Friday, August 14, 2009

Done

All done with work! I managed to wrap everything up into a semi-coherent package for the researcher who's going to be continuing the work, so hopefully the project will go on smoothly.

Last night, the lab took me out to dinner as a goodbye, and they surprised me with a custom-made, hilarious t-shirt (Mastercard "Priceless" ad spoof), EMBL pens, an EMBL USB drive, and A REALLY SLICK EMBL POLO. It's like they've known me all my life. In all seriousness though, everyone here has been so nice to me, which made leaving today pretty sad.

Dad's arriving tomorrow! We fly out to Rome on Monday, then to Paris next Friday, then home on the 26th. I'll see if I can get dad to write a guest column here this weekend before we leave...

Thursday, August 6, 2009

All Quiet on the Science Front

Crisis averted. My PCRs overnight have cleared things up considerably, and the news is pretty good. While I still have to redo some data, it doesn't invalidate everything I've done so far as I had feared. So, well, that's good.

Wednesday, August 5, 2009

Internet

Oh yeah, tonight I am getting 0.36 Mb/s down with a 70 ms ping to Frankfurt. I suppose this is better than the nights where there's no internet at all, but come on, what is this, the 90's?

Waterskiing Part Deux; Lab Cookout; The Agony and the Ecstasy

On Sunday I went waterskiing with Jan again, and it was a great success; unsurprisingly, it's even more fun when you're able to stand up. I fell at the first turn on my first run, but I did the whole loop on my second run! The best part was definitely letting go of the rope at the end of the loop and just slowly sinking into the water as friction slowly got the best of me. By the end of the day I had made it around the loop four times, so I was pretty pleased with myself.

Yesterday, I gave the presentation at lab meeting (again), and it went pretty well. I wasn't really sure what to make of some of my data, so the talk was very helpful in the sense that it allowed me to put my thoughts in order and get a lot of feedback from people who actually know what they're talking about. The ecstasy: after the meeting, Jan asked me for a writeup of what I've done so far because he's planning on using it in a grant he's writing, and he said it might develop into a paper later. Cool. The agony: today, some of my repeats shed doubt on about half the data I already have, which would imply tens of hours and many hundreds of Euros in enzyme wasted. Not so cool. Needless to say, I'm in a pessimistic mood right now, but hopefully some of the PCRs I have running tonight will provide a clearer picture. Ugh.

Last night, we had a lab BBQ at Jan's. They had pretty much the standard stuff: burgers, (German) sausage, chips, salad, etc. Along with all of the regular lab members, we also had a new postdoc candidate and his wife. He's British; she's Italian. Both seemed very nice, and his talk today about the HHMerThread pipeline he developed was really solid. We have another two postdocs coming in for interviews before I leave, one tomorrow.

In my free time, the last few days have seen me writing and laying out the Freshman week issue of The Princeton Tiger, the humor magazine for which I'm the head writer. Since everyone else on staff is feeling particularly lazy this summer, this issue is mostly mine; I've done the actual writing on literally 90% of the content in it, at least so far. (One of the editors helped out a lot with ideas for probably half of the articles.) Fortunately, the advertising we've been doing to the class of '13 is paying off; I have a ton of interested recruits emailing me.

So that's the long and the short of what I've been up to lately. Excuse me while I go do laundry and mope about my data.

Thursday, July 30, 2009

Munich

Sorry this update has taken me so long, but I have been mad busy. Tuesday night I saw Harry Potter; best Potter film yet, though still nothing near LOTR levels of goodness. Monday night I went over to Adrian's house for an epic Guitar Hero battle. Katharina made authentic Austrian Apfelstrudel, and we tried to make it through "Through the Fire and the Flames" on medium difficulty. We made it, but barely. All in all, great week.

But back to Munich.

On Friday, I left early in the morning for the main train station, the Hauptbahnhof. I arrived at the station at 8 am, even though my train wasn't until 10 am; I'm just neurotic like that, especially when it comes to travel. Basically, I listened to podcasts and twiddled my thumbs.

My first train was a short ride to Mannheim, then I switched to a larger train direct to Munich. The second train was very very nice; it felt like an airplane, but with much more leg room. After some work finding my seat, I settled in for a two-hour ride to Munich. Barring one minor moment that could have been disastrous if I had been stupid enough to get off the train (München Pasing is definitely NOT München Hbf.), the ride was uneventful.

