He of the Lion

touleontos @ 2009-03-26T12:48:00

2009-03-26T18:23:44Z

Once upon a time, livejournal used to be really great for keeping in touch with my friends. Most of the people I cared about that I didn't see every day used to be on my friends list, and we would all post interesting things about our lives and then have interesting conversations in the comments. These days, most of the people I'm interested in following never even had livejournals, and those who do only post very rarely. Facebook has some usefulness for certain kinds of communication, but really doesn't form a community the way livejournal used to. Twitter seems to have potential, but a glance at my friends page shows that the way people actually use it is horrible, and four out of five tweets are totally uninteresting to me.

Well, I don't know. Maybe I'll come up with a solution. In the meantime, if you need me, I'll be in my lab doing science.

touleontos @ 2009-02-13T10:30:00

2009-02-13T15:31:09Z

Last year, I lost a girl to med school. This week, I lost a violinist to med school.

Med school and I are not friends.

touleontos @ 2009-02-13T09:00:00

2009-02-13T14:05:21Z

Another song is posted.

I'd like to try to get higher-quality audio recordings of these things, by laying down instrumental and vocal tracks separately, adding vocal harmony, &c ... but I can't decide whether to focus on recording new videos or making audio recordings. Any opinions?

Also, for those of you who know the rest of my songs, any requests for what you want to see next?

touleontos @ 2009-02-05T22:24:00

2009-02-06T03:26:56Z

http://www.youtube.com/lessersounds

Tell your friends.

touleontos @ 2008-12-12T12:00:00

2008-12-12T17:10:49Z

I have just arranged to join Shamil Sunyaev's lab for a rotation in January. In a few weeks I will have more information about what project I will be working on.

Relatedly: some of you may remember that last summer I spent some time trying to calculate my Erdös Number. I have finally come up with a number, which is 8. The path goes:

Erik Zuiderweg
Gerhard Wagner
Eirik Flekkøy
Gianni de Fabritiis
Francesco Mainardi
Hari Srivastava
Joel Brenner
Paul Erdös

Shamil Sunyaev, though, has an Erdös number of only 3, through Eugene Koonin and Lazlo Szekely. So if I publish with him, my Erdös number would be cut in half.

You know, one must be concerned about these things.

touleontos @ 2008-12-08T09:54:00

2008-12-08T14:56:42Z

This is a little (okay, a lot) overdue, but hey, I published a paper last year! As first author! Here's the cite, if anyone's interested:

Jordan, DM, KM Mills, I Andricioaei, A Bhattacharya, K Palmo, ERP Zuiderweg, "Parameterization of peptide ¹³C carbonyl chemical shielding anisotropy in Molecular Dynamics simulations." ChemPhysChem 8 (9) 1375-1385 (2007).

doi:10.1002/cphc.200700003

It currently has 3 citations, giving me an h-index of 1.

touleontos @ 2008-11-16T10:26:00

2008-11-16T15:52:42Z

In actual news: Either I've gotten worse at school since college, or school has gotten harder. Probably a little of each, combined with the fact that I've lost the knack of caring about my classes. Joining a lab might make me feel less like a waste of space and taxpayer money. I've currently got two or three names on my list for my first rotation. These two also do really cool research, but might not be the best places to work. Maybe I'll join a lab when I come back from Thanksgiving.

touleontos @ 2008-11-16T00:23:00

2008-11-16T05:27:36Z

If I could have any woman in the world, my first choice would probably be Vienna Teng. The rest of the list varies from day to day, but numbers two and three are currently the crown princess of Sweden and Freema Agyeman, not necessarily in that order. My plans for meeting these women involve (respectively) becoming a successful singer-songwriter, winning the Nobel Prize, and, I don't know, wishing really hard.

I don't really have anything resembling a point. Wish me luck, I guess?

touleontos @ 2008-11-06T15:11:00

2008-11-06T20:17:53Z

Interesting side note about the election: the statehood party in Puerto Rico (called the Partido Nuevo Progresista or New Progressive Party) appears to have won the governorship, the non-voting seat in the House, and a massive majority in the commonwealth legislature. Could we have a 51st state in a few years?

touleontos @ 2008-10-25T11:47:00

2008-10-25T15:50:25Z

"This is a matter of how we prioritize the money that we spend. We've got a three trillion dollar budget, and Congress spends some 18 billion dollars a year on earmarks for political pet projects. That's more than the shortfall to fully fund the IDEA. And where does a lot of that earmark money end up? It goes to projects having little or nothing to do with the public good -- things like fruit fly research in Paris, France, or a public policy center named for the guy who got the earmark. In our administration, we're going to reform and refocus. We're going to get our federal priorities straight, and fulfill our country's commitment to give every child opportunity and hope in life.

