Wednesday, December 31, 2008
Also there are lots of minigames that I don't remember; I am more used to FFVIII or FFX (neither of which have I beaten -- my brother is an absurd backseat gamer and that took much of the fun away from video games), which are much more straightforward. I think I like the small varieties of gameplay, although I have to admit that I am terrible at just about all of them (just like I'm terrible at most video games).
I had all of these really good resolutions planned, too, but I think in the short term I won't even keep a resolution of "Don't spend every waking moment playing FFVII". So I might have to revise those. We shall see.
Friday, December 26, 2008
“Don’t touch that!” the shout rang out across the room. “Don’t you dare!”Saw "Frost/Nixon" today. It was really well done, and sparked a conversation about corruption in government and what Nixon did other than Watergate and whether (to simplify horribly) he was just a total slimeball and a crook or an overall decent president who did some really stupid corrupt things at the end of his tenure and got caught. (Diplomacy with China and Russia? Founding the EPA? wha?)
Jacob stared quizzically at his niece and the decorated paper plate in his hand. Most of the glitter had worn off, the bright colors faded. “What?”
“Put it down, now.”
Jacob set it down, still confused. Annie glared up at him. “That is the special-est award I have ever gotten. It is one of a kind. No one can touch it.”
Jacob stared up at the large mass-produced trophies that adorned the shelves, and the paper plate covered in tempera paint, and thought that maybe he understood.
Also had an adventure trying to get a custom calendar made for my mother. Ritz Camera stores appear to have problems employing non-obnoxious people, and also keeping their printers working. Two stores later, we still had not found a place that could print the calendar anytime in the known future. Which was not the result my mother and I expected, or desired. Especially since my father had received an e-mail telling him not that they had gotten his order, but that the calendar was printed and ready for pickup. Which was quite something in our opinions.
Thursday, December 25, 2008
“So, what do you do?” he asked, leaning too close for Sarah’s comfort.To a certain extent, my stubborn angry determination has defeated my writer's block. At least, this drabble was quicker than the last one. So that's good. Also, I've started going over November's Novel and will be posting it starting Jan. 1, with posts every week. It would be nice to be regularly posting something longer than 100 words, again.
She coughed lightly. “You’re psychic. Why don’t you tell me?”
He paused; perhaps offended. “Clever.” No such luck. “You work with Janice.” That wasn’t a surprising insight. “So, HR.” He grinned. “Impressed?”
“Forgive me if I’m not,” she said bluntly.
He smirked. “You have a useless degree in Philosophy from Cornell. You work long hours, without thanks. You don’t go out; haven’t since last year. Janice talked you into this and abandoned you, ‘for your own good’.”
He paused; she stared.
“No, Janice did not tell me.”
Christmas was quiet; no one in my family could sleep last night (as in, everyone was awake at 4 AM), so we didn't do too much today. But I did have time to watch four Doctor Who Christmas Specials (all of the new ones, for those who know or care). I have to say, the newest one (The Next Doctor) is probably my favorite; vying with The Christmas Invasion. I would lean towards saying I like the new one better, largely because some of the themes that they've been playing with -- humans almost as clever, and therefore almost as powerful, as the Doctor, for one, and the Doctor's central loneliness, for another -- are done nicely in The Next Doctor and not even touched in The Christmas Invasion. And I like those themes.
Wednesday, December 24, 2008
I'm sitting in the living room; the rest of the family has gone to sleep after watcing Wall-E (to Kevin from Santa), while tomorrow's dinner boils and bubbles away on the stove (I was bored and overambitious -- yes, it is past eleven here). I have at least an hour's worth of cook time left, and not much of anything to do. I cleaned up the living room (all wrapping paper is gone); I even got my brother to help. And now I'm back to my standard state this break: boredom.
I have not been posting largely because I have not felt like I had anything to write; I have been trying to write this break and have not had much success at all (2 pages of beginning to nothing in particular doesn't count). I think the creative deficit is finally hitting me (last night and this afternoon especially), which spurred the decision to cook, certainly. It was something to do, at least, but it didn't really make me feel like I had brought anything new into the world -- except a batch of pasta sauce that is still incomplete and could have been done hours ago if I had done it the way mom always does it instead of adding too much liquid. And a loaf of cornbread which turned out nicely.
It's been forever since I had an idea for a story, basically, and I'm really beginning to feel it. The drabble below is my attempt at forcing myself to re-enter the fray, even if I feel like I'm rusty and out of shape and have run out of any unique ideas. Honestly, I'm not; I'm burned out intelletcually after finals week and out of practice with writing after my Nano-inspired break. I just need to get back into it. Which is, perhaps, easier said than done.
Perhaps that can be a New Year's resolution. That and a few other things, like "Excersize outside of Silks class" and "Ask more questions" (this is my favorite).
On NPR today a TV critic listed his top 10 TV shows of 2008. Making the list was Pushing Daisies (ABC, I hate you for cancelling one of the few good shows on television) and Doctor Horrible (Yes, even though it was not on television -- it was so awesome they bent the rules).
Drabble: Made Up, inspired by the word "Narcissism"
Juliette primped for the mirror. She smiled at it winningly. Her mother called something from downstairs, but she disregarded it, adjusting her hair infinitesimally.On a completely unrelated note, I am glad the Doctor Who Christmas Special shows in the UK tomorrow; this means I might be able to see it sometime in the next century. (Boo to BBC America for showing the last three Christmas Specials here tomorrow, and not the new one!) And you know you've gone into Doctor Who withdrawal when you start dreaming about the Doctor. I was Martha (I was not "his companion", I was specifically Martha). There were plant-people. I woke up before discovering what their intentions were, but the Doctor was not the least bit afraid. Last night was a big night for dreaming; there was also something about Chicago, but much more of that has faded away since waking.
She looked lovely.
Her date was, of course, waiting. She checked her appearance one last time, making sure nothing had gone awry. No, still beautiful. She almost cried at the beauty of her own visage, but she stopped for the sake of her mascara. She stood, carefully, and turned for the steps.
When she got to the front door, he was gone.
“Where is he?”
“It’s been two hours. Did you expect him to wait forever?”
Wednesday, December 17, 2008
But somewhat more seriously, as I was walking (slowly, slowly) up from aerial class today towards the MUNI stop, breathing in the cold fog and breathing out slightly warmer fog, considering eating the chocolates I had been given for christmas as dinner (they were delicious), I had one of those movie-homecoming moments. You know, the last scene of the movie that goes with the epilog of the heroine having found a home and a new life and going off to change the world? It just felt comfortable and right. Which is pretty awesome, since I didn't really feel at home in Chicago until the end of my second year or something like that. I think, in part, it is related to the fact that I am doing things that force me out into the city more often than I was in Undergraduate, and also because everyone here is super friendly. Like, whoah.