I arrived in Munich's massive train station around 1:30 pm and headed straight to the hostel to drop off my bag. It was a short 10 minute walk from the station, so I didn't bother with the tram system, the S-bahn. I checked in and left by bag at the hostel, then headed out into the city.

The first order of business was transportation. I bought a three-day MVV (Munich's public tranport system) pass for 12 Euro, which was surprisingly cheap compared to the individual fares (2 Euro per ride). It turned out to be a real money saver.

Following the advice of my invaluable Frommers guidebook to Germany (which pretty much made the trip ~732 times more enjoyable), I first headed to Marienplatz, the city's center (pedestrian-only!). There I saw the Karlstor ("Karl's gate" for you non-German folks), the Neues Rathaus ("New Town Hall," "new" being a relative term) with its famous Glockenspiel, Frauenkirche, Peterskirche, and Michaelskirche (churches). I climbed every tower I could find, and took a bunch of pictures.

That night, I met my roommates for the evening at the hostel: a Chinese couple in their mid-forties and their ten-year-old son, who all live in Austria; a young Spanish couple from Madrid (I think the girl was 17); and another Spaniard in his mid-twenties. I spent the evening translating from Spanish to English and back again so that the Spanish and Austro-Chinese halves of the room could communicate. I talked a bit with the Madridians (mostly in Spanish, since my Spanish is better than their English), and it was a pretty cool evening.

The next day I left early in the morning for Schloss Nymphenburg (Nymphenburg Castle), which was the summer retreat for the German Electors, and later the Holy Roman Emperor (?). It's built in an Italian villa style, and it is SO pretty. I took an audiotour of the interior, which is done in a ludicrously ornate style. I then walked around the 500-acre (!) gardens, and looked inside some of the other mansions hidden on the grounds. Most had plain exteriors that belied their awesomely-ornate rococo interiors. This visit was probably my favorite part of the trip.

Next, I toured the Residenz, which was the daily residence for Germany's kings over the years. This one was truly massive, and all of the rooms eventually started to blend together. Highlights: the collection of holy relics, including John the Baptist's skull; the Antiquarium, a gorgeous banquet hall; and the Ancestral Gallery, a gilded hall of portraits (think Hall of Mirrors, with paintings instead of mirrors).

On the same ticket as the Residenz, I also had access to the royal treasury and the Cuvillies theater, so I decided to check them out. The treasury had, well, treasure. My favorite part? The solid gold statue of St. George on horseback that was literally covered in diamonds and rubys. The Cuvillies theater was also neat; it's a rococo theater from the time of the electors.

Next, I decided to head a few minutes out of town to see the concentration camp at Dachau. The visit went about as you would expect: terribly cheery, and loaded with museums and documentaries. It started to rain as I was walking around the grounds, but it felt appropriate. Somehow, Dachau wouldn't have seemed right in the sun. I didn't have time to take a guided tour, but it was depressing enough even without a guide.

After an hour wait for a bus back to the S-bahn that took me back to Munich, I went to the Hofbräuhaus for dinner. This is Munich's famous beer hall where Hitler jumped up on a table to outline his ideas, but it's also simply a gathering spot for locals and tourists alike. They sell their classic beer in one size and one size only -- a massive barrel-like mug that only a Münchener could consider to be a sane unit of volume for beer. I had Weiβwürste, a traditional white Bavarian sausage, and it was fantastic.

After dinner, I walked around the Englischer Garten for a bit, which is Munich's massive park. It turns out it was a good thing that I only had time to go at dusk; that way I did not accidentally stumble into the part of the park where Germans of the FKK persuasion sunbathe on warm afternoons. (FKK stands for Freikörperkultur, which roughly means "Free body culture." And they are very "free." With their bodies. In public.) It would have certainly been a sight to behold, but I had little desire to see old sweaty Germans as nature intended. I then took the U-bahn (subway) to Olympic Park, saw the stadium from the '72 games, and went back to the hostel.

