Alice in Wo-- Wait, what the hell?

As we waited for the new Alice in Wonderland movie to begin, I was giving a friend book recommendations; in particular I was describing what I liked so much about the 'Nightwatch' series of books. It seemed a fitting discussion just prior to watching a Tim Burton movie, in a way, because what I like about the Nightwatch series is that the world has a very unique, and imaginative, set up (mechanic?), which twists the world as we know it into something much stranger, and that every book in the series is unfailingly dark.

And then we watched the Alice in Wonderland movie, which might have looked like something out of the most tripped-out Goth's fever dream, but had the emotional murkiness and darkness of, perhaps, Cinderella. Oh, Disney.

To top things off, I just finished Jasper Fforde's latest book, which is also incredibly quirky (Fforde pretty much defines quirk for me, because everything he does is illogical until you realize it is powered by a pun) and also incredibly dark. Dark in that my vision of the world is mostly in gray scale, with a few bright points of - usually red - color (perfect for a Tim Burton movie, perhaps?) and dark in that after reading it my heart almost broke and I was left blinking and thinking "Oh no, this is the first book in the trilogy. Just how bad is it going to get?"

Which brings me to a bit of a quandary. Tim Burton didn't set out to make Alice dark, he set out "to try and make Alice feel more like a story as opposed to a series of events." (Quoth Wikipedia, Quoth a Comicon 2009 interview). But because it was Tim Burton I guess I pretty much assumed that it was going to be dark, emotionally as well as visually. To be fair, he did make a movie with considerably more plot than the episodic and often diffuse nature of Alice's Adventures in Wonderland. But given that he wanted a concrete plot, why choose one which ran so shallow? Given that he needed a good-versus-evil battle, why make good synonymous with 'likes fuzzy animals' and evil synonymous with 'callously abuses fuzzy animals'? I mean, I'm all for fluffy puppies, but give me an ethical quandary bigger than "We have to kill this vicious, man-eating dragon in order to end the iron-fisted, tyrranical, and arbitrary reign of Queen Evil McTortureson, but we don't want to kill anything because we're the Good Guys and Good Guys Don't Kill Things (TM)!"

So, a continuum:
1) Murderers versus cute puppies, and the puppies win! Tea and cookies all around!
2) Murderers versus cute puppies, and the puppies win, but sustain heavy casualties! Tea and cookies for those who survive!
3) Murderers versus cute puppies, and the puppies win, but sustain heavy casualties and end up compromising and/or killing other, even more innocent and/or cute, puppies who just wanted to keep their heads down and go about their business. Somewhat tainted tea and cookies for those who survive.
4) Murderers versus cute puppies, and the puppies win, but in the process realize that they're no better than the murderers. By now the tea has gone cold and the cookies are stale bricks of remorse.
5) Murderers versus cute puppies, and the murderers win. Murderers don't so much like tea and cookies, but they have some Lipton and a box of Chips Ahoy for appearances' sake.
6) Murderers versus cute puppies, and the murderers win, and in the process you realize that this is the only possible outcome. Lipton is cold and/or already steeped, and the Chips Ahoy has been left out and gone a bit stale.
7) Murderers versus cute puppies, except the murderers and the puppies are revealed to be exactly the same, and no one wins, because the battle goes on eternally, causing untold destruction for no real reason. There's no one left for tea or cookies, and no tea or cookies to be had anyway.

On that scheme, Alice in Wonderland is reveling in its (1)-ness, I think the Fforde trilogy is (3) or higher, and the Nightwatch series is squarely (7). Does the fact that I like Nightwatch best make me callous, cruel, depressed, or just realistic? (And does the fact that (7) is possibly overrepresented in Russian literature reflective of Stalinism, the cold Siberian winters, or both?)

Pablum

A drabble. I think I finally have a beginning for the invisible-motorcycle story that has been bumping around my head for at least two years now, but I don't have a middle or an ending. We'll see if I can turn that into anything readable in the near future. Probably not.

Pablum: Something that is trite, insipid, or simplistic.

In other words, you should be very surprised that this is not about DNA. Or a collection of the responses I get when I say "I'm a geneticist."

There’s something that legitimizes dying wishes; your own rosy-tinted memory makes you comply, even if the request is absurd. I think my grandfather knew that, and that’s why he whispered, on his death bed, “Avenge me.”

It calls up all sorts of fairy tales, doesn’t it? Kill the evil baron who poisoned my grandfather’s wine, right countless yet-unknown wrongs, back in time for supper.

But things are never that simple. My grandfather died of a stroke. High cholesterol and higher blood pressure did him in: genetics and a lifetime of smoking, drinking, and eating red meat. Whose fault is that?

Disclaimer: I am not a poet

I had to write a short explanation of my research (to be put on the lab's website), and in the process of figuring out how to explain it concisely, I, in a fit of conceit, proclaimed that it would be just as easy to write it as a sonnet. My father suggested a Haiku. So here is the published (drabble: 100 words) version, a haiku veresion, and a sonnet version. I know the Haiku doesn't get into specifics, and the sonnet has some dodgy rhymes and phrasing, but they were written rather quickly.

Drabble:

I am interested in the epigenetic regulation of placental development, in particular the role of DNA methylation. The epigenetic profile of the placenta appears to be more flexible and dynamic than the embryo proper, as evidenced by significantly lower levels of total DNA methylation and striking loss of imprinting at many loci in extraembryonic tissues. However, knockouts or inhibition of the DNA-methylating enzymes (DNMTs) result in malformation of the placenta. I am examining the role of DNMTs in the placenta with tissue-specific knockdowns, and using high throughput sequencing techniques to clarify the extent of loss of imprinting in the placenta.

Haiku:

Epigenetics:
How cells interpret genomes
And environment

Sonnet:

Though strictly controll'ed in embryo
The genome seems more flexible outside
And where development will progress slow
Environment must always be denied

Those marks which seem to regulation tied
Are rarer far in afterbirth than son;
And in placenta both alleles transcribed
Which fetus sees the choice of only one.

And yet those tissues with controls undone
In both the embryo and extra part
Are compromised and stunted every one
So necessary the controlling mark

I study why this freed placenta fails
And what its flexibility entails.

The first Friday of the Month...

Is, generally speaking, the worst day of the month in terms of getting anything done for me. Reason being, the first Thursday of every month is a fellowship meeting during which people present their progress over the course of the past year, and these presentations have almost always shaken my dedication to the scientific enterprise as a whole. They're poorly done, inconclusive, misrepresented, and it seems like almost everyone is just doing random, unconnected experiments, most of which do not work, in the hopes that someday they'll be able to find a thread that ties their experiments together and publish.

Seriously? This is science?

Yesterday's talks were made worse by one person who actually said that, as he was writing a manuscript at the time, he intentionally removed all identifying information from his single data slide. That, more than anything, struck me as very strange. I'm used to talking about everything to everyone. Talking through a problem is often my most effective way of figuring out how to solve it, and explaining a success is often my most effective way of figuring out where to go next, where the holes remain in hypothesis and theory that need to be shored up. What was he afraid of; that we would rush off and tell a competing lab, who would scoop him? Were he working with a company, and dealing with the nondisclosure and confidentiality clauses that allow for competition between biotech firms, I could understand his reticence, perhaps. On the other hand, in my idealized version of academia it is progress and the spread of ideas that is important, and not who thought of it first: Newton or Leibniz, the Calculus is the same.

Conferences and seminars can be full of unpublished or soon-to-be-published results; which is one reason why conference abstracts are largely misleading and often disproved later. And grants, of course, must be based on preliminary data; some comes from previous papers and my sense is that in the best grants, some comes from unpublished results. So in a way, it is true that communicating one's research even before it is ready to be published in a journal is an important part of science. What's more, this was a fellowship meeting -- a group which was designed and existed largely to support the research of the students who were presenting; it was not a thesis committee meeting, certainly, and it wasn't a lab meeting, but it was the next closest thing. What did this student have to fear, or think he had to fear, that caused him to remove all trace of data? On the other hand, I have several times balked from posting any specifics of my research here, in part because I don't think it would hold many people's interest, but mostly because it seems terribly unprofessional to post unpublished information on a private blog. That justification falls apart as well, I find, in an internal scientific meeting designed to be an annual litmus test of progress and provide support and ideas for those in need.

I'm not certain I remember this correctly, but I think when I went to hear James Watson speak, he said that the biggest difference between successful scientists and unsuccessful scientists was that successful scientists talked to everyone, absolutely everyone, about what they were doing. At the same time, fear of being scooped plays a huge role in The Double Helix. Maybe it would have been safer for them to say nothing, but to worry that every single thing they said would make it back to Linus Pauling, and provide for him the key to the riddle they were trying to solve, was not constructive. And in the end, it's hard to say whether the final breakthrough in that particular story was the result of any particular conversation, but it's likely that without as many conversations with as many different people as they did have, they would not have been able to make the discovery.

I'd like to think I live in a society (academia) where openness and collaboration is paired with success and progress more often than not. I think that the scientific enterprise requires communication, and not just because we see farther standing on the shoulders of giants. And when I feel like the status-quo, on the other hand, is secretive and reclusive and more focused on order of publications that spread of knowledge, it is yet another thing that disillusions me. On the up side, there was free food, and leftovers for today. It seems like a strange trade: we'll feed you, if you give us your hopes and dreams and idealism. But in a depressing sort of way, perhaps that's the trade that most people make every day of their lives. At least I only have to be reminded of it once a month before retreating back to my ivory tower.