On the other hand, I went to a stretching class today. Trust me when I say it was seriously hard core. No intro to yoga class, this. As in, they nicknamed it contorture. It appealed to a somewhat older audience than the aerial class I usually take, I think, although I am uncertain as to why -- flexibility goes before strength does, at least as far as I knew.
I'm going to start by saying I am not a contortionist. There are people who are bendy, naturally, and there are people who build muscle mass naturally. I am fairly squarely in the latter category, given my gender and age. When I was a gymnast, I hated it when my coaches would push me into stretches, because it hurt. And I was still not as flexible as my little brother, no matter how much my coaches pushed and pulled and stretched. Now I am perhaps a little more flexible than my little brother (he stopped stretching, I didn't), but I have discovered that it still hurts. And, if I thought that the pushing my gymnastics or diving coaches would do was bad, it was mostly because I had never trained with contortionists. Ouch.
The moment when I realized that I simply cannot do this ever again was when I couldn't breathe because the coach was compressing my lungs against a balance beam (pulling my shoulders back), while critiquing me that I should stop holding my breath and just relax (oh right because that is a perfectly natural thing to do when your arms are being torn out of their sockets); "See? When I said that you stretched farther!" he said as I almost passed out. I should have perhaps said the safe word (you know a class is going to be bad when there's a safe word. It was "Papaya") but I would have felt like a wimp, and my stubborn determination in the face of pain in general serves me well (I will not say whether it served me well in that situation or not, I have not decided yet). Also I couldn't really choke anything out (no air, and all) and settled instead for shaking my head madly.
When I do aerial stuff, I feel challenged and pushed but not that I am trying to get my body to do something it absolutely positively was not made to do. This time, I felt like saying "No, I cannot do that, I have organs there."
I was unaware, up until today, that one could stretch so much one felt sore the next day. I'm worried that tomorrow I might not be able to walk. And this class came highly recommended, too!
I'm also wondering if stretching out my pike and not so much my bridge for years in diving has made my arch worse than the rest of me, which is another explanation for why I was thinking "this class is maybe pretty okay even though it hurts like none other, and it would be super useful to get more flexible" until they started stretching out our backs, when it turned into "O God O God I am in pain and I cannot breathe haallllppp!"
As if to make matters worse, a dancer dropped in to the aerial class who would have been a great contortionist. Part of me is really jealous of people who can bend like that, in part because I think that their poses look so much cooler and prettier than the ones I can do. This is only made worse after 1.5 hours spent undergoing huge amounts of pain in order to... not bend that much. I mean, really. Even just being able to do the splits would be nice. On the other hand, she couldn't really do a straddle-up, or climb the silks. And I think I would be much more disappointed if instead of being able to climb to the top of the silks (or ropes or lampposts or trees or what have you) I could, I dunno, put my leg behind my head, or kiss my foot without bending my knees.
Time for a hot shower and sleep. And fingers crossed that I can get out of bed tomorrow! It will be lucky if I can.
Friday, December 12, 2008
2. My PI for my first rotation lives in a redwood forest. She invited the lab to her home for a Christmas party, and we went on a hike to get to her house. Better yet, she has a slackwire in her backyard. For her five year old daughter. A slackwire! Which is, in my opinion, possibly the most awesome thing ever. I climbed on it, but did not feel comfortable letting go of the balance ropes.
3. My cheesecake was a success! It was tasty, but next time I will 1) put more sugar and more lime in (the filling was a bit bland for my tastes), 2) use unsalted butter + salt on the crust for better control, and 3) possibly try the method where you put the spring-form pan in a dish of water to bake, thus making it cook slower.
4. After close contact with a Saint Bernard and the rain, I smelled like a wet dog. The dog was pretty much the sweetest animal ever. I really like Newfoundlands and Saint Bernards, I've decided, even more than I like big Labradors. Their mellowness is nice. I might like them better if I wasn't allergic, however.
5. Watching the fog come in over the redwood-covered mountains is amazing. Absolutely amazing.
Tomorrow is the latke party; I'm about as prepared as I want to be at this point (cookie dough in the fridge, etc). I just have to hope I don't burn the potatoes. *fingers crossed*
Wednesday, December 10, 2008
She feared becoming the teacher from Charlie Brown – standing in the front of the room, pontificating, while all anyone could hear was “wah wah wah”. She could envision her students’ eyes glazing over, the boy in the back of the room falling asleep, the two girls in the corner passing notes.I have many reasons to celebrate today. First (and most important): I am done with my first quarter of graduate school! W00! I finished up my last final today, hand it in tomorrow at 10 AM, and so that leaves me with a week or so more time to really dedicate myself to my rotation lab before I go on vacation and start my next rotation. This is pretty thrilling to me.
That was, if anyone asked her, why she chose to speak so clearly. Sharp consonants and round vowels would keep her from fading into the ignominy of incomprehensibility.
But she couldn’t explain all that to Johnny when he asked, “Why do you use your teacher’s voice all the time?”
Second: my silks instructor today (I celebrated by going to the city for lessons. This was not an abnormal activity for me, but it was celebratory anyway.) looked at me at the beginning of class and said "You know lots of tricks. You should start trying to tie them together. Your job for today is to make a phrase of two or three tricks." Which was happy (I know lots of tricks!) but terrifying (What do I know about stringing them together?) But I did it, and at the end of class she had everyone (which meant both of my classmates and herself, so not many people) watch while I did my little phrase. It was probably terrible, but I didn't fall down -- I actually came out of the last trick gracefully (which is a big deal for me) and so I was happy with it, especially for the first time. Chris (a classmate) had the same duty, and while his had a lot more cool tricks, he got tired halfway through and it was sloppy afterward. On the other hand, he has a lot of dance experience so he probably has a better idea on where to start with this "choreography" thing.
Saturday, December 06, 2008
They said it was impossible to get past the sentinel; that no one had ever reached the castle unknown. But Daniel had his ways. He was better than the others.Also, my mother laughed at me when I said I was surprised that strangers on the street have conversations with me. She pointed out that I once lent my phone to a (probable) drug dealer on Michigan Avenue. In my defense, I did not think he was a drug dealer, just a man without a phone. (Although it is a good story). She also laughed at my assertion that I was a cynical, east-coast, city-type and not a friendly California type. However, I stand by my assertions and my surprise.
He was not, however, as good as the girl he tripped over in his way through the forest. “Sorry!” she yelped, smiling warmly and moving out of his way. “Are you going to the castle?”
Daniel nodded instinctively. He realized too late that he should be keeping his secrets.
“Marvellous!” she said, cheerily. “I am too!”
“Why?” he asked.