On Sunday, I toured the Deutsches Museum and the Alte Pinakothek (Old Art Museum). The Deutsches Museum is one of Germany's largest science and technology museums. I saw the original V2 rocket, the bench on which the first atom was split, and original Leeuwenhoek microscopes. Pretty cool. After I finished there, I swung by the Alte Pinakothek until I had to catch the train home. The museum had works by Rafael, Da Vinci, Rembrandt, and it was incredibly well put together. I was very impressed, and I spent probably four hours just wandering around in there.

So, in short, I had a great trip. Traveling alone definitely let me see much much more and be more flexible than I could have possibly been in a group, so that was nice. I probably saw a week's work of stuff in 48 hours, which was pretty impressive.

As always, all-new 100% natural organic photos may be found here.

Wednesday, July 29, 2009

Coming Soon

An update, as haiku:

Munich was awesome.
Much too busy to blog now.
Updates soon. (Tonight?)

Thursday, July 23, 2009

Munich, Predeparture

Long time since I've posted! The has been the result of the confluence of a number of factors:
  1. The internet has been spotty
  2. Blogging is work
  3. I've been busy
  4. Nothing much out of the ordinary has happened
But all of this is about to change! I am headed to Munich for the weekend, so I should have plenty of photos and stories when I return. I'll try not to die, and it should be fun.

More updates soon.

Monday, July 6, 2009

New Rule

I propose a new amendment to the constitution:

Amendment XXVIII. If the only two songs you know how to play on the piano are "Twinkle Twinkle Little Star," and a poor approximation of the first 8 bars of the piano intro to "How to Save a Life," you shall not play the piano in the lobby of Heidelberg's ISG Hotel. Or anywhere in public. Or anywhere. Ever.

I expect it will pass quickly.

Sunday, July 5, 2009

Waterskiing

Waterskiing was *awesome*. I am writing this about an hour after getting home, and I am still on an adrenaline high. I’m pretty sure I just came home and stared at the ceiling while listening to the entirety of Coldplay’s Parachutes. And for you ISC kids, I was watching a fly in my room using the E. coli run and tumble locomotion paradigm. Not even kidding. So about the actual event:

Jan picked me up at 8:20. We got to the lake a bit before we were scheduled to start at 9:00, so I was able to scope out the situation before my first run. The first thing I noticed was the contraption that pulls you along the lake. It’s pretty cool. It’s a suspended wire loop, about 800 m long in total, and it goes around the lake about 30 ft above the water – it reminded me a lot of a ski lift, but in a big loop. You hold on to a rope attached to this loop, and the rope itself uses a catch mechanism to grab on to one of eight hooks along the wire when you’re ready to go.

My first run was… graceful. You start out squatting on your skis on this slick platform right at water level, and the operator hands you the rope. When one of the hooks comes along, you just feel a gigantic tug, and suddenly you’re speeding over the top of the water. At least, that’s the theory. I made it about 50 m my first run before I pulled a bit too hard on the rope and sunk back into the water, at which point I was promptly jerked head-first over the top of the skis. It was awesome.

After this first glorious faceplant, I was able to jump right back on since there was no line at this point. The second run was better, about 70 m before a faceplant. And then maybe 150 m for the third run. On my fourth run, I managed to do the entire first straightaway, but got in trouble on the turn. Ah, the turn. See, the problem is that the wire makes a sharp turn, but you are not able to change direction so quickly. As such, you have to start the turn way before the wire actually goes off in a completely orthogonal direction. I didn’t. I got to the turn, feeling pretty proud of myself, when I am instantly pulled to the left at 30 km/h. Again, it was awesome.

On my fifth and last run, I actually managed the first turn (not graceful, but it worked), but took an epic dive on the second curve.

Overall, I think it was a pretty successful hour. On Friday, Jan told me that I would probably be able to do the straightaway on my first day but probably not a curve, so I feel pretty good about my efforts.

A few pictures here.

Wednesday, July 1, 2009

New Postdoc

A new postdoc arrived in the lab today -- Meg, the woman from Harvard whom I think I mentioned before. She seems like she'll fit in well, and it will be cool to have someone to fill up the empty-looking desk next to me. We all had coffee outside as a lab to celebrate, and it promptly started to rain. Ominous? Perhaps.