Momentous Occassions

Two absolutely life-shattering things happened today at work (and it's only 3:00!). The first is that I finally figured out how to submit stories to Futures (science fiction published in Nature). The second is that, for the first time ever, my cloning worked the first time around! Well, to be perfectly fair it worked in 3/5 cases, but I the remaining 2/5 are less essential, and possibly toxic to bacteria. I'll work on that.

It's a rare day when the experiment that is supposed to take a week actually only takes a week and a half. And all of that just goes to confirm once again that thunderstorms are my lucky charm.

Dancing!

At least two significant things happened at dancing tonight. First, I finished the accelerating waltz with my feet on the ground and some semblance of rhythm and/or grace (a personal first!). All credit should go to my partner, of course, for taking smaller steps and reminding me to hold on for dear life. Otherwise I almost certainly would have skittered across the dance floor like the ball-bearing in the pinball machine, causing dismay, mayhem, embarrassment, and possibly a few broken bones. Not fun. But as opposed to previous accelerating waltzes in which at the end my feet leave the ground either out of centripetal force, my own clumsiness, or my partner's idea of something funny/interesting to do at 370 bpm, this time I ended on my feet. A miracle!

Second was a "difficult" Zweifacher -- a dance composed of waltzes and pivots in a repeating pattern -- which we were actually getting (by the end of the dance). The pattern was hardly a pattern at all: Waltz, waltz, pivot, pivot, waltz, waltz, pivot, pivot, waltz, waltz, waltz, waltz, pivot, pivot, waltz, pivot, pivot, waltz, waltz, and repeat. When the repeating unit is 9 and a half bars long (and since it's 'and a half', it's not really a repeating unit -- you then have to do it all on the other foot, which is different enough -- so the repeating unit is really 19 bars long), it ceases to be a step and becomes, well, a choreography. The only difference being that you could really hear it in the music. But it was great fun and my partner was a very good sport about the whole thing and by the end we were totally getting it.

Oh! And that's forgetting the wonderful cross step waltz/schottische cover of "Lucy in the Sky With Diamonds." That song made my night; the intro was 3/4, slow, and somewhat syncopated -- a cross step -- and then halfway through the first verse it switches to 4/4 and a bit faster -- a schottische. Besides the part where schottische is one of my favorite dances and Lucy in the Sky with Diamonds is one of my favorite songs, I was lucky enough to have a partner who not only knew what he was doing, but had a fondness for pivots and the "role-reversal" schottische (also known as the "sex change schottische" because for the second half the woman dances the man's part); fun times!

It is perhaps worthwhile to note that the most dizzying dances (the ones listed above) were probably also my favorites. At one introductory lesson a woman asked the teacher how to avoid getting dizzy while waltzing, and the teacher chuckled and informed her that the point of waltzing was to get dizzy. I don't entirely agree with that, and in any given waltz I'm unlikely to get dizzy (and glad that I don't get dizzy easily! How inconvenient would that be?), but one of the things I enjoy about waltzing, and especially fast waltzes, is the almost-dizzy feeling of one too many pivots (or is it just the right number since it's almost-dizzy and not outright dizzy?). So I guess it isn't surprising that the dances I generally like best are the ones that leave me slightly out of breath and slightly dizzy. Well, those and the Bohemian National Polka. You've just got to love the Bohemian National Polka.

Although, given the number of pivots in the BNP, and the fact that I often subconsciously try to add pivots (I mean, who wouldn't want to do 16 pivots in a row?), perhaps that one could be classified with the above as well.

Draconian

Inspired by the word-of-the-day; "Draconian", in addition to a conversation I had in lab today where someone asserted that a woman could get killed for committing adultery in the United States. I said "Um. No," although I was surprised to learn (thanks, wikipedia!) that some states have yet to decriminalize adultery (although it is hardly ever prosecuted anymore, and apparently there's at least one Supreme Court precedent that makes it difficult and questionable to apply any laws that still do happen to be on the books). The most amusing example was Maryland, whose punishment was a $10 fine -- which to me seems so very lenient as to be the worst of both worlds; it puts what is really a private thing between three people into the public, judicial, domain and it leans towards mocking the distress of the cheated-on. No good for anyone. And that sparked this:

You don’t seem to understand; I found her in bed with another man. In my bed, in my house, bought and mortgaged with my hard-earned money. With another man. I found my wife in bed with another man, she’s leaving me, and you seem to think that a ten dollar fine will just make everything better. Sorry for cheating on you, turning your suburban paradise into a twisted mockery of love and matrimony, how about I buy you dinner and we call it even?

Actually, you can’t buy dinner for ten dollars. That’s hardly even a cup of coffee anymore.

Clearly, my work today involved too many incubations/spins where I had fifteen minutes of empty time. Not enough to really read a paper, too much to just stare at the wall. So skimming wikipedia it is.

A drabble, off of the Word of the Day - "Torpor" - which I would have liked to be more rigid and angry but instead comes off instead as clinically depressed:

The dishes needed washing. The dishes needed washing, as did the laundry, and the bathroom should be cleaned, and the entire apartment was covered over by a fine layer of scrapbooking supplies. And the trash hadn’t been taken out. At the very least, she should get out. And instead, she sat, sheets smelling slightly of sweat, staring at the wall and then the ceiling and then the wall again. It was a peace-that-was-not-peace: if she didn’t acknowledge the outside world (or the mess), it didn’t exist. But she had never been good at isolation. And the dishes still needed washing.

More Circus Videos!

Because I have them. It's unedited, and somewhat poor-quality by virtue of "I wanted it to actually load in Blogger".

The first part is a trick I just learned which is terrifying but fun and cool-looking. I balk twice because (1) it takes a lot of strength to pop up like that, and it's at the end of practice, and (2) it's scary! The only good thing I will say is that I keep my toes pointed and my legs straight and my feet together (mostly). Also I can totally remember when tossing the fabric over my knee to wrap the first trick was prohibitively difficult (I'm sort of a klutz, don't tell anyone). So that's happy! But as usual I get tangled in the fabric at the end, because that is just how I roll. I need to learn how to do it without getting the fabric caught on my foot, and I need to build the strength and courage to do it without balking, but it's pretty neat-looking. Interestingly enough, there's another wrap that does similar drops in the reverse order: first the front somersault-ish thing and then the sideways flip (although there isn't a pause between them...). In any case, you could do that into this one as well, which would be wonderfully palindromic, so I might try that out in January.

The second part is a short sequence I put together because I thought everyone was putting together sequences which we would share. Turns out I was wrong, and I was the only one with a sequence. So no sharing, but I got my coach to take a little video of the sequence. It's even more right at the end of practice than the last one, so I'm even more exhausted, which is my only excuse for not being able to climb the fabric smoothly. Also the second-ish move (where I drop to hanging by one knee) gave me rope-burn, because my leggings didn't come down far enough or something. As above, the one good thing I have to say is I have decent form, although I still cringe watching myself getting tangled in the fabric at the end (that's why I laugh, because I'm thinking "oh goodness, she's still filming. How awkward," and I don't know how to make resting look graceful. Yes, those awkward hand-sweeps are my attempt at being all "Oh I am totally not resting, of course not!" I know, I know, it would have been better to, er, keep my hands to myself. I think what all this means is that I'm getting pretty decent at tricks, but I still think like a diver -- I'm approaching this without caring about transitions, beginnings, or endings (you're not being judged on how you get onto the board or out of the pool, after all). Which means that I have one physical thing and one mental thing to work on -- flexibility and transitions, respectively.

Steampunk? Steampunk.

Seven months ago, I met some friendly looking steampunks at maker faire, who happily handed me a card with an e-mail address on them, and ever since I have been bemoaning the fact that I lacked one crucial piece of paraphernalia. Yes, it's true, I didn't have a single pair of air-ship-suitable goggles.

And, because I am stubborn and foolish, my response was not, say, to buy and modify a pair of welding goggles or swim goggles or some other form of goggles, but to scrounge around and ponder for a while and finally decide to make something passable out of a piece of leather I bought in high school and the lenses from a pair of cheap Harry Potter costume glasses. I had to add a bit of wire I had lying around, two brass purse buckles (for fasteners) and a toilet paper roll (to support the eye sockets), but my apprentice goggles are finally done. I'm reasonably happy with how they turned out, although I already know several things I should have done differently. I have been utterly incapable of getting a good picture with them on my face, (due in part to a couple of the things I should have done differently) so these two of them on a table will have to suffice.



I'm thinking lose or re-attach the nose bridge because it's lopsided and it makes the entire thing look even more lopsided than it has to be. That should be a reasonably quick fix and it should help quite a bit. Next step would be adding an LED flashlight, and possibly jeweler's loupes. Although I'm not positive where to put them so those plans are still on the drawing board.

