Only at the U of C, ish.

WARNING: RAMBLY. I might clean it up later, make it more coherent, but probably not.

Every so often, something happens that reminds me of why I went to school at the U of C and not somewhere like MIT. Well, it's fairly often because this quarter it's been every Monday and Wednesday at 3:00 when I have a philosophy of literature class that certainly would not occur at a tech school. But every so often, something (other than Ted Cohen telling a joke) happens that reminds me of why I went to school at the U of C and not somewhere else, like MIT. Often enough, that thing involves Tom Stoppard. Today it was my glee upon finding an article talking about "postmodern science" or, rather, the use of science to explain postmodern life and vice-versa as epitomized by Stoppard's use of Quantum Physics in Hapgood (Quantum Physics + Espionage = fun times!) and Chaos Theory in Arcadia. Although the Arcadia analogy is not nearly so good, in my opinion, because in Hapgood the whole thing is tied up tightly in uncertainty and such (of every sort), whereas in Arcadia chaos theory plays much more of a sub-role, being discussed alongside other subjects, but never really encapsulating the whole thing; really Arcadia to me seems as much about thermodynamics as chaos theory, and as much about Byron as either of them (the link between Byron and thermodynamics is drawn, and beautifully so, by the simple statement "the action of bodies in heat"). I couldn't read the entire article, because Questia is a bastard that way (and the U of C network goodness doesn't give me access). But nothing is lost to the march, and so I can reconstruct it.

Ooh. I should re-read Hapgood now that I know some Quantum. Heh. And I should read Arcadia again after I finish Thermo, just because. I wonder if Stoppard has a Kinetics!Play, but I probably won't be taking 3rd quarter Physical Chemistry, so I suppose it's immaterial.

Also, I should maybe finish my work for class before going on a Stoppard binge. Although in one week I think such a thing will be entirely called for.

OH MAN. I just had a hilarious idea. Absolutely wonderful and hilarious. I'll post more on it later when I have my book next to me and have enough time to think it out more fully. BUT, to give you a sneak peek into how weird it's going to be, well, for a second there I imagined the Doctor philosophically interrogating Tom Stoppard's characters. ("No more it can, for time needs must run backwards" (or something like that) versus "From a non-linear, non-subjective point of view, time is more of a ball of... wibbly-wobbly... timey-wimey... stuff." (or something like that)) I realize, of course, that one is "real" philosophy while one is goofy, but I don't much care about that (have I ever? There's philosophy in Harry Potter, I tell you, just not very complex philosophy!). Anyway, if science fiction is good for anything, it should be good for blowing apart the paradigm and fostering imagination. Pointing out what should perhaps seem odd to us.

And that brings me back to Ted Cohen, and the Stories class, and the order: "Don't take it as a matter of course or an obvious fact that pictures and stories please us." And the burning bush. And that noticing that something is odd, or striking, or interesting (nothing more and nothing less) sometimes says something about you, and teaches you something about yourself and the world. Hah.

That's overwrought philosophy for you!

I may have just finished the second-to-last problem set of my college career. Hooray!

Also, at lunch today my bottle of tea came with a quote from The Doctor: "First things first, but not necessarily in that order. -- Doctor Who" This only makes it easier for me to obsess over Doctor Who until the next season begins.

Now, on to dinner and a lab report (not hooray!).

I almost forgot

When I was waiting at the airport for my shuttle to get to Stanford, this was brought to my attention.

Whenever anyone asks, from now on, I'll say that I'm studying the likely genetic underpinnings of Magic in Harry Potter, and point them to this article. Excellent!

Updatexors!

Quick update before I go back to frantically studying thermodynamics:

I still have to hear back from UCSF and Princeton. However! I have been accepted everywhere else! Hooray for me!

My choice, it seems, is coming down to Stanford versus MIT. They are both absolutely stellar programs, they both focus on actively promoting interactions between disciplines, they both seem like great places to live and be (with great cities nearby if not next door). What I consider to be the differences:

1) At MIT, you do not start research until halfway through your first year, whereas at Stanford you dive right in to rotations. At MIT, this allows them to require a "core biology" cirriculum and inundate you with classes your first semester. At Stanford this allows you to get a sense of projects during rotations.

2) At MIT, wackiness seems to be smiled upon, while people at Stanford seem more laid back and traditionally "cool" (if you can actually say that about graduate students). I might be able to find wackiness, or bring wackiness, to Stanford. As a city, San Francisco is much, much cooler (and probably wackier) than Boston. However, MIT is much closer to Boston than Stanford is to San Francisco.

3) MIT seems very post-doc heavy, as in there are tons of amazing post doctoral opportunities there. Stanford seems more focused towards Graduate students, which would be good for graduate students.

4) Stanford has much, much better weather.

5) In neither place would I be able to assistant coach diving. In Boston there would be more high schools with potential openings for me to do that. In San Francisco, there would be circus arts for me to do, but that would be a 30 minute commute.

6) Stanford is about 3.5-4 hours drive from Kevin, but to get home to DC would take the whole day and to get to Chicago would take most of the day. Boston is more generally accessible, but I would probably want to get on an airplane to see any member of my family (or my college friends).

7) Mango might go to MIT, but he might not. He won't go to Stanford. PCBio people are going to Stanford.

8) Stanford's campus is drop-dead gorgeous. MIT's campus is kind of... ugly.

After some research, Yale appears to have a program very much like Stanford's, but it is a brand new umbrella and might therefore not facilitate cross-talk as well during my prospective tenure. Plus it's in a rather ugly town (sorry Easha and Ryan), an uncomfortable distance from airports or family members or large cities, with fewer coaching opportunities and no circus stuff that I know of.

Back to thermodynamics!

Graduate Programs

First of all, some very exciting news for those of you who I have not already told: I have been accepted to four schools! Yale, Harvard, MIT, and Johns Hopkins! I am absolutely, incredibly, and stupendously pumped. Honestly, and I know many of you have said I was silly to think this, I started this process thinking I would get in to one, maybe two schools. And I have been accepted everywhere so far. Which is... charmed, I guess.

While I am thinking about it, here are one sentence (or less) summaries of the schools I have visited.

Princeton: Arcadia, but overwhelmed by undergraduates.
Harvard: It seems that the stereotypes are true. (They think their faculty are better than anyone else, and the graduate students seem to live in awe of the professors).
MIT: It seems that the stereotypes are true. (Oddball, clever, exciting, emphasizing a strong basis in biology in general before specialization in lab, and proud but not stuck-up.)
Hopkins: A small program, with a stellar medical school, whose star is rising, but is overwhelmed by undergraduates.
UCSD: They're trying to be the Harvard of the UC system in biology, and therefore stress the "top-10" nature of their school as well as the "unparalleled" associations with biotech and research institutes in the area. La Jolla is a designer community for the life sciences and in a gorgeous area of the country, but the closest big city is Los Angeles (shudder).
UCSF: A "Party School" compared to the others -- students are less mature, causing them to "lose focus" and take upwards of seven years to finish, but who wouldn't fall in love with the city?

Perhaps more info eventually. But my flight is boarding in the next 10 minutes, so I should sign off, pack up, and get ready for my incredibly long, probably unpleasant flight. Oh boy.

But, as a post script, does anyone want to weigh in with insider information about Princeton, MIT, Yale, and Stanford (which are my favorites so far I think)? In particular MIT and Yale; since I am awaiting judgment from the other two.

Notably not Interviews

So, I have quite a bit to say about Harvard and MIT (and I will happily babble to anyone who wants to hear it) and I'm trying to write a poem or a song about developmental genetics (because it's cool, and the joy and giddiness of it doesn't really fit into prose very well), and perhaps I'll post about that stuff later, but for now I have something totally unrelated.

In one of my many literature searches for articles related to ChIP (Chromatin Immunoprecipitation, the subject of the presentation I'm giving today and another thing I'll happily babble about to anyone who asks) I found the following, which is notably not about molecular biology. Now, I don't know why that popped up when I was searching for, most likely, different authors and "Chromatin", but I do know (now) that the Plague of Athens was possibly caused by small pox, typhoid, anthrax, bird flu or the bubonic plague, but was probably not caused by purely human influenza (at least, according to these researchers).

Did I find a way to put that tidbit into my presentation?

The answer, my friends, is of course I did.

Princeton (Interviews Part 1)

So I am back from Princeton (hooray! Elizabeth: 2, Chicago Weather: 0) (make that Elizabeth: 2, Chicago Weather: 2 since both my flights were delayed in a feat of blizzard). And, on top of that, I have a working computer. Put these two things together, and you get one mammoth blog post about Princeton (and about the trip there. The trip back was so horrid that I'm not thinking about it).