“To tell the king you’re here,” she chirped. “I’m the sentinel.”
It would have been remarkable to run into Brian even if he hadn’t been a subject of conversation at dinner. After all, who expects to run into acquaintances from Chicago when one is in California? But there he was, at the ice cream shop.Yes, this actually happened. I was out with friends tonight, and as such my creative energies were spent being witty. But we did run into another Chicago-ite after talking about him (mostly the fact that he is in Palo Alto) at dinner. Another funny (and ENTIRELY TRUE) story, however:
“Wow! It’s you again! How’s the quarter been?”
“Alright. Busy. Yourself?”
The conversation was short: two people who don’t really know each other but want to keep up appearances.
“That was cool,” Roger said, as Brian walked away.
“Yeah, but if we had known this would happen, we totally should have talked about Scarlett Johannsen.”
So I was waiting for friends to get frozen yogurt (there is a new trend in Palo Alto, which is sour frozen yogurt with fresh fruit), and this older woman (older than my parents) stands up right behind me. She almost bumps into me, and then suddenly sits back down, so I sort of move out of the way and apologize, assuming that I've gotten in her way somehow. She says that I wasn't in her way and should not be sorry. This sparks a conversation. (Do not ask me how this sparks a conversation, as I do not rightly know.)
She likes my (red wool double breasted) coat, and asks if it is vintage. I say that I made it, and she is impressed, asks me to model it (turn around). She likes the flare (which is my favorite part, so I appreciate that). Asks me what I do, is surprised by "genetics". She is from the midwest, (Michigan, I think) and loves the fact that it doesn't get too cold in Palo Alto over the winter, but admits that icicles and snow in Michigan are beautiful. An older man comes to pick her up, and she asserts that he has had a stroke, and he is totally bonkers, and they aren't married but she has to look out for her fellow students. I am not sure what this meant. As she leaves, she gives me a hug, remarking upon the fact that I am skinny.
I turn back to my friends, who ask "Who was that?" and I have to respond, "I don't know. I've never seen her before in my life." On the one hand, I admit that it is probably odd I have just conversed for five minutes (and hugged?) a woman who I have never met. On the other hand, it seemed the most natural thing to do in the situation. And it's not sketchy if she's a motherly or grandmotherly sort of person. Although it certainly was odd.
Thursday, December 04, 2008
The envelope was fluorescent pink, and still Andy almost discarded it with the rest of his junkmail.
The sender was “The Department of Supernatural Affairs.”
He opened the envelope. An application fell out, and a cover letter.
“Dear Sir,” it proclaimed in big, bold letters,
“You have not come to our attention in a search for applicants for a position at the Department of Supernatural Affairs.
“Are you constantly overlooked? If so, the Department of Supernatural affairs may be perfect for you! Meet other people like you, who use their remarkable unremarkability to be extraordinary and unnoticed.”
Andy blinked. What?
Wednesday, December 03, 2008
People were rarely surprised that Caty worked with the circus; they were more surprised, however, that she was an acrobat. How could she perform with her… disability?The aerial fabrics class will be offered again next quarter, which is excellent, and I do not think it clashes with any of my classes, which is also excellent. I will keep my fingers crossed!
But she put up with their stares, with their ogling, because once she got on stage everything changed. Suspended, she was as graceful as a prima ballerina standing on the tips of her toes. She floated in silks, and twined with rope; even cold chains lifted her up rather than keeping her down. Freed of gravity, her freakishness was turned to beauty.
After all, who needs feet when they can’t touch the ground?
“I’m just a simple sailor,” he claimed, glancing warily at his interlocutor. “I have no idea what you are talking about.”In other news, I think I totally freaked out a couple on the MUNI. I was riding home with Chris (from Silks), debating quarter versus semester, and lauding the joys and despairs of a liberal education. The funny thing was that I had forgotten my water bottle, and so had water in a cup without a lid, with which I jogged to the MUNI, spilling water all over my front while Chris held the bus for me. His reaction upon seeing me: "Are you okay?!"
His interlocutor, from the shadows, laughed. “It’s no use hiding anymore,” the gravelly voice came. “I might have believed you once, but now? Your performance on the rigging was not that of a simple sailor.”
“I’ve been at sea all my life.”
“All the other sailors were hiding from the storm; you were climbing like a monkey. And the back flip onto the bulwark? It was a little excessive.”
He winced. The back flip had been his favorite part.
Yes, they stared at us for the rest of the time on the MUNI. I think it helped that the first thing we talked about was dedication, and how it is easier if your friends know you have a strange habit and support it -- this morning, to my "Ugh I only got four hours of sleep last night. Maybe at six I'll take a nap instead of going to the city" the biochemists (Ruth and the Rooses, to be particular) responded instantly "No! You have to do your circus stuff!"
Maybe they just wanted to avoid me, but I'd like to pretend that they had my best interests at heart. And since I learned this really nifty new trick that looks like you're sitting on the silks (without, mind you, tying up your foot), I have them to thank. (It's one of those deceptively easy-looking tricks: where, if someone can do it well, it looks so simple and restful -- you're just sitting there with your legs crossed -- and then you realize that the only reason they're not slipping down the fabrics is because they are pinching it for dear life between their knees.) Also because my roll-down (a trick in which you wrap the fabrics around your waist and roll down them; you control your speed by how fast you feed the fabric through the loop, and you can spin as many times as you want until you hit the ground, but it's easy to lose the silks and get tangled, and body-position is supersuper important and supersuper difficult: it is, in fact, remarkably difficult to hold a hollow position while suspended from your waist, feeling the pinch of fabric and gravity on your lungs, kidneys, liver, etc) is making progress; I can almost sort of do it! w00!
Monday, December 01, 2008
The passing of November is the passing of adventure. November is a time when anything is possible, when the sun still shines through the crystalline winter cold. In November, there is still time for this year to surpass all others, still time for one more frantic burst of energy before the long nights and short days of winter curtail our efforts. December is the beginning of the end; December is the bells tolling, slowly, counting down the days, hours, minutes, seconds until the New Year: another year gone, and where are we now?In other news, we discussed the Immortal Strand Hypothesis in journal club today. It postulates that stem cells retain older copies of DNA in their cells, thus preventing or at least reducing the risks of DNA lesions and mutations. Which implies, in turn, that sister chromatids segregate non-randomly. Which is pretty cool, and pretty weird, at the same time. I might edit this post later tonight to explain, if that isn't clear. (One common question is "If each chromatid is made up of one mother and one daughter strand, how can you have newer or older copies?" -- for now, the short answer is: think of the next cell division.)
What have we done that was worthwhile?
Sunday, November 30, 2008
1) Turned on the pilot light (with help). Now my apartment is toasty warm instead of chilly.
2) Cooked a Turkey breast (without hardly any help!). It turned out absolutely delicious, if I do say so myself -- the breast meat was tender enough that even I (a sworn dark-meat person) loved it. I still have some in my refrigerator. Sammiches? Yes. The rest of Thanksgiving dinner (challah, mashed potatoes, vegetables, apple crisp, gravy) was a riotous success as well. With the possible exception of the gravy, which was... very thick. In my defense, I had not made gravy before, and my father did say "equal parts drippings and flour". But, all in all, I need more excuses to make large meals and bake bread. Also the time to do so.
3) Fixed the light in the kitchen. This was, admittedly, in no part my doing. It was also in no part within my abilities, since it required someone to fix wiring somewhere inside the walls. But the landlord is fixing things in the apartment next to mine, and halfway through making the turkey, the light came on. Thanksgiving miracle!
4) Strung Patio Lights (they are not christmas lights if I leave them up after new year's). They are warm and welcoming.
5) Made a desk (w00!). It is just a shelf built into the wall, but since I hate powertools and this required using a power drill, I am proud of myself nonetheless. After all, I have a battle scar from when a power drill attacked me. The desk is pine, stained bright red, and sitting in the nook in my bedroom. I love it!
6) Finished this year's NaNoWriMo novel! All told, it is 76,440 words long and 156 pages. It is not my worst work, but not my best either, in my opinion. I think it is, however, a good sequel, so I am not ashamed. At least, I will not be ashamed once I have edited it.
7) Investigated another clue for the scavenger hunt. I now have 3 clues written and 4 more planned out. I can stop now, or come up with one more clue. Woo!
Hopefully, now that November is over, I will return to a more regular posting schedule. The plan is to go back to posting a word-of-the-day drabble every day. We'll see about that.
And, to inaugurate my return, a drabble! Inspired by the word "Incursion".
Professor Randolph knew that 150 people were registered for his class, but he also knew that only one quarter of those people ever attended lecture. So he was not prepared for a full classroom on that dreary Monday morning. Unless he was very much mistaken, there were more than two hundred students in the lecture hall.
Frankly, it distressed him.
He cleared his throat. “I don’t mean to be obtuse,” he said, “But you can’t all be registered for this course.”
A rolling laughter swept the audience, but there was no specific reply.
Professor Randolph, baffled, turned to the board.
Sunday, November 23, 2008
Also, the closer it comes the more I realize that I have no idea what the hell I am doing. It will, potentially, be an exciting Thanksgiving. At least there will only be four other people to witness my crazed humiliation.
Wednesday, November 19, 2008
I guess what this means is that I am an extrovert. (Gasp; who would have thought? Although I must admit that I did not think I was an extrovert until fairly recently. Yes, even though I like getting up in front of people and performing, and even though I talk to strangers, and even though I talk to as many people as I can about even the most minor of decisions, and even though I get lonely really really really easily. I can be dense sometimes.)
Point being that at 7:00 tonight I was feeling next to dead, from want of sleep and sociality and who knew what else. And so I dragged myself to a coffee shop, where I had the (good?) fortune to happen upon a monologue slam (like a poetry slam, only with dramatic monologues, which, fortunately, I am not quite as bad at writing). One of the performers sat next to me; I complimented her on her performance (it was quite good), and she said I should write something. I only had five minutes to go, and had not thought of anything in particular, so I frowned and told her as much.
A minute later, I had an idea.
Four minutes later, I had half a monologue, which I performed. I could tell that everyone wanted it to go on, to reach a conclusion, and was shocked when it didn't -- when I stopped halfway through a thought. But I wasn't going to improvise. And for the roughly ninety seconds when I was reading in front of them, pretending not to be a geneticist but rather to be an uncertain undergraduate once more, dallying and dabbling in all sorts of things while I still could, and when people cheered when I said I was from Chicago, and when people laughed at my attempts at humor, I was outside of myself, and it was wonderful.
For a moment, I wasn't an awkward first year genetics graduate student desperately trying to make friends and get a program to work correctly for once so that she could have made some progress, somewhere, sometime, in her rotation project. I wasn't even, as one of the other first year genetics students said, "[practically] a biochemist", due to the fact that I was practically ostracized from my own department socially simply because of my outspoken, extraverted (okay, I said it) personality. (According to him, all the biochemists are the same person, with the possible exception of Ruth, who is "quiet". Ruth objects to this, saying that she is gregarious and sociable and extraverted and just doesn't talk in class -- which is probably true, but even if she is outspoken compared to the geneticists, the biochemists make her seem shy and retiring -- and Alex objects to this as well, saying that he is different because he mumbles -- which is a less compelling argument.) Instead, I was special, because I could go up in front of people and read two hundred words that I had just written about who-knew-what (I believe it was winter, and the fact that I keep expecting it to come and it never does), two hundred words that I knew could be better or cleaner or wittier if I could sit down and edit them carefully and consider each of them, two hundred words that I hadn't had time to think about how I would deliver or even learn to the point that I could read them without looking mostly at the page, read two hundred words of a rough draft of an essay I will never write and have it be fun, have it be exciting, have it be goofy and exhilirating instead of embarrassing and scary. And simultaneously, I was surrounded by people who were more special than I was -- my monologue was not the cleverest nor the best delivered, by any stretch of the imagination -- but were shared by the common bond of, perhaps, "we like doing scary things".
I forgot to tell them my last name; everyone else was "Joe Smith" or "Diane Wang" or even "John Do" (I don't know if that's his real name, I hope it is, because that would be hilariously awesome), and I was just "Elizabeth". But it was okay. No one cared, least of all myself.
And afterward, the performer who I had complemented found me again, and told me "Your spontaneity is delicious," which I took as a huge compliment. I aspire towards brave spontaneity; towards not giving myself time to worry that something will go wrong, towards not always needing a plan and a backup plan and a backup backup plan.
Hopefully, that will have given me the boost I needed; enough energy to push me through the rest of the quarter. Or at least until I can go Christmas Carolling with the Biochemists. (Since I might as well be a biochemist, according to some, and since Krystal has agreed to assist with the carolling endeavor.) Or rather, at least until I can get this scavenger hunt party underway (it is a traditional scavenger hunt (one clue leading to the next leading to the next) in which the prize is fixings for a party, and everyone gets to join in at the end). Which will not be performance-based, but will be tons of fun. I have several ideas that will possibly cause injury and/or hypothermia, unfortunately. So maybe some of them will be postponed until summer, when at least one of those risks will be abnegated.
And, because the Big Game (TM) is on Saturday (might or might not go up to Berkeley for it):
Go Cardinal! Beat Cal!
Saturday, November 15, 2008
And, since word count no longer is of primary importance, I can talk about something else. Namely, this past week's New York Times Science Section, which focused on a subject close to my heart: epigenetics. (Epigenetics and fiction, I just need to mention circus stuff in this post and it will be a summary of my life.)
If you haven't read it, you should -- it's a pretty good read and a decent introduction to epigenetics. Here's a summary article.
And here is my caveat, in which I say that I have a bias. I am a geneticist. I study epigenetics. And, reading this article, I felt the need to stand up for the power of the gene, or at least the DNA sequence.
Robert Tjian gave a talk at Stanford two weeks ago. He's the next President of HHMI, and studies how genes are regulated in a cell-specific manner. And he said, something like three times in his talk and in a smaller discussion afterward, that it all comes down to transcription factors, specific cis-acting binding sites, and, effectively, sequence. Sequence is still everything, sequence is dictating the changes, even when the changes result in variable interpretation of sequence. I asked him about epigenetics, in part because anyone who studies cell differentiation in this day and age has to consider epigenetics, and what he said was, I felt, particularly revealing. He didn't deny that methylation marks, histone modifications, nucleosome positioning, and whatever other epigenetic mark you can think of are certainly important in development and in differentiation, especially in producing stably differentiated cells. However, he said, even these marks, eventually, come down to sequence.
Take, for example, something that seems overtly epigenetic. A cell divides, and upon division, whichever daughter cell is closer to an external signal remains a stem cell while the daughter cell that is farther away differentiates. How does this come down to sequence? Well, there are specific genes for specific receptors on the surface of the cell which interact with that external signal and cause a signalling cascade resulting in a set of transcription factors being upregulated to cause the differentiation, for one thing. And there are other specific genes which organize and create the mitotic spindle such that when the cell divides, one of them actually is closer to the external signal than the other. Even what appears to be an epigenetic effect based on the location of the cell relative to other cells is, in the end, controlled by genes. There are protein-coding genes which you can knock out which disrupt many, many parts of this process, and each causes a defect in differentiation.
Likewise, consider "position effects" in eukaryotic molecular cloning. Depending on where a researcher inserts an ectopic sequence into the genome of a eukaryote (for example, yeast, or mammalian cell culture), that same ectopic sequence will be expressed at different levels, perhaps very highly and perhaps not at all. Surely this is proof that, finally, sequence doesn't matter: same sequence, different expression, right? Only it's not the same sequence, if we look at a slightly larger level. Neighboring genomic sequences differentiate one situation from the other, and dropping in large sequence buffers called "insulator elements" to situate the ectopic sequence in a more neutral genomic environment goes a long way toward ameliorating "position effects."
The article I linked from the New York Times says, basically, that since only 1% of sequence codes for protein, 99% of sequence is irrelevant, and hence, sequence is 99% irrelevant. However, I would argue instead that since only 1% of sequence codes for protein, the remaining 99% is where all the really interesting stuff occurs. It still comes down to sequence; we just need to redefine what we mean by sequence.
Tuesday, November 11, 2008
But in the spirit of bad chinese take out, my fortune was, probably, the second most oddly specific fortune cookie I have ever seen. (It still doesn't beat "You will see the Great Pyramid in Egypt.")
While the rest of my cohort was opening cookies to reveal pretty standard fortunes (Good luck comes to those who wait, A significant change is just around the corner, Beware Japanese waitress bearing fortune cookies), I cracked open the shell and read "You will attend an unusual party, and meet someone important."
I think there is only one possible explanation: sometime soon, I will be blindfolded, kidnapped, and taken to an underground sumo-wrestling party, where I will meet Joey, a talking Orangutan sumo-wrestling champion who will lead the ape rebellion. Our conversation will mean that when the revolution does comes, I will not be torn to pieces by screaming monkeys.
Not a bad fortune, all said. Probably better than those poor sods who got "A significant change is just around the corner."
ETA: Updated word count (for those of you who care, and those of you who don't): 40,002. I am 4/5 done with my nano goal, and only 1/3 done with the month. Time to sit back, relax, and coast to the finish line. Or spend lunch breaks, evenings, early mornings, and every free moment I have writing because, hey, who wouldn't use an excuse to write a hilariously bad novel when they could be doing useful things?
ETA2: I am sitting outside, and had missed, for quite some time, the large airship flying across the sky above campus. As in, white blimp labeled "Airship Ventures" with a sign painted on its underbelly: a number to call to schedule your own zeppelin ride.
The (steampunk) future is here, for the rich and famous, and apparently it takes place on a zeppelin. Although the airship could have done with some more brass, I feel.
Sunday, November 09, 2008
I think, to be honest, that the kind of writing I have been doing lately does not suit itself to the kind of writing I am comfortable posting on this blog. For the following reason. Most of the fiction I have posted on this blog are drabbles; very short, and hence I have had time to look over every word and carefully choose it as I go. While the longer (full short story) pieces I have posted have definitely improved by being looked at by Ayn, especially, even they were more ready to be looked over than my Nano piece. Nanowrimo is, if anything, the antithesis of how I write drabbles and short stories: in order to make it through the month, I can't edit as I go. I have to just write something and promise myself I'll look throug it and make it better later. That's what January and February are for. I've already told anyone who asks that they can read my novel, at the earliest, in March. (Apparently novel-writing science graduate students are rare enough that my friends are surprised and at least play lip service to wanting to read my work.) That's when it will finally be fit for other people to read. There might be some sections that need less editing than others, but all of it will need to be gone through with a fine-toothed comb before I even come close to posting it in total online.
She did not begin to run until she felt the spring sunlight on her face, and smelled last night’s rain in the ground. And when she finally did, after months of a concrete cell with no contact with the outside world, she almost broke down and cried with joy. She ran, she slipped, she skidded, she fled and she flew through the foggy forest surrounding the prison, but even this forest which would have scared the bravest human was home to Nerissa Zephyr. She could taste the sunlight and the dew in the air, and she could sense how desperately they had missed her during her incarceration. She was free, again; free from her cell and more importantly free from the future depicted in the crystal ball. The world was hers, and the arms of Albion and Naid and Corundum stretched to welcome her back.
But nothing, no smell of rain or warmth of sun or feel of earth beneath her feet, nothing compared to the homecoming of finally, once more, after so very long, feeling the breeze against her skin. It enveloped her, caressed her, and she thought for the first time in a long, long time that this was what it meant to be a fairy, and especially, this was what it meant to be Nerissa Zephyr. Not beauty, not grace, not cleverness, not the magic she had used to make herself invisible. To be herself was to be one with the wind, to hear it whisper in her ear, play with her still dingy straw-colored hair, brush against her prison garments, warm her skin and her heart. She thought back to her lessons with Professor Johnson, and her sessions with James, and all the nights making up magic in her cold jail cell, and she frowned in concentration. If she could make herself invisible, then there was no limit to what she could do. She lifted her hands, and made herself lighter than a feather, and the breeze picked her up tenderly, carefully, like a child. And then she spread her arms wide, willing the wind to carry her home.
And, with that, my nose goes back to the grindstone!
Wednesday, November 05, 2008
Prop 8, at the moment, is ahead by something like 4 points, with all precincts reporting and only absentee ballots etc to count. It could still change; but it seems to me that this is, at the very least, more certain than Ohio was at 9 PM Eastern Standard Time last night, and so I am (perhaps prematurely) disappointed. This morning my sentiment (and desire to make sweeping generalizations) could be summarized by "Fuck Los Angeles, San Francisco is the only place in this state that makes any sense." (The SF bay area came out against the proposition, while the LA and San Diego areas and much of rural California came out for it). I've calmed down a little bit, (emphasis on little), although I think that Chicago would be a much happier place to be right now.
My remaining problem with the Yes-on-8 campaign is that, if they win (it's close enough that we need to count absentee ballots), they won on a combination of misinformation and straight-up lies. They made it about protecting children from being taught about homosexuality in schools when existing laws in California ensure that parents would be able to take their children out of any such class. They made it about the freedom to practice religion when no one would force a priest to marry two men if he didn't want to. They spun a fairy-tale of a world in which homosexuality is the norm and someone could be prosecuted (they said this, although I feel like they must mean persecuted) for being adamant that it is a sin. However, in the end, proposition 8 does one thing and one thing only. It eliminates a right for a specific group of people. It isn't protective; it is discriminatory. It isn't about wider issues; it boils down to straight up bigotry and one group of people imposing their beliefs on another group of people.
I hope this doesn't boil down to religion. I really hope it doesn't, because some of the best and brightest people I know are very religious and I do not think they would have voted for prop 8 (in some cases, I know they wouldn't and/or didn't). The only way I see this being about religion is if it is about moral absolutism; religion allows you to say "this is morally wrong" in a victimless crime (such as two men who love each other dearly and have been in a relationship for 21 years getting married). But in general I don't think that it is about religion, and I don't think it is about right and wrong, I think it is about something far more difficult to pin down; something far more subtle. I think that this is about the careful distinction we have to make between "what is wrong" and "what should be illegal". The two are not the same. There are some things which may not be wrong but are illegal (rewarding people for voting, without asking how they voted). There are other things that may be wrong, but should not be illegal (making racist statements, for example, which might not be the best parallel in my opinion because no one is hurt by two people getting married, whereas people are hurt by racist comments).
One last thing that I thought of today, while trying to distract myself from worrying about this by doing experiments. The proponents of prop 8 claim that if it fails, it will usher in a new era in which it will not be acceptable to be religious, and in which kindergardeners will be taught that homosexuality is okay. I, as an atheist pinko commie starbucks-drinking hippie liberal, didn't want to do any of that -- shut down churches, preach to kindergardeners -- until they said I did. But their lies and accusations make me angry enough to turn me into the very villian they make of me. It's something that I have to fight, not to lash out at people who make false accusations, and it's something I consciously do fight, but I feel like those accusations are a self-fulfilling prophecy. Accusing people of being evil and wanting to bring you down is as good a way as any of making people want to bring you down.
My next post will include part of my November's novel.
Saturday, October 18, 2008
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
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.”
“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
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
"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
Actually fairly interesting. I will try to edit this post with my thoughts when I get home. We'll see if that actually happens.
Monday, September 29, 2008
In fact, it was only when I realized that the paper wasn't one research study but four independent experiments that I could understand what on earth was going on. At which point, since none of the experiments were particularly compelling, I was left with an even more sour taste in my mouth about the whole experience. Perhaps they assigned this paper simply to frustrate us; to see who could read a paper and who couldn't, who could determine the weaknesses and analyse and generally understand the steps of a paper. And to see who wasn't afraid to look at a published work and say "That paper was crap." Because this one was particularly hard to understand: no organization, no background, and no continuity from one part to the next.
As best as I can reproduce it, for your reading enjoyment, here is a summary.
First off, most people think that this one protein (A) interacts with the cellular scaffolding proteins to make cells asymmetric (btw, cells are asymmetric. nifty.) Except, if you prevent scaffolds from forming, you still get asymmetry, so this can't be it.Honestly, I shit you not. Now put that over 13 pages of techno-babble with appropriate (or inappropriate, you know, to spice things up) figures, and you get the paper I had to slog through today. Delightful, right?
If you look at a cells that mess up their asymmetry -- don't bud/divide correctly -- you find that a lot of them have problems with another protein, B. (This protein is totally unrelated to protein A.) If you cut out B, along with some other proteins that let the cell know which way is up, cells become symmetric. If you add back B, they lose their symmetry. If you add back various mutated forms of B, effective and deficient in various functions, you can see that certain things, like binding to the cellular scaffolds, are necessary for cell survival and asymmetry, and other things, like binding to itself, are not necessary for anything in particular as far as we can tell.
Protein B might interact with protein C. Protein C is thought to serve as a +/- marker, like an on-off switch. But it might not work quite that way. If you force it to be a switch, you get symmetry, so it's most likely not a switch.
By the way, if you add lots and lots of the switch-version of Protein C, you can in fact get asymmetry back. But those cells aren't happy, so they don't count.
The one thing I take from this paper is that as a biologist, I need to learn how to design a study, in a way that is not just a collection of various and sundry experiments, because otherwise I will end up writing a paper like that one.
And that would be very, very saddening.
Also that stream-of-consciousness, while very effective as done by James Joyce, is not an appropriate literary device for a scientific paper. But I already knew that.
Sunday, September 28, 2008
Perhaps a more substantive post this evening when I get back from the dance on Mars. (Clearly, by "dance", I mean "hiking trip" and by "on Mars" I mean "in Big Basin Redwood Forest". Unfortunately, reality cannot live up to some expectations.)
We have just discovered an important note from space.
The martians plan to throw a dance for all the human race...
Friday, September 26, 2008
When he looked back on it, Alan knew exactly what he should have said. He knew exactly what would have avoided all the strife, all the awkwardness, and all the sideways glances whenever Anna walked into the room. Just because they knew the story, people thought they were in on some great big secret – when really, Alan and Anna seemed to be the only ones who had moved on. And one sentence could have spared him all of this. One simple, straightforward sentence that summed up his feelings exactly:Wrote my first functional, useful PERL script today. w00t! Which means, basically, that I have a free weekend, since my weekend's worth of work took all of three and a half hours. Also, I learned regular expressions in order to write said script. And yes, yes I was wearing my tee shirt that said "STAND BACK! I'm going to try Science!" while I programmed regular expressions in PERL.
