditative philosophizing that Unnamed Cat cultivated (shown here contemplating the life of birds).

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: