Saturday, October 18, 2008


The title of Tom Stoppard's latest play never fails to remind me of Guitar Wolf and Wild Zero. Which is among the better of reminisces. And, perhaps, among the better of comparisons?

Rock'n'Roll tells the story of Soviet-occupied Czechoslovakia, from the point of view of someone who couldn't care less about Vaclav Havel, but absolutely loved Pink Floyd. In the point of view of the main character, a band called "The Plastic People of the Universe", a rock band, really brought about the end of the soviet republic, and were able to "live in the truth" (not his words, Havel's) even when the intellectual dissidents of the time were inable to, simply because they didn't care about the power structures, they cared only about music.

The general sense that the play gives is that freedom, and change, comes from the uncontrollable -- art, music, love; possibly Sex Drugs and Rock'n'Roll in particular -- and not from your ideals, your opinions, or other intellectual bases. (He brings Sappho into this. I now want to read Sappho. And re-read Havel, of course). So, in Rock'n'Roll, Rock and Roll saves humanity from invading soviet communists enforcing conformity (as opposed alien zombie hordes in Wild Zero).

Of course, my favorite parts were (1) an argument about Havel between two characters, and (2) Possibly the most feel-good ending you will ever see in Stoppard (the good guys won! love and music triumphed! The Rolling Stones played in Prague!). The last scene and a half were the kind of thing that, while watching, I was worried my smile muscles would cramp up. "Will you come with me?" "Yes." "To Prague?" "Yes." "Right now?" "Yes!" And the main character arguing that a bunch of disengaged mediocre rockers were the only people able to bring about the fall of the Soviet Union (as opposed to Havel and the intellectual dissidents) because they uniquely didn't care about fame, money, or power structures and therefore couldn't be bribed or bullied into conforming was, well, the circularity of it was awesome. And just the sort of thing I love Stoppard for.

I think I still like Arcadia better, for lines like "...we will be alone on an empty shore." "Then we will dance.", and for the fact that it provides, in my opinion, a direct contrast to the depressing determinism of Rosencrantz and Guildenstern are Dead with Thomasina; we know how her story ends and yet I feel like at the end of the story we don't know as well. Of course, the philosophy that allows Thomasina's uncertain fate in Arcadia is in fact the same philosophy that brings down the Czech Soviet Union in Rock'n'Roll, which is quite possibly an even greater achievement, unless you're a fan of the Doctor, in which case saving the life of one ordinary person is of more import than single-handedly causing Vesuvius to blow or (one assumes) bringing about the fall of the Soviet Union in Czechoslovakia.

I have put off this post since Thursday because my thoughts are not yet crystallized (that will require reading it several times I think) and because life got crazy. Well, sort of. Two weeks ago, I was bored and had nothing to do, so I signed up for a bunch of new activities. I may have signed up for too many activities, it turns out. I don't think so, not quite, but the thought crossed my mind when I didn't get to sleep until 2 or sleep past 7:30 for five days in a row.

Now, if only I could find a friend; someone who I could talk into going to see Tom Stoppard's latest play with me on a Thursday night, even if we both have discussion session at 9 am on Friday. I talked to about 20 people, all of whom had other commitments (in many cases, sleeping). Really, the only thing that would have made the evening better would have been someone to gibber with about the play while taking the train home. Or at intermission. Or, you know, ever.

Sunday, October 12, 2008

Invisible Motorbike

I dreamed of an invisible motorbike (among other things) last night. This story is the result of that dream, and a warm up (maybe) for Nanowrimo (3 weeks!). [Note: this is the edited, and much less bad, (I can't guarantee it's any good) version.]
Faith didn’t usually stay out late at night. She was a little bit too quiet and a little bit too introverted to thoroughly enjoy the club scene. And when she did stay out late, she almost always arranged for friends to walk her back to her apartment. She was a little bit too small and a little bit too spacey to feel entirely safe by herself late at night. So it was more than a little bit unusual for her to be staggering down the street at two AM, slightly tipsy from her night on the town and mostly just chilled to the bone from the walk. So she was worried at every corner that someone would appear and assault her, at the same time she told herself the crime levels in the city were at an all-time low.

If only Michelle hadn’t met that cute boy from across town. Or if Jeremy had been with them. It was on his way home. But no one else lived anywhere close and so she was left alone. Which wasn’t, really, much of a problem. She was already just across the street from her apartment, and her wonderfully warm radiator exuding its steam heat. She smiled just thinking of her cozy bed and stepped across the street.

It was thus, preoccupied, that she almost ran into the man on the invisible motorbike. She screamed and fell back, landing heavily on her wrist. He swerved out of the way and screeched to a halt on the pavement, staring at her quizzically.