I ordered my PCR primers yesterday, and they should arrive early next week. This marks the transition from pure bioinformatics into a mixture of computers and wetlab for the next part of my project. All is going well, and I'm excited about it. Jan went before the Ethics Committee to try to get approval for the human gamete experiments we had planned, but we need to make a few revisions for informed consent purposes before they'll accept it. It's a very strict process, which might delay my work a bit, but I suppose the stringent oversight is a good thing.

A few observations from this week:
  1. Air-drying laundry in humid weather takes forever. I stopped paying the extra Euro to dry my clothes, but I didn't realize we were coming up on a humid week. It took them three days to dry, and I'm just now able to put them away.
  2. Note to self: searching for "human sperm" on Google doesn't give you biotech companies that supply male gametes. Use more specific search terms next time to avoid creepy results.
  3. I can be obsessive when I am excited about something. Last night I meant to go to bed at 11:00, but I was on a roll working on a programming project. Next thing I knew it was 2:00am. Whoops.
  4. Corollary: I am now tired, so I am going to bed.

Thursday, June 25, 2009

EMBL Lab Day -- and Terminator

This week has been pretty great. Last Thursday was the EMBL “lab day,” where members of all of EMBL’s different outstations come to Heidelberg to meet, have graduation for students who have completed the program, and generally party it up. We went to talks all morning about next-gen sequencing and the work that’s being done at EMBL, then afternoon consisted of free food, socializing, the poster competition (which our lab didn’t win, somehow!), and a concert by EMBLers who play instruments. After a nice BBQ dinner, there was live music and free drinks. And that was day one.

The next day was the 10th anniversary of the founding of EMBLEM, which I’m told basically brings EMBL ideas to the business world. After work, Andreas, Adrian, Adrian’s wife Katrina, and I attended the fancy (free!) Mediterranean dinner. The food was fantastic (and free!), and I probably ate twice the capacity of my stomach. After dinner, the party began with a pretty good band, a magician, a fire show, drinks (free!), and dancing. I hung out with Andreas’s friend Tanmay and a few other grad students. Did I mention it was all free?

Then on Saturday I went out with a bunch of grad students and postdocs: Andreas (Austria), Tanmay (India/UK), Rob (UK), Norm (Ireland), Vinnie (Switzerland), Eric (Switzerland), a girl whose name I didn’t catch (Hungary), and another guy (Iran). We talked politics, Germany, science, and Norm’s impressive facial hair. Thank goodness Andreas has a car and lives very close to me because the buses and trams stop running at midnight. (Or, at least he has a car for now. The car is about as old as I am, and the brakes were not sounding good. I think he said he took it into the shop today.)

We had another visit from the postdoc candidate I mentioned before. Jan is making the final decision about whether to offer her a position or not, so we had another round of talking to her about her research and answering her questions. Obviously, I can’t actually be of any real help, but we chatted for a few minutes while she was waiting to see Jan.

Then on Tuesday, I went to see Terminator Salvation with the other members of the lab in one of the local theaters. I give it mostly positive reviews, and the dubbing wasn't even noticeable.

And for those of you who are saying, “A movie? In German? I thought you couldn’t speak German,” I can’t. But you would be surprised at how much you can glean from a movie by just paying attention and picking out a few phrases here and there. I admit, the language would have been a bit of a problem for a character-driven, brooding, thoughtful snore-fest, but seriously folks, it’s Terminator. This movie is about killer robots from the future, and it contained no less than two nuclear blasts. I did all right with the plot.

After the movie, I went out with the lab and Marcus (a fellow EMBLer) for a soda at a really old student pub in the center of town. Over the years people have carved their names into the tables so much that the surface is really a solid wall of names. It’s pretty neat. We talked about the movie and retro geeky things, like the Commodore 64 and D&D. Yeah, I hang out with cool people.

Finally, can someone who has seen Transformers 2 tell me if (1) it has cool special effects (2) if Princeton gets blown up at all? K thanks.

***TERMINATOR SPOILER ALERT***

Really, John Connor? If you’re fighting a war against machines, the second a half-man half-machine shows up in your base, you kill it. I don’t care if it’s a nice robot or if some woman on your team thinks it’s hot, get rid of it. Immediately. I’m really glad it worked out for you in the end (Sappy heart transplant? Really?), but, honestly, even letting it get to that stage was just sloppy.

