Sunday, June 28, 2009

Mini-Update

Posting this from the Hostel in Mendoza. We're getting ready to leave, which is terribly sad because this place is incredible.

Super short version: Making Friends, Bikes and Wine, Hiking and a crazy trip to the zoo.

Details on Monday or Tuesday; I'm giving a seminar on Tuesday and may not have time to write tomorrow.

Amazing trip though, full story and photos soon!

Friday, June 26, 2009

The Art of Other People's Photography

Posting this before I head off to work today.

I finally got some pictures; that is, the girls took lots of pictures on our last major outing so I'm taking them from facebook, isn't modern technology great? Just because I suffer from the family curse of never having a camera, doesn't mean I can't get pictures anyway!

This is from our trip to the cemetery where Evita is buried.

First is at the girl's apartment before we left. Daniela and I are sitting, Darimar is standing behind us.

Dani got us lost going to the cemetery. Neat looking building we saw in said process.



Walking around the cemetery. The guy with the jacket that looks suspiciously similar to mine is Alex, a highschool friend of Daniela's who happened to be in the country (he has family here), and joined us for the day. He's a physics guy, so we got along quite well. The girl in front is Julie, the newest (and final) arrival.

Some neat cemetery stuff.

Evita's grave. Flowers!




We were quite amused to find that a scientist (Leloire) actually had a bigger tomb than Eva.
Hangin' out, down the street, same ol' thing we did last.... er, sorry. Anyway, here's us except for Darimar who was taking the picture. From left to right, for clarity, is Julie, Daniela, Alex, and of course your 'umble narrator.

Lastly, we went to the movies to see UP.
So here's Darimar and I making faces (well mostly me) in front of the Ice Age 3 cutout.

Okay, off to work!
-J

Wednesday, June 24, 2009

Thieves, Communists and Wine

"All around the world,
we can make time,
roppin' and stompin'
because I'm in my prime."
~ All Around the World, RHCP

Thieves
Or, An Expensive Tale to Tell
The other day some of the girls got robbed. Darimar and Julie were coming back from the bank, or a restaurant, or something (I'm not real clear on the details). They got stopped by an old lady and a some guy telling them that a bird had crapped on them or something and in any case apparently Darimar had some sort of substance on her clothes. The pair of strangers offered to help and then proceeded to produce a bottle of water and some napkins or cloths to help clean the substance off. That done, they hailed the next taxi that came by and left.

Odd behavior, no?

Awhile later Julie was planning to head out and checked her purse, then noticed her wallet was missing. She carries one of those purses that doesn't zip up. Luckily, she didn't lose that much; credit cards are easy to deal with (if annoying), certainly had that problem myself before. Nothing else major but the cash in her wallet, which was only AR$150. Annoying, but not really much more than US$40.

On a similar note, Aisha also got swindled by a taxi driver. She made the (often cited) mistake of paying for her cab with a large bill, a AR$100 in this case. But then she realized she had enough cash to pay in small bills instead, and payed that way, asking for the $100 bill back. The cab was quite dark however, and Aisha is, it seems, a little too trusting. When she went to pay for her meal later at a restaurant, she found only $2's in her purse. Surprise!

Communists
When I reflect on it, it's amazing how much the concept of communism has actually shaped both my personal life (mostly in terms of humor) and my academic life given that I've lived the majority of my life in the post-Cold War era, and even then, the part of my life that was technically in the Cold War era was really quite cold as far as wars go, even cold ones, and I was too young to really be influenced by the impact of the "looming threat of communism". If that was even around anymore.

That said, I've grown up with jokes about the source of every problem being either communism or a lack of sex on someone's part (and in my experience, this holds true quite often!) Then consider that a large portion of my education was centered around the concept of Communism. This is not as odd as it sounds, as much of the modern culture of the US is also centered around communism, specifically, the US has defined itself as the opposite, even the enemy, of Communism. In my own life, much of my humanities education has directly or indirectly been influenced by Communism, whether it's been the explicit study of communism and the Bolshevik revolution in history, followed by the Cold War (possibly the defining struggle of the modern US), or the indirect study through literature of communist era struggles and certainly the study of literature about both times and fictionalised events in military revolutions (I'm thinking specifically of House of the Spirits here, for any of my IB English compatriots who may be reading).

That said, Communism has always been an idea, with examples shown in class and discussions of the theory (and often it's flaws) in History classes. Then there's the occasional nutjob on my college campus who spouts such silly things (and I'm no hard-line right-winger). But that's been my experience with communism prior to landing in Argentina.

Imagine my surprise the first time I came to the campus and found not just one, but entire boards filled with political posters (also common at UF) for the communist party, complete with hammer and sickle! (Not common at UF) And they're not even a fringe group! Actually, I have been informed that the equivalent of my views in the US (centrist, more or less), would be the socialist party. Meaning that the actual position I would take probably corresponds to the hard line conservatives of Argentina.