“You can see me,” he said bluntly, puzzled.

“Well, you’re not invisible,” she answered, taking what she decided were deep, calming breaths. She didn’t feel terrified anymore, not now that the motorbike had stopped moving. She thought maybe the alcohol was preventing her from processing it. “That’s just your motorbike.”

He frowned. “If it’s invisible, how do you know it’s a motorcycle?”

She blinked, and was about to answer that he was sitting on it like a motorcycle, and it made a growling sound like a motorcycle, and so it had to be a motorcycle, but he had disappeared, and all she could see was a single headlamp shooting through the dark.


The invisible motorbike had been Peter’s idea, although Morgan often claimed it for herself. Back when they just had a red Yamaha bike and a massive load of debt, making it invisible had seemed like the sort of obvious gimmick that a certain group of people would go for. It had, slowly and only among those keen enough to see it, become his trademark. If you ever saw a boy – no, rightly a man, although at high speeds he looked even younger than he was – crouched over, clutching invisible handlebars, flying down city streets, it was Peter on an errand or another.

“I’d appreciate it if you at least wore your helmet when you went out joyriding,” Morgan said without even turning to look at him entering the office.

“I met a girl on my way here,” Peter answered bluntly, ignoring her comment. Morgan raised an eyebrow. “She almost ran into me.”

Morgan shrugged. “People are always running into you, Peter,” she said cattily. “It comes with the territory of having an invisible motorbike.” When Peter didn’t seem surprised, she added, “It’s one of the reasons you should wear a helmet.”

“She could see me,” he answered thoughtfully, and Morgan was suddenly silent. “She knew I was riding a motorbike.”

“She could see the bike?” Morgan snapped.

“Of course not,” Peter replied, grabbing his helmet from its high shelf, tugging at the chinstrap. He hated the way it mussed up his hair like a small child’s. “But she knew what it was anyway.”

Morgan snorted. “What was her name?”

“How would I know? I didn’t stay to chat.”

Morgan rolled her eyes and sighed in frustration. “Why did you tell me, then?”

Peter shrugged. “You take an interest in my life, sometimes,” he said softly, and fell into the worn eyesore of a couch that soiled the wall of the office. “I can never tell when you’ll be interested and when you’ll be sour. Give me a break, Morgan, what do you want from me? I mean, just yesterday you were --

“Enough,” she said. “If you don’t hurry, you’ll be late to pick up the keynote for the voodoo convention from her hotel.”

“I’m never late,” Peter said, frowning as he slid his helmet onto his head. “Which hotel?”

“The Omni, on Franklin. And the convention is at the Hyatt. After that, you’re travelling north to pick up some Mandrake for old Mrs. Smith.”

“She can’t pay,” Peter said. “She never pays.”

“Consider it a charity case, then,” Morgan replied. “Giving back to the community.”

Peter sighed. “And then?”

“Then come back. I’m manning the phones; the psychics told me they’d be late to get back to me about their order three weeks ago. So I’m expecting a phone call any time now.”

Peter nodded, and was gone.


Faith woke up with a splitting headache, a throbbing wrist, and the strangest recollection of a man on an invisible motorbike. She looked at the clock beside her bed; 10:00 AM on a Saturday. She had been out with friends last night, late. The headache must be a hangover, and the motorcycle must have been a dream.

She stumbled into the kitchen and put on the kettle for tea. She had read somewhere that the best way to cure a hangover was hydration. She had never needed to test that assertion before. She winced as the kettle whistled cheerily and poured her cup of tea.

It had really been the most vivid dream. She could remember his blue eyes in the two AM darkness, and his wind-blown hair. He hadn’t been wearing a helmet.

Why hadn’t he been wearing a helmet?

And why would she remember something like that about a dream? And how could she tell he had blue eyes if it was two AM?

By the light of the headlamp, of course, a small voice said. But she just sighed and sipped her tea. She had errands to run, and resolved to let the dream fade into the mist of forgetfulness, like the rest of her dreams.

But all day, she kept flashing back to startled blue eyes, and a single headlight. And after dinner, as she washed the dishes, she had a resolution. She called Michelle, just to make sure her plan wasn’t too crazy.

“I had the strangest dream last night,” Faith finally said after Michelle had gone on about Darren (so that was the cute boy’s name) for a few minutes.


“I was walking home from the metro at two in the morning, and I was almost run over by a man on an invisible motorbike.”

“How did you know it was a motorbike if it was invisible?”

“He asked me that,” Faith said. “From the way he was sitting on it, I guess. And the single headlight. And the sound.”