Tuesday, June 16, 2009

Tour und TV

This weekend was spent doing more in Heidelerg. On Saturday I took an English tour of the Old Town. My tourmates were a couple from Alabama and their children, two English women. The tour was supposed to last an hour and a half, but it took three. The tour guide was fantastic, and we were allowed to go to a few places normal groups wouldn't have seen since we had such a small group, especially after the dad and kids dropped out after an hour.

We saw all of the usual sights in Heidelberg, such as the old bridge, the churches, the famous pubs, and the student jail, along with some really neat lesser-known things, like the Alta Aula (Old Auditorium) of Heidelberg University. Both Kirchoff and Bunsen worked here, so the university has some pretty solid history -- it's no Princeton, but, hey, not too shabby. Plus, it's much older than Princeton. Like, 250 years older. Impressive.

The student jail was also very interesting. It was the small prison where they kept unruly students way back when, but it was an honor rather than a punishment. Our tour guide told us when the police came, it was an easy experience:

Police: "We're here to arrest you."
Student: "This is a rather inconvenient time; I'm off to the opera."
Police: "Ok, when may we arrest you?"
Student: "How's next Saturday?"
Police: "That should be fine."

In the jail, they covered the walls and ceiling with graffiti, drank heavily, and partied all the time. It was so much of an un-punishment that the spikes on the gate point *outward* -- to keep people from getting in.

On Sunday, I took a cruise on an entirely solar-powered boat a short distance down the Neckar river. It was a really cool piece of technology -- it stores all of the power it generates in batteries so it can operate at night or on cloudy days too. I also went to the top of a church steeple and took a bajillion pictures, and I got a few random people to take pictures of me. Sketchy, but it worked. Pictures are, as always, here.

I tried to watch TV last night for the first time here, but it didn’t work out so well. First, I tried to watch CSI dubbed in German. It was vaguely amusing, but I don’t follow the show enough to enjoy it without understanding the dialogue. I then stumbled upon MTV, spoken in English with German subtitles. The show was “Rock of Love 2,” which I gathered is sort of like “The Bachelor,” but without the thin pretensions of decency. (I’ve never seen “The Bachelor,” but I can imagine.) I was originally attracted to the show by the fact that I could understand what they were saying, but I was quickly repulsed by the fact that I could understand what they were saying. Here’s a bit of dialogue to give you some idea of what this show is all about:

Fully-Tattooed-Arm Girl: “Why are you calling me a stripper?”
Vapid Too-Much-Makeup Girl: “It’s your profession!”
Fully-Tattooed-Arm Girl: “Yeah, but you keep repeating it.”
Vapid Too-Much-Makeup Girl: “I give up.”

Me too, Vapid Too-Much-Makeup Girl. Me too. I went back to reading a Nature paper. I love science.

Christina turned me on to MIT's Open CourseWare, so I've been watching some biology lectures over dinner. It's a pretty cool concept: you're able to download all of the lectures and course materials from some selected classes for free, so you can essentially take the class at no cost. MIT's approach is also very slick and easy to use. I would recommend it.

Friday, June 12, 2009

Ganz Heidelberg auf einen Blick

It's been a long time since my last update, but it's not my fault, I swear! I had to fight with the hotel for awhile to get a new unlimited internet account after my first one mysteriously broke. I had been using free 24-hour accounts, but I finally got a new unlimited one yesterday! Unfortunately, it was on a holiday, so they decided to do maintenance on the EMBL network's connection to the internet. So I had no net access at all yesterday. Hopefully, this is all sorted out by now, so it shouldn't be an issue any longer... then again, now that I say that...

On Wednesday morning, I went to get a visa so I can actually work here. I had set up an appointment with the semi-fluent-in-English agent on Monday, so I went down to the Ausländerabteilung (Alien's Office of the Heidelberg Government). The office is located near Bismarkplatz, which is basically the center of town, so it was very easy to get to. The agent was very nice, and I pulled out whatever German I could in an attempt to seem respectable. Luckily, I had all of my documents in order so it was a fairly smooth process. (Though she did want a full letter from my HMO saying I was covered, which I managed to talk my way out of...) Since I did some paperwork before I came, I was able to get the visa that day, which was really nice. Unfortunately, I was not able to talk my way out of the €50 fee, which EMBL had said I might not have to pay. Whatever. I have a visa.