"For many parents of children with disabilities, the most valuable thing of all is information. Early identification of a cognitive or other disorder, especially autism, can make a life-changing difference. That's why we're going to strengthen NIH. We're going to work on long-term cures, and in the short-term, we're going to work on giving these families better information."

- Sarah Palin (emphasis mine). And yes, these two paragraphs were consecutive.

So, Palin wants to cut fundamental research in developmental biology while searching for cures for developmental disorders. Interesting.

touleontos @ 2008-10-07T11:50:00

2008-10-07T15:56:24Z

What do you mean, my grades don't matter? They're grades, that's all they do, is sit there in my transcript mattering all day long. You mean to tell me that nobody will ever look at them again? That all anyone cares about now is how well I learn the material? That it's entirely up to me to decide what I do and don't need to know? And, more to the point, that I don't have to finish this problem set if I don't think I'll get anything out of it?

... weird.

touleontos @ 2008-09-28T09:37:00

2008-09-28T13:49:17Z

I just got an email from Microsoft's Mac Business Unit, saying they got my resume at WWDC and have a job I should apply for. They're about a year late, of course — I now have a much cooler job on the opposite side of the country as a scientist, though I suppose it pays about a third of what these jobs pay. And the other thing, of course, is that I haven't been to WWDC in two years. A little odd, no?

touleontos @ 2008-09-27T21:41:00

2008-09-28T01:54:13Z

The fact that I order lattes at coffee shops has led to a lot of people calling me a "latte-sipping arugula-eating east coast liberal," which is, I suppose, more or less what I am. But lyster and I want to print up t-shirts: one for him that says "black-coffee-sipping Chinese-speaking martial-arts-practicing novel-writing liberal" and one for me that says "latte-sipping viola-playing computer-programming Midwestern liberal."

touleontos @ 2008-09-27T21:26:00

2008-09-28T01:41:18Z

Things I like:

Cambridge.
My house.
My new guitar.
My new iPhone.
My classes, amazingly enough.
Dudley House.
Biophysics students.
Systems Biology students.
Law students.
Boston accents.

Things I do not like:

Harvard.
Harvard undergrads.
The Harvard IT department(s).
The writing ability and style of scientists.
Matlab.
Spending an average of 2 hours going to and from class every day.
Flooding.

touleontos @ 2008-09-03T17:52:00

2008-09-03T21:54:31Z

Moving to a new city and starting a new school has prompted me to change nearly all my contact information, including my phone number and my google talk address. I've posted a friends-only entry here and a note on facebook telling you how to reach me; if you want my new contact information and are neither my facebook friend nor my livejournal friend, drop me a line and I'll send it to you.

touleontos @ 2008-09-02T23:02:00

2008-09-03T03:15:14Z

I just watched a stadium full of Republicans waving signs that say "Service" and chanting "Country First." Is it just me, or are they actually starting to sound like fascists?

Life with Dan and Max

2008-08-22T04:07:36Z

From a conversation with lyster:

The philosopher Xun Zi is largely known for two views: first, that academics are the highest form of human endeavor; and second, that human nature is basically evil. These views seem (to Max) strangely unconnected, but he thinks there is an answer in the etymology of the Chinese word used for "evil" (恶). The word acquired its current meaning around, let's say, the 16th century AD, when Christians used it to translate the word "sin" in the Bible; Xun Zi wrote c. 300 BC. The character itself depicts a deformed man and a heart, and appears to have originally meant not evil so much as incomplete or malformed of soul. Xun Zi's meaning, then, might be that humans are born incomplete or malformed.

So why was this word used in this way? Because the word is actually a faithful translation of Greek "ἁμαρτία," which has a root meaning of falling short or missing a target, and a pretty reasonable translation of Latin "peccatum," which has a root meaning of failing or being in error. These words are used as approximations in the Bible because, as Nietzsche was fond of pointing out, Latin and Greek do not have native words for the Judaeo-Christian concept of sin. Classical philosophers used these words in a moral sense, but one slightly different from the sense in which the Bible uses them. So this means our modern misinterpretation of Xun Zi's philosophy is based on a confusion in terminology between Western Classical philosophy and Biblical ethics.

I know I'm a geek, but I am highly amused.