I've gotten used to the communist posters, but it's still a little surreal walking by actual posters for a real, legitimate, not crazy fringe communist party.

Wine
Okay, I got Julie to play translater for me today, and I now officially hold a ticket for a bus ride to Mendoza this weekend. That's right, wine country! And I'm going with four girls, how much better could it get, right? If only we had time to hit the slopes as well, maybe I could learn to ski or snowboard.

Off the topic of wine, work is going quite well now. We're really starting to dig in, and I've surpassed my professor in my particular area, as he's now relying on me to understand, interpret and even ask some questions about the biochemical network we're studying. I've managed to learn a great deal about both simulation work and some complex network dynamics. Furthermore, my background in mathematics and physics is really helping here, as I've been able to rapidly understand and make (often quite accurate) predictions about the complex network dynamics we're trying to understand. I'm not top notch at the biology portion, but I've already suggested to Adrian (and he legitimately appreciated) network based reasons why certain mutations in the phosphotase proteins responsible for MAPK-cascade dephosphoralation would lead to cancer pathologies (and note that, in fact, they do!) I figure that's pretty legit, yeah? Anyway, the nice thing is that my work load is still rather light. I'm doing my best to keep it that way, balanced against returning interesting and high quality results. So far it seems to be working. I'm not working hard or really all that much, but I always have interesting ideas and results to show, so everyone I work with seems quite happy about my work. I like it that way; I figure I'm not really going to gain from working super hard, but if the work I do is top quality, then I'll get the recognition, respect, and reference letters I really want (plus some publications!) while keeping with the mathematician's work ethic. You know, laying on the couch, eyes closed and claiming to be working. Hey, I've done it that way before!

Okay, that's enough for now. Also, even though I don't really respond, I do read and appreciate everyone's comments. Even the one's about my foul language ;P

-J

Thursday, June 18, 2009

IHTFBS

"We'll ride the spiral to the end
and may just go where no one's been..."
-Lateralus, Tool

Okay, so the other night was fucking terrifying. In a bad way. It went like this: I missed my bus stop on the way home, since presumably the bus didn't take a different route than normal. We were heading home the normal way and I knew where we were and it was good. Then, quite suddenly we were somewhere that looked just a little bit wrong. It was a little darker than normal, and the streets looked a little sketchier than normal. But I didn't recall passing Av. Independencia, which is the edge of my neighborhood and a pretty big, well-lit street. The kind that's hard to miss. Somehow I did though.

Anyway, once I realized we weren't where I was expecting to be, I started rationalizing (because I sure didn't want to get off the bus in this sketchy looking area): maybe we took a detour. There's construction all over the place, so that's probably it.

Wrong. Almost certainly we had passed into the section of town just a little ways past my apartment that Adrian described to me as "somewhere you probably don't want to go." I stayed on the bus, hoping to see something familiar.

That didn't happen though. Quite the opposite, we were soon in an area with very little light, graffiti on every surface, and some very old, falling apart buildings. Great. To my great fortune we left that area fairly soon, crossing a bridge (what, a bridge?) into the industrial sector. Or what I assume was the industrial sector, given that there were factories around and not much else.

It was about this point that I went from feeling uncomfortable to thinking "Oh FUCK where am I? What the HELL have I done?" I was pretty sure that if I got off the bus I would get stabbed.

Then we turned into another area that looked rather slummy. People started getting off the bus. I was pretty sure I was fucked at this point. I didn't know where I was in Buenos Aires. I don't speak enough spanish to ask someone for help or directions. I had very little money on me (not enough to get a cab, ripoff or not). There was little lighting and no way to figure out where I was. And even if I was capable of finding my way back home on foot, I'd have to walk through some very dangerous sections of town.

I was so freaked out, I didn't register much as we passed through a bus station and went further into hell.

Then, quite suddenly, we were somewhere else. There was a big street with lights and stores and another bus station! Excited, I looked around only to realize that I, yes, I was on a major street, but no, it wasn't any place I even remotely recognized. Then we turned down a side street into a small neighborhood. Like a suburb.

What the fuck?

Most of the rest of the people on the bus started getting off. At this point I decided I'd had enough. Although there wasn't a lot of light (still), the suburbish area looked safe enough to walk through without getting assaulted. I got off the bus and immediately started fast walking toward the main avenue. At this point I was pretty upset: it was cold, I was hungry, it was late, I was very, very lost, I had no money, and no help or a way to get help whatsoever.

Then I decided that it would be more helpful to focus on figuring out a way home than mentally listing how shitty my situation was. So I did just that.