Michelle sounded nonplussed even over the phone. “You don’t think it was a dream.”

“Well, no. My wrist is awfully sore today.”

Michelle sighed. “You probably just slept on it funny.”

“I don’t think so. It’s bruised and everything, like I fell on it.”

“Might it have been a black motorbike, and you just couldn’t see it well in the darkness?”

“No. I could see his leg through it.”

“What are you going to do about it?”

Faith paused. “I’m going to wait outside, see if he drives by again.”

Michelle sighed. “You’re going to stand around outside until two in the morning? Need I remind you of all the reasons that’s a bad idea?”

Faith, truthfully, knew all the reasons it was a bad idea. Even in her relatively safe neighborhood, standing on a street corner for hours was a wonderful way to attract attention of exactly the wrong sort. “He was on an invisible motorbike. I can’t just let that sort of thing pass me by,” she said slowly.

“Notwithstanding the fact that you probably dreamed him up,” Michelle said, “You certainly can let something like an invisible motorbike pass you by. In fact, it seems like it being invisible would make it particularly easy to pass by.”

Faith snorted derisively. “You have absolutely no imagination, Michelle,” she said.

“And you, my friend, have too much. Keep safe, and warm, and don’t get mugged.” Michelle paused for a moment. “Call me tomorrow morning, okay? Promise?”

Faith smiled. “Yes, mother,” she answered wryly, before hanging up and looking out the window, pensive. It was as much as a blessing as she was likely to get from Michelle.

At twelve-thirty AM, she pulled on a few layers over her pajamas, grabbed a thermos of hot chocolate, and crept down the stairs to sit on the stoop and wait.

It was quiet, and cold, with a fresh sprinkling of snow on the ground, but her thermos kept her hands warm and her wool socks and insulated boots kept her feet warm, and she felt a little bit like a small child again, waiting for Santa Claus to come down the chimney.

Around one thirty, she was dozing off, when she saw a single headlight approach. She stepped to the edge of the street.

He was moving fast.

She threw herself out in front of him. So it can be said, this second time, that it was entirely her fault.

There was a screech of brakes, and a muttered curse, and she stood, smiling broadly.

“You again!” he said.

“Sorry,” she answered, not looking very sorry at all. “I have an answer to your question.”

“What question?”

If it’s invisible, how do you know it’s a motorbike?” She recited. “I’ve been thinking about it all day. And it’s the way you’re sitting on it. And the headlight. And it smells like a motorcycle, all burned rubber and worn leather and waxed metal. And the humming, revving sound the engine makes.” She smiled. “But you should be wearing a helmet,” she said, looking at his once again windblown hair.

The man looked marginally impressed. She hopped from one foot to another and glanced from side to side. The cold was finally getting to her. “I have hot chocolate,” she said, holding out her thermos.

He laughed, blue eyes sparkling in the lamplight, as he gulped down some hot chocolate. He handed her back the thermos, grinned and held out his hand. “I’m Peter,” he said.

“Faith.” She grabbed his hand and shook it, but he didn’t let go.

“You want a ride? As payment for the hot chocolate,” he said. It wasn’t an offer, it was an assertion.

And Faith found that, when it came down to it, there was no reason for her to have stayed out the second night if she didn’t want a ride. “Sure,” she said with a smile. And then he was pulling her onto the motorcycle behind him, and he said only “Hold on tight,” before they were off.

It feels like the beginning of something bigger. But I can't decide where it goes from there, in part because that's where the dream ended.

Also, planted Pansies and Poppies in my garden. They are yellow and blue and generally beautiful. I loved picking them out, and I loved how dirty my hands got when planting them. Hopefully they will survive! If they do, I'll go back to the gardening shop next weekend to get more flowers for the back. Maybe some herbs too for a real kitchen garden. If they die, I'll have to reevaluate my ability to do things like have plants.

Friday, October 10, 2008

The joys, and despairs, of data

So, I started out this rotation in a situation fundamentally different from any other lab I have worked in -- whereas in the other labs I have gone through, I have been given a project in its infancy, with no data and (in most cases) not even a system set up, and have worked through the beginning parts of a project, months after months with no results, this time I was given a partial data set.

Of course, I can already think of a few more libraries that would be interesting to add to the data set, but as a start this is absolutely and fundamentally different -- for the past three weeks, I have had to analyze massive quantities of data, rather than starting a system with which I could collect data.

The remarkable thing is, at this point, I think said data will turn out to be actually interesting; I have reasons to believe that something very significant is happening over developmental time. The epigenetic markers that I am assessing correspond to transcriptional markers at slightly later time points. It's wonderful; I can show the cells reprogramming epigenetically as well as in gene-expression patterns. In many ways, a perfect study. I have more things I want to do with this data before I'm sure, but I have (I think good) reason to be very, very hopeful.