Report from the road

2008-08-16T19:41:43Z

Our truck has a governor that won't let us go faster than 75 mph. Since our truck is called the Dawn Treader, we have named this imperious circuit Reepicheep. It seemed appropriate.

Yesterday: take US-23 south from Ann Arbor to Toledo. Just past Toledo, turn east on I-80, a.k.a. the Ohio Turnpike. Stay on I-80 through about $10 worth of Ohio and a whole damn lot of Pennsylvania. Once safely in the middle of New Jersey, take I-280 towards Newark and Jersey City. Stop for the night.

Last night: Upon arriving at our destination in Jersey City at about 2 AM, we discovered that our padlock had suffered a fatal injury and would now not open, meaning our suitcases and my viola were trapped in the back of the truck where we couldn't get to them. We called a 24-hour locksmith, who said he would be there in half an hour. Two hours, four phone calls, and $120 later, we had a new working padlock on the back of our truck. We got to bed around 6, which is something I usually try to do only for reasons involving a girl in my bed.

For what it's worth, we checked the contents of the back periodically along the way, so we know that the lock did not break until we got on I-280. I-80 is our friend and would never do us wrong. She is, as Dave Carter will tell you, a mighty good road.

Today: wake up at noon, hang out in New York City, go to bed at a somewhat reasonable hour.

Tomorrow: take I-95 across the George Washington Bridge, through New York City and up to New Haven. Wave hello and then goodbye to Mother Yale. In New Haven, take I-91 to Hartford; in Hartford, take I-84 to the Mass Pike; from the Mass Pike, take exit 18 to Cambridge. Arrive at the new house and rejoice. Then start lifting some heavy furniture, which is not quite as joyful an activity.

Disjointed thoughts about Boston

2008-08-12T15:05:38Z

I'm leaving Ann Arbor probably for good on Friday, and arriving in Cambridge on Sunday. I am, as you may know if you've been paying attention, insanely excited to get on my way. Packing, however, is a bit of an ordeal. As will be the journey out.

redbaker and I are renting a Budget truck and taking an epic 3-day road trip into the Utter East, also known as New England. We are naming our truck the Dawn Treader, for obvious reasons. We will make good friends with I-80 and the middle of nowhere, Pennsylvania. Chances are I will be ready to kill him by the time he leaves Cambridge.

Speaking of redbaker, over the weekend we discovered that he has a tendency to think women I'm interested in are kind of high-maintenance and significantly crazy. In retrospect, I think this is probably true of the women in question. A day or two later, he announced that he knew a woman in Boston who might be perfect for me, which appears to mean more trouble than she's worth and dangerously insane. Somehow I'm still excited at the prospect.

I have realized that, rather than just being vaguely unhappy and bored, I may have actually been suffering from depression for a good chunk of the last two years. This means that being in a new place with new people and new things to do might not really help. On the other hand, maybe it will. I guess I'll keep you posted.

I guess I'll actually have to wake up in the morning and be on time for things in the fall. Too bad.

Over the course of the last two years, I have written seven songs I think are good and significantly revised one. Together with the three that I was happy with from college, this makes enough to record an album. I'm not sure how to proceed at this point. At the very least, I'll start showing up at open mic nights in Boston and singing them. Hopefully they're as good as I think and I won't get booed off the stage.

Relatedly, I have a shiny new guitar, which is very pretty. Astonishingly enough, I can actually play it passably. It's pretty easy if you already play a string instrument.

In the last two years, I have learned to play guitar and brew beer. I've switched from being a physicist to being a biologist, which worked out well, since I never would have gotten in to a program this good in physics. I've also lost about 40 lbs, shaved my beard, cut my hair, and started wearing contacts. You might not recognize me.

I have completely lost touch with my TD friends. If any of you still read this, I'm sorry and I'll try to do better once I get to Boston. That goes double for Marc, whom I haven't spoken to since before I graduated, even, and have no idea how to contact. Marc, are you out there?

I think that's all I have to say at the moment.

touleontos @ 2008-07-22T12:24:00

2008-07-22T16:34:37Z

Things I have called "the bane of my existence" in recent memory:

Microsoft Excel
Line endings
The Conservative movement in Judaism
Teleconferences

Things that I have not called the bane of my existence, but it might be kind of funny if I had (courtesy of redbaker):

Non-black non-ravens
The void at the heart of existence
Stefan's mom
Kittens

Things that actually are the bane of my existence:

Stupid and unnecessary relationship-related drama, both mine and others'

touleontos @ 2008-06-08T17:49:00

2008-06-08T22:02:52Z

Today is Sunday, June 8. I woke up this morning in Scott's apartment in Manhattan.

One week from today, I will wake up in a hotel in Changsha.
Two weeks from today, I will wake up in a hotel in Xiuning.
Three weeks from today, I will wake up in one of Perry's apartments in Hong Kong.
Four weeks from today, I will wake up in Charles' parents' house in Washington, DC.
Five weeks from today, I will wake up in my house in Ann Arbor.
Six weeks from today, I will wake up in my house in Ann Arbor.
Seven weeks from today, I will wake up in my house in Ann Arbor.
Eight weeks from today, I will wake up on a sailboat in Lake Huron.
Nine weeks from today, I will wake up in my house in Ann Arbor.
Ten weeks from today, I will wake up in my house in Ann Arbor.
Eleven weeks from today, I will wake up in my house in Cambridge.

Thus, at least, is the plan.

23

2008-05-19T23:14:28Z

I turned 24 yesterday, so it seems like a good time to review the events of my 23rd year. This may be a long and self-indulgent post, but I didn't post about most of this stuff as it was happening, so I feel somewhat entitled.

All things considered, I'd say 23 was a pretty good year. I went to Asia for the first time, visiting various parts of China, and I'm planning on doing it again this summer. I went to Puerto Rico too, also for the first time. I learned to brew beer, which I'm getting pretty good at; at this point Marshall and I have made somewhere around 70 gallons. I wrote three new songs, each of which I think represents a good stylistic advancement for me, and I have two or three more in the works. I've started to learn guitar, which, by the way, is pretty easy. I've lost about 15 pounds, making me nearly 30 pounds lighter than I was in college and easily in better shape than I've ever been before. And on top of all this, I've had a lot of time to do things like read books, work on hobby software projects, and just relax in general.

And, weird as it is to use the word, my career is also going fantastically. This year I took on a lot of responsibility at work and worked on some very difficult problems, and everybody involved has been very happy with my work. I published a paper in a respectable chemistry journal. And, most importantly, I got in to graduate school. In fact, I got in to five out of the six graduate schools I applied to, and will be going to the Harvard Biophysics program, which is a really fantastic program that I am incredibly excited about. And, for what it's worth, US News and World Report ranks it first among Biophysics PhD programs. I bet you didn't know they ranked Biophysics PhD programs, did you?

Romance, as always, is a different story, though maybe a more interesting one than usual. I don't really feel the need to go into great depth, but a theme does emerge as I think about it. There is a Chinese proverb (said a certain beautiful girl to me this year) that says romance requires two things: compatibility, and timing. She went on to say that she and I were certainly compatible, but timing might not be on our side. She was right, as it happened, and not just about her and me; for timing in general, it looks like 23 was just not my year. And 24 doesn't look too promising either, consisting as it does of three months and change left in Ann Arbor, followed by the first two semesters of graduate school. But maybe I'll be surprised.

At any rate, as I recover from the emotional rollercoaster that was my 23rd year, I can't help thinking that we're not supposed to live this way. We're not supposed to have careers that take up all our time and energy, and we're not supposed to be able to fly all over the world and leave important people behind. As Marc liked to say in college, all I want is to meet a girl monkey who will bring me fruit and groom me, and then raise a family of baby monkeys with her; and the part of me that wants that just can't understand why it doesn't work that way anymore. But still, as a friend said when I told her this, isn't it nice that we haven't adjusted to this new world yet — that we can still feel this kind of affection, or desire, or hope, or loss? No matter how pointless or irrational these emotions may be, they're still real, and I don't think they're wasted.

So that was 23. And as for 24, as busy as I'll be in grad school, I'm thrilled about it. I'm excited about living with friends from Yale again, I'm excited about making friends with all the fantastic people I met at the Harvard admitted students weekend, and I'm incredibly excited about the labs I'll be working in. And, though it might be a little slow compared to the fall, I'm also looking forward to everything I'll be doing this summer — wrapping up my job, working on some pretty cool hobby software projects, going to China again, going sailing, and generally enjoying my remaining months with my Ann Arbor friends.

So that's my story. Happy birthday to me!

touleontos @ 2008-05-15T19:05:00

2008-05-15T23:05:58Z

I just got an email from the Biophysics program administrator at Harvard with orientation and registration dates, instructions for scheduling my lab rotations, and a Harvard ID number. To which I say: holy shit, this is actually happening, isn't it?

