A busy week. I've set to programming in earnest. With datasets this big, there really isn't any way to answer certain questions unless you write a program to explore it.
Now I see why Mike has such affection for MATLAB in this setting. It's an astoundingly flexible tool. Only problem is that much is up to whether you're capable of writing a program to test your hypothesis.
I'm learning, but I'm also fully aware how inefficient and memory intensive my code is. Especially when it comes to manipulating matrices, there are things I take 50 lines to write that a good MATLAB coder could do in a few.
I suppose this is what you get when a liberal arts major starts programming--verbose code.
Enjoying myself though.
The other day we stopped by the apartment the Chius have rented. His wife, from what I've seen, a cheerful, poised woman, started crying. My Mandarin is poor, but I understood it to be her frustration being the main caregiver and Mr. Chiu getting annoyed at her for hen-pecking him about exercises he should do, medicines he should take.
Sitting there, listening to them, reawakened something that I've always puzzled over: we never *really* know how someone is feeling. If a friend has a headache, I'd never know it unless she told me. I'd never know Mrs. Chiu's frustration unless she expressed it. Certainly there are times where we might guess or infer things, but we never reach a state where we feel exactly what someone else is feeling.
It's sort of sad--there's always that otherness, and the only thing we can do is make good guesses or just try to be considerate all the time.
Dave turned about into the increasingly tumultuous sea and I paddled on to scout the landing. Under more sanguine conditions it might be idyllic: a sandy crescent tucked below Mt. McArthur, (a XXXX ft peak) on Sitka. With Dave long behind me, without the comforting sounds of someone paddling alongside, there was only the solitude of the deep green water moving, the wind blowing, and the pathetic splash of my paddle in that big, prehistoric place.
The surf landing wasn't excessively difficult, I kept one eye cocked behind me to mark oncoming breakers and backpaddled as they washed under me. Kayaks don't have much of a skeg, and if you let yourself surf on a wave, you're bound to get pushed sideways and rolled. So forward and backward it was until I felt the rasp of the beach on the bottom of my craft. I swung out quickly before the next wave crashed into the beach and hauled the kayak up the sand, half-thinking that whatever Aaron had packed in the kayak that morning might be all I had for weeks if disaster struck and the party never made it in.
I sat for a moment on the grey beach. The dark hemlocked Tongass forest--I it's think the most northerly rain forest--marched to the edges of the cove, a "C" nibbled by the ocean from the hard substrate of Sitka. There were rocky points on the North and South edges and another deeper-set cove on the South. A huge boulder interrupted the sandy verge.
Seaweed wreckage marked the tideline far in front of me. This beach was quite shallow and the difference between high and low tide looked to be several hundred feet. I decided to pull the my kayak further up towards the trees.
If worst came to worst, at least I had my sea bass for dinner. Nick was long forgiven. I'd be ecstatic at the sight of his hooded green Patagonia shell, or of Doug's hunched, bearded form, or Leslie (lovely), or even John, despite the disfavor his behavior of a week ago inspired.
There was no evidence of anyone on the distant, stirred horizon.
Today I went up to 3100 to visit Mr. Chiu and his family. Though they can count themselves among the endless Taipei tycoon crowd over there, they are the nicest people. I like them. Otherwise I wouldn't have visited them.
I was alone in the elevator from the 3rd to 1st floor. As it accelerated downward, I jumped. A good one that nearly cracked my head on the ceiling. I do that everytime I'm in an elevator alone, unlike Charlie whom I remember farting in the elevator only to have the prettiest girl in the dorm come in on the bottom floor.
"While the Americans say they have learned much from the Afghans, the Afghans seem to feel they have gotten the better end of the deal, like economy passengers suddenly bumped into first class. They are wearing sturdy American-made uniforms. They spend their nights in warm American sleeping bags."
I don't know if this is really the case, but I sense that the writing at the New York Times has loosened up a bit. I've just been noticing passages like the above sprinkled throughout the paper over the last couple months. New editorial policy? Or just new writers? I like it though.
To kick off the transition I'll be making from the grad school back to the med school, I met with my advisory dean. Even though I won't be officially back in the med school until probably August, it already feels good to be back. I want to start doing things, and really start the career I've been training for for a gazillion years. Ultimately medical science is about application. Curiousity is exceedingly important, but it doesn't help anyone until it's applied in a way that makes sick people better. And I look forward to being in the more goal-oriented environs of medicine. Scientists really are> nerdy. I don't think this is bad, but before applying to med school I joked about how I wanted to sink my hands in the guts of life, well yes, that's exactly what I want to do, the lab is a little to removed for me now.