“I’d rather not say.”
Hindsight is twenty-twenty, and all that rot.
And yes, I did explain the comic and the relevance of my teeshirt to the rest of the people in my program and year.
$elizabethGeek += 10;
All in all, it was a nice way to start grad school. Loads of geeked-out-ed-ness, and a free weekend afterwards!
Although I do have a biostats problem set to force myself to look at. Which is made exciting only by the fact that the book is somewhere en route. Time to go to the library.
Perhaps there will be a trip to Big Sur on Sunday? That would be awesome. And perhaps gardening tomorrow, which would be good, but less awesome than hiking around Big Sur. If there isn't a hiking trip, I'll lounge about in Palo Alto and work on Statistics. Perhaps it's time to put PERL on hold and teach myself some R.
So as not to get too out-of-balance, you know.
Thursday, September 25, 2008
Juliette refused to call herself a child prodigy. Her parents despised the word, with its implication that she wasn’t on a direct path towards success, but was rather a bright shining star that would burn out soon enough and let the other kids have a chance.Graduate school, so far, is full of Computer Programming Languages. (To be honest, it is also full of epigenetics, and genetics, and my wonderful genetics clique which is being broadened to perhaps include biochemists and developmental biologists, but mostly it is full of Computer Programming Languages.) This quarter will be the quarter to learn how to analyze data; I am learning both PERL and R for that purpose. Well, not exactly. I'm learning R because it's part of a totally worthless statistics course I have to take (mostly I sit in the back and pass notes with the rest of my genetics clique). I'm learning PERL in order to analyze a data set for my first rotation.
“That’s not fair,” Andrea said, “plenty of child prodigies grow up to be successful.”
Juliette dried up that sanctimonious phrase with a single look. Stuck behind the Starbucks counter all day, making Espressos for young investment bankers, the last thing she wanted to be reminded of was what a bright child she had been.
It's a very novel experience; being confronted with a massive data set. I don't rightly know what to do with it yet. I mean, I have a vague idea of what sorts of graphs I'd like to eventually have. But it's very vague and I have very little idea of how I would go about making those graphs. But what's awesome is that my job for the next ten weeks will be to analyze someone else's data set: I'm so used to doing benchwork for ages and ages and getting maybe 10 data points. This time, with no benchwork at all, I was handed an enormous data set: something like 5 million points. I'll likely do some benchwork as well to make a library (read: sample) or two, but it's all procedures I know well already (read: molecular cloning, PCR amplification. The hardest step? Gel purification. From a kit.) and even if I started yesterday, since the lab I'm working for sends out their libraries for analysis, and the analysis is backed up like whoah, I wouldn't get data back until the rotation will be over. So I'll do it to stay in practice, I guess, but the focus of my project will totally be analysing all this data. And since I have a lot of data to analyse, I am (finally) teaching myself PERL.
So far so good with that; I'm pretty comfortable with basic control structures, arrays, and hash tables (and since I picked up the book yesterday, and since I am a biologist, I count this as progress). I'm finding my biggest frustration to be 1) Vista, which has nothing to do with PERL, and 2) the fact that all variables are stored, basically, as strings, so I have to remind the program that any given variable is a number, say, by adding zero to it, every time I want to do a comparison -- or else 9 > 10 since it's sorted alphabetically by ASCII value. Say what?
Next topic to cover is file input and output.
On another, unrelated note, I am riding my bicycle faster than I ever have before. I know this because I actually passed someone on the road today. For the first time in my entire life. As in, when I said "I passed someone on my bike today!" my dad thought it had to be a four year old with training wheels. I still feel big, slow, and vaguely turtle-like: since I carry textbooks and my computer, lunch, and various sundries on the back of my bike every day, as I slowly wheel my way the mile-or-so to work. But at least I am not the slowest turtle on the road!
If only my textbooks would protect me the way a turtle's shell protects the turtle. That, indeed, would be nice.
And, finally (I mean it, finally), I found a market that looked like it has been designed for a specific short story I wrote, which basically made me run out of reasons not to submit the story. So I did. I am keeping my fingers crossed, but to be honest it would not be the end of the world either way.
Wednesday, September 24, 2008
I couldn't resist.
Neither could I resist shouting at the screen in anguish repeatedly while watching the Heroes season three premier.
I could barely resist gouging my ears and eyes out.
Since the premier was not tonight but last night, I'm going to assume that I'm not posting spoilers for anyone who cares about reading spoilers. But:
I didn't like Heroes for the random powers, for the world it created, for the special effects, or for the simple fact that it was a super-hero show. I liked Heroes because I go to know, and like, and empathize with, the characters. Take Hiro, who I think is probably most everyone's favorite character (if he's not your favorite character, then you're silly). In the first season, he was just sustained awesome. In the second season, I put up with that ridiculous Takezo Kensei plot mostly because Hiro was in it, and Hiro was being his faithful, puppy-dog self. If it had been the naturally suspicious and serious Noah Bennet (who I like, don't get be wrong), or the takes-himself-waaay-too-seriously Peter Petrelli who had been sent back in time, the side-plot wouldn't just have gotten dull fast, it would have been impossible to watch. Like that feildtrip we took to Ireland with memory-wiped-now-morally-ambiguous Peter (that might be a hint -- keep Peter the good guy, unambiguously, please?).
Now, Hiro in season three is already suspicious and keeping secrets from Ando, something that would be unbelievable in previous seasons. And their justification of "Hiro thinks Ando will kill him, because he saw the future where that happens" doesn't make sense because, well, old!Hiro saw New York City blowing up several times, and instead of running away from it he tried to stop it. In this case, why not try to stop your best friend from attempting to kill you. By, say, NOT turning on him and becoming a secretive, suspicious idiot?
The thing is, this isn't just a sudden, unexplained character change in Hiro Nakamura (although since Hiro was so close to my heart previously it is particularly troubling to me). Peter, Clare, Mohinder, Nikki, and to a certain extent even Nathan, Sylar, and Noah Bennet have all undergone similar bizarro-tranformations. Evil!Future!Peter is just annoying (for once I agree with Mrs. Bennet -- bring back her son and get the Hell back where you belong), Emo!Numb!Clare is something I thought we grew out of at some point in season one, Lizard!Mohinder I shouldn't even have to qualify (seriously, bring back awkward, earnest, well-meaning Mohinder. The one who could have lines directed at him like "He's adorable. Can I keep him?" I want more adorable and less random!hookup!sex.)
Oh, and on a side note, why must everyone be a Petrelli? Next thing we know, we're going to discover that Hiro's a cousin many times removed and Matt Parkman is Nathan's older half-brother. I mean, really?