The next project is the big one: Corset. (Dun dun dunnn)... I'm somewhat more confident on this one for several reasons: first, I'll have a pattern; second, I've already made a few boned bodices, and the step up, while a difference in magnitude, is not one of substance; third, I'll have a pattern; fourth, it will not involve leather; and finally, I'll have a pattern. Did I mention I'll have a pattern? Because that's pretty important. I'm about up to drafting patterns for dresses (and I did the goggles free-form, which is why they came out lopsided), and I'm 99% confident I'll have to alter the corset pattern, but I must admit that I'd really rather not have a lopsided corset, which sounds like just about the most uncomfortable thing on the face of the planet. (Ouch.) I'm trying to decide whether or not to (photo-)document my progress re:Corset. I'll probably end up not doing it because I am a lazy bum and after painstakingly writing down everything I do at work, I don't know if I could handle bringing that amount of rigor to my "for fun" projects as well. Also because I don't think anyone much cares.

Along the way, I think a pair of spats are up (I still have all this leather), possibly followed by gloves (if I still still have all this leather), and/or a petticoat. But those are all relatively quick projects.

Tomorrow: Circus, or Science. I promise.

How I have been wasting my time

To celebrate its 350th birthday, the British Royal Society put 60-odd papers online. I've been reading through them, as a method of procrastination which is hard to tell from my 'real work' of reading a slightly different set of papers. There are some real gems there; I particularly like the early medical papers on dogs, and the one about the effects of standing in a furnace on body temperature (read: homeostasis ftw!). But possibly the coolest thing about it is you can see the modern scientific format being born: those early papers read more like letters between friends than prestigious scientific publications, (Ben Franklin's 'I've heard you've been talking about these lightning rod things. Here's a cool experiment I did with a kite' is especially nice in that light) but slowly they become more rigorous and formalized. On the other hand, I still haven't gotten through the Bayes paper, if only because it is mathematics and hence much more formalized and technical. Oh, and it's fifty pages long.

They provide background info and commentary, too, and generally it's review articles that are reasonably accessible to a lay audience I think.

http://trailblazing.royalsociety.org/

Punctiliousness

Taking "precision" and adding "puncture"?

Doctors with bad handwriting should not, Sarah thought, be tolerated. Poor penmanship was a sign of a lack of precision – either in thought or in motion – which could be deadly when the hands exchanged ballpoint pen for forceps and scalpel. Or even syringe. Try arguing that to the madman with the needle.

“You won’t let me stitch you up because of my handwriting?” he asked, graying eyebrow twitching upwards condescendingly.

“No fine motor control. You’d make a mess.”

“Would you rather a scar?”

Sarah gritted her teeth and shook her head. Her penmanship, of course, was perfect. “I’ll do it.”

Lightning Bug Costume

Below: Pictures of how the lightning bug costume turned out! I believe there are more (or will be more shortly) on Facebook. In particular, pictures of me making my funny "Why are you taking a picture of me?" face. And other funny faces. Because... yeah.

First, one with the lights on, so you can see the antennae and the green sparkly petticoat:



And then one with the lights off so you can see the actual cool part; the glowing hem:


At the dance on Saturday, the lights were dimmer, so the hem showed up better, and people picked up on it a lot faster. On Friday, the lights were fairly bright, so people kept asking me why I had a battery pack on my hip. Also, on Saturday, there was a toddler dressed as a witch (most adorable witch ever) who was absolutely fascinated by the fact that my skirt lit up -- in part I think because the hem was at eye-level for her. So periodically I would go to move and she would be tugging at my skirt, staring. It was 1/2 adorable and 1/2 "Oh no, one of these times I'm going to step on her and her parents will be furious."

On a side note, I'm debating whether I should participate in Nanowrimo as usual or make a new costume in November instead. I don't think I can do both, simply for lack of time.

On another side note, my antibodies came in today so I started experiments! Woo!

Thoughts

Today was a blur; or possibly three blurs; or possibly innumerable blurs -- so many blurs that they all start blurring together. Everything about the day felt detached from anything else, but not in that pointillist sort of way where each event stands out in stark contrast, nor in that infinite day sort of way where there are just too many things happening to take them all in. In a buzzing, absurdist-philosophy sort of way where I'm walking down the street but it feels more like I'm watching myself walk down the street (and if I had a gun in my hand and the sun shone a little brighter, I might just fire the gun, but it wouldn't really be me doing it, it would be the sun and the heat and the... I don't know what. On a side note, I never really appreciated Camus before I started feeling like this; Sartre seemed -- for lack of a better word -- more constructive. There's something about internality/externality and free will there that I won't get into because it would be unimaginative regurgitation of something I heard somewhere, probably).

Lately, I feel like if I stop moving, even for a second, I don't really recognize myself, or I don't like what I see. It's like; I started dancing because I was bored and I was looking (probably) for someone (which I know and I knew was not a reason to start dancing so I insisted that I was looking for something, namely, a hobby), but now the dancing has just taken over in a way. That doesn't make any sense. Maybe what I'm saying is just that when I stop dancing, the vague dull loneliness comes back and I wonder why I can't get any of my student friends to go dancing with me and why I don't really feel comfortable calling my dance partners 'friends'. And so I didn't write this weekend because I was dancing, which was certainly nice. But it left me feeling (always leaves me feeling?) sort of detached from myself, in a strange way.

On the other hand, I'm already dancing basically every Monday, Tuesday (if you count silks, which I do), and Friday (and quite a good number of Saturdays as well), with dances I've been meaning to check out on Wednesday and Thursday as well. So, it seems to me, it very well might be possible to never stop dancing. Except on Sundays. I don't know if that's a solution or not. Or even if I have a problem. Perhaps I am just very, very, tired.

And that's as close as I can come to an explanation for this drabble, which popped into my head almost fully formed.

Brooke stared at the mirror; dark brown eyes stared back.

She blinked. So did they.

She pulled a face. The mirror mimicked her grimace.

She touched the smooth glass surface.

She frowned, and turned away, not knowing what to make of it.

Gary was still in bed. He yawned blearily and grabbed her hand as she sat on the edge. “You’re up early,” he mumbled.

She smiled indulgently. “It’s almost noon.” And then, on a whim, “What color are my eyes?”

“Blue,” he answered. “Is this a test?”

“No,” she said, and kissed him, and resolved to sell the mirror.

Almost, because as initially written it wasn't unsettling; it just sounded like he didn't know what color her eyes were. Maybe it still does, I'm not sure -- I think some ambiguity in that direction is good. But it should be ambiguity, and not "Oh, well obviously..."

An Attempt at a Return

I think my relative absence of late can be described in two words: qualifying exams. Namely, they were just over a week ago, and I passed. Hooray! Now, perhaps, I can actually start research. If I'm lucky.

(On that note, and somewhat predictably I'm still waiting for antibodies to come in. The exciting life of the biologist.)

And, since I'm now into the long phase of graduate school, the one that takes four or five years and ends (if you're lucky) with a thing or two you can publish, I'm trying to use this transition to get myself back into some habits that I enjoyed, back when I did them regularly. (Things like, say, "cooking" things other than ramen and canned soup, and getting more than four hours of sleep a night.)

Also, writing. 100 words a day, either fiction or science, although I predict that the science will be harder on account of needing to get through a lot of definitions. Hopefully, sticking to one conclusion of one experiment will help. As an inauguration (reinauguration?) I've done two: 100 words of fiction inspired by the word "aesthete" and the fact that it was defined not as someone who was sensitive to beauty, but someone who cultivated sensitivity to beauty:

To be done properly, the experiment needed a control. It was a fact: you couldn’t test a hypothesis without a control. And the best control was… well.

The student thought it clever to name him Damien. Of course, the student who named him reaped the rewards of Damien’s first three years, took a few fMRI scans and graduated. That student was long gone before Damien stitched a sentence together; already tenure-track at a remote institution when Damien hit his troubling teenaged years.

The police found him, transfixed by the gore. He turned to them, smiled, and said, “Isn’t it beautiful?”

And 100 words of science, summarizing one finding from this article in Nature last week (which fits a current paradigm of science today which is: When in doubt, sequence!).

Methylation is a chemical modification of cytosine bases. The prevailing dogma is that mammalian genomes are methylated at cytosines found in the dinucleotide CG; and only in a genomic context where CG is rare. DNA methylation in promoters of certain genes has been associated with repression, and this association has been generalized to a differentiation hypothesis: cell-specific methylation stabilizes cell-specific expression which yields morphology. However, we may have been looking in the wrong place. A recent paper found methylation in embryonic stem cells at non-CG cytosines, and these sites were the ones that most changed between ES and differentiated cells.

I'm thinking, perhaps, that a sentence limit or a larger word limit on the science might be good. I don't think that turned out very well.

A little randomness...

When I'm explaining my research to laypeople, I usually start out with something along the lines of "With a few exceptions, every cell in your body has basically the same genome." The obvious exceptions are usually places where genome modification plays an integral role in the differentiation process itself -- for example, B and T cells in mammals, whose rearranged receptor loci are responsible for antibody diversity, or the massive numbers of copied, lined-up (polytene) chromosomes in Drosophila salivary glands. In each case, the rearrangement is specific: you don't see rearranged immunoglobulin genes anywhere but in B cells, and you don't see polytene chromosomes outside of salivary glands. These are the mechanisms that the body uses, in certain very rare occasions, to tell one cell from another in a permanent way, or to leverage a genome into doing something that it might not otherwise do. Most cells, on the other hand, are differentiated by chromatin state, protein expression, and other mechanisms which are relatively stable, and relatively permanent, but don't touch the genome sequence below. That is the basic reality which allows a skin cell to be reprogrammed by a certain set of transcription factors into a stem cell: the modifications may be different - the clothes may be different - but underneath it all it's still the same genome - it's still you.