I. I entered the red line train car and sat down to the sadly familiar sound of what I thought was someone panhandling. He smiled and waved at a man wearing a Carhartt jacket who entered with me. I prepared to tune the beggar out, to stare blankly at the floor and not move very much, hoping he wouldn't notice me, acutely aware of the fact that I was the only white person in the car. I don't know why I notice that; I often wish that I wouldn't notice it, but it is increasingly the case that I will realize suddenly, standing on the platform or sitting down in the car, that I am in a way an outsider.

I realized, then, that he wasn't a beggar. He was speaking in the same tones and rhythms that panhandlers use to decry that they aren't out to get anyone, but they have some sob story or another and they're just down on their luck and they pray to Jesus every day and they know he'll look down kindly some day, but in the meantime couldn't somebody please just spare a dollar to get a sandwich. He was using that same affect of talking at people instead of to people; disregarding the fact that everyone in the car was doing exactly what I was doing, looking away sadly and pretending not to hear him. But he wasn't asking for money or giving us a story about how his younger brother just died and he was raising money for the funeral. He was advertising temporary employment opportunities for people who were down on their luck. For people with felonies on their record - it doesn't pay much, he said, but oatmeal is better than no meal, and if you put some sugar on it it tastes all right. For people over fifty, who are working on fixed incomes and have prescriptions to buy or grandchildren to take care of, who needed a little something extra. And he handed out little green tickets, green slips of paper with this information.

Then he talked about a show he was doing; he was a poet. I thought, okay, here's where it will become obvious to me why this man is standing on a train and reading his poems instead of sitting at home, snug and secure, or going to work at what middle class America calls "a real job". He'll read a bad poem and he'll "sell" it to someone, and I'll be able to go back to my cubby-hole definition of the real world. But I had to admit that it was unlikely; the man had proven himself unique already.

The poem he read was good; it would be the kind of rap I liked if I liked rap. Positive and self-affirming without being too trite and with a cadence and a rhythm to it that moves quickly from one rhyme to the next, emphasizing the beat and the sound and the shape your mouth makes when you say a word.

Really, it was exactly what I should have expected. He sold a copy of his poem for a dollar, and sat down to talk to the man in the Carhartt jacket. They talked about people they knew, upcoming shows, everything and anything.

In Ayn's latest issue of Paste, there's an article about Hip Hop as a nascent cultural artform, or at least as an artform and a culture unrecognized until now. One that is all about rags-to-riches stories, self-made men. I've always been skeptical about that, because I think so often its messages are more of misogyny and violence and materialism than good positive determination and success. So often it's performed by someone who is violent and angry and jealous and maybe doesn't even believe in the self-made idols he holds up. But the guy on the train was real, and good. Or at least, I could imagine it that way, and I have no reason to force myself to be so jaded.

II. O'hare was a blizzard. I couldn't see to the end of the runway because of the snow, and the flight monitor flashed CANCELLED in bright red for most flights. Orange delay times appeared beside most others. Please, I thought, let me get out of O'hare. I don't want to stay here. And, an island of white in a sea of red and orange, my flight to Newark was on time.

It wasn't until we were in the air and the plane was shocked by a crosswind that I realized I should perhaps have asked to get to Princeton rather than to leave O'hare. I laughed.

And I realized that my questioning, my pleading, was not a plea for mercy from the author but rather a plea of sympathy from the reader. I think it's odd that I can so calmly laugh at how ironic it would be if my plane crashed in a ball of fire (it's easier since I didn't think it would), and how I seek identification with a judge or an audience, given that I so strongly disavow the very existence of a higher being ala author. I can tell myself this is because future generations could hear or read my story, but they wouldn't know that I was laughing with them; they would never know any of my little pleas for sympathy.

III. Newark Liberty International Airport is like a vision of the future from the sixties: touch screens and chrome and a magnetic monorail called an "Airtrain" that comes every three minutes and talks to you cheerfully as you ride.

IV. The Nassau Inn is a colonial relic - It used to be a changing post for horses between Philadelphia and New York City. The elevators are tiny and jury-rigged and the walls would be crumbling down but instead they're remarkably well kempt. And in one room, "The Library Room", they've saved the money on bookshelves and books by simply painting a bookshelf and books on the wall.

The best part is that the pattern is on a short loop.

V. The graduate students here live in a dorm - a castle called "Graduate College" with a basement bar called the Debasement Bar, or D-Bar. I note that one doesn't actually want to go somewhere where one will be debased, and they look at me strangely as if they haven't heard the word debasement before outside of the context of their bar. I shrug.

VI. Fox advertises American Idol in the same breath as Super Tuesday Primary Coverage, tacitly equivocating the two. Because which teen gets a record deal is at least as important as who the next president is going to be. Or at least, it is for most Americans. Or maybe just most Americans who watch Fox.

VII. The outside of most of Princeton is granite, and paradigmatic, but the molecular biology program is new and exciting (perhaps in relative terms) and therefore has new buildings. All are connected by convenient tunnels. The inside is bold and bright and feels like something out of an animated movie, somehow younger than I expected. The tables and chairs are big matching sets in lightly varnished wood, the walls are white with trim to match the tables; it feels like an elementary school with an adult color palette. And, suitably, all the break rooms seem to have miniature, rather than adult-sized, furniture. Everything is big, bright, pretend colonial to as to be Classic. Like an old lady who only has one suit, in a 1950s cut, immaculate, adn looks stunning in it, but it's all she wears. Classic.

They're pouring money into the program; they guarantee funding for as long as you need it, and the money comes from the University, not individual labs or TA-ships, so in theory at least, you have complete freedom. Everything, it seems here, is handled by a benevolent God of Funding. In a climate where that is very much an issue, no one here seems much worried. Which is refreshing, but it makes it seem even more like a painting or a myth. Arcadia. Here we are, in the center of civilization, midway between New York and Philly, hidden in a picturesque suburb where you can see the stars at night, where everyone knows eachother and everyone likes eachother and strangers will talk to you in a coffee shop about David Hume's views on Religion. Everyone is happy, healthy, excited about work, and part of me is always looking over my shoulder for the real world, for death, for hardship and mortality, marring even this beautiful canvas. Part of me says that maybe these people really are just that good. Part of me wants to believe that money, and having the purse strings in friendly hands, really can change a lot. That this is what I always wanted academia to be and I should be happy to have found it. But part of me is reminded that this isn't every weekend, that real life likely comes even here, and that Death mars every canvas, no matter how lovely it is to look at. Here, I am in Arcadia, instead of Even in Arcadia, there am I.

Or, you know, not.

VIII. Two professors talk about research they're doing and I won't (can't, shouldn't) bore you with the details, except that it is so obvious from both talks the passion with which these people live. And they do it so differently, to boot. The one wants to change the world, she wants people to live forever, to have children without birth defects for as long as they care to, she wants to cure humanity of Death; or at least aging (which fits in so very well with my Arcadia metaphor, eh?). I talk to her later, and you can see it in her eyes when she talks about the therapeutic possibilities of her research. You can see it through the makeup she wears and in the wrinkles around her eyes. She has a young child, I learn later. I wonder if her passion, her mission, was selfishly motivated in that way. I think probably I'm imagining things. Creating characters. Writing stories, fictions that might not only be false but also offensive. I try to stop but my brain automatically makes connections. I cant' stop it.

The other, it is obvious, just gets such glee from the work that he can barely keep himself from jumping for joy. He loves the stories, the problems, the questions, the mysteries, the discoveries. He looks at a video he's seen so many times he must have memorized it, and still stares at it in awe, transported by its meaning to him. He giggles, his voice rising in a slow crescendo from a tantalizing whisper to a sanglante cry - how could someone not feel the emotion dripping from his voice when he talks about it? He is a child, still looking at the world with wonder, still gasping in delight at the sheer majesty of it, still stopping dead in his tracks when he thinks of the mysteries still in store for him.

I spoke to his wife, later, about my science and hers and science in general. She was attentive to my description and even asked me about the implications of my procedures on her work. I answered her quickly and correctly (I know that much) and didn't think about it until it was pointed out to me; a tenured professor had just asked me if I had any advice.

A yeast geneticist showed me amazing data about nucleosome rearrangement and transcriptional control, which is an interesting outgrowth of my current niche. And some more common stuff about reversible DNA-DNA interactions. I felt almost guilty I didn't have more questions to ask, but he e-mailed me this morning saying he enjoyed talking to me and hoped my return home was not too bad (it's Chicago in the Wintertime, so hoping it's good is hoping for the impossible, I guess). And if I have any questions, I should call him.

