Tuesday, May 29, 2007

Coal is a four-letter word

From the New York Times, we learn that Representative Nick V. Rahall, Democrat of West Virginia and chairman of the House Natural Resources Committee, believes that
“For so many, filthy coal is a dirty four-letter word. These individuals, I tell you, have their heads buried in the sand.” Indeed, it has recently been discovered that coal has a hidden fifth letter. The illuminated amongst us are now embracing the cleaner spelling: coale.

Monday, May 28, 2007

Basal Ganglia: FTS

On a more positive note (since anyone reading this probably has little interest in my emo-style mooning about), I feel like I'm beginning to get a grasp on the function of the basal ganglia. This article, which I'm presently reading, provides a reasonable foothold. Apparently, the notion that the basal ganglia inhibits competing (motor) programs is fairly well-established in the literature. Interestingly, I think you can reach the same conclusion from purely computational considerations, given that the basal ganglia is structured as a feed-forward loop. It also seems like it will integrate nicely with an understanding of the cortex in terms of undirected graphical models. Everything would be sunshine and lollipops if the people who write about the basal ganglia weren't so damn dry. I don't understand how these people don't fall asleep while writing their own articles.

Thou art that

In high school, I read Catch-22 and belly-laughed through the whole thing. The desperate situation of the World War 2 bomber pilots and their absurd responses to the impossibility of their predicament had the ring of truth, but seemed alien to the consensus understanding of reality. In college (admittedly during finals), I read Catch-22 again, and found the book utterly depressing. Whereas at age eighteen I had seen Catch-22 as a fun-house mirror, distorting underlying reality into grotesque and obscene shapes, at age twenty-one it seemed like a corrective lens, undoing the effect of the rose-colored glasses which we wear to make the otherwise untenable human condition bearable. Humor is sometimes used to gin up a dull evening, but it is also a coping mechanism of last resort when the world takes off its kid gloves.

When I first read the Chuang Tzu, it was the most insightful book I had ever seen. It seemed as if, by acknowledging the mundane position of humanity in the universe, we were freed from our self-imposed burdens and obligations. What I failed to see was that freedom can be a terrifying thing. The same chains that weigh us down and restrict our actions also serve to bind us to the structure of human society. By accepting the arbitrary obligations and expectations which comprise a culture, we gain a framework within which to understand our place in the world and the meaning of our lives. In loosing these fetters, we obtain absolute freedom, but lose the context which made that freedom so desirable. The question of "what shall I do today" sheds its cast of childlike wonder, and takes on menacing overtones. We are no longer selecting a single permitted treat from the almost overwhelming variety of the candy aisle. The entire grocery store is open to us and we have a fistful of cash, but after the third consecutive gallon of ice cream, we find its taste suffocating.

I think my ultimate frustration with Taoism (or at least my limited understanding of it) is that it is fundamentally rational, whereas humans are at their core emotional beings. Just because I have everything I want, or in the case of Taoism I have realized that I don't in fact want anything, doesn't mean that I am satisfied. My wandering may be free and easy, but I have no direction, so I might as well just sit down where I am. I think this sense of malaise is common, but generally misinterpreted. People assume that they can stuff the hole in the core of their being full of physical acquisitions or sexual conquests or workplace accomplishments, and achieve completeness. But absolute freedom from social structure dissolves these societal constructs, and they pass through our grasping fingers like so much air.

We are left at the mercy of ourselves. Some activities are still intrinsically more enjoyable than others, but each moment stands by itself and must find its own justification.

Saturday, May 26, 2007

Sucking dust

I cleaned my room today. This is an activity in which I engage only occasionally. I suspect I last vacuumed was at least four months ago; the empty boxes in which I shipped most of my things from LA were sitting folded against the wall up until 4pm today; I still don't think I've emptied the trash can in my room since I purchased it (although admittedly it still isn't quite full - there's always a little more room if you compress the current contents). Partially, I think this is an expression of my refusal to fully admit that I've moved to Switzerland. I still feel like a foreigner here. Keeping the empty boxes is like saying "I may be here now, but I'll be leaving soon, so I shouldn't get too comfortable."