(Also, you should see my visa picture. You can't smile, so I look rather angry.)

On Monday, we had a first year master's student named Gavin arrive from our collaborating lab at the European Bioinformatics Institute (EBI). Gavin is from Vancouver and goes to UBC, but he is working at EBI this summer much like I am at EMBL. He's here for the week to pick Jan's brain (at EBI's expense!) for ideas relating to his thesis. He's really friendly, and it's nice to talk to someone who has an American/Canadian accent for a change.

Yesterday (Thursday) was a holiday here, so Gavin and I saw Heidelberg. We started out with Heidelberg's most famous attraction, the Schloß (castle). It's perched on the hillside overlooking the oldest part of Heidelberg, and it's actually quite massive. We had a great time touring with our rented audio guides (in English, of course). Pictures, as always, are on my Picasa album.

Next up was shopping for souveniers in the local market, then lunch at a local restaurant. I practiced my German with the waitstaff, and I got through the whole meal without saying a word of English to our server. I'm getting good enough at German to fool the locals into actually thinking I can speak the language. Of course, I then have to backpedal with a few well placed phrases, like "Wie bitte?" ("Pardon?") or "Sprechen Sie langsam, bitte" ("Please speak slower"). Still, I count this as progress.

Finally, we hiked back up to the hotel. It took us a good two hours and a little bit of getting lost, but it was fun. I'll have to do some hiking around here.

Sunday, June 7, 2009

Faul Sonntag

I was planning on seeing Heidelberg and its famous castle today, but the weather conspired to keep me indoors. Instead, I'll learn some German, read a few science papers and A Prayer for Owen Meany, and watch a movie.

Saturday, June 6, 2009

Zeugen Jehovas

Last night, I went out with Andreas and a few other PhD students. I met Peter, one EMBLer from Switzerland, who told me all about the Swiss system of government. Apparently, the country is run partly by a seven-member executive council, and the citizenry can force a country-wide referendum on any law that the parliament passes by gathering enough signatures. Interesting system.

After, Andreas, Peter and I went to a student party thrown by the politics department of one of the local universities. It was like an American party in that there was dancing, but unlike an American party in that the music was good and the guys danced as poorly as I do. They played all English music, including "Feel Good Inc." I met a crazy German guy who stands probably 4' 5" but could talk his way into anything... including the party, without paying the one Euro entrance fee. Impressive.

Today, I was eating lunch in my room (PB&J... hadn't been shopping yet...) when someone knocked on my door. I was surprised that anyone knew I was even there, but I looked through the peephole and it's an elderly woman and a girl about my age. Ok. Maybe some EMBL business?

Not quite. I opened the door and the girl starts speaking rapid French at me. I just kind of stared and looked confused. The elderly woman suddenly realizes I have no idea what's going on. "Oh, you speak English. We saw your last name and assumed you were French." (I guess they read it off the buzzer.) So she continues in English, and she asks if I have a Bible with me.

I was bothered by *French* Jehovah's Witnesses. It was awesome.

With my afternoon, I went out shopping and got a backpackfull of food. My favorite purchase? Garlic salt. Life is complete. I also tried to buy a prepaid cell phone -- they call it a 'Handy' here -- but I needed my passport to buy it, so I'll have to go back. Until then, I'll just have to entertain myself by chuckling silently anytime anyone says the word 'Handy.'

Thursday, June 4, 2009

Fotos...

Pictures are at http://picasaweb.google.com/jrvalcourt/Germany2009?authkey=Gv1sRgCP3eq9mszqv4KA# as I think to upload them.

EMBL, Abendbrot, und Heidelberg

What a quick few days! I started work on Tuesday and met the lab. There are three other lab members: Jan, the group leader; Adrian, the lab technician from Austria; and Andreas, the computational guy, also from Austria. Everyone has been really friendly, and they're making me feel like a part of the lab right off the bat. For instance, just yesterday a potential postdoc candidate came in and I attended her presentation. After, Adrian and Andreas talked with her about their research and sort of did an informal interview. Jan had me do the same -- though obviously much shorter and not interviewey -- and he even called me in to his office to ask my opinion on her candidacy. This was obviously kind of for show, but it still was pretty cool.