Bean: Ethiopian Yirgacheffe, Gr.2, '99/00 Crop
: er setting 5.5, into the 2nd crack--"Full City"
Grind: Grinder setting 1.8
Hard tamp with a quick polish
Pull was a bit too fast. I should back the grinder down to 1.2 for a finer grind.
Last night I had the windows partially open and woke up somewhere in its hourlessness to the wind combing itself through the trees. It sounded like the tide, and in that semi-conscious state, I forgot myself, and was innocent, and heard the wind for the first time. Startled by this novelty, I arose, glad to live in a world where there's wind that, unprovoked, arrives from some direction that I can't fathom with my local mind, and that I can hear it drag and rattle through the forest.
Many thanks to nationalgeographic.com's Map Machine.
The sea lions were barking, and the wind picked up. Our first morning paddling on the open Pacific had started with a calm, undulating swell--amplitude about six feet, but slow and almost imperceptible. To port was Sitka island's timber strewn Western coastline, and starboard, nothing but Hawaii between our kayaks and Japan. The late morning hours we spent jigging for sea bass among cackling, larcenous gulls. I had gotten a couple of bites and only one fish worth keeping. Nick's mother was French. He tended to say preposterous things, but he was a much better fisherman than me. He had an impressive looking bass, but being a classic catch-and-release type, he couldn't drive himself to kill the damned thing. He awkardly paddled alongside, trying to manipulate his paddle and the jigging rod at the same time.
"Erich, can you kill this for me?" He handed me the club we used to dispatch our piscine dinners. I grabbed his line and held the fish against the side of his kayak. Clubbing a fish against a bobbing kayak, not your own, is pretty difficult. I splashed sea bass blood all over my spray skirt--the bastard refused to die and gaped vapidly at me. A few more clumsy swings. Cal Ripken would be ashamed--I felt a bit sick. Kill your own damned fish next time, Nick.
As we meandered our way to early afternoon, the sky hardened to a murky concrete. The sea became acute. Comrades disappeared behind pitched, barrack-sized swells. Wind skimmed spray off the water. The lead instructor snapped an order for the group to "pod-up" and pointed to me and Dave, one of the other instructors, to paddle as hard as we could for the sheltered cove we had marked on our maps as our destination early that morning. We were to assess the surf at the landing, report by radio and direct the rest in.
At a normal paddling pace, we were 40 minutes out. It didn't seem as if the weather was going to be getting any better in that interval. We had to haul ass.
One thing I had learned by that point was to be an efficient paddler. And now I was free of Charlie--athletic as he was (Morehead Scholar no less)--he was deadweight in a double. He could dunk a basketball, but in a kayak he was all arms and wasted energy. The only reason I was in a single that morning was that Aaron, poor chap, had gotten quite seasick in the morning swell. We switched places and now I felt as free as a bird. Doubles are fun, but ponderous. I also don't like having to depend on a rudder when a well-handled single can run rings around a double without the benefit of a wire and metal contraption hanging off the stern. Rudders represent yet another thing to break in an environment that will challenge anything mechanical.
Like any physical activity, paddling a kayak depends on finding a rhythm. In this case it arises out of the "power box" you make with your arms and paddle, how deep you dip you blades, the way you feather the paddle in the onrushing wind, how far forward you lean. Dave and I paddled hard in the freshening weather. We could hear the sea lions barking behind us.
After about twenty minutes, shoulders burning, and within sight of our cove, Dave pulled out his VHF to contact the pod. No answer. He looked mildly worried. We paddled further and he tried again. We certainly couldn't see the group by now. If the rollers had not converted into mountains, they were at least foothills. There wasn't a chance from our low-slung kayaks that we were going to see them in the undulating, roiled seascape. We pulled out our binoculars and assessed the surf. We turned around and looked for the pod. No one. A landing would require caution, but was doable. After a moment's consideration, Dave told me to head into the beach by myself, land, wait for the group, and direct them in when they showed. He was going to paddle back and fetch them.