I kind of wish I could skip the next three months and just get on with it. Well, hopefully I can get in some quality relaxation this summer. But, y'know, probably not.

touleontos @ 2008-04-22T14:04:00

2008-04-22T18:10:00Z

My brother sent me this story, asking for a comment on whether the primary campaign does, in fact, resemble a Wagnerian opera. As it happens, the mention of Wagner in the article is a poorly executed reference to a quote of Rossini, who supposedly said, "Wagner's music has some beautiful moments, but some terrible quarters of an hour." This is probably an apt observation about the primary campaign. Otherwise, though, it bears little resemblance. Maybe if Barack Obama were the last scion of a race of heroes prophesied to to save the world from certain destruction; Bill Clinton a vengeful god sworn to stop his ascension; Hillary Clinton his ex-wife and/or sister, recruited to the Clinton cause by her hatred for her ex-husband and/or brother; Howard Dean a benevolent god determined to see Obama triumph, but bound by a solemn oath to give him no aid; and John McCain the human incarnation of the wolf Fenrir, come to devour the world if Obama fails in his mission.

Grad School

2008-04-01T17:08:36Z

Okay, here we go.

At Columbia, I've been accepted to the Biological Sciences department. "Biological Sciences" originally meant Zoology and Botany; these days (according to the department's materials) it means Cellular & Molecular Biology, Developmental Biology, Neurobiology, Structural Biology & Molecular Biophysics, and Systems & Computational Biology. So, it's a pretty broad department. I would pretty much only be interested in the latter two, but the core courses required for the PhD include some pretty intensive study of all five areas. This is probably a good thing, actually, since it would require me to learn some things I might otherwise not. For such a broad department, It's very small — only about 30 faculty, with about an equal number of affiliated faculty in other programs (including some departments at the Medical School), and about 120 students. One the one hand, this makes it a very cozy and welcoming environment; on the other hand, it does limit research options somewhat.

The ordinary stipend is somewhere around $29000 (they haven't calculated it exactly for next year yet), along with subsidized housing near campus. They don't give a dollar value for the subsidy, but a good estimate is probably about $6000. They've also offered me a Presidential Fellowship, which is good for an extra $5000 my first year.

Some faculty I might work with:

At UW Madison, I have been accepted to the Biophysics program. This is an interdepartmental program, encompassing some 50 faculty, about a third each in the Chemistry and Biochemistry departments and the remainder scattered around other departments, and about 30 students. Coursework is pretty light; you need to take 3 out of the 4 core courses, plus a research seminar. The biggest selling point is that there is an incredible about of research being done there, and they have an absurd amount of funding. Their facilities are basically all gigantic and brand new. I'd be a little worried about departmental politics — professors have nothing but good things to say about the Biophysics program now, but apparently about two years ago it was not so highly regarded and antagonized a lot of professors outside the chemistry department. I also didn't particularly get along with any of the current students or my fellow prospectives.

The stipend at Madison is $23000, which in terms of actual cost of living is probably a little bit more than Columbia's normal stipend. They have also offered me an NIH training grant, which guarantees my research funding for 3 years regardless of what lab or project I'm working in, giving me some extra freedom to choose my research project.

Some faculty I might work with:

At Harvard, I have also been accepted to the Biophysics program. Its organization is somewhat similar to that at Madison, with a difference in scale. The program gives access to some 80 faculty at Harvard, Harvard medical school, MIT, and a handful of other medical research institutions around Boston. The coursework is similarly flexible, with few specific requirements and the ability to take courses at Harvard grad school, Harvard med school, and MIT. And unlike at Madison, the program is very well established and appears to have few political difficulties. The program contains about 50 students, who in general seem pretty pleasant. Another important feature is that the other prospectives, who will be my classmates if I go there, were great. I thought we all liked each other much better than the groups at other schools, and most of the other prospectives agreed about this. My biggest concern is that the professors I met with didn't seem as excited about working with me as some of the professors at the other schools — probably a reflection on the quality of the rest of the admitted students.

The stipend at Harvard is $39500, which is about equivalent to Columbia's normal stipend. Harvard has not offered me any extra money or funding, but they do guarantee two years of funding out of program funds for all Biophysics students.

Some faculty I might work with:

I've also been admitted to UC Santa Cruz's Bioinformatics program, and to UW Seattle's Biomolecular Structure and Design program, but I've already pretty much ruled them out.

So ... I guess it sounds like Harvard, doesn't it?