Sunday, November 30, 2008


This was a weekend full of successes, large and small.

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

Turkey Week

There is a turkey in my refrigerator. Rightly, not a whole turkey. A whole turkey would neither have fit on my bicycle nor in my miniscule oven. A significant portion of a turkey, however, with some light meat and some dark meat. Newsflash to Elizabeth: Turkeys are surprisingly heavy. As in, I was unprepared for the fact that although I tried to balance my bicycle with potatoes, apples, and other produce, it was (unfortunately) impossible. My bike was still dangerously tippy until I worked up the momentum to stabilize it (and even then). Slowing down was exciting. Honestly, had I sat and thought about it for very long, I would have realized that frozen meat was going to be denser than brussels sprouts. But I didn't. Fortunately, I got home safely, and so did the turkey, and now it is sitting in my refrigerator thawing, and I am dreading going back to the grocery store tomorrow after work to get the apple juice (and other things) I forgot. It is not the end of the world that I forgot them; they would not have fit on my bicycle anyway.

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

"Your Spontaneity is Delicious"

If there is an advantage to living alone it is that I have no roommate to bicker with about dirty dishes, or the rent, or utility payments. If there is a disadvantage, it is that I have no roommate to socialize with. Which means that I stay out until an average of 10:30 every night, and don't sleep very much, and slowly am being worn down to my very core.

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

Genome versus Epigenome

For those of you who care (and those of you who don't, I suppose), I have surpassed the word count goal of 50,000 and am now in the realm of "As long as I finish my plot, I will be happy." Which is a much more laid back and calm place to be than those people who are at 20,000, or 15,000 or (eek!) 5,000 words right now.

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


Since everyone seems to be posting about food (or at least mentioning delicious pumpkin pies in their posts), I feel that I have no choice but to post about my meal yesterday, which consisted of free (yay) bad chinese take out (boo.).

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 have written a total of 33,359 words of fiction so far this month, so it surprises me that I have no scene or excerpt I want to post. I've finally come to it, about 1/2 of the way through my plot, I think. My main character has just broken out of prison in a matter best explained by allusion to the Count of Monte Cristo. It was helped by the fact that she can make herself invisible.

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.

It did.

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.

And, with that, my nose goes back to the grindstone!

Wednesday, November 05, 2008

I should maybe not be posting this

Because I don't know how much good it will do. But it's been a long long while since I posted (and it will be a while; I'm focusing my energies in November on writing a novel, just as in October I focused on making a Halloween costume. And this is what I'm thinking about right now.

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.