I'm on cloud nine.

A bacteriologist talked me through a recent discovery; it's part review of basic genetics and molecular biology (Bacteria have operons, where genes that are similar in function are clustered for co-regulation) and part theory of science (you can screen based on decreased viability, but you can't select based on it), and part joy of discovery and a cool story.

With all of the professors, I talked about the weather in Chicago and the programs and where else I'm interviewing. It's fun, but part of me wants to spend more time with a single person, to really get down to the nitty-gritty of a project or the program, rather than a whirlwind tour of the offices of five professors.

And that's how I feel about a lot of the people here; I want to sit down and have a real conversation, unlimited time, just get to know one person really well rather than meeting twenty.

IX. The graduate students give a "panel" discussion. I ask, if they're living in a dormitory and eating in a dining hall, if this wasn't just "College 2: This time we mean it" or if it didn't feel that way. They say that it's different because you're older (why, yes; well spotted) and people are more mature, and there aren't crazy parties all the time. And besides, it's awesome to live in a castle and eat in the Great Hall of Hogwarts. I smile. I have lived in a castle, eaten in the great hall, and had mature beer nights where no one gets drunk rather than crazy frat parties. And I decided that, rather than than that, I wanted my own kitchen and my own living room. The more I think about it, the more significant it feels - I want a place to call my own, I want my own space above all, I don't want a randomly assigned roommate and I do want my own kitchen. But the people here say no, it's better for you to do it our way so you don't turn into a hermit. When all I can think of it the fact that really I want a kitchen where I can throw a dinner party and no randomly-assigned roommate to be stuck with. I don't want to clean up other peoples' messes, and I don't want someone else cleaning up my messes, and I don't want to get into arguments about it. And they will happen, I know. They just do.

I guess part of my problem is that Duff and Ryan went to Graduate School and got single bedroom apartments; it felt like they were beginning their adult lives. TO me. Or something. There's something so nice about Yotom's studio or Christian's place; I have created a dream surrounding it that's hard to let go.

X. The campus is beautiful, old colonial brick buildings and lawns with big trees and a picturesque style. Everything tastefully arranged. The chapel is Rockefeller only bigger, and the Graduate College is BJ only nicer kept, the grounds are Snitchcock Quad without the divet and the concrete path. It's what we would build if we had unlimited money. I find out they have the largest endowment per student in the world and it doesn't surprise me. Everything here is well cared for, in a way that makes University of Chicago look old, dank, crumbling, or tacky. It's amazing. Almost unbelievable. But it is certainly for real.

XI. Chicago wants to make its undergraduates into graduate students; Princeton seems to want to turn its graduate students into undergraduates. They push heavily for graduate involvement in undergraduate student organizations. They create a new post: resident graduate student, who is simply a grad student living with undergrads and holding social events every couple weeks with no disciplinarian aspect to it. To me, it feels a little bit backwards.

XII. At dinner at a professor's house, we talk about hacks. A kid from MIT is there who was involved in a plan to steal the cannon from Caltech. They took it cross-country, put an MIT class ring around it, and replaced it right in time for Caltech's prospie weekend. I told a couple stories about Scav. The professor, not to be outdone, told a wonderful story. He used to be dean, and have an office overlooking Cannon Yard. He walked into his office and looked out of the window to see a huge hole in the ground and a pile of dirt. The cannon, having a history of forced transitions between Princeton and Rutgers, was liable to theft, and so had to be buried in the center of the quad. He called various administrators to tell them. They came down to the square and poked around, appalled, until the then-Dean noticed something else; the hole was off-center. Someone had dug a hole and, with the dirt, buried the cannon. They never figured out who did it.

And that's it for Princeton; Harvard and MIT are next so more on them next week.

Now for studying. So much to do!

In case there was any doubt...

I went to the bank to deposit checks and withdraw some money today. And as I was filling out the deposit envelope, I heard this odd whirring that appeared to be coming from the other side of the wall. I leaned towards the wall and it got louder, more distinct.

My first thought was "That's a sonic screwdriver."
My second thought was "Holy shit. Is the Doctor real?" Or rather, the image of the Doctor (David Tennant version, of course) on the other side of the wall - which would put him inside the UC hospitals.

My third thought involved looking into my bag and realizing that my books were being pressed against my toy sonic screwdriver and thus creating the whirring sound.

Note that it never once occurred to me that someone other than myself or the Doctor would have a sonic screwdriver. Also that my first reaction was not that I had a toy sonic screwdriver in my bag, but rather that the Doctor had to be real, and adventures were afoot. Apparently I am still subject to the same flights of imagination that caused me to adamantly believe I could fly across the backyard when I was five.

If there was any doubt that I am really a small child at heart, well, I think this dispels it.

Craig Venter is an evil supergenius.

Okay, I know that I said that before, in this post, but it remains true. Or rather, I have discovered new information that confirms my belief. Namely, that he "informed" the Department of Homeland Security that, should be want to, he would be able to manufacture a virus in a week, and a devastating killer virus like Ebola in a month. Just, you know, so they would be more aware of the dangers of biological terrorism.

Because everyone knows that Osama Bin Laden has all these state-of-the-art genetic research laboratories. Such as the one that tied the NHGRI for sequencing the human genome. Oh, wait, no, that's Venter.

Honestly, why would any real terrorist (i.e. one who was not also a mad scientist) make a virus when there are perfectly good ones lying around? Why manufacture Ebola when you can get a sample from a dying village instead? Seriously... There is an easy option here and a hard option, and only one of them requires synthesizing a genome from its component bases. And, I mean, you don't even have to use Ebola (although that does kill people quickly, efficiently, and in ghastly ways). There are a myriad of diseases and chemical compounds which should strike terror into our hearts at least as much as Al Qaeda making a killer virus -- such as Plutonium 209, Ricin, drug resistant TB, Bird Flu, nuclear dirty bombs, and so on and so forth. Seriously.

In fact, the only kind of person I can imagine making a designer virus, for world conquest or otherwise, is someone who honestly derives a great amount of pleasure from the designing of virii. Such as, oh, I don't know, J. Craig Venter.

Watch out -- he's working on bacteria from the family that Tuberculosis belongs to next.

On a completely unrelated note (honest, I swear), I know that I have not posted hardly anything in, well, quite some time. The reason for this is that I have 7 graduate school interviews scheduled for the next 5 weekends (not counting this one). But! I think I will post about my trips, maybe, so that means I'll be posting once a week for a while. Right. Or maybe I'll just... not. Either way.

EEEEEEEEEEEEEEEE

I got into Yale!

Not even an interview, not even past the first cut, I got in. I am so excited it is hard to breathe. Well, not hard to breathe but at least very, very hard not to smile, and squeak excitedly every time I remember it.

I AM GOING TO GRADUATE SCHOOL NEXT YEAR, and it will be at a school I like AS MUCH if not MORE THAN YALE.

Oh my gosh.

The best part is, I no longer have to stress about any of it. I can relax and enjoy. From here on out, I have just about nothing to worry about in College.

Time and Relative Dimension in Space!

(From http://www.zetacity.com/insidethetardis/)

My roommates and I are huge Doctor Who fans. Between the three of us, we have at least one, and probably two, sonic screwdrivers with us at any time. And so it always seemed natural (and perhaps necessary) that at some point we would transform part of our apartment into a TARDIS. Now, we had two options -- the back end of a closet that jutted out into the hallway, was roughly of the correct proportions and size, but had no door, and our coat closet, which of course has a door (as coat closets tend to do) but was improperly shaped. We decided that the ability to enter and leave our Tardis was more important than getting the size just perfect, and so for the New Year we transformed our coat closet into a time-traveling space ship, or a blue police box, whichever you like.

First, we covered the walls with blue butcher paper -- here is Ayn covering the first wall and cutting out the hole for our buzzer. (David, who is superhumanly tall and not pictured, stood on a chair to affix the paper to just below the picture frame molding high up on the wall.)


Here's what it looked like when one wall was finished.

Next we covered the other wall and cut out a hole for the door -- and wrapped the door in blue paper.

We cut out a little hole for the latch so it would still be functional.


Next step: The sign that goes over the phone. (Police telephone for use of public...) We decided to put this over our buzzer/intercom just for the gags. We had thought of making a little box out of foam core or poster board that actually could be pulled open to reveal our buzzer, but that seemed like a bit too much work for not enough extra awesome. And too much work to buzz someone up to the apartment, too.