I think that most of it, though, is some sort of practical Taoism, divorced from the usual realm of application. If you live in the moment, and you don't recognize an external morality, let alone an overarching ultimate goal or directive, then you need to choose your actions on a minute-by-minute basis, with little other than personal preference as a guide. At any given point in time, I don't really feel like cleaning. It's not very amusing when done without the aid of powerful stimulants. I know that if I do clean, the second law of thermodynamics will just blow through and make everything messy again. I'm all for romantic, unwinnable battles, but only when both the goal and the method of combat hold some considerable aesthetic appeal. A clean room satisfies neither criterion.

Moreover, were I to clean, the only one to benefit would be the me-of-the-future. While he seems like he's probably a nice guy, the me-of-the-future is not the me-of-right-now. I'm no great philanthropist, and I don't think the appreciation the me-of-the-future would have for a cleaned room will equal the irritation faced by the me-of-right-now in rendering my room into such a state.

So I almost invariably choose to do something else instead. I don't think my choices are particularly good, but since I lack a framework in which to evaluate their quality, I'm hard-pressed to identify better choices, even after the fact. I feel like I'm perpetually just getting by. I can survive from day-to-day without too much trouble, but I don't think I'm accomplishing anything meaningful or worthwhile with the passage of time. dx/dt = 0. I think that life would be more amusing if I were able to commit to a grand objective, but nothing seems sufficiently important. I can think of no mountain for which, having achieved the summit, I would feel satisfied for more than a few weeks. I don't think this is a matter of living selfishly versus living for the benefit of others. In the end, both approaches are equivalent, since actions for the benefit of others have an immediate and obvious impact on yourself. And assuming I am not uniquely unworthy, why should I work for others in the first place? It would be an awfully ironic world where everyone was toiling for everyone else and ignoring their own happiness.

In the end I'm left with only questions and the imperative to act.

Tuesday, May 22, 2007

Twenty-six years later...

Is it odd that my birthday makes me think about death? I don't feel like I have much to show for the past twenty-six years, not do I expect to accomplish anything meaningful in whatever time I have left, mostly because I can't imagine what a meaningful contribution to the world would look like. Everything done today will be gradually eroded by the tides of time, washing back and forth over the perpetual present.

Death would be more intimidating if I thought that what I had now was qualitatively different. But the person I am today is not the same as the person I was yesterday; the me of five minutes ago is already dead. Existence consists solely of a sequence of moments, disjoint but for the tenuous links forged by memory and anticipation. Sometimes I try to see myself as existing in each moment independently. I envision time as a spatial dimension, and see myself extending into the past and future, each instant existing beyond the ravages of temporal dynamics. I think this is a better understanding of reality than the more traditional model of directed time moving at a constant rate.

This essay was worth reading. My mother thinks that I am devoid of empathy. She is wrong. I have empathy to spare, but very little sympathy. The Mean Monkey doesn't care if you are sad, but he does feel your pain.

Thursday, May 17, 2007

The mean streets of Zurich

Last night I went out dancing with two guys from lab. Today is Ascension day, which is a major holiday in Zurich. In honor of the resurrected man-god flying up to heaven, everything is closed, so the blasphemous goth club was packed last night with people who didn't have to wake up at the crack of dawn for once (which is almost as ironic as the store-front Pentecostal church which regularly had services on Friday evenings directly across the street from where the black-leather-clad masses were waiting at the velvet rope to get into Das Bunker in LA).

Dancing was less enjoyable than usual, since there was little room for mad gyrations and even less air to fill my empty lungs, but I did see one of the girls who went on the ZNZ retreat last weekend. I don't remember if she presented a poster or a talk, so I can't look up her name, but she was the only competent dancer at the horrible restaurant where we were serenaded by a seventy-year-old paraplegic singing American hits from the 50's accompanied by his trusty auto-programmed Casio. Think Wesley Willis without the schizophrenic street cred or camp-cool lyrics (I really did whoop Batman's ass).

Anyway, my friends were goth club neophytes, and their will to convulse rhythmically to harsh electronic beats waned after two hours, so we called it a night at around 2am. The walk back to my apartment, where one of my friends left his bike, passes through a few relatively narrow and poorly lit alleyways. In Hell's Kitchen or Compton, these are the sorts of places where a nice Jewish boy from the suburbs would not dare to tread even in broad daylight, but Zurich's notion of gritty generally doesn't go beyond titty bars where both the glassware and the lavatories are sanitary. On this particular evening, while walking back through these alleys, we encountered a young black man and woman; an unusual enough occurrence in Zurich. As we walked past, the girl asked us if we had any cigarettes. I certainly didn't understand her German, so my friend answered that we didn't have any, and we continued without breaking our stride. Before we could go more than a few additional steps, the boy requested cigarettes in a considerably more aggressive manner. I understood him no better than the girl, so I continued on without response, and my friend, having nothing more to say, did the same. As we walked past, I saw him raise his arm out of the corner of my eye, and our departure was saluted with the crack of a handgun fired into the air.