I headed back to the bus station on the main avenue I had passed a little earlier and caught the first bus of line 45 that was headed back in the other direction. I wasn't quite sure it was the right bus (the sign was for a different place than the one I usually take to get to the university), but I figured I had enough coins for two more bus rides, and I'd be able to at least get back to the station I just left and find a different bus.

I was luckier than that though. We went back along the same route I had taken to get out to the suburb area and we eventually got to the bus station I had initally seen after leaving the industrial looking area. And of all things there was a subway station there for the line that has a stop two blocks from my apartment. I jumped off the bus and ran down the steps to the station.

The subways in BA close early. They officially stop running at 11 PM. They stop letting passengers in sometime around 10:15-10:30. I had left the university at around 8 PM and I had been on the bus for a very long time (not to mention walking and taking the bus back).

It was 10:23, and the last train of the night was about to leave. I got a pass, and got on.

Less than 10 minutes later I came out of the subway next to Av. Independencia. I walked two blocks to the pizza place down the street from my apartment, greeted the guys there and ordered some empanadas.

"IHTFP"
-MIT motto

On the other end of spectrum, today I decided on an argument for why I should get into a place like Caltech or MIT or whatever for graduate school. It's easy: I should not be the first to figure out the biology paper that a computational biology grad student and a professor of bioinformatics are trying to understand. Both of these guys have better backgrounds and many more years of experience in the field than me.

Maybe the study of mathematics just gives one the magical ability to interpret graphs. In any case, I think Adrian gained some respect for me today when I was able to explain what the hell the guys who wrote the paper were doing with their simulation.

To their credit, I did spend a good bit of yesterday programming a simulation like the one in the paper, so I had some idea of how the network works. But it's much cooler if they only see me do the Will Hunting thing.

-J

Wednesday, June 10, 2009

Caturday!

There are a lot of stray dogs in Buenos Aires, it seems. Today I saw a stray cat. It was different.

I also saw some young boys teasing a little girl until she cried. It was not very different (just in Spanish.) So it goes.

So, I have been given my own office space at work, which is cool. It's in a common room for graduate students, there's five of us in there, but there's plenty of space (the room is really big, we could easily fit 3 more people). I've got a corner desk and a computer, which gives me the best set-up of any of the students here, since everyone else is doing experimental work (as opposed to in silico simulation work), so they have to wait for machines and equipment and spend a lot of time waiting. I spend a lot of time doing nothing too, but at least it's not because I'm waiting to use equipment.

On the other hand, there is a slight problem with my setup. I do all of my simulation work using Matlab's SimBiology package, which is not installed on my system, so I use the lab server's copy by accessing it remotely. Except that the network is heavily firewalled and there's a lot of information going back and forth when I do, well, anything. Plus, I swear the network relys on a single photon laser to communicate it's information, it goes so slow. And by slow, I mean glacial, opening a menu takes 5+ minutes!

Luckily the problem is solely in the network, so I was able to circumvent the issue by running matlab through the command-line in the UNIX terminal. Which means I have to set-up my simulations hard-core programmer style, but honestly I kinda like it. It'll give me more familiarity with UNIX (more or less, it's still mostly matlab), and I'm learning Matlab much better this way.

On another note, a tree fell on the truck in front of my bus the other night coming home. Seriously, we were in traffic and, at least from my perspective, the tree just suddenly fell over onto the truck in front of us. It was wild.

Also, I found this great pizza place less than a block from my apartment. It's this tiny place with three guys who make pizzas and such, and is really great (also, cheap!). They seem to be amused to have an American who doesn't speak spanish in the place, and the one guy who makes the pizzas likes to try to teach me some basic spanish as it relates to pizza making. It's kinda cool.

Okay, all for now.
-J

Thursday, June 4, 2009

Mr. Gregory Lane, Please Take a Bow

Okay, so today was another "meh" kind of day. I accomplished almost nothing at work today, simply because I had no real work to do. I mean, I fixed a small error in the model and added a second version with some different parameters, but nothing major. I mean, that all took me less than an hour. I spoke to Adrian about my work. He was telling me about his "ideas" for where we could go with our analysis. Apparently he has a lot. Which means little in the specifics department. Which means it's going to be a pain for me, because I am not a biochemist. I'm just the math guy. I do the modeling, not the science (not here, if we were doing combinatorics or physics or computer science even, sure, I could probably think up questions, but I am not a molecular biologist nor do I wish to be one. So it goes...) Anyway, I interpreted this as "you're going to be on a wild goose chase for a while". Hopefully I'll just get to work on writing code for some software tools or something. Hell, that'd be better than a paper if I apply to grad school in CS, which is what I'm thinking these days (I mean, I like theoretical computer science and machine learning, goddamit, I wrote a paper in cryptography!)