I woke up this morning with a headache. Not a promising start. Ironically, today is about the mildest, most pleasant day this Winter's given us. When I got into lab I managed to start programming but gradually reached a point where the fluorescent lights were beating me into the ground with their cold, inhospitable light. My head felt like a spirit level; if I leaned too far to one side, the bubble would touch my inflamed membranes and touch off that metallic pain I know too well. I retreated to my bay--closed the blinds, closed the door, turned off the lights and nestled in the beach chair I keep in lab for late nights. I sucked down a Coke (I have caffeine cravings when this happens).
Gradually things cleared, I was able to start programming again, and punched out some nice figures. Days seem so much better when a migraine evaporates. The grey, leaden haze lifts, and the colors become more vivid, people more amiable.
I wish I could predict when these guys hit.
I'm increasingly sensing that I need a break. Not just a change of milieu (after all I spent two weeks overseas in December), but something deeper, more fundamental. I don't know what would constitute the change. I was certainly flagging at our CODEx meeting today. Escape. That's what I wanted. Dublin is an emerald dream. of Gaelic accents, and coppered colored hair. Only a month and a half more before I seal myself into a metal tube and emerge in a completely new place, hopefully new, albeit evanescent adventures...
I'm writing my paper, but progress is fitful. Part of it is due to the "new" nature of the work, but most of it is due to the sclerotic condition of my mind currently. I feel a bit oppressed, and oddly the source of this oppression is myself. I mean this in the way Ethan Hawke, in Before Sunrise, talks about how you can never get away from yourself; that you can never go somewhere where you aren't, or think things you aren't thinking. Sometimes, I think (or should I say "we" think) it would be darned nice to take a vacation from myself, hang out with some fresh thoughts, see the world in ways I've never imagined I might.
I just logged onto Expedia to look for a flight to Bora Bora. It told me no flights were available.
It's futile anyway, because I'd just be there too.
How do you get a respite from yourself without being certifiable?
Making your own espresso is a ritual that belies the casual pulls tossed-off at a million Starbuck's coffee stands this moment. I shouldn't be too snobby about this because coffee is better overall in the US than it's ever been. People just don't know what they're missing when a barista actually knows to give a damn about the beans, the grind, the tamp, and the pull. I think it would be misanthropic to spend too much time railing against bad espresso, since a bad one is probably still way better than Folger's.
So what is this ritual? A couple of times a week, I green coffee beans. I usually have several varieties in the house at any time. ing it yourself gives you an opportunity to play with the darkness of the and creating your own blends. It also means that your coffee is as fresh as you can imagine it. What a difference. Pull a shot with a month old versus one you did the previous night and a glance at the crema will show you the difference. The old gives you a thin, bubbly head that barely covers the edges of your drink while the fresh gives you a thick Guinness crema that's a tight, almost custard-like glory of emulsified coffee essences. It's rare that I see good crema even at a good restaurant. Never seen one at Starbuck's, but sometimes you have to live in the Real World and can't run home just for a shot.
So back to the ritual. I usually leave my machine on overnight so it's hot. A good espresso machine has a minimum of plastic--you want thermal stability, and big chunks of metal give you that. The machine I use has a head unit that's 9 lbs of marine brass. Next to my shrine is my burr-grinder. I have nothing against propellor grinders, they're fine for a French Press, but they don't give you a fine enough grind to do justice to your espresso. I only grind for the shot I'm pulling. Sometimes, depending on the weather, I have to adjust it. An ideal shot expresses a "mouse tail" of espresso over a span of just less than 30 seconds for a shot's worth of volume. This is the ideal amount of time to pull out the "good" essences in the bean while stopping short of the "bitter", more caffeine-laden essences. Believe it or not, there's less caffeine in an espresso than in an equal volume of supermarket drip coffee. There is more flavor though. The point of espresso is to extract only the good stuff, and a properly-timed shot gives you that. So part A of a good shot is the grind. If it's humid out, you'll probably have to back off the fineness, if it's dry, you'll probably have to dial it in. Part B is the tamp. Every coffee bar I've been to, they just touch the puck. An important part of a pull is compressing and polishing the ground coffee in the portafilter. I keep a folded towel on my countertop for this and put my whole body into compressing the puck. I finish it off with a quick, clockwise turn of the tamper. You want to make the hot, pressurized water have to push it's way slowly through the puck and extract, rather than sprint through the ground coffee, only managing to bring along a fraction of the flavors that make good espresso. If you've done it right, to fill one espresso cup should take that magic 27 seconds. The liquid should be heavy with emulsified coffee oils, rich with microscopic micelles of flavor. It should even hang heavily from the portafilter spout.