Of course, there's another kind of genome instability that's covered in every genetics class: this is the instability caused by transposons, or jumping genes. This kind of instability is the bad kind, the kind that is unregulated, random, can alternately do absolutely nothing or fundamentally alter the expression of important genes. They are semi-autonomous genetic parasites; the remnants of long forgotten viruses which live on in our DNA; the rats in the lower deck whose numbers must be kept down for the health and safety of the ship itself. Most organisms go to extraordinary lengths to keep these transposons silent. DNA methylation seems to have been evolved for this purpose: by chance, organisms which put a chemical modification onto repetitive sequences of DNA, thus shutting it down, were less likely to be prey to transposon insertions and thus had more stable genomes and better reproductive fitness. DNA methylation of transposon sequences is the one constant of DNA methylation; even in Drosophila, transposon sequences are highly methylated, while the rest of the genome shows no sign of the modification whatsoever. Transposons are reactivated very rarely: a few seem to be important in placental development to do typically viral things like repressing the mother's immune response, and in one example in plants, transposons are reactivated in the endosperm in order to provide RNA templates for RNA-mediated DNA methylation in the embryo (I think). Notice one similarity for both of those examples: transposon reactivation occurs in extraembryonic tissue, not embryonic tissue. What a thrill, then, to learn that this 'bad' kind of genome modification could serve an entirely different purpose.

A paper published in Nature this week shows that L1 elements (a certain kind of transposon that happens to be particularly prevalent in humans), and in particular human L1 elements, are unmethylated, expressed, and capable of insertion in human neural progenitor cells (NPCs). They go on to show that brain tissue contains more copies of the L1 sequence than heart or liver tissue. What does this mean? It means that your brain is likely a genetic mosaic, with different cells harboring these L1 insertions in different numbers and different places. Some insertions could do nothing, and some insertions could kill the cell (in which case they would be lost), but some insertions could prove disabling-but-not-deadly, and some insertions could be advantageous. And since different neurons might have different insertions in different places, this means that there might be a(n epi)genetic reason why different people think in different ways. Even better, this process would be ongoing in neural progenitor cells -- as your brain develops, it is changing and redefining itself by which cells have insertions in which genomic loci. And, since the entire thing happens in the brain, none of these rearrangements are passed down to any children you may have, which might go some distance to explain the non-heritable portions of intelligence. Finally, and perhaps beautifully, as NPCs accumulate these insertions over time, they will, by chance, pick up an insertion in some essential gene that causes their own death (there's a Russian roulette metaphor there that, for once, I will spare you).

The fact that the neural connections in your brain are a plastic, ever-changing structure has been known for quite a while. The idea that the very genome of your brain could also be plastic is, as far as I know, fairly new.

Aside: Personally, I think that this is one of many similarities between extraembryonic tissue and neural tissue, which is yet another reason why the placenta is a very interesting thing to be studying. Also, if you want a cool genetic phenomenon, you should look up "chorion gene amplification" in Drosophila and perhaps "endoreduplication" just in general (it happens in mammals too -- in the placenta, as a matter of fact!).

Edited to add: If you want to read the editorial in Nature, go here. Or, if you want to read the original paper, it can be found here.

An interesting article

Scripts are running, and although this afternoon is "Bench Organization Time (TM)", for the present I'm just waiting for results to filter through the server (hurry, computer, hurry!). Which means checking on the progress (line 1277 of 4648) rather obsessively, and reading NYTimes articles on teh intarwebs.

And I found Sam Harris' critique of Obama's nomination of Francis Collins as head of the NIH very interesting, which got me thinking about something sort of tangentially related. (Find it here -- he says it much better than I could.)

The basic gist: Collins is a wonderful choice because he has found an intersection between devout faith and modern science, but his belief that people are endowed with an immortal soul/moral law which can never and will never be explained or explainable by science is at odds with recent advances in neuroscience.

There's a bit of Ivan Karamazov there, too: “If the moral law is just a side effect of evolution, then there is no such thing as good or evil.” (Which is a discussion for another time...)

It's interesting to me because what is being argued is not, in fact, whether it is possible to do good (great, brilliant, world-changing) research while holding these views. Because that would be an incredibly stupid argument. It is self-evident and obvious that it is entirely possible to do good (great, brilliant, world-changing) research, in biomedical fields, while holding these views. Period. The question that is being asked, instead, is whether or not there exists worthwhile biomedical research that is inherently counter to these views, and as such, whether such views are desirable in someone who will be controlling the direction of a huge portion of the funding for biomedical research not simply in the United States but worldwide.

And so the question becomes: are we capable of addressing the development of and action of the human mind, the sense of ethics, and altruism in a molecular scientific fashion, in an evolutionary fashion, and in a fashion which (here's where I might step on some toes) abnegates the hand-of-God in the origin and continued existence of said characters? (And second, will Collins' belief that such questions are unanswerable without the hand of God effect his decisions on which research to support?, but that's not particularly interesting on a philosophical level.)

I would posit that at this point in time, the question 'Can we come to an understanding of the human mind through molecular, and evolutionary, means?' can no longer simply be answered 'no'. Advances in brain imaging techniques, in our understanding of neurological signals and circuitry, in our understanding of cellular memory and feedback mechanisms, in computation, and in many other fields have combined to allow us to study the mind, and model the mind, with heretofore impossible capacity.

An example to illustrate the point: there is an artificial brain that is being built in a supercomputer (my mother pointed me to a description here). The idea that we could build, out of purely material things, a human brain, would have seemed patently ridiculous (to the point of being horrifying) to most people at most times. (To the point that one character describes building a mind out of aluminum cans in Stoppard's "Rock And Roll", to the eventual point that for her there has to be something more, not that that's particularly relevant, but still.) However, here they are, trying to build a mind out of transistors and wires and circuits. And to those of you who think that this is just a brain, and not a mind, the last line is particularly relevant: "Is it really possible to put a ghost into a machine? "When I say everything, I mean everything," he says, and a mischievous smile spreads across his face."

For a more molecular/cellular/basic scientist (as opposed to engineer?) approach to it, I would suggest reading just about anything by V.S. Ramachandran. But there are tons of neuroscience books for laypeople that are being published, which is evidence in and of itself that neuroscience is going through a rather significant paradigm shift at the moment.

In the end, no one is going to prove (or disprove) the existence of God. Even evidence for a center in the brain that, when activated in epileptic patients, causes intense religious/spiritual experiences, is neither proof of nor evidence against Him. And I think that Ramachandran also rings a bell when he says (in this interview) that science enriches the spiritual experience and spirituality enriches the scientific experience. But spirituality, in my mind, is not any given formalized religion.

Which is I think where the concern about Collins comes in. What it comes down to is, basically, that any specific line you draw in the sand to corroborate a strict religious tradition with science will, eventually, be torn down. Galileo did that, Darwin did that, and many others along the way. And so whenever someone draws a line in the sand, and says "Science can explain this, and this, and all of this, but not that, because that is special," it raises a red flag. Instead, it seems easier, and truer, to say that there will always be mystery in the world, and spirituality and science will always offer ways of understanding, and investigating, that mystery.

EDIT:

I find this article from nature interesting in a similar way. I find the conclusion nicely worded -- "Perhaps it just takes a rare person to advance a scientific career while balancing belief and bioscience — without corrupting either." It's not impossible, just difficult to balance?

I think I must have told quite a few stories about one person I had the (mis?)fortune to meet by virtue of my newly inherited Kindle over spring break; but the fact of the matter is that sitting for a couple hours at a bar in a coffee shop, sipping tea and reading Sherlock Holmes off of a piece of flashy technology garnered me more than one conversation. And although the ridiculousness and idiocy of the one might have pushed from my mind another, it was only a matter of time before subsequent coincidences brought it back again.

To be brief: While sitting in a coffee shop on my first day in San Diego for Spring Break, I crossed paths with a raving madman and a barista on his lunch break. The madman told me things about DNA that were not covered in my Advanced Genetics class (or in fact any class I have ever took). The barista recommended to me a spanish author by the name of Carlos Ruiz Zafon, a name which I wrote down on the back of a receipt, and promptly forgot.

3/4s of the way through "The Shadow of the Wind", however, and I have just realized that this author -- the author of this book which I cannot stop reading, busy as I am -- is exactly the one recommended to me some four months ago, in San Diego. The book is wonderful; gothic and frightening and full of beautiful language that I am sure only just barely comes through in translation, bringing a city to life with all of its grime and disease, believable characters who you love even as they barrel through life, selfish and oblivious, and a main character who really develops - a boy who slowly grows up through the pages of the book. It has been the wonderful antidote to the dry, technical nature of the rest of my late reading.

So, to all the baristas in San Diego who give out book recommendations to tourists on their lunch breaks, thank you.

How to Catch a Koala

Oh my goodness, is this a drabble? I think it is. I suspect it may be the first in a series. Today has been rife, I tell you, utterly rife with inspiration.

Really, you just wanted a teddy bear. And he looked so cute with his fluffy ears, munching on a leaf. “How hard could it be,” you thought, “to climb up there and grab him?”

You hadn’t quite realized how he was staying up there himself – the three inch long claws embedding themselves into the branch. But it’s hard not to notice them now that they’ve been intimately acquainted with your face, arms, and chest.

“See, that’s why we use the flag,” she says, holding back a laugh. “Gets ‘em to climb down.”

You groan.

“I warned you about the claws.”

Don't get your hopes up or anything, for regular (or even semi-regular) posts. (All four of you.)

Can't get this idea out of my head

So, I just read Plato's Symposium (my new favorite Platonic Dialog, hands down, and up there with favorite works of philosophy in general). Well, to be precise, I read it about a week ago. But it gave me an idea (a ridiculous idea) and that idea has been entrenching itself more and more firmly in my brain until I can't ignore it any more.

Idea: Socrates the Player. Like all of those terrible (some only mediocre) remakes of classical works of literature set in modern times, only this time it's a series of Socratic Dialogs! I imagine it like a movie; set in "Generic Urban Setting", with a semi-unintelligible, slang-speaking hip hop Socrates dishing out all sorts of wisdom to his bros and his hos, saying all the time, "I ain't no smarter than any of y'all. And eventually being killed by the rival, Sophist, gang. Or possibly put in prison for being a public menace. I haven't decided. But, seriously; Apology: "Y'alls just hatin' on me 'cause I talk funny and tell it like it is!" Crito: "C: We can bust you out, Socrates," S: "Naw, man, that ain't how I roll." And, of course, Symposium, which is the night of drunken debauchery turned oddly philosophical. Um. Right. Hopefully teh intarwebs will take my idea so I can start having other ones. Preferably, you know, ones that could possibly be related to my studies. That would be nice.

In case you were wondering...

I can post video here! In celebration of that, I've uploaded a short video of me doing silks tricks (what did you expect?). I see a bunch of things I did wrong (including the ever-present "look at the camera!") and a few places where, in retrospect, I should have done a completely different trick. I also know that I am pretty awful about pointing my toes. In fact, the only reason I can watch this without cringing is that it shows that I can suspend myself and do tricks for nearly four minutes, at the end of practice. And it spurs me on to do something better -- my goal by the end of the summer is to have something actually presentable, choreographed to music and everything. Who knows if I'll make that goal or if I'll just metaphorically fall flat on my face. (I do not expect to literally fall flat on my face, despite the danger associated with circus arts.) Hopefully, with this video in hand, I can convince the people at the rock wall to let me hang my silks in the off-hours and practice. (They already let other people do so.) (Let me dream, at least.)

And, since I know my parents needed something else to worry about, here's the video:

The past few days have been eventful, to say the least. The most blog-worthy news is that I am learning how to write fancy image processing algorithms like watershedding to find cells and nuclei. It's a blast, and it'll be even better if (when?) I can get it to work.

Well-rounded Success!

And scientific fail?

So, today so far has been the day for well-roundedness. This is manifest in two ways:

1) I did an aerial for the first time ever! Admittedly, I had a bit of a boost from a mat, but I am still thrilled about it. I have never done aerials before (not even in my previous life as a competitive acrobat), and I did something like seven of them. Hooray!

2) NSF results came back; (I got honorable mention, hence "and scientific fail?"; I know it's not actually scientific fail, because Honorable Mention is still good and all that, but... still.) I was reading through my rating sheets, and the very first one included the following (italics mine): "Perhaps most importantly, her application demonstrates that she has extraordinary written communication skills. Her personal statement and statement about her research experience are very professionally written and novel - perhaps she should write a novel in her spare time!"

I find this especially funny for three reasons: first, my other rating sheets are dry and straightforward where this one is chatty. Second, I don't understand the jump from "you can write a good personal statement" to "you should write a novel" -- there are a lot of people who are incredibly good at short-form and essays (i.e. personal statements) and can't or don't want to write novels. The hint at the novel hits really close to home; almost as though this person actually knew that I actually wrote novels in my spare time, and wanted to share the inside joke. (Google search unlikely -- I checked and my name turns up nothing on me for the first five pages.) Third, this isn't the first time I have sent out an application consisting of a personal statement and a research proposal only to get back a comment along the lines of "you should make sure to keep writing non-science."

Validation of hobby choices, anyone? I sort of want to print it out and tack it on the wall by my desk. Man.

Finally, a picture!

I took the picture above last night, looking out from behind the Gym into Golden Gate Park. It doesn't really capture how ethereal and beautiful the swirling fog was, but it's the best that I could do. It was warm and sunny and summery in Palo Alto, but in San Francisco (and in the mountains) it was cool and foggy (which I guess is "summery" for San Francisco and the mountains, but I still have trouble getting used to that concept).

At class, I learned the "no-hands wheeldown" which would be great except for the fact that the more I roll down, the tighter the silks get around my waist until (after only two turns, lame!) I can't breathe. I asked Monica about that, and I think that it's something with how I'm rolling, but I'm not sure. In the morning, I went to the "intermediate" gymnastics class, and went so far as to do a front handspring. Which I was pretty happy with, especially since I haven't done any tumbling for about a year. Also worked on presses; I can almost do them. My goals for the end of the quarter: a front handspring that isn't a full stop (maybe front handspring into roundoff or something) and a press. It's not a long time, or I would be more ambitious. The coach is chill and friendly, the people are goofy, and in general it's a fun time. The gym is amazing; of course all of the apparati (sp?) (and a full-sized spring floor), but also pits for all of the apparati. Which is awesome for learning new things (front handspring from tumble-track into a pit was not something I was in the least bit afraid of, although if scrambling awkwardly out of said pit looked half as ridiculous as it felt, well, I'm sure I'd make a good clown). Plus it's fun.

Had an interesting conversation yesterday. People were talking about learning to read, and remembering learning to read in the first grade. These were brilliant people -- five PhD students and one tenured faculty member. And they all remembered learning to read in the first grade. They were puzzled why anyone would want to teach a kindergartener how to read; kindergarten, they proclaimed, was about cutting things out and pasting them, play time and naps. I, by some strange quirk of fate or UChicago-educated parents, was reading chapter-books by that time (bad ones; the Oz series mostly, but chapter-books nonetheless). I can't remember a time before I knew how to read; two of my first memories are of trading books with the neighbors, and reading the words to sing "Somewhere Over the Rainbow" for a talent show (according to my mother, no one believed I could read then, either, but I didn't notice). I remember the librarian in my Maryland elementary school remarking upon my predilection for bad young adult novels when I was in kindergarten -- you don't want to read those, they're boring and they're at a fifth grade reading level. And my response that I knew what I liked and I wanted to read those. (I guess some things never change, I still have a predilection for fluffy young adult novels, although I intersperse them with "literature" which, as I see it, is the same thing but either with a larger vocabulary, more sex, more philosophy or -- if you're really lucky -- better writing.)

I just find it so strange to think about even a five-year-old kid not knowing how to read. All the stories they're missing out on, all the adventures they could be dreaming of that they aren't, because they don't know how to read. I guess part of that is peculiar to me -- I have always been a storyteller (and I still am, even my science I think of as a logic puzzle and a story waiting to be discovered). I define myself by the stories I know and the stories I tell. To me, before I could read, I wasn't really a person in a way; I couldn't access this vast history of human stories. If that makes any sense at all. I'm not sure it does.

Of course, when I said, quietly, that I could read before kindergarten, and that I was reading the Oz novels in kindergarten, my friends' response was (I guess predictably), "Why am I not surprised?"

I told the story of my brother organizing his friends and dividing the labor of writing/drawing/coloring for writer's workshop, to defuse the situation. It's a funny story, and very Kevin. I know only two things that I wrote in the kindergarten, and I remember them only second-hand: first, a confession that I was angry my brother got moved out of the daycare because he threw a temper tantrum, whereas I had no such choice in the matter (it sparked a parent-teacher conference, I think) and second, the treacherously naive statement: "The world would be a better place if Bill Clinton was President."

It wasn't until first grade that I started writing the beginning of the same story every day. But that has lasted for almost seventeen years so far. Maybe one day I'll finish that story; but then I'd have to find a new one, and that would be terrifying.

Photographic Memory

So, I have a camera. I brought it to silks class last night. And foolishly forgot to exchange the standard-installed 32MB SD card for one of my 2GB SD cards. Which means that after about 10 seconds recording the preparation for the cool new drop I learned (Monica calls it the 'mission impossible'), the card was full and no more pictures or videos of Elizabeth. It pretty much looked like 10 seconds of me flailing about midair. So I'm not posting it, much as I'm sure a few of you would get a laugh out of that.

On the other hand, the trick (which I promise to get video of sooner or later) is really wacky, and somewhat terrifying. It's one of those things that you have to train your body to be used to -- on the verge of very painful, and half the neurons in your head firing saying "I should be falling to a concussive death right about now; the only thing that's holding me up is this tenuous knot that I don't trust." Of course, the other half are firing to say "Wait, what the heck do I do next?"

And then there's the moment when you're suspended fifteen-or-so feet up, horizontal, arms as wide as you can, fabric over your shoulders in an impromptu harness, holding on tightly, and paused midair. And then you slowly let the fabric slide through your hands, and you rotate head-over-heels as you sink to the ground. Flip, flip, flip.

And then there's the best moment of all, which is when you land on your feet, shrug the fabrics off of your shoulders, step out of your impromptu harness, and walk (or in my case half-walk half-skip half-trip) away.

So, to those of you to whom I promised pictures, well, maybe next week? I am hopeful. I am more hopeful about taking pictures of the garden this weekend, which will almost certainly happen, 2GB SD card or no.

In other news, I have fabric burns on the backs of my knees. There's this evil, evil climb (called a knee climb?) which if I ever figured out probably wouldn't give me rope burn, but apparently my knees are not strong enough to clamp on to the fabric, and as such they slide, to interesting (and not altogether pleasant) result. Honestly, I can see the choreographic value of the climb -- it keeps the silks separated and you in the middle, which is the starting position for a large number of tricks, and besides it looks fairly cool -- but... ouch.

In other other news, I think I have a strange talent for remembering lots of random details about a person but not their name. I ran into a post-doc by the coffee machine today (strange only because it's the Pathology coffee machine and we're both Geneticists), and she said hi, and "I think I remember you from the retreat," and I responded, "Oh, I remember you, you're in so-and-so's lab, you're a post doc, and you presented in CIG this fall."

Of course, I couldn't for the life of me remember what her name was. Score one for creepy!Elizabeth. I guess it's better than one alternative -- which is, remember absolutely nothing about anyone, rather like my father -- but I'd sort of like to remember people's names every now and again. Maybe I should write them down, like flashcards. If I work really hard at it, I could become good at remembering people's names. I wasn't too terrible when coaching, although there were definitely a couple of kids who got the worse for it. But that's how I am, I guess -- I'll remember that your second cousin from Missouri's new husband does R&D for GM, but I won't remember that your name is Jim.

She asked how the rotations were going, I told her they were going quite well, and that it just came down to choosing a lab -- and that I was a bit nervous to do so. She said to choose based on the relationship with the PI over the science, because the science is good at pretty much any lab here, and having a good mentoring relationship with the PI can make or break a PhD. Which I sort of agree with, and I sort of already knew, and my "problem" is not really a problem so much as a surplus of good choices -- two out of my three rotations have been interesting projects, with good and accessible mentors, in friendly labs that I could get along with. A couple of the more significant differences between them have recently dissolved, as well. So that's awesome, because they dissolved in the 'potential downside disappearing' way instead of the 'potential upside disappearing' way, but it means there are fewer clear-cut differentiators to make my decision on.

What even makes a good PhD lab? I've heard everything from "The science. The science will sustain you." to "The environment; good environments lead to good science, bad environments lead to burn-outs and misery." I think it's probably somewhere in between, especially someplace like where I am, where everyone is doing "good science", and the question becomes more what is personally interesting to me. But that's never been much of a guide, since "what is personally interesting to me" has always been a terribly broad category (at least I've gotten out of the 'a' word careers: I will be neither an Acrobat nor an Author, or perhaps I will be both but neither as a profession).

I went to a talk on Wednesday, and the majority of each of the three labs I rotated in was present. The talk was very good, and very interesting, and the fact that all three labs I rotated in were there was a demonstration of one thing: even though I have interests in a wide variety of areas, I have narrowed it down in terms of what I want to study. (Of course, narrowing it down to something like "Chromatin Regulation" doesn't say very much; what aspect of chromatin?) I guess I just need to start drawing up a flow chart, full of positives and negatives, and really thinking seriously about the choice I'm faced with. Talk to people outside of any of the labs; they will most likely have advice. Because general subject won't get me anywhere and managerial style or size of the lab will only get me so far. Any suggestions?

Inspired, interestingly enough, by the word "Crepuscular" (the world might be worth a whole story, but I don't have a main character, an antagonist, or a plot (yet?). On the other hand, it might be too similar to something I've already written.)

The clouds had been designed to reverse global warming. At first, everyone rejoiced as the temperature dropped, children running out in the rain after an oppressive summer day. The inventors of the miraculous technology were made Nobel Laureates – for peace, no less. I saw the old newspaper headlines: “The Climate Change Dragon Slain”; “Man Triumphs Over Nature.”

But the clouds kept growing.

Grandmother says there used to be hot, sunburnt summer days, when you had to shield yourself from the bright light, and golden sunsets as the sun gradually crept beneath the horizon. But now, everything is gray, and cold.

Started (and finished) Pride and Prejudice and Zombies this weekend; I highly recommend it to anyone who enjoys Pride and Prejudice, Zombies, or both. The first line is undoubtedly my favorite:

It is a truth universally acknowledged that a zombie in possession of brains must be in want of more brains.

I think it's most people's favorite as well, because that is a truly wonderful first line.

Round one of the Genetics v. Biochemistry Olympiad was Friday (challenge: Trivial Pursuit). I am proud to report that even though the Biochemists had a ringer in the form of one Journalism student (notably not a Biochemist!) the Geneticists were victorious! It was as close as could be -- we won on the tie-breaker, by a single question. And some of the questions (in particular the one about Timbuktu) I should have known and didn't. Next year, we will be even better!

Round two (next Friday) is Rock Band; I have hopes, but not particularly high ones, since I have only ever played Rock Band with the Biochemists (and I am one of the worse players at said game). On the other hand, since there is no clear competitive mode, perhaps any victory or defeat will be debatable.

In other news, I have not yet killed the plants I planted (hooray!) and Rose Season has begun, this time in earnest -- in that twice a week (at least) I have to go out and cut roses from the bushes outside my apartment. I have a vase sitting full on the table and I am sure that by Wednesday I will have another vase's worth of roses and nowhere to put them (my apartment is rather small). I guess I shall bring some into lab, and give them to friends. I gave most of the ones I cut Saturday to my neighbors (their response to my cutting the roses: "Well at least someone cares about the landscaping!"), and then when I left the apartment today there were even more blooms than I had cut (in my defense, I cut almost a dozen and a half) looking about ready to be cut. Wow. On the upside: roses! On the downside: so many roses!

Also, I set up my first fly crosses this week! It was truly exciting. Hopefully they are very fecund, as insects tend to be. Have I mentioned that I feel like a real geneticist now that I'm doing fly genetics? Because I do. It's like... everything I was doing before was fake genetics; half molecular biology and half genetics. On the downside, there is not so much computer/statistical work to do in my current rotation, and it was one of the things that I have liked the best about my first two quarters. I'm not sure exactly how I could do computer stuff in my current rotation, but perhaps I'll find a way. And at least I have a class that demands programming every week. (Hooray for image processing!)

At silks class, someone came in to practice for a show; she was doing an aerial loop bungee act on roller skates. As in, she was on roller skates, climbing and securing herself in various impromptu harnesses from a loop of strapping attached to a movable point with bungees. Someone else was pulling the movable point up and down to make her bounce. She would move outwards in increasingly large circles, and spin and twist. It looked like just about the most fun thing ever, and I was almost certain that if I tried it I would break my ankle. Perhaps even without the roller skates. But it might have been worth it. Wow.

On a more personal front, I did a wheel down from the very top of the fabrics and got out of it, and moved into another trick. It doesn't sound like much when I say it that way, but I was very proud of myself. Also, I learned/relearned a move called the "elevator", with a tee-shirt this time, so I didn't get more rope burns on my armpits. It was much more enjoyable without the burning pain!

Genetics has a summer softball team, and practices start on Tuesday. I need to get a glove!

The seder went off without a hitch. Lots of delicious food, and enough people that they ate almost all of it. Which was happy because everyone was goofy and happy and well fed, but sad because I did not have much by way of leftovers for the rest of the week. Also, they are still talking about the matzo ball soup. (Which I thought could have been much better; I used a funky recipe for matzo balls with lots of parsley in it, and the leaves did nothing for the texture. Next year, back to the cayenne-spiked matzo balls. Also, more liquid for the brisket, which was well-flavored and not tough but not so tender it fell apart on my fork. They ate all but one slice, which amounted to more than half a pound of meat for everyone eating it, so it couldn't have been too bad). I didn't pull off my crazy afikomen idea, either, and given the size of my apartment and the number of people searching (very small, and 11, respectively) it would be the only way to make the search last any significant length of time at all. I did fool them, however, on where I had put it -- it was not in the first place which anyone looked.

July 20th is the 40th anniversary of man walking on the moon, as well as being Biff and Alex's birthday; they are going to have a Moon Party -- first, moonbounce in the form of a room full of trampolines (my favorite is the "all trampoline walls"), and second, in the form of a two-room party in which one is decorated to look like the moon, and the other to look like Mission Control. Upon entering Mission Control, you would have to put on a white, collared, short sleeved, buttoned shirt, with a thin black tie. Possibly also be handed a slide-rule. I'm getting plastic fishbowls and decorating them ala astronaut helmets for the two birthday boys, as my present to them. I also put in a vote for the moon room having "Ground Control to Major Tom" and maybe a few other space-themed songs on a short loop. It will be awesome.

Much else has happened, but those are the principle things.