First we tried to put both bays of windows on the door, which would correspond to the Tardis being the same width as the door frame. That looked okay but not great.
Next, we made the Tardis twice as big as the door frame, with two sets of six windows, one on the door and one off. Since the wall with the buzzer is about the length of the door frame, it only got one set of windows.

Here's the telephone sign with windows above.
Next step were the "Police (Public Call) Box" signs on the top of each side. They're white lettering on black, so we couldn't just print out a banner for them (at least not without using up a whole lot of printer ink). We cut the letters out of white paper and glued them on to strips of black construction paper. Here's Megan cutting out letters, and Jonathan making windows (okay, so this is a little bit out of order. So sue me.)



We made two sets of letters - here they are all cut out! We only used half of the second set, since the wall with the buzzer on it is about half the length of the wall with the door on it.


Here's a close up of the finished and mounted sign.

And here's the Tardis with the signs glued together and mounted on the wall!


The only thing that remained was to give it a bit of the wood-paneling look. So we drew on panels with a sharpie. They aren't very obvious, and we'll maybe draw in shadows or at least make the lines broader over time, but we have a completed Tardis, and at the moment we are just basking in the glory of the shining gold time vortex housed inside. Or maybe that's just a bunch of coats. We're not too certain.

One final picture: Megan loves her Tardis; now she's just hoping it comes with Jack or the Doctor inside.

Credit goes to Ayn, David, Jonathan, Megan, Pat, and myself, in alphabetical order.

FILES!

I started - or rather, continued - rewriting it tonight. And I have some passages that don't give much of anything away, because I had to tell people and Mango and Kate had already gone to sleep.

This was the most humiliating situation he had ever found himself in. Except perhaps that time he had gotten caught in the dolphin tank without his trousers, and everyone insisted they hadn’t seen a foxy red-headed dolphin training seductress anywhere near the aquarium.

This was almost as embarrassing as that. And it was made worse by the fact that the person pointing and laughing at Roger's predicament wasn’t some pimply janitor who probably couldn’t get a sexy red-head in (well, half-in) a wetsuit to lure him to almost-certain death in the dolphin tank if he asked nicely, but rather Roger's own coworkers. And as much as Roger would like to deny it, while Michael would be too much of a prude to be caught without his trousers, well, he had after all inherited his father's looks as well as his employment, and so it would probably not have been for lack of trying on the part of the woman in the tightly fitting neoprene.

That's probably my favorite quote from the new stuff.

Roger is such a melodramatic character though, so over the top. It's such fun to write, even if he's rather despicable.

Is this Biochemistry?

I have reached the unfortunate conclusion that I am a molecular biologist pretending to be a biochemist. Most of the time I do not even pretend. After all, I chose to be a molecular biologist and not a biochemist for a reason: Namely that I am more interested in genetics than in protein science, and not particularly interesting in reaction kinetics (whether that be for a folding reaction, a binding reaction, or an enzymatic reaction). Also I, in general, appreciate working with more natural systems rather than more artificial ones (namely, if studying biological systems, we should perhaps use biological systems, like cells and animals, rather than non-biological systems, like test-tubes and monolayers). (I also note that there is a time and a place where the non-biological systems are incredibly useful and that my own systems are, in many ways, very artificial themselves). In any case, none of this would be an issue if I didn't want to write an honors thesis. Which I do, and since I am majoring in biochemistry (primarily), I feel like that should be in biochemistry. So my question: does this sound like biochemistry?

Gene regulation in eukaryotes is an incredibly complex process which is not completely understood. Until recently, the model for transcriptional control has been based on a view of DNA as linear, neutral, and controlled by the function of transcriptional activators and repressors – proteins designed to interact both with DNA and with the transcription complex. However, DNA is, in reality, in a dynamic nuclear environment not solely determined by the various transcription factors present. Long-distance DNA-DNA interactions such as chromosomal kissing disprove the linearity of DNA, and the effect of nuclear localization on gene expression disproves the transcription-neutrality of its position in the nucleus. My project attempts to determine the significance of this localization effect in gene expression. To do this, I have created a system called TCIS (Tagged Chromosomal Insertion Site) with which I can repeatedly insert pieces of DNA into the same, easily visible, genomic location. This site is usually found in the center of the nucleus but can be tethered to the edge of the nucleus as well. I will insert various promoter regions into this TCIS, tether them to the edge of the nucleus, and measure the difference in expression levels between tethered and untethered samples.

I know it's rough, I'll work on that once I get something that actually might convince someone I'm almost a biochemist (if they're being really generous).

Well, this is not that celebratory, but I NEED to post it

Or rather, it's absolutely awesome.

First, www.freerice.com is awesome in that it makes you less guilty for procrastinating with online video games; you're helping the UN to end world hunger with each correct answer. (I've "bought" 13690 grains of rice. Woot.)

Second, it shows you awesome (and counterintutive?) words like the following:

Pulchritude == physical beauty
Fuliginous == sooty
Panjandrum == self-important dignitary
Gallimaufry == hodge-podge
and many others.

Also, quote of the day: "For real, though. Who threw that wedding at me?" - Ayn.

99th post

My next post is my 100th post. So it should be significant.

But since this is just the 99th post, well, it can be about something silly; like a teenager beating up a bear.

http://news.bbc.co.uk/2/hi/americas/3667399.stm

My favorite is the caption:
"Unarmed humans rarely come off best against bears."

In defense of biology in the classroom

Emblies posted about education in general, and Duff (in his comment) suggested that Biology should be taught in lab and not in class, since largely it does not use a mathematical framework. You should read their posts if you haven't already because they have many interesting things to say. But Duff's comment about biology not being appropriate for class learning piqued my thought and so as not to totally clog Emblies' response page, I'm responding at length here.

Duff says: "In biology, I've long wondered if things would be better served if they did away mostly with lectures, perhaps limited it to once a week for an hour and a half, and the rest of the time was spent working in the lab."

First (and foremost) is that "Biology" is an incredibly broad term. There are some areas of Biology (phylogeny, for instance, or most forms of ecology) which I know less about than I know about physics. Even in a specialty or sub-discipline such as Genetics, there are a huge range of things that people study. The principles may be the same, but the procedures and the questions asked in Harinder's lab (where I work now) are very very different from the procedures and questions asked in Bill's lab (where I worked in high school). I absolutely could not (cannot?) choose a field of genetics, much less a field of biology itself, without classes to introduce me to topics before setting foot in a lab. I know that ecology and phylogeny bore me because I've had to study them for classes at some point and they bored me. I know that molecular biology is interesting because when I read even text book sections for them, I find things that are amusing, interesting, and intriguing. I know that DNA studies interest me more than protein studies because I have taken classes focused on proteins, and I find them less interesting than the classes I have taken focused on DNA. I think that I want to be a molecular geneticist because of experiences that I have had in classes as well as lab. There would have been no feasible way for me to be introduced to as many fields and disciplines as I have been introduced to if I only had class 1.5 hours a week: a year of rotation for a graduate student typically has them visit and do small projects in 3 or 4 labs (as far as I am aware). And one hopes to actually do a substantive project at some of these places, which means that 2 years of rotation needs to be enough to find a lab. But only having interacted with 6 to 8 possible specialties (and that's maximum, with specialty very specifically defined) is certainly not enough to give people an idea of the variety that is biology. So I think that biology classes are a necessary part of training a biologist.

Secondly is the fact that walking into a lab without an understanding of lab principles or procedures is a very very foolish thing to do. My first year, I was in a biology lab class (an advanced introduction, so these were presumably more biologically-inclined people than most classes at the U of C, even for biology majors) in which people did not know (or could not figure out immediately) how to use micropipetters (or, as I like calling them because it's more awesome, pipettemen). They didn't understand sterile technique in the slightest, they got Bacteria everywhere and freaked out instead of swabbing with ethanol and trying again with more finesse, they couldn't load a gel, etcetera. Even in my biochemistry class in my Junior year, there were people who were graduating with a BA in biochemistry and could not load a gel without a guide. My TAs have been consistently impressed with my ability to do things that I consider very simple, such as load and run gels, set up PCR reactions and so forth. All of which tells me that most people are, at base, completely and totally incompetent in lab, and that that incompetence needs must be trained out of them before they set foot near any valuable experiments. I have trouble in lab about keeping everything sterile, pipetting accurately, and getting reactions to work without hitch - so if someone was worse than me at those standard procedures, well, I wouldn't know what to do with them. They would be a waste of time and money. It is ridiculous to expect post-docs and graduate students, who have their own work to do, to also take on training every single biology student who comes through a program. If they were expected to do so, they would never get any of their own work done. So putting people into laboratory situations right away is silly.