That's the ritual
This makes me happy though. I love the curved cast aluminum.
The last two days I've been feeling washed out, colorless. This happens sometimes. I'm not depressed, just listless. It's even hard to articulate myself. My mental processes are fitful.
This morning I decided to try a 1/1 blend of some more Brazilian Corrado, Monte Carmelo 17/18 with some Ethiopian Yirgacheffe, Gr.2 '99/00 crop. I think the 6 er setting was a bit aggressive so backed it down to 5.5. My pulls were a bit fast, so I set the grinder to a finer 1.2. Haven't tried the blend yet. I'll let the beans rest overnight and try the blend tomorrow.
Today was a truly lazy Sunday. I didn't finish the Times--just monkeyed around with this blog and the templates all day long. I feel genuinely guilty that I didn't do one productive thing today. Tomorrow is another day.
I have to say that I'm very impressed with Movable Type. Once I've learned a bit more about Cascading Style Sheets, look out.
Bean: Brazilian Corrado, Monte Carmelo 17/18
: er setting 6, into the 2nd crack--"Full City"
Grind: Grinder setting 1.8
Hard tamp with a quick polish
Randy and Cindy are in town for the UNC game, so we caught Mel Gibson's film adaptation of We Were Soldiers Once, and Young. A.O. Scott reviewed it to the effect of "square and effective", which is pretty on target. No post-modern angst or time spent wondering what we were doing in Vietnam in the first place. It was a World War II epic set in Vietnam--a good commander who trains his men as well as possible for the maelstrom, men who trust a good commander, and a long set-piece battle that encapsulates all that is best about American loyalty, perseverance, and flexibility. There isn't a drop of cynicism throughout. No ellipses. No ambiguity. I confess that a tear rolled down my cheek when Moore's wife comforts a black woman who loses her husband in the battle. I don't think there is anything wrong with the full-throated decency of the movie. Like Blackhawk, it is clear that a soldier's greatest loyalty to country is loyalty to his comrades. Who can find fault with that sentiment? It's simple, but simple is fine sometimes, Red Wheelbarrow fine.
Disappointing Occurence(s): We went to Borders after the movie for a cup of coffee. Since I couldn't find Richard Ellman's Oscar Wilde biography at Barnes & Noble, I thought I'd look for it there.
Bad sign #1: There's no "Biography" section
Bad sign #2: The clerk, a not unintelligent-looking middle-aged woman didn't know who Richard Ellman was (bookstores are now staffed by people who don't know books); and after "perusing" the Books-In-Print database, insisted Richard Ellman did not exist (he is a Pulitzer Prize-winner after all). Even worse, after searching on "Oscar Wilde", insisted that no such biography exists.
Since Ellman's literary biographies are considered definitive, among the most treasured by literary critics, and I know he exists and his books are still in print (I studied Joyce under his daughter for God's sake), I suggested very nicely that she was FOS. Seeking to vindicate herself (and I really was being very polite, even if she called me "insistent"), she asked me to come behind the counter and look for myself. After scrolling down, 'Lo and Behold, there's Richard Ellman.
I'm going to shop at the Regulator or McIntyre's from now on.
So I'm writing (my paper) now. It took a little time to absorb it all--I've just sat and played with the data for a while. I think much of this "new" science is going to demand just diving into the numbers and running your fingers around its contours. The data sets are big and more complex than anything a molecular biologist is used to dealing with. Part of the process is merely getting used to the data and getting comfortable with it. Inevitably, since I'm a tinkerer I twist and stretch the methodology (not the data!) to see how it responds. Where I harbored a lingering, irrational fear that this was all artifact (every scientist's nightmare), I'm feeling more and more that this is real--it's an accomodation with complexity.
But then come new challenges. This way of looking at data is different. It isn't completely unprecedented, but it demands a new perspective on the science. And in this dream of recognizing complex phenotypes based on thousands of characteristics, comes the responsibility of "selling" it to the broader scientific community. This could potentially be very hard indeed, or assuming sympathetic reviewers, could be relatively easy. What is evident, in spite of all of this, is that I have to pitch the paper rhetorically. I have to sway the readers no less than an effective politician sways voters.
I guess I was never going to get out of the writing business entirely.