On the other hand, I don't feel like I'm doing any work. No matter how much time I program, crunch numbers, make charts and graphs that accurately display the data (a misleading graph made right off caused me and my PI to be even more hopeful than it turns out was prudent), I don't feel like I'm doing any work. In part because it's analysis, and I've always been in the mindset that work was getting data, and the analysis didn't take much time at all. That's not the paradigm in the lab (and in particular the project) I'm in: here, getting huge amounts of data is relatively easy, and figuring out what that data means is much harder. In another part is that there are very few clear stopping points, or perhaps too many clear stopping points. I end up spending far too much time (more time than I can perhaps afford) on my rotation project as opposed to my classwork. (At least no one really cares about grades anymore.) I program and crunch numbers until 7:00 and only then realize that perhaps I should leave lab.

I've signed up for activities to try to fix that. Starting next friday, I'm volunteering to teach science to small children. There are journal clubs as well, and a couple people who hang silks in the rock climbing room (also just hanging in the rock climbing room, or perhaps more accurately bouldering in the rock climbing room until I can find a partner). And I'm on the listhost for any swing dance events (although it didn't look like there was anything as regular as Java Jive in Chicago). So hopefully my days will fill up with events, so that I won't just hole myself up in lab crunching numbers -- since Mr. Pham mentioned it, I have been afraid of Ning's fate: a hermit, sitting in lab all day calculating constants.

The other thing that I seem to be tripping up in is how much independence I need, want, and should have. I'm used to research as an undergrad, with a post-doc mentor who, to put it kindly, was very mothering. She wanted to know every step, and she supervised many of them. Not only would this make absolutely no sense with regards to analysing this data set, but that is very much not what the post-doc I'm working with now is like. She is, it seems, barely older than I am; just out of her thesis work in, if not the same lab, then certainly Stanford. (On a side note, it seems like a ton of people do that here -- there are so many people starting postdocs in the lab in which they did their dissertations, so many very young post-docs. I'm used to an older group, for whatever reason.) She seems more like a friend than a mentor. Add to that the fact that she's been working on other things while the data analysis is all me, and I'm left very much on my own. Which is not a bad thing, especially since I think that this sort of data analysis is not as nicely adapted to supervision and mothering as day-to-day labwork. But I have been left feeling a little bit confused. Pleased, that I can set my own hours and figure it out on my own and as long as I get results to my own satisfaction, everyone else will be thrilled (at least so far), but a bit discomfited because I am used to a certain variety of connection and I am notably not getting it.

I think that it's entirely possible that over the course of the quarter I will grow to enjoy my newfound independence so much that moving to a lab where I once again have a mentor-babysitter the way I sometimes felt I had in the Singh Lab would be a grave disappointment. And it is certainly true that this novel experience will be good for me. After all, the two things (two of the things? the two primary things?) that I wanted to learn in Graduate School were 1) how to stand up and be independent (not reclusive, but independent) in lab and 2) how to finish a project.

Hopefully, this lesson in data analysis will help me along my way towards both goals.

Monday, October 06, 2008

Misfortune, Serendipity, and Life

For those of you who don't know (which is probably most of you), I recently sent one of the stories I have written out to an anthology, hoping to get my name in print somewhere. Today I received back a very kind, very encouraging, but unavoidably negative response. The part that I most particularly am struck by is the very beginning:

"I found [your story] to be a touching and charming story, with much to recommend it. Indeed, I am rather hard pressed to say what it is that causes me to pass on it."

The kind editor goes on to say that he thinks the anthology, in general, is a good match for my work and that he hopes I find someplace to publish the story I sent in. As I said, very kind and very encouraging. But it brings into bright, shining contrast something else I've been thinking of lately, which is the fact that so much of life seems not designed and not determined but simply arbitrary and random. The rest of my life is conspiring to reinforce that feeling as well, drawing me towards the inevitable conclusion of the absurdity of the universe: there is no reason, things just happen.

It's strange, because finally I feel like I've reached the point Camus wanted to reach; where absurdism is neither optimistic nor pessimistic, where it just is. Good things just happen, and bad things just happen, and things -- of all sorts -- just happen. It would be easy to say that I am feeling existential doubt because I have received a rejection letter, and that I will get over my short-lived depression soon enough, and go back to being a grownup rather than a teenager filled with Sartre and Camus.