Duff goes on to say: "I've always been curious as to what it means to think about biology outside a lab context. That is to say, not that abstract thought about biology cannot be had, but that it must be tied to the laboratory, as biology often does not have a mathematical framework that one can think within."

Admittedly, I laugh about the idea of "theoretical biology" as well, but it does exist. (Harinder is especially good at it, actually.) And there are some principles of biology that can be learned in a classroom very well (and that are actually suited particularly for classroom instruction). Yes, biology is based in observation and experiment rather than theoretical mathematical systems, but that does not mean that it cannot be taught in a classroom. Because there are theoretical underpinnings to much of biology that can be taught, and a worldview that can be exposed, in much the same way that mathematical acumen is necessary to understand and practice physics. I'm trying to think of a really good example and I'm going to go with Dobzhansky's Dictum. Dobzhansky's Dictum is the following: Nothing in Biology makes sense except in light of Evolution. When I first heard it I was dubious. But that's just the point -- it's a theoretical underpinning and a way of looking at the world specific to biology. It forces you to see the connections and relationships between our environment and ourselves, between different parts of our environment, etcetera. It also forces you to see the relationship and interdependence between molecular biology, genetics, and macroscopic biology. Evolution works on all levels, and you can talk about it at the genomic level, at the gene level, at the organismal level, at the systems level, and it's always the same principle. But you have to learn how to look at the world before you start seeing the interconnectedness. You have to hear Dobzhansky's Dictum and think about it for a while, apply it to specific situations, before it makes any sense to you whatsoever.

So the point is that while all kinds of biology don't necessarily have a mathematical framework that one can be taught and can "work within" -- although many kinds of biology do, in fact, have mathematical frameworks that you work within; protein folding problems come to mind -- all kinds of biology do have theoretical frameworks and postulates that you can think about and use to hypothesize. After all, theory != math.

Speaking of which, then, what makes physics so much different than biology in its capacity to be theoretical, then? Because Mango, earlier, had the following gem: He had always thought of physics as science and biology as engineering. For Mango that came down to purpose: the purpose of physics was to understand the world, the purpose of biology was to make people's lives better by finding cures and treatments for diseases. Again, physics as a discipline is theoretical and abstract and attempts to understand existence while biology is tied to the day-to-day realities of life and disease.

But it doesn't have to be this way. At least, not in my estimation.

I've sort of lost my train of thought here, so I might come back and clarify/add later. But I think that's enough for now anyway.

COAT!

I just finished sewing the pockets + collar for my new coat!

It is bright red, double breasted, knee-length, and super awesome!

I will have it done by thanksgiving at the latest!

This is very exciting to me!

Pictures will be forthcoming if I can get a camera.

Genetics, Epigenetics, and Life

As promised, the overuse of gene post.

I read, on one of my molecular biology binges, that the notion of a gene was becoming increasingly hard to identify. I don't know if I agree with the argument, but here's the general idea. A massive oversimplification of molecular biology says that each DNA sequence is transcribed and translated into a protein, and that each protein has one function. Given that assumption, then there is a one-to-one correlation between DNA sequences and proteins, DNA sequences and functions, and proteins and functions. Hence, a gene is a single DNA sequence, which corresponds to a single protein and a single function (or trait). We can, therefore, isolate the gene for blue eyes, the gene for tall pea plants, and the gene for purple flowers.

However, if we define a gene (as we have done above) as the DNA sequence which is transcribed and codes for the blue-eye protein and causes the phenotype of blue eyes, well, we have a problem. First off, not all of the DNA sequence that causes the phenotype of blue eyes is transcribed. Second, not all of the DNA that is transcribed codes for the protein. Third, not every protein that effects the decision between blue and brown eyes is coded by a single piece of DNA or even effects only that decision. Should things like transcription factor DNA sequences, which are necessary for "turning on" specific sequences and thus for the observed phenotype, be counted as part of the gene? Probably not. But should introns, which are transcribed regions of the DNA that have little effect on activity be counted as the gene? How about promoter regions immediately upstream? Enhancers that can be located long distances removed? The intervening sequences?

No matter how you look at it, it's a mess. Of course, there are rigorous definitions of gene (i.e. coding sequences) but if you use them you leave out the vast majority of the information in the genome (i.e. promoters, enhancers, insulators, microRNAs, other nontranslated RNAs, ...) . The authors of the book I was reading went on to say that, perhaps, the notion of the gene is obsolete.

Of course, I don't follow their final leap of faith that removing the word "gene" from the picture and using only the longer descriptive terms -- enhancer, promoter, coding sequence, exon, intron, etcetera -- would simplify matters. I think it would, if anything, make it harder for any non-biologist to understand what on earth geneticists were talking about. And I am decidedly against making myself harder to understand. But the central point of the argument; that the very idea of a single, isolated gene is an oversimplification and perhaps a fallacy, remains. Genes do not exist on their own. They exist in context and that context is incredibly important to determining what they will do.

In my last post I talked about birds who learn the calls of the birds in the nest where they were raised. That's a typical example of something called epigenetics. That call helps the bird find a mate and eventually find a nest to insert its eggs into, and is therefore heritable, but it is in no way "genetically coded". It can even be the basis of evolution by natural selection: birds who put their eggs into the nests of species who take care of their young well, who find food everywhere and are safe from predators will be more likely to have more of their young survive and therefore will be selected for. But it is not, at base, encoded in DNA and therefore is not genetic.

Epigenetics works at all levels; from the organismal level I've just discussed to levels of gene control and regulation, such as what I'm working on right now. Where a gene is in the nucleus has huge ramifications on transcription and regulation. The state of histones (the proteins that DNA is always wrapped around in the nucleus) creates a "histone code" that is independent of genetic code and controls much of gene activity. These things aren't coded for in the genome, but they are heritable and they do yield phenotypes.

Epigenetics (on both microscopic and macroscopic levels) is a growing field. Scientists are increasingly coming to the conclusion that, well, it doesn't just come down to your genes, even on a molecular level! Yes, I do believe that the entirety of my organism can be described with sufficiently sophisticated chemistry, but also that as a being I am constantly learning and adapting to my situation. I am always making connections between neurons, and those connections make it easier for me to make more connections and so on and so forth. My genes provided a scaffold upon which I could build, but it was only that.

And so whenever someone says that they want to isolate "the gene for intelligence", I cringe a little. Because everything I've just said holds true. The chance that there is a single DNA sequence mediating the immensely complex trait we call "intelligence" is tiny. The chance that there is a single protein mediating that trait is similarly tiny. The chance that we could select for a single gene and therefore raise our intelligence without other, unfavorable side effects is almost infinitesimal. The fact of the matter is that this subtle and complex trait is mediated by an enormous number of variables, from genetic elements to epigenetic ones to cultural ones. And saying anything else is a pathetic oversimplification.

Genetics and Racism

I think that this is a pretty nice summary of Watson's latest blunder. If you haven't already heard of it, well, you must have been under a rock.

James Watson made a few racist remarks, for whatever reason, and the backlash has been remarkable, swift, and decisive. Which is nice in some ways and not in others. The point, for me, is that Watson started from a scientifically relevant position - "there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically" - and applied it to a situation where it doesn't necessarily belong - basically, black people are stupid.

Personally, I think that it's entirely possible Dr. Watson made an honest blunder, or just got carried away or wanted to piss people off to sell more copies of his new book or something. As the article says, he has marketed himself as a trouble-child, so it's a lot to expect for him to toe the party line, no matter what party line that happens to be. (There's no such thing as bad publicity). And besides, in most circles it is well known that Dr. Watson is off his rocker (although not as much as some others, like Craig Vetner) and while brilliant scientifically, not someone to go to for advice that doesn't relate to molecular biology. (That puzzled me; many of the questions at his book signing at the U of C were not related to molecular biology. Part of me asks, what do I care what Watson's views are on religion or politics or... although his comments on religion were certainly hilarious. He's a good scientist, and I care about his views on scientific issues.) In any case, what bothers me more, to a certain extent, is the reaction that those comments have received.

First off is the feigning shock, the outrage and the revulsion, to the point that he's been suspended from his job and had interviews canceled. As I said, Watson has been marketing himself as someone who makes politically incorrect remarks since his first book, and the fact that anyone is particularly surprised that James Watson said something that was outrageous, politically incorrect, and just downright ridiculous is somewhat troubling. In the scheme of things, this ranks right up there with making all girls pretty, aborting homosexual babies, and saying that black people have bigger sex drives. It's stupid, it's prejudicial, and it's pure James Watson. That anyone should be surprised by it shows something about us that isn't necessarily a good thing; our ability to turn a blind eye and actually forget about the idiocies and unpleasant elements of our public figures. James Watson has always made this sort of absurd, bigoted remark. He has also always been a good scientist. Why should we think that anything has changed?