Good deeds, roses, and lemonade

I gardened today! Went to the store to get drought-resistant plants (they remembered me! Asked me how I was settling into the area. I was shocked, and quite pleased. I guess they don't get many customers on bikes, and that would make me memorable? Also I went in just about three weeks in a row to get books + research + supplies and finally plants.) Pulled up all the weeds I had let grow over the winter (eek!), applied pesticides to and turned over the proper soil (in preparation for tomatoes, basil, and possibly another herb) and planted flowers (iris and geranium) in the two clay pots. If the iris and geranium are bigger in three weeks or so, I'll plant tomatoes + herbs. The weeds were these low-lying, mostly water (hence grows faster?) plants that smelled vaguely of honeysuckle and had big lily-pad like leaves. They covered everything. It was really quite impressive. My goal for next winter: Do not let them take over my garden. My goal for the next three weeks: water the plants twice weekly. I haven't taken up the strawberries, and I should pinch off the flowers until June if I want them to produce more fruit, but they look pretty pitiful and so I'm not sure what to do. I really can't have strawberries next to tomatoes (tomatoes harbor a fungus that kills strawberries), but I think my strawberries are dying of said fungus anyway, so... yeah. I have to think. I have a big raised bed, which I'd like to turn into a kitchen garden, but I know I need to start small, or I'll just do nothing at all.

I was on such a roll from pulling out weeds that when I finished cleaning the back, and packing them up, and watering my plants, I checked on the roses on the common walk. The land lord does all of nothing to take care of them (it seems), so there were (already?!) all these rose hips. I cut off as many as I could reach without drawing blood; hopefully more roses will bloom. And I took one mostly-gone rose, and a bud, for myself, because they are pretty. But seriously, this rose bush was more like a rose tree than a bush. It was kind of absurd getting the blooms from them, because I had to pull them down from the roof. Maybe it'll be a project for this winter to actually prune it (they say, for places without true winters, to prune in December and January, and for people with true winters to prune in early spring -- it's late for either case; drat! Also, I do not know if I have a true winter or not -- that sounds like something to ask the people in the gardening store). I would feel a little bit strange about doing it, and would probably want to talk to the landlord first, but... seriously; you can't hardly see the blooms because they are above the roof. Sheesh. I consider what I did a good deed for my neighbors, because now we can share many more roses. Hopefully. I wonder if the landlord waters the roses. I wonder if my hose stretches far enough. My hunch: not, on both counts. They only take about an inch of water a week, so maybe I could go back and forth with the watering can. Hmm. (Since it will likely not even drizzle again until September at the earliest, this bears thinking about.)

Anyway, now I have washed all the dirt from my knees and hands, put the rose + bud in water in a wine bottle, and am drinking lemonade. (I made two glasses. I will drink both.) There is something very satisfying about a day spent outside, planting and tending things. It is more concrete than the typically intellectual problems which I face on a day-to-day basis. Plus, I don't have to do in on a daily basis, which makes it much more fun, by definition.

This week: preparing for the seder! I will likely be cooking eight pounds of meat. The reality of that just hit me. Huh.

A productive morning

I missed the post on Boingboing last week entitled "Marx Was Right", which I find mostly amusing because it's the same oversimplified worldview that I told my P.I. in the fall (to which she responded "You sound just like my husband"). But Marx's theory seems more and more relevant as time goes on, or rather does not seem less relevant as time goes on, at least to me. Of course, whether it leads to a worker's paradise or a paternalist authoritarian state is harder to tell. Also, unsurprisingly, the boingboing comments are 2/3 inane drivel (along the lines of either "Marx was a fascist!" or "Marx was righter than Adam Smith!"), 1/4 trolling, 1/12 moderators chastising the commenters, and 1/12 actually insightful. Actually, maybe a little bit more inane drivel there, and a little bit less insightful. But you get the picture.

One of the actually potentially insightful comments brought up socialism in Scandanavia, and why it seems to work so well there. Which in turn led to this wikipedia entry, which sort of confirms my view that in societies in which individualism is prized, Socialism has a harder time getting a foothold and it would be neary impossible to work on a large scale, whereas in societies in which the collective is prized over the individual, Socialism is almost workable: http://en.wikipedia.org/wiki/Jante_Law. Of course, that's an oversimplification too, and basically comes down to the idea that "Well, if everyone believes in Socialism, it'll work", and the drawbacks on an economic system based on collective belief (fantasy?) can be shown pretty clearly by the current economic collapse.

In any case, a few more wikipedia articles later, I happened upon the trailer for 2081, a movie based on the short story "Harrison Bergeron" by Kurt Vonnegut, which I am now very excited for: http://www.finallyequal.com/. It looks very cool, although trailers usually do.

... now if I could just get my apartment cleaned like I meant to do to begin with. (oops).

Yesterday's Drabble

Why even pretend anymore? I didn't post this because I am lazy and distractable.

Nothing reminds me of my childhood as much as the song of the mourning dove: Coo-ee-coo-coo-coo. Doves were as common as crows and noisier in the twilight hours. It always sounded not like a mournful wail but a lonely whistle – there were birds in my parents’ backyard that cried like children, but the mourning dove was the sound of wind through a flute; empty, sweet, and alone.

Now, its longing call, through the gray mist of memory, reminds me that I am no longer a child.

Coo-ee-coo-coo-coo; you have left.

Coo-ee-coo-coo-coo; you can never go back.

Coo-ee-coo-coo-coo; it is gone.

I have discovered that I cannot write my short story without reading some more Sherlock Holmes mysteries, and possibly that I should read Frankenstein, The Island of Dr Moreau, and The Moonstone as well. This whole trying-a-different-style thing is interesting. And non-trivial. Next step: download an anthology onto the Kindle.

So, it will be a while (especially when the next quarter starts and, again, I drop off the face of the planet).

Drabble: This time, with the same number of words.

I know immediately the flowers aren’t for me. No one sends me flowers. The only occasion upon which I have ever received a bouquet was my twenty-first birthday; a bottle of champagne nestled in a small yellow, white and pink arrangement. When someone wants to please me – when I need to cheer myself up - a used book store is a better bet. So the vase squatting at my doorstep cannot be mine.

But I don’t know who, or where, the rightful recipient is, and so I indulge in a brief, harmless fantasy.

And throw away the card, strangely guilty.

There's another one in my head. Perhaps that one will be tomorrow! Or perhaps (gasp) I'll actually write a full-out short story. I have the recipe for one: a first line, a premise, and an idea for a plot.

OMG Bioperl!

So, I've been doing a lot of thinking and have not had much time to actually put any of that thought into action. I have two short stories that I swear I'll sit down and write... sometime. I'm thinking spring break, which fortunately enough starts oh-so-soon (by which I mean, basically, Tuesday).

BUT, what I have been doing is programming in Perl. Specifically, bending those wanton BioPerl modules to my will. And I am (fairly ridiculously) proud of the output, so you all get to see it. I think it's pretty darn beautiful, if I do say so myself. Once I figured out how to print anything in an image, the rest of it was fairly straightforward (surprisingly, since it took me basically a full day to find a server I could run my script on and get it to print anything even close to what I wanted). The overlay at the bottom took me quite a bit of puzzling to figure out, because online there were three tutorials that described ways to do it (none of which worked, of course), and because the parts of BioPerl that our instructor even vaguely went over were all "here's how you download a sequence" and "here's how you find enzyme digest sites on that sequence" and not "here's how you output a picture".

Next quarter: Computer Analysis of Biological Images, in Java! I will learn how to deal with the data I was getting last year; all those pictures of nuclei I dreamed about. And given that my favorite parts of this quarter have been learning Perl, I think it's fitting that I'm now taking a class in Java. I'm pretty excited, but I predict that my friends will not be in that class, since they (by and large) did not enjoy Perl nearly as much as I did. Which is sad. *sigh*

Continuity

Today was a beautiful April day, and my neighbors were complaining about how bad the weather was -- oh my gosh, clouds in the sky. The fact that it is still February is not lost on me. I'm sort of amazed. I feel like I'm halfway through spring quarter already, and winter quarter isn't even over. It's pretty wonderful that a warm Saturday sitting outside and reading a new book (Last Watch; so happy it's out, so sad the series will be over) can make everything -- absolutely everything -- feel happy. Even a book about (possibly?) Armageddon.

I got to thinking, however, about my NaNoWriMo piece. It's fairly interesting, because I feel like I have too many characters that aren't important enough. In many instances this is a small deal and fixable (swapping out one new character for a reappearance of an old character, for example), but it's somewhat interesting to me because one of the main characters in this story is entirely new, which doesn't jive so much with it being a sequel and all. Of course, I like the character too much to do away with him entirely, but it got me to thinking, and my sense is that in order for the later story to flow the way I want it to, I need to edit the earlier story to make it more sequel-able. Since when writing the first one I was not thinking "You know what this needs? A sequel."

A good example that everyone knows about -- in book one of Harry Potter, Hagrid borrows Sirius Black's motorbike. It's a throwaway reference that no one pays attention to, and doesn't stand out particularly, but it introduces at least a name so that when Sirius becomes a main character in book 3, readers aren't up in arms saying "If Sirius was James' best friend, where was he the night that James died?" The character isn't really developed until book 3, but he exists in the world as of book 1. (Of course, Remus and Peter aren't mentioned, but the fact that one of them was makes the other two more believable, somehow; mentioning all three would have been overdoing it.)