But I don't think that I failed; that's the interesting thing. Failure would have been a form-letter: "Thank you for your submission of [Title]. We are sorry to say that we will not be printing it in [Anthology]. Good luck in your further endeavors." But the fact of the matter was, the editor admitted that I had written a successful story that was a good fit for the anthology. My writing was a success, my discriminating taste at where to submit my story was a success, and the fact that I will not be published is simple arbitrary fact.

There is also the point that I am not, at base, afraid of failure. Indeed, being bad at something often reinforces my will to get better: I would likely not have taught myself how to sing had my mother not told me I was tone-deaf. I would likely never have learned how to ride a bike had I not been faced with the fact that my little brother could do it, I couldn't, and no one thought I would ever learn. My anger, in both of those cases, allowed me to prove everyone wrong and become competent.

But there is no anger in this case. I find I cannot get angry with the kind editor who liked my story and rejected it simply because certain things happen - stories are rejected, bike tires go flat, trains come early or late, it rains in Palo Alto. It was his choice, but to my experience he is simply the hand of the arbitrary, and absurd, universe.

And I don't know if I want to (or if it is even possible to) translate this into anger and become "good" at getting published. Everything I have heard, and everything I have read, on the subject says the same thing -- who is published and who is not is essentially arbitrary, the basic mirror of the absurd universe. No one is good at it except someone whose name is well-known: someone with a well-known name will naturally be more readily published, and naturally be more readily read. But most of us are not in that lucky (and also arbitrary) position.

I feel, increasingly, that this is mirrored in my social life. I have found a group of friends (miraculously? more rightly, serendipitously) at Stanford, and am active and sociable on weekends, and it seems like I fell into it -- that this group was none of my own doing. I see people who have not fallen into such groups, who are aliens or wallflowers or outcasts. And I cannot tell any quantitative difference between them and me. It seems like something outside myself, some (in this case, lucky) roll of the dice that allowed me to have a group of people to hang out with while others are exiled, or bypassed, or avoided, by the same group.

Or the conversation(s) I have had about relatively sparse love lives -- no matter how much work (if it should be called work, I guess) you put into finding someone, there is a certain element that is purely random: the only way to tell the people who are in happy relationships from the people who are not in happy relationships is that the former drew until they got an ace (or settled for a ten, I suppose) while the latter has not yet had the lucky hand. And so the only thing to do, and the only way to ensure eventual "success" (which, since it seems to be an arbitrary and not a skillful process, seems to me to be a misnomer) is to keep pulling cards. There's got to be one in here somewhere.

The paper I'm (supposed to be) re-reading right now, to discuss tomorrow, is about crossovers in mieosis. It is a mostly random process: as taught in introductory biology, crossover events occur without bias everywhere in the chromosome (except near the centromere). And it's a mostly essential process, both for mieosis to work right and for genetics to work right. Genes would not assort independently (one of Mendel's laws) were it not for crossing over and homologous recombination in meiosis: genes on the same chromosome would remain linked, and the shuffling that takes place in sexual reproduction would thus be greatly reduced, and the added diversity we gain from sexual reproduction nullified. But moreover, without crossing over events on the order of 1-7 times per chromosome (in humans), nondisjunction becomes a significant issue: chromosomes do not separate in meiosis, and terrible diseases (mostly, death) result.

The randomness (arbitraryness?) of the location of crossing over is another thing that is taught as fact, and seems important for good independent assortment: since no one place is guaranteed to recombine, alleles sort by a random flip of the coin, and therefore independent assortment is guaranteed. But, it turns out, recombination is much more likely in certain places than others, and different kinds of recombination are more or less likely in different places (a certain kind of recombination does not result in a crossing-over event). And it turns out that nature has rewired this randomness to create more randomness; removed the true random mechanism in favor of one that is skewed towards seeing phenotype: areas in genes, or promoters, or otherwise "useful" regions of the genome are much more likely to be the sites of these recombination events than other parts of the genome.

It's like the computer methods for playing a random song -- they are non-random, on the basis that in a truly random sample people see patterns, and do not believe in the randomness. In the world, so much seems totally random, which must really be skewed one way or another. But researchers couldn't find that out about recombination in meiosis until they did a full genome scan, and beginning students will still be just as well-served by treating meiotic recombination as a random event. You need a lot of data points to prove that something isn't random, when the randomness is so subtly changed. And here's the question: for any of the other arbitrary, absurd things in life (being published, bike tires going flat, trains being early or late, whether you make friends or find love, rainstorms in Palo Alto) is it really worth it to find the pattern, or is it just as useful to approach them as though they were totally random?

Friday, October 03, 2008

The Good Samaritan

This is what I read while my code runs:

Actually fairly interesting. I will try to edit this post with my thoughts when I get home. We'll see if that actually happens.