My friend was convinced that it was some sort of fake gun, perhaps an air pistol, but I can't imagine why someone would carry such a useless show-piece on the street at night. Then again, I'm not exactly sure what he hoped to accomplish by firing a gun of any sort after we declined to give him a cigarette. It isn't as if, hearing the gunshot, I was about to turn around and say "Oh, when you put it that way, I think I just may have a pack of cigarettes in my pocket." And I don't think being denied a cigarette by a passing stranger is really reasonable cause to flip out. People are strange.

Wednesday, May 16, 2007

Involuntary expatriotism

When I was a sophomore in college, I went on a two week whirlwind tour of Europe. I saw a whole bunch of cathedrals and discovered a liking for Belgian ales, but I came back wondering why I had gone so far to see foreign lands when (a) I haven't seen most of my own very large country and (b) I think that seeing things for the sake of their novelty without actually understanding them is basically without value. (Like science museums. Few things anger me like science museums. You go in all googly-eyed and stare at crystals and bubbling liquids and magnified images of insects and protists and maybe see some demonstration of vortexes in fluids, but you leave without any deep understanding of the principles underlying the gee-whiz demonstrations. In the end, it's roughly equivalent to watching an action movie, with an added air of intellectual superiority. Science is not about special effects. Science is the application of mathematical models to reality. If you take out the math, all you have is a picture show.) I really like this comic. Perhaps unsurprisingly, even after living in Switzerland for 10 months, I've only ventured beyond Zurich a handful of times, and I haven't found any of those experiences particularly enlightening. When I have gone out, I've seen things roughly equivalent to what's available in America, but everyone was speaking some funny language.

Cat and girl is really funny.

Tuesday, May 15, 2007

Basal Ganglia? Sucks!

It strikes me that, perhaps foolishly and certainly with a touch of unjustified self-confidence (I think this is what the rest of the world calls arrogance), I think I understand how cortex works (at least at an abstract, algorithmic level). In contrast, I have absolutely no idea what the hell the basal ganglia is doing. Unlike the cortex, where connections are almost entirely bi-directional, the basal ganglia consists of one-directional loops. In this respect, it is like the hippocampus. But whereas the hippocampal cells have been studied ad nauseum and a considerable amount can be said about what each individual cell is doing, the basal ganglia has not been subject to such microscopic scrutiny. I can say with certainty that this hippocampus is essential for the formation of new declarative memories (memories which you can consciously access and render into words, like the capital of France, rather than procedural memories, like how to ride a bike, or a variety of other types of non-declarative memories). If you take the hippocampus out, you can't form new memories. In rats, cells tend to respond when the animal is interacting with a particular combination of stimulus and context. Since rats are very spatial creatures, this usually takes the form of particular places in a room. In a different room, the same cell will respond to a totally different place. The only crazy thing about the hippocampus is the same loop structure which makes the basal ganglia so confusing.

So back to these loops. In the hippocampus, I've long been frustrated by the problem of getting memories out in the same for in which they are pushed in. Since the output cells in the lower layers of the entorhinal cortex are not the same as the input cells in the upper layers of the entorhinal cortex (not to mention other outputs directly from CA1 and subiculum (I think)), I don't understand why these cells should be expected to project to the same regions as the inputs of which the memory consists. This seems like putting all of the stored information through a random permutation function. Every time I ask the hippocampus to remember "cat" it tells me "20 foot tall pile of marshmallows." Eventually, I guess I'd figure out that "20 foot tall pile of marshmallows" is just it's funny way of saying "cat," and I imagine this is what the brain is doing.