Um. So I'm not sure if it's even worth continuing. If I can find a group of people to throw popcorn at the screen with, then I might keep watching. But as is, ugh. I dunno.
In other news, Grad School is going well so far. I have a Genetics Clique. We are too cool for those Dev Bio and Biochem students in our classes (haha yeah right). Also, I have a rotation project. It's pretty much better than expected.
Monday, September 22, 2008
“It’s a bad time to be a science writer,” Stephanie said, and everyone agreed, shouting their outrage to drown the pounding on the doors of the barricaded conference hall.Does it count as procrastination if technically I have nothing to do until five?
“Journalism is dying with the newspaper,” she proclaimed. “And we’ve been deemed expendable. Things will only get worse.” There was a round of grumbling assent. “The outlook is dark: no new jobs, massive lay-offs, and lack of public interest.”
Keegan snickered from the back of the room. “That’s a gloomy prediction. But you’ve left out the mob with torches and pitchforks.”
At least, in the end, they made the front page.
After lunch I'll try to find the mythical post-doc I'll be working with on my first rotation. Maybe he or she will give me a paper to read. That would be distressingly like productivity, since Julie seemed to think I couldn't go in to lab until tomorrow, earliest.
Saturday, September 20, 2008
“Last time we talked, you were seeing someone.” It was a statement, not a question. I laughed bitterly.I failed at tailgating, mostly because I failed at properly transcribing phone numbers. Lame, Elizabeth, Lame. Also lame was my thought; "That's okay, I can just wander around until I find them. How big can a college football game be?"
“Funny thing about that; turns out I wasn’t.” He said nothing in response. “How about you?”
“My boyfriend is moving out here in January.”
“Long distance is really hard.”
“Yeah. But if you can do long distance, you can do anything.”
It was his turn to laugh. “I hope so.”
We fell into silence. Finally, “There’s something to be said for a fresh start.”
I nodded. “Don’t I know it. But there’s also something to be said for having someone.”
Um. Don't answer that question. Just take it for a start that I have never been to a football game, and actually thought University of Chicago's football games, where even free food fails to draw a crowd, were normal.
In any case, after thirty minutes of aimless wandering through the thousands or millions or whatever it was numbers of people tailgating, finding no one, I called it quits and biked home. *Sigh* Maybe next time I will not be so stupid on so many levels (seriously, this afternoon was a comedy of errors, complete with being mistaken for a man and breaking into my own apartment. Or something like that).
In more positive news, I finally met up with Becca, and we hiked around the "lake" (more like a meadow) and up to the satellite dish. It was tons of fun!
Also, when I got home, I got my check (I can pay the rent! W00!) and my neighbor said to me, "I have a year's worth of Nature. Do you want it?"
It is now proudly sitting on my bookshelf, in chronological order. I've been reading them online, but I should go through them some afternoon (read: tomorrow?).
Friday, September 19, 2008
In other news, I've been hazed and vetted by the genetics department. I actually, like, know people now. Highlights:
Sally hated to present to physicists. It wasn’t that they were loud or raucous; every question was politely held to the end. It was just…
“Are you sure your data is significant?”
She sighed. “The trend goes up,” she answered.
“But not by much,” her interlocutor responded. “And it sort of oscillates,” someone added.
“What’s important is that we’re hiring more diverse applicants,” she insisted.
“But we’re not getting more diverse applicants,” someone called from the back of the room. “If the pool is unchanged and we’re accepting more people, doesn’t that just mean we’re lowering our standards?”
On my way to catch my ride to Monterey, I got lost in a golf-course. I didn't even know the campus had a golf-course, but in retrospect I'm not too surprised.
The first event of the weekend was our introduction (read: public humiliation). Doug (who knows Steve from grad school, I think, wacky!) asked me what the U of C mascot is and quizzed me on the date of the Great Chicago Fire. I don't remember (1873?). Man-Wah pointed at me and said "You have an interesting hobby. What is it?" to which I responded, after a moment, "I take classes to be a circus performer." The crowd was half-full of people who didn't actually believe me (which I find sort of amusing) and people who did (mostly professors or students I had told this to on a prior occasion, and who remembered). It also set the tone for the rest of the retreat: one out of every three professors, before giving their short talks, would say "My circus trick will be [x]", where x = doing this talk without coffee, doing this talk in under fifteen minutes, impersonations, and in one case a cartwheel (I'm doing my first rotation in her lab).
I have a first rotation lined up! I'm not sure what the specifics will be, but I will be working for the next 10 weeks on DNA methylation in induced differentiation, or something like that. I have been told I will be e-mailed about it. Now I just have to worry about not embarrassing myself the moment I set foot back in a lab. Eek.
Somewhat surprisingly, my incoming class is full of gay men. (Edward, Erik, and Ernesto. I swear I am not making this up, their names do all start with the same letter.) As in, there is only one straight guy. (His name is Biff, but he is not named after Back to the Future. Again, I swear I am not making this up.) There's a bet going between two upper-classmen that his sexual orientation won't last a year. The girls are, perhaps, less straight-out-of-a-wacky-and-poorly-conceived-television-show. But except Lia they mostly stayed in at night, which was lame. So for the first night, and for volleyball (which we were terrible at), I was one of the guys (TM). It was fun.
I got to the winner's circle in the first-night poker tournament! And then promptly felt pressured to bet less cautiously in order to move the game faster, and lost. But I beat two poker sharks in the process, and they were shocked. I should have stayed cautious. Oops! But I've been challenged to a rematch, so I should work on my poker face in case that happens sometime. (Next year, for instance).
The karaoke competition was more like a talent show than a karaoke competition: costumes, altered lyrics, song and dance numbers, the whole shebang. We (the incoming class) was pressured to sing, so I convinced them to sing "I Will Survive", and everyone joined in. Unfortunately, I had a migraine and basically had to leave half-way through. Lame! Instead of doing karaoke, one of the smaller labs put together a presentation on studying the bsh-2 (pronounced bush two) knockout mutant in C. Elegans. They found two mutations had arisen that abnegated the effects of bsh-2: mcn-1 and obma-1. It was actually reasonably well done, but most everyone was drunk at the time so they all found it hilarious.
PEOPLE HANG SILKS FROM THE PULLEY SYSTEM IN THE ROCK CLIMBING WALL! (Sorry, I had to shout that.) This is something I wanted to do SO very much, and they already do! My first-week job, perhaps, will be to find these people and ask them to be my friends. Or, you know, at least let me practice with them (I have my own silks and everything).
Also, in the interest of honesty, I'm going to issue a warning: classes are about to start (on monday), so I won't be posting to this blog as much as I have been. I'll try to update at least once a week. But hopefully, you know, I'll have a life.