That was, again, my first reaction, and it has remained pretty much unchanged since I heard about his comments a week ago. What is new, however, is something that was only brought to light by the comments at the bottom of the blog post I linked to. I understand the impulse to defend what could be potentially valid remarks from a perceived over-political-correctness that makes much political discourse in this country utterly meaningless. However, some people go too far. Ignoring the one comment that seemed to tie Watson's lack of tact or forethought to the moral bankruptcy of the scientific establishment, slavery to abortion, and the second coming of Christ (more on that later, or rather, not), many of the comments seemed to be taking "Watson's side" on the issue - advocating to a larger or smaller degree the genetic basis for an IQ difference between blacks & whites, Americans & Africans. There are several problems with this, large and small. First, that I do not believe there is a significant genetic difference between blacks and whites, Americans and Africans and especially not one that would lead to a consistent and statistically significant difference in intelligence between those groups. Second, I think that people overuse genetics at the expense of environment and epigenetics. Third, people downplay the extent to which de juro or overt racism in our country and in the world has been replaced by a subtle, pervasive, and condescending sort of racism and sexism. Fourth, measures like IQ tests are inherently inaccurate. Finally, how can we say that Africans are genetically bad at governing themselves peacefully when there are obvious examples to the contrary?

If I talked about all of that, I would be here all night. I'm just going to cover the first part for now: my strong belief that there is no reason to assume that a genetic difference between populations causes the perceived intelligence gap.

I'm going to start from a few assumptions, which I'll probably dismantle in later posts (or not if I get distracted). Basically, what is the most valid I can make this argument that there is a genetic basis? I'll assume, to start with, that IQ tests give an accurate picture of intelligence. I'll also assume that there is a proven, significant correlation between how well your parents and relatives do on an IQ test and how well you do on an IQ test. That still doesn't prove to me that ability on an IQ test is necessarily genetic.

I'll give a few counter-examples. I doubt that anyone would argue (except perhaps Dr. Watson?) that religious belief is genetic. (Not even just belief in God, here, although that works too, but specific denomination and religion). However, the single greatest determining factor in someone's religion is the religion of their parents. Here it seems obvious that children who are raised in the faith, taught the faith from a young age, and (to an atheist's eyes) indoctrinated are more likely to profess that faith when they grow up. It has nothing to do with genetics and everything to do with environment; parents raise their children in the church and that experience of growing up in the church makes devout people out of their children.

You can even consider a species of nesting parasites (birds who insert their eggs into the nests of other birds). These birds develop the call of the birds whose nest they were hatched in. In fact, I believe that if you move the egg, the bird develops a different call. And the call determines mating patterns later in life - so it is not purely incidental. Here, where the bird grows up is a bigger deal for who its mate will be and what it will be like as an adult than its necessary genetic makeup.

Finally, it is (perhaps) a little known fact that the smartest children are not born to the smartest parents. Even given a correlation between IQ of parents and IQ of children, if Einstein and Marie Curie had children it is by no means necessarily true or even likely that their child would be particularly good at physics. In fact, the best determinant of childhood success in school appears to be the number of books in a house, which, like religion, is not genetic.

Given all of that, the question that I pose myself is: is it likely that environmental factors in a child's life could lead to the phenotype that we see, namely, a significant difference in IQ test-taking ability between Africans and Americans? And I am forced to answer that yes, it is very likely that environmental factors in a child's life could lead to that phenotype. Compared to the availability of books in middle class white neighborhoods, the number of books in most places in Africa is pitifully small. That alone would explain a significant difference between the populations.

So it seems obvious to me that even given a significant, apparently heritable difference in IQ between populations, there is no reason to believe that this difference is genetic and no reason to believe that any baby born in a remote village in Africa might not do very well on an IQ test were he or she raised from birth in a house with a lot of books and parents who read regularly.

Next up: Overuse of Genetics and the expense of more interesting subfields.

Andrew Bird

Makes preparing graduate school applications and studying for midterms so very much better.

My favorite so far: Imitosis --

He's keeping busy, yeah he's bleeding stones,
With his machinations and his palindromes
It was anything but hear the voice
Anything but hear the voice
It was anything but hear the voice
That says that we're all basically alone

Poor Professor Pynchon had only good intentions
When he put his Bunsen burners all away
And turned into a playground a petri dish of single cells
That would swing their fists at anything that looks like easy prey
On this nature show that rages every day it was bound,
a part his intuition
To say we were all basically alone

And despite what all his studies had shown
What was mistaken for closeness was just a case for mitosis
Why do some show mercy
When others train for the show
and tell me doctor can you pull my file
'Cause he just wants to know the reason why

Why do they congregate in groups of four
Scatter like a billion spores
And let the wind just carry them away?
How can kids be so mean
Our famous doctor tried to glean
As he went home at the end of the day
In this Nature show that rages every day
It was bound a part his intuition, Say

We were all basically all alone
Despite what all his studies had shown
What was mistaken for closeness was just a case for mitosis
So fatal doses, malcontent to osmosis
Why do some show mercy
When others are paying for the shot
Well tell me doctor can you pull my file
reason why

OOTSSOERAAAP

This is amazing. I want to be a member!

Passion and Power

I was told today that when I present about my research, I have "Power" and that that "Protects me from people like Steve Kron." I find this greatly amusing, especially since I am reading the second book of the Night Watch series, Day Watch, in which that would take on a very specific meaning. I imagined myself casting some sort of shield spell to protect me from Steve's criticism.

What Elisabet meant was that when I present for PCBio I am obviously enthusiastic and excited about my research, and Steve sees that and appreciates that and so he won't find fault with what I do because the important things - learning about how to do research and how to discuss research - are two things that I am obviously enthusiastic about. Also that when Steve does make sarcastic comments or nitpick, I can rebuff or answer him succinctly and confidently, possibly because I am in presenter mode. (I go into presenter mode a lot. It is the mode I go into when I explain science to people. I enjoy explaining science to people.)

All the same, it would be much more awesome if I was really an Other going into the Twilight and casting awesome shielding spells or something.

Speaking of which, if you have not read Night Watch or its sequels by Sergei Lukyanenko, you should. Now. Or possibly yesterday. They are awesome. And I had a thought about them today that will not ruin them for anyone, so I will expound upon it here!

The premise of the books is that there are magically adept people among us, called Others. They are human in the biological sense that they are the children of humans and give birth to humans, but they are not human in the sense that they can do magic, live for much longer, and can access an alternate reality world called "the twilight". (of course it's more complicated than that, but I'm explaining very broadly here). They're witches and wizards and enchantresses and warlocks and magicians and werewolves and vampires and shapeshifters and so on and so forth, and there are Light Others and Dark Others.

Every Other gets his or her power from the emotions of the humans he or she comes into contact with. However, one principle difference is that Light Others feed on happiness while Dark Others feed on unhappiness. Which brings up an interesting point: when a Dark Other takes Power from a human's unhappiness, he or she takes away that human's unhappiness as well, leaving the person happier than previously. And vice versa for a Light Other: taking Power from people's happiness leaves them unhappy. Which brings up an interesting point, in my opinion, because if Light Others (who are, of course, supposed to be "good"), get power by making people less happy, and Dark Others (who are, of course, supposed to be "bad"), get power by making people more happy, then why are our classifications of "good" and "bad" set up the way they are? Possibly because if there were no misery in the world, Dark Others could not get any power, and hence they could not exist, and therefore Dark Others want there to be misery, while Light Others by the same logic want people to be happy.

But it's an interesting point, and merges nicely into another key difference between Light and Dark Others; that Light Others need to validate what they do constantly as "for the greater good" and so forth, while Dark Others just do whatever they please and don't care. Which makes sense if Light Others are basically making people less happy - people would get upset about that! - and Dark Others are basically making people more happy - people would not get upset about that.

In any case, some of the things that Lukyanenko does are obvious from the beginning; Light Others are obviously not all good and Dark Others obviously not all bad. Some of them are moralistic and preachy, but in general he does a good job of keeping you on your toes and the plots are amazingly intricate and well-woven. I can't talk about that without giving anything away, obviously, so you'll have to take my word on it.

Finally, and perhaps most awesomely, is this. Because you really wanted to know how to knit a Dalek.