Okay, work complaints aside, it wasn't all that bad a day. I fixed the toilet and found an irish pub. Okay, less found, more realized that my bus stop is actually in front of an irish pub. So today I worked up the courage to go in alone (usually I have someone who can interpret for me). So worth it. I had popcorn (apparently the argentine equivalent of free bar snacks?) and three pints of guiness. The guiness was expensive, but oh so worth it. I've been dying for a drink from home, and this was just what I needed.

Anyway, getting to the title of the post, I'd really like to thank my stepdad here for taking the time to teach me valuable life skills like finding good wine and fixing basic plumbing problems. My roommate is totally useless when it comes to things like the toilet is busted, and given that I speak no (useful) spanish, it really comes in handy to know a few basics about plumbing and other household handyman kind of issues. I may not be that good, but at least I can survive a clogged toilet in Argentina!

JC

Wednesday, June 3, 2009

cp /abstractions/pain/physical/upperback /people/jamescrooks

Okay, so my back is killing me. I have this terrible pain in my upper back/shoulders/neck region. Not sure if it's because I'm sick or if it's because my bed is two planks of wood with something that passes for padding on it or both. Probably both. I hope it goes away soon.

Lab is improving. I've gained access to the file management system, completed the new test model (and successfully got the proper oscillations to show up in the simulation data) and actually taught the grad student who's overseeing my work something about bash. Which makes me thing he must not be a computer scientist at all. I didn't think it was legal to graduate with a degree in CS without knowing wildcard characters.

In other news, I bought this premade pizza (not frozen, but all made up, just pop in the oven for a few minutes) from the store on the way home from work. Thought it would make for a nice afternoon snack. Then I got home and realized I don't have an oven.

So I cut it up, popped it in a pan with some oil and stuck it on the stove. Worked surprisingly well! I mean, it had a flavor that actually resembled palatable, or good even. Which given that it comes from the supermarket across the street and doesn't contain a significant amount of alcohol, is really saying something. So far restaurant food has been great; stuff from the grocery store however, much more questionable.

Anyway, it looks like there's this art and music festival coming up soon. Daniela sent me a link, should be interesting.

http://www.ciudademergente.gob.ar/home09/web/en/index.html

JC

Tuesday, June 2, 2009

No Bandwidth

Okay, so, first entry. I'm starting this blog because, well, I couldn't find any more Big Bang Theory episodes to stream and I'm incredibly bored. Woo!

Alright, I've been in Argentina for about a week now, and things are finally going pretty well. It was a rocky start, as most of my friends and relatives have had to hear about, with no bank access, some power and water outages, and a total lack of direction at the lab. But the banking, power and water are fixed, and I'm finally starting to get somewhere (or at least an idea of somewhere to go) at the lab. Which is great, because I was running out of comics to read while I was supposed to be "working" on something I finished last week and had no idea how to proceed with.

I have sort of an odd situation at the lab, I think. Well, maybe odd in a general sense; I suspect it's not terribly uncommon for someone in my field though. So, I've got this mathematical biology/computational biochemistry work to do: basically I'm designing and implementing biochemical simulations. Well, so far it's just implementing with not so much designing, but that's going to change soon. I think. I hope. Of course, at least so far it's been nice and easy. Anyway, basically I have to admit that I have pretty much no interest at all in the biochemistry I'm working on. I don't know why it's important really (my labmate mentioned something about cancer pathology, but I wasn't clear on the details). I do however, quite enjoy the actual techniques and methods we're using (i.e. coding and running simulations in MATLAB). It's kind of weird, I think, because most scientists would be the other way around if anything. The techniques may or may not be of much interest, but the data, and the results, are important. But I guess that's the issue with being in applied mathematics. It's more about the tools than the results you get with them. I mean, your results should be correct, but the results aren't really the point: it's how you got them. Results are just for confirming the correctness of method.

Thinking about this, I am so glad there is a computer scientist in my lab, because if they were all biochemists, I'd probably never get anything done. Really, it's nice to have someone I can talk to who actually has a similar background as I do, and gets the chemists, so I don't have to filter all the chemspeak (coupled with the whole english/spanish language thing) through my own understanding. Of course, it'll probably be a mark in my favor when I talk about doing interdisciplinary work and such on my NSF Fellowship application.

As for the rest of life here, well, I've started to pick up a very small amount of spanish. Not really even a day of classes worth really, but I can get around on the bus system and order food and wine at restaurants (more or less. Got the wine down though.) You know, the important things.

And the wine, it is cheaper than water. Seriously. It's pretty great. A glass of house wine usually runs about AR$4-5, which is about US$1.15. A bottle of water is about AR$6. Okay, so the water is still cheaper per mL, but not by much!

More later,
JC