My problem is that, since I first set out to only write one story, those references are conspicuously absent. I don't mention a character just for kicks, or on the off-chance that I would be writing a sequel. Most of the new characters in the piece I wrote in November I hadn't even thought of when I was writing the first story. So there are characters that logically should have been present in some of the events I describe in the first story, and aren't mentioned. Places and things that should have made an appearance, and didn't. Because I hadn't thought of them. Nothing contradictory, necessarily, but just strange -- the long lost brother or sister who is never mentioned until he conspicuously shows up. So I want to rewrite the first one, to add those elements -- nothing big, but enough to make it not seem strange that I'm bringing up these characters, places, and things in the second one. Also maybe change some names (that's a separate issue). But I know that I don't have the time to make the second one readable and the first one better at the same time. (I barely have enough time to get the second one readable on any sort of schedule). So I'm just sort of puzzling about what to do. The obvious solution, of course, being to go back and change the first one when I'm through with the second one. Which I might do. We'll see.

Andrew Bird!

Concert was last night. It was awesome. My brother's (and my) only disappointment was that he did not play "Not a Robot but a Ghost" from his latest album. But that's not much of a complaint, and those older songs that he did he did in new ways. ("Why" -- which I want to choreograph a silks act to as soon as I get good enough to do so, and a song titled "The Water Jet Cilice" but which I call "Serendipity" instead). He's very... affable on stage. And the crowd sort of just sways to the music, in part because it's not dance music so much. And by far the best part of his concerts, in my opinion, is that they don't sound like his albums. Which means that even if I can't see a thing because there are all of these tall people standing right in front of me, I still get a different experience than just listening to my mp3 player. (other than the tall people standing right in front of me, the smoky bar, and the volume)

He had the audience sing a part of "Tables and Chairs" -- instead of playing the melody on his violin and looping it, he just sort of held out his hands like a conductor and hoped that people would pick up. My brother and I did, of course (I always sing along with the violin at that part anyway), but I think much of the audience was sort of mystified. In part because he plays with rhythm so much in his concerts (less so in his albums) that even if you wanted to sing along with the vocals, it would be nigh impossible. And in part because instead of something like "You guys sing the chorus!" he instead said "You guys sing the melody to the instrumental interlude!" (actually, he didn't even say anything; he just stopped playing and singing and pretended to conduct us. I think it would have been cool in a really strange, eerie way if no one had sung at all -- just gone silent right then, and he's conducting, but there's no noise).

Also, some woman shouted out, about halfway through the concert, "We love you Andrew, welcome to San Fran... (cisco)". To which one guy standing near me responded: "You're not from around here, are you?" Because yeah; no one in the bay area calls San Francisco "San Fran". It's "San Francisco" or "SF" or "The City". Or, if there are some people, they're very rare. I can, of course, understand why she didn't want to shout San Francisco (it's rather long) or "The City" (it's rather vague). And maybe she just moved here, or something.

And we got free posters! Mine will be up on my wall as soon as I figure out where I want to put it. Possibly in the kitchen.

A plot, to go with my idea:

Thought this up last night. I'm pretty pleased; it's very goofy. Might post a rough draft up here, when/if I write it:

Imagine a world in which digital clocks really caught on; so that no one used analog clocks or watches anymore. In this world, because time appears to be quantized and discrete, peoples' perceptions of the world change fundamentally. Also, since velocity and thereby motion is based on limits and continuity, in a world with no continuous time motion becomes illusory -- you still think that you're moving, but really you're jumping from (stationary) place to (stationary) place in very small leaps. Basically, in this world, motion (and hence progress) is an illusion ala Xeno's paradox of the arrow.

This wouldn't be an issue, but it means that conceptually, this world is stalled out circa 1990. And so my hero will go back in time (using a tea kettle; you knew it was coming) and destroy (or ridicule) the digital watch in order to save continuity and progress.

An Idea

A very goofy idea, in fact. Perhaps two, in the form of a conversation, because that's how they came to me.

"You've heard of time dilation?"
"It sounds familiar."
"It's the idea -- if you move fast enough, time moves differently. So you can go faster, and depending on how fast you go, you either move forward or backward in time."
"Is that the idea?"
"No -- everyone is working on that, just like everyone is working on wormholes. Everyone and their prehistoric ape cousin. But there are plenty of other ideas. For example; what if you stop moving?"
"What?"
"Time dilation; it works with acceleration, basically. But what if you slow down? Or stop?"
"You mean, like just sit around all day?"
"No! Even if I don't move a muscle, I'm still moving; the planet is spinning on its axis and traveling around the sun, and that in turn is torquing through the galaxy. And every molecule, every atom, every subatomic particle in my body is flitting around even faster than the earth is moving through the universe. I can't stop; can't break the inertia, can't go lower than ground state, but what if I could? If I could stop moving..."
"The world would move without you?"
"Time would move without me."
"So, you'd be taken to the future."
"Perhaps. Even if I was, I'd be floating out, who knows where relative to the Earth's place in the expanding Universe. And I might not travel at all; I might just spontaneously decompose into dust."
"Is that what you're studying? How to do it safely?"
"Heh. Not quite. I'm studying tea kettles."
"Tea kettles?"
"Well, and pasta pots. Containers for heating and boiling water, basically."
"Um. What does that have to do with time travel?"
"Haven't you heard the phrase, 'A watched pot never boils'?"

Literature

So, one of my Stanford friends is turning twenty-three soon, and to celebrate (I think this will become a birthday tradition) we had a ladies' brunch and watched a Chick Flick. Since this was the first time, we started with the paradigm: Pride and Prejudice. While three out of four of us knew the story incredibly well, the remaining woman had not seen, nor read, nor heard told, the story. (She thought that it was "A love story between a white woman and a black man in the deep south." I kid you not. Personally, I thought that Pride and Prejudice was required reading for every twelve year old girl, but I must be wrong).

Now, while this created problems when the three of us had to bite our tongues to stop the words "The perfidious Wickham!" from coming out of our mouths the first time he was on screen (and come on, you have to admit that perfidious is a very, very fun word to say), what was most remarkable about watching this movie with this woman was that she didn't like Mr. Darcy. It is usually a safe bet that any woman watching Pride and Prejudice will, by the end of the story, like Mr. Darcy. But my friend's response to the comment of "Man, Mr. Darcy is awesome," was not affirmation, and not even denial, but staunch disbelief. She argued that he could not have existed in Victorian England, and she much preferred works like "The Awakening" (which, as far as I can tell, follows roughly the same plot as Anna Karenina).

I don't really want to spend much time here picking apart that argument -- but it seemed to me that she was operating under several inaccuracies which she stalwartly did not accept: mostly, she assumed that Georgian England (i.e. the time of Pride and Prejudice) was the same as Victorian England. In fact, "The Awakening" was written in 1899, and "Pride and Prejudice" in 1813, and as such comparing the two eras as being synchronous is, in fact, roughly equivalent to drawing the same parallel between the aforementioned late Victorian era (circa 1900) and the mid 1980s.

The Georgian era was marked by social upheaval, unrest, and as tends to go hand-in-hand, relative social freedom. The other authors one associates with Austen (Bronte, Eliot) are also Victorians and, once again, not her actual contemporaries. On the other hand, the most famous novelist of the time was Walter Scott, who certainly had strong female characters. The most famous writer? Lord Byron (hah). And a few other well known personages who were actually Austen's contemporaries were, wait for it: Casanova, and the Marquis de Sade. I mean, I have trouble thinking that the era which gave us Casanova, Don Juan, and sadism was also known for its repressive social norms. The late Georgian period showed a lessening in restrictions in everything from class (trade and industry were becoming respectable) to undergarments, and those restrictions subsequently tightened right back up in the Victorian era. And although I told her several times that Pride and Prejudice was not Victorian but earlier, and that social mores were actually much less strict in Georgian/Regency society than they were in Victorian culture, she resolutely refused to believe me, and went on and on about how Elizabeth obviously should have killed herself because Darcy wouldn't actually fall in love with a liberated woman, being a product of Victorian society.

Why does that bother me? I mean, yes, it is one of my favorite books, but why should it matter to me what she thinks of it? Or if her opinions are legitimate or founded on false assumptions? Would I have found it easier to deal with if she had compared to an actual contemporary of Austen's, instead of someone writing some eighty years after her death? (And what would she have compared it to, Ivanhoe, which is itself historical fiction? Don Juan? Justine? That would have been a good one -- Darcy is not realistic because he is neither as depraved as de Sade, nor as womanizing as Don Juan.) But why should I care if my friend prefers Queen Victoria to Casanova? (Even if I find that rather odd?)

Except that wasn't entirely what she was saying -- instead, she was implying that Jane Austen failed at what Jane Austen was perhaps best at (creating realistic, three-dimensional, and compelling characters). She was saying Darcy wasn't realistic. Which rankles with me, because I think the strength of Austen's writing is in her characters. Not just the main characters, but even the very characters she satirizes: Mr. Collins, Lady Catherine, Lydia, and Mr and Mrs. Bennet. To say that even Mr. Darcy was unrealistic and impossible, and especially basing that statement on the social mores of the time (which I am fairly certain Jane Austen understood better than my biochemist friend), strikes me as the kind of ridiculous stubborn vanity as would make her, well, more akin to Lady Catherine than any other character in the movie we watched. And that is the sort of baseless condescension which I really dislike.