Chocolate Ice Cream

Is better than God. At least, according to Jim Watson. I quote: "I like chocolate ice cream so much I don't need an afterlife. I can fulfill myself every day."

The talk was awesome. That was my favorite quote, followed shortly for wackyness by "I think Erectile Dysfunctional Disorder, which we can now treat with Cialis, has been evolutionarily selected for."

In terms of substantive stuff, he talked about how we can't get young people to want to be scientists unless we make it a fun place to be; interminable and badly paid graduate school, long postdoctoral careers with no way out, and the end-goal being paid less than a major league baseball Umpire. He also said it was silly for the P.I. to get his name on every paper leaving a lab, unless the P.I. really did contribute significantly to every paper in the lab. And that he thought going into science now was grimmer than when he was going into science.

He had his standard crazy things, talking about "new ways of thinking" that amount to pseudo-Darwinian semi-nonsense, for example the idea that Jews are smart because they were polygamous the longest; so extraordinary men had more wives and more children. His comment that "it might be wrong, but it's a new way of thinking" pretty much sums that one up in my opinion.

My favorite substantive comment that he made was on congeniality and science. What he said was, basically, that you absolutely have to talk to everyone you can in science. It doesn't matter if that person is mean, nasty, if you're afraid of them, if you're competing with them, whatever. You need to be able to walk into their office unannounced and talk about your project. Especially, he said, with competitors. Reason being that your competitors are the other people interested in your subject. One of the most interesting things he said was actually about Rosalind Franklin. He said that had she been able to sit down and talk to Crick, shown him her data and her stumbling block, Crick would have given her the missing piece to her logic and we would all be talking about Franklin's structure of DNA instead of Watson and Crick's structure of DNA. But she couldn't, and so she didn't, and so Watson and Crick are famous and have movies made about them and she died alone, bitter, and four years before she could have won the Nobel prize. Which is an interesting way of looking at it.

In any case, the talk was great, I have his new book, and man does James Watson have an annoying laugh.

A couple things

Craig Venter is an evil supergenius. See here. His comments on "A new philosophical age" and "Not everybody is going to be happy" are particularly creepy. Also the fact that he is knowingly and gleefully playing God, and seems to think this is purely a good thing. I particularly like his comments on our potential to make bacteria which pull carbon dioxide out of the air, since I have never, ever, ever heard of or seen an organism that could do that, and I'm sure that you haven't either. Also because there wouldn't be any problem with, for instance, pulling too much carbon dioxide out of the air, or deciding which byproducts these hypothetical organisms would turn the carbon dioxide into. I mean, honestly.

It has been said that I do not think like an evil supergenius. I am not sure I am ashamed of this. But I am sure I am going to be a mad scientist for Halloween. Possibly with a glowing rat. I think that would be fun. I would have something more traditional, like a ray gun or whatever, but I am after all a geneticist. A geneticist who has finished her GREs, though, which is exciting. Just in time to stress about my presentation to PCBio, where I will probably get yelled at by Steve for not making enough progress *wince*. But I can blame the fact that in the 100 clones I have screened, only 1 was good and only 1 other looks promising. AND I can say I'm trying new techniques to get clones, which will hopefully have better results. (I have 25 more clones ready to look at whenever Karen has time, and more on the way, but Karen is busy with paperness so I am on hold, working on getting bacterial constructs made for the next couple weeks.) That's not a lack of effort. That's a lack of luck?

Speaking of, I (hopefully!) get to hear James Watson speak tonight! I hope I have questions to ask him. I have also decided that Watson > Yoga and Heroes. Which I feel is the proper choice.
I should get his new book from the seminary coop. I liked Double Helix, it was really funny. (If you are a scientist, you should READ IT NOW. If you know many scientists, you should also READ IT NOW. It's wonderfully tongue-in-cheek making fun of paradigmatic scientists, and if you are one or know many, well, you'll see yourself and/or a lot of people you know reflected in the characters.)

In any case, maybe I'll post later tonight about the speech. And maybe I'll work on my problem set instead. We'll see, won't we?

While working on a problem set...

I happened upon this monthly blog: http://ca.expasy.org/spotlight/snapshot. They talk about one protein each month. Some of them are obtuse, like the cupidin article (their article is a poem; the protein is also called Homer2 -- it is involved in neuronal signalling and cocaine sensitivity and apparently its deletion in mice makes them act like cocaine addicted rats. I think that the researchers would have compared to cocaine addicted mice except maybe we don't have those to study. Go figure). I still don't know why they called it cupidin. Some of their articles are also fictional -- such as the lamborghinin one; I really wanted there to actually be a protein named lamborghinin -- which is also unfortunate. But mostly the articles are pretty good. And now I am full of useless information about several random proteins!

Hooray!

Public service announcement

Aristocratic Octopus is no more.

GRE

I have vanquished the GRE! Go me! Now I just need to similarly vanquish my subject test and the math methods test and I can maybe get into graduate school!

Yay?

Also

Is it just me, or is the Eckhart library set up particularly well for a rousing performance of "Marian the Librarian?" I mean, the partial second floors are just too perfect. As is the large central area full of desks for dancing on. Unfortunately, there aren't any of those rolling/sliding ladders that are so awesome. At least, I couldn't find any.

But it still bears thought. Seriously, guys. Take a look if you haven't.

I am no longer dead to the world!

In fact, I am out and about today! Hooray! If by 'out and about' I mean 'at work and studying' then... yes.

I recently got an e-mail about the test that I have to take to prove that I can do some math, so the Chemistry department won't disown me and ostracize me from the elite group of Biochemistry majors into to the masses of Biology majors. That would be scary. There are so many pre-meds there.

I laughed at first, because the concepts on it (n-space, linear dependence, eigenvalues) were all things I remembered learning in high school but have long since vaguely forgotten about. I don't mean to sound snide -- I'm sure the college course here on basic linear algebra is much more demanding than my high school course on basic linear algebra, even if it isn't the course here on abstract algebra which sounds like so much more fun and I'm somewhat disappointed I never really got a chance to take.

However, I understand now why the Chemistry department won't simply take my year of Analysis as proof that I can do this math - because while some of the concepts in Analysis are based on the concepts of linear algebra, and while Analysis is really much much easier if you know a little bit of linear algebra, the topics above, especially eigenvalues, are not covered in Analysis. So it would be entirely possible to pass through Analysis and not know what an eigenvalue is. (Which would be a shame because then you couldn't throw things at Peter Parker when he mistakenly gives one a unit.) Of course, I've almost forgotten what an eigenvalue is, so it's time for me to break out the book and get studying.

I can't believe that it's the weekend before first week and I have 1 test to take and 2 to study for. This year is going to be awesome. If I survive it.

What is so hard about getting my name right on an ID?

I am 1 for 4, on people getting my name right on IDs at their first try. But at least DMVs are full of hijinks for me. I guess that's a good thing. Certainly makes something very boring somewhat exciting.

Today there were two adventures: First, I presented my 19-year-old social security card (with stub containing an address in Roger's park) and my much more recent Maryland Driver's License. They accepted the Social Security card as proof of my residency in Illinois. I am now registered to vote here. At no point did they ask for any sort of more recent mail. I know that they do for some people, because I heard them asking people in line in front of me. They also tried to put the roger's park address as my current address. But I caught them there. When she asked "Is this your current address?" I was shocked enough to sort of double take. I was not aware that the stub to the social security card contained an address. But it does. What's more, I think that wherever I go in life and whatever I do, I will be able to get an Illinois Driver's License. Which is more than a little bit absurd.

The name mistake is much less funny, because it wasn't really their mistake. My (and my brother's) social security cards say "Hauener" instead of "Havener" for the middle name. The woman, therefore, typed my middle name with the U instead of the V. This was, fortunately, easily corrected with my passport which clearly says "Havener". I didn't show her the erroneous social security card again, and I am perhaps lucky she did not ask. But she was fairly apologetic, which was nice. Or something.

Also, the inside of the DMV in Chicago (on a weekday at about 2 pm in the middle of the month) is actually not much of an ordeal. The people are polite, friendly, and intelligent, and they move you through remarkably quickly. (for a DMV).

That is all.

Wacky?

In this week's Science table of contents, this caught my eye:

Production of Trout Offspring from Triploid Salmon Parents

Now, at first I stared at it and said, well, how can a Salmon give birth to a Trout? The answer, it turns out, is if the Salmon is only externally a Salmon, and has Trout-derived reproductive cells. The researchers took sterile Salmon and transplanted by microinjection (so basically injected into the fish eggs) Trout progenitor cells for reproductive cells. Surprisingly enough, the fish grew normally and were, for all intents and purposes, Salmon with Trout eggs/sperm cells.