The basal ganglia is even worse, though, since I don't even know what the hell it's doing. In Parkinson's disease, disruption of dopaminergic modulation of the basal ganglia induces tremors and rigidity and slowed motion. In sleepy sickness (also known as encephalitis lethargica, or "that disease in that movie with Robin Williams"), similar disruptions of dopaminergic modulation of the basal ganglia render patients almost entirely motionless. What's more, if I recall correctly, when they are briefly revived with L-Dopa, they report perseverative thinking as well. It's as if they don't move because they so occupied counting their fingers that they can't be bothered to interact with the rest of the world. Various summary-type things I've read have suggested that the basal ganglia is necessary for motor planning of various sorts, and a paper I read today claimed that basal ganglia disruptions due to Parkinson's disease prevent patients from learning subtle correlations in the environment.

So I'm left with a part of the brain which seems simultaneously absolutely essential and completely mysterious. Sucks!

Edge of Sanity

The danger of working hard on some blog posts is that it makes one reticent to post except when one has the time and energy to write something thoughtful and interesting. Unfortunately, creativity often comes from setting pen to paper (or fingers to keyboard) regularly, and waiting for inspiration to work its fickle magic. This is definitely the approach I take in science, but there I have the added impetus of other people's papers to prod me to think about new things.

Anyway, today I'd like to share with you my appreciation for Dan Swano's band Edge of Sanity. I have physical CDs for Purgatory Afterglow and Crimson II (the second of which is really just Dan Swano, not the entirety of Edge of Sanity), and I've heard Crimson many a time. Today, though, I'm listening to Spectral Sorrows for perhaps the first time. I'm feeling a bit abstracted, and don't really want to re-read the paper which is the basis for this week's assignment in the class I'm TAing, but this album is making it go down smooth as melted butter (which is to say, it's a bit too thick and I want to gag a little, but at least it's smooth). Swano does a good job of infusing classic rock sensibilities into what remains very clearly death metal. Most of his melodies have a distinct groove to them, and his songs are rarely short on the sort of hooks that make pop music so infectious. Someday I'll work up the energy to give his Pan Thy Monium albums, which are a Frankensteinian combination of jazz and death metal, the careful consideration they deserve. Today though, I want something a bit simpler, and Spectral Sorrows is definitely hitting the spot.

Friday, May 4, 2007

Neuroscience is hard... Let's go shopping!

Classic quote: "Thus, although neuroanatomical information will be central to understanding how the brain processes stimuli and forms representations, our current knowledge of neuroanatomy is sufficient to constrain neither the problem of binding nor its solution." - Adina L. Roskies, writing in the introduction to a special issue of Neuron on the binding problem.

I recently read (well, listened to, at any rate) Surely You're Joking Mr. Feynman and Further Adventures of a Curious Character, both semi-autobiographical works by famed physicist Richard Feynman. Although these books are mostly about Feynman's extracurricular adventures, he does touch upon his philosophy of scientific pursuits. I was struck by what he described as the radical honesty good scientists must bring to their work. Feynman claims that it is not sufficient to simply present all of the details of your work, he asserts that the good scientist must lay bare all of the potential flaws in their theories and experiments. He particularly warns against scientists lying to themselves and failing to recognize weaknesses in their work. This idea initially intimidated me. I make a point of remaining convinced that I am on the cusp of a (or perhaps THE) great discovery regarding how the brain works. It makes going into lab more fun, it seems mostly harmless, and some days I'm even convinced that it's true. However, none of my work can stand up to this sort of merciless intellectual assault. Yes, there are some interesting ideas in there that bear a passing resemblance to the experimental data, but I can't quite jam my higher-level ideas into a neuron by neuron, receptor by receptor, and ion by ion map of the biophysics of the brain. I can't pretend to have read even 1% of the literature on these detailed phenomena. Moreover, it is a truism of neuroscience that for every paper there is an opposite (but not necessarily equal) paper claiming a mutually exclusive result. Creating a model which matches a set of consistent, correct data is hard. Creating a model which is compatible with an undifferentiated mass of mutually contradictory data, half of which is necessarily wrong, is by definition impossible. I think the real answer is that the brain is a messier affair than particle physics. Cloud chambers are neat and sterile. The brain is squishy an amorphous, and you need to peer into it through the tiniest of tubes (generally, a bunch of solid wires). In this sense, neuroscience is much more akin to statistical mechanics than to particle physics. Asking how the brain works is like asking for a detailed description of the turbulence behind a large truck. It's possible to write down rules describing the interactions at the smallest scale, and it's possible to make some hand-wavy measurements of phenomena at the largest scales, but ne'er the twain shall meet.