Which raises the question, biologically, are they closer to Salmon or closer to Trout?

Also, how wacky and awesome is it that Salmon can give birth to Trout?

Those terrorists...

So, I need to renew my driver's license. I went to the Illinois DMV armed with my old driver's license, my passport, a canceled check, and a piece of mail, thinking that with all of these things I would be set. However, they turned me away immediately for not having my social security card with me. I told them I knew my number, they were not impressed (this is understandable), I told them I could get it faxed to them in a matter of minutes, they were not impressed. Finally, in a bit of a tiff, I asked them why they needed my social security card when I had two forms of U.S. photo I.D. with me, as well as proof of my residency in Illinois. Their response, and I quote, was "To prevent fraud after 9/11."

Now, excuse me for a second while I ponder this statement. First off, I was unaware that there was a particular increase in identity theft concurrent with the attacks of September eleventh. Second, I am confused as to how preventing people from getting an Illinois driver's license will a) prevent them from getting on an airplane and crashing it into a building or b) prevent them from committing any other form of atrocity except, perhaps, living in Illinois and owning and driving a car. Third, I am very baffled, since social security cards are perhaps the easiest piece of identification to fake, as they have only a number, name, and signature, and they are printed on plain blue paper. In fact, had I actually lost my social security card, I imagine that it would be easier and less time-intensive for me to forge a new one using photoshop and online images than it would be to go to the social security office and get a new one sent to me.

Fourth, I am unaware as to how giving my social security number to the idiots at the DMV will prevent fraud. Excuse me if I am wrong, but it really does seem to me that the reason we have a problem with identity theft and social security fraud is, quite simply, that there are quite a few transactions where the only identifying information on them is a social security number and name. Every time that I give my social security number to someone else, it goes into another database to be stored with a bunch of other people's social security numbers. The more times I give out my social security number, the more possible times there are for someone to steal it. Making an easily forged social security card necessary for a driver's license in fact does nothing to ensure the safety of my social security number; if anything, it makes it more dangerous for me.


Finally, since this doesn't prevent terrorists from flying in our planes, trains, buses, and taxi-cabs, perhaps with dirty bombs tucked away in briefcases or boxcutters with which to hijack whatever, well, the question is what does this rather useless rule do? It seems like a simple rule to, generally, make life harder for immigrants and keep those gosh-darned illegal immigrants off of American soil. One more hoop for them to jump through before they can be treated as human beings. Of course, it's easy to hijack the public's fear of anti-American terrorists coming over and doing evil things to keep everyone else out as well, which in some ways we've already done (one look at the signs on American customs outposts convinces you of this - the 'welcome measures' include fingerprinting for all non-U.S. Citizens who enter the country, I believe). This is just one more example.

Of course, it could also be to prevent terrorists from stealing my social security number and crashing it into a building. You know, like they do.

Evolution!

People from societies with diets that have historically been rich in starch are twice as likely to have at least six copies of the Amylase gene.

Amylase is one of very few genes that exhibits significant differences in copy number between individual humans. It encodes for the protein in saliva that begins the digestion of starches, and is necessary to get nutrition out of grain. What's more, contrary to what happens in some other places, the "extra" copies of the amylase gene are fully functional and do lead to more amylase protein being produced, which in turn leads to faster and more effective digestion of starches. Also, since the differences in sequence between the three copies of the amylase gene in the reference human genome sequence are so small, it seems that this duplication might have happened quite recently; even perhaps since the birth of modern humans. Which means things like the development of agriculture and therefore the increased levels of starch in some societies' diets might very well have effected the evolutionary path of those societies. Which is cool -- we are effecting our own evolution. And not just by killing genetically diseased babies, like certain geneticists would want us to.

Nature, Futures, and the coming dystopia

The past two stories in Nature's "Futures" column have both been in reference to a futuristic society in which certain aspects of life (photography and weapons manufacture, respectively) are monitored automatically via computer, ala failsafe. In the first, guns turn against their owners and start deciding who gets shot based on entries in a police database-in-the-sky. In the second, all photographs are stored online (by requirement) for some reason - and darkroom procedures hence outlawed, a compromising picture of a government official appears in a chemistry lab.

It vaguely reminds me of the Cybermen; the little ear-bud phone service that turns against you, hijacks your brain, and turns you into an automaton. And I wonder what the fascination with such dystopic futures is. At one point, progress was considered universally good, we were on the path to utopia, and so forth. Now it seems more imprinted on the common imagination that we are descending into a police state, that our parents were freer than we are and we are freer than our children will be, and that there is no turning back on this irrevocable path. When did we go from Marx, with the revolution being imminent, to Mill, with no more revolutions and the gradual death of our species from lack of freedom, argument, and passion?

EDIT: I know the answer to that question is, potentially, when Marx's communism turned into just such a controlling police state.

Fall

There is a certain joy that can only be achieved by nestling into freshly washed, still-warm-from-the-dryer, sheets with the window open and letting in air that is just a tad colder than comfortable. And it is a joy that cannot be had in summer in Chicago. (There are plenty of awesome things about summer in Chicago, such as swimming in the lake and sudden thunderstorms, but that is not one of them). But last night was just such a night, and that is a sign, perhaps, that fall is on the way (or already here).

Joy!

My experiments worked! Joy!

Also, I have a new project: Bright red wool coat with polka dotted lining; double-breasted and really full bottom; approximately knee length; big white buttons. Wish me luck! I will post pictures if I ever get a camera that works.

November is closer than you think

I just realized, recently, that November is really quite close. Which means that the insanity of writing a novel is closer than I think. Which also means that the insanity of applying to NSF grants and graduate school while writing a novel is closer than I think. I tried the writing-a-novel-in-December last year, and while I succeeded it wasn't nearly as much fun without the online community (or any community to speak of, really). It was my second year doing it, and I think that the product I ended up with was better than the first year. But I can do better. I have a few ideas for my novel this year. Most of them are stories that I want to write eventually, so I'll have plenty of fodder to keep doing this for years to come no matter which I choose. The three best ones are as follows; first, the story that I originally envisioned as a fanfic, but doesn't have to be, second, the story vaguely based on my experiences with circus people and diving, and third the science-policy dystopic story. I've had ideas for first chapters to all of them in the recent past, but I'm working on the fic-one right now. At the moment I think I'll do that one, but I think the other two are probably better stories. Or I could combine the first two, but that seems a bit much perhaps? It would need outlining to work right. The problem being that the first two are both vaguely retellings of Peter Pan or The Wizard of Oz (or Alice and Wonderland I guess, but I'm less familiar with that). I feel a little bit like that is the only plot I can really write, because it is arguable that the story I wrote last year also follows that paradigm in plot:

Main character runs away from/is spirited away from normal life to adventures, has adventures but in the process realizes that they really want to be home having normal life/normal life is the true adventure/some corny moral and returns home to cheers and fanfare. It's the typical children's story I guess. So maybe I want to write the science one simply because it's different.

In any case, this useless post brought to you by the fact that November is NATIONAL NOVEL WRITING MONTH. You should all write novels in November with me, so that I will have company.

Now this is cool.

It seems like it is a corrollary of the theory of Natural Selection that the most highly conserved regions of the genome will be those which are necessary for existence -- if a region is not necessary then it will slowly mutate away and if it does not do this there must be some reason why mutations in that region are selected against. This is particularly interesting in the context of certain "ultraconserved" regions which do not code for proteins -- long regions that are conserved between fish, frogs, and men and which can be very distant from any coding region. For a while, it was supposed that these regions were necessary regulatory elements. However, conservation does not imply necessity, a recent study points out:

It is widely believed that the most evolutionarily conserved DNA sequences in the human genome have been preserved because of their functional importance and that their removal would thus have a devastating effect on the organism. To ascertain this we removed from the mouse genome four ultraconserved elements—sequences of 200 base pairs or longer that are 100% identical among human, mouse, and rat. To our surprise, we found that the mice lacking these elements are viable, fertile, and show no apparent abnormalities. This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature.

I find this very cool. I have no idea what it means, but it's very very cool.

My new project?

I am probably certifiable, but I am going to try and make a jacket based on this for a part in a halloween costume (I'll make the whole costume as pictured, with a slightly different jacket). My idea being to make it black + off-white, with trim around all the seams and a design on the front bottom openings and around the neckline and on the sleeves, instead of everywhere. Probably a more tailored and fuller cut too, because I like those. Wish me luck; if I succeed it should be totally awesome.