As for what I'm doing, it's a but hard to explain, but I'll give it a shot. I'm looking at certain structural variations (basically large insertions, deletions, or inversions in the code of your DNA, abbreviated as "SV") in the human genome. Now, there are certain spots in the genome where more of these events are observed than in the rest of the genome, so we call them hotspots. Likewise, coldspots are where few of these SVs are observed. I'm basically picking a few SVs and trying to (1) confirm that the SV exists using PCR (if you don't know what that is, don't worry), then (2) determine why the hotspot or coldspot is like that. Is it because these SVs happen more or less often in these places? Is it because these SVs are removed from some places but not others? Is it a selection process, where individuals who have SVs in certain locations don't survive, so we just don't observe them in those places because we get our DNA samples from adults? All are possibilities.

Anyway, back to everyday life. On Tuesday I went shopping for groceries at Famila Center, basically one of the Wal-Marts of Germany. It was exciting to figure out the bus system to get there, and buying all of my food in German was actually pretty easy. It's hard to disguise food too much. Since German food stores don't supply bags, I brought my backpack. I looked kind of sketchy, but it worked, and it was fun.

Last night, the lab took me out for dinner in Heidelberg. I had Flammkuchen, which I think means something like "flame cake." It looks a bit like pizza. It's made with a very thin, crispy dough covered in sour cream and toppings (mine, the "Traditional," had bacon and onions). After dinner, we crossed the Neckar river into Neuenheim ("new town," which is the nicer and more expensive part of Heidelberg) where we had eis (ice cream, in kind of a gelatto style). I had Himbeere (raspberry) and weiße Schokolade (white chocolate).

So life is settling down into a rhythm here, and it's been a great experience so far. More updates when I can...

P.S. Thanks to everyone who wrote to tell me that the rice in salt thing is not just German. Clearly, I just don't know American culture either.

Monday, June 1, 2009

Zweiter Tag


I woke up this morning at 3 AM. And 4 AM. And finally 5 AM, when I just decided I was up for the day. It was hard going to bed at what was until very recently 4:00 in the afternoon and sleeping until what my body still thinks is 11 PM. Oh well. Such is jetlag.

The hotel had what would be a very generous continental buffet by American standards; it even included some eggs and bacon. While I was eating, I noticed a few odd things:
  1. They put a few grains of rice in the salt shakers... presumably to give it a satisfying shaking sound? (If that was the intention, it worked.) Maybe this also happens in the states and I've just never noticed before, but it struck me as odd.
  2. The radio was playing Enrique Iglesias's "Do You Know," in English. Really, Germany? Really? You had to pick that particular bit of Americana? Actually, it seems that much of the popular culture here is imported; they watch American movies and TV shows dubbed in German. As my driver put it, "American film, good. Deutchland, eh. Turkey, ewww."
  3. The buffet had tons of bread options, with open face cold cut sandwiches as a prominent breakfast option. Everyone knows German sausages, but I hearby nominate German bread to share the title of best local food.
Then I packed up my backapck with water and energy bars and went exploring. It's a holiday here in Germany (the day after Pentecost), so no stores were open. It seemed like a waste to go into town today if I couldn't buy food, so I walked around the town where the guesthouse is (Eichwald/Boxberg). I also made the 20 minute hike up to the EMBL campus, but nothing was really open yet, so I didn't find much.

Then the afternoon was spent reading Dune, falling asleep (oops), sorting through all of the papers I've amassed, and unpacking.

Tomorrow is my first day at the lab! Getting excited...

Sunday, May 31, 2009

Willkommen in Deutschland

I've finally arrived in Germany! I am staying at the ISG Hotel tonight until my guesthouse apartment is ready tomorrow. The front desk receptionist is very nice; he got me food, so he's on my good side. The room itself is about what you would expect from a hotel in the states (though I do have a balcony, which is a nice touch).

The flight and connection went very smoothly. I left Boston at 7:00 PM eastern on a 7 hour flight to London, then switched to Lufthansa for the final hour to Frankfurt after a two-hour layover. Listening to all of the British security guards speaking was inexplicably funny -- either I really love British accents, or I'm simply overtired. On second thought, it was probably the latter; I managed a few hours of sleep on the plane, but that's all. I just woke up from a much-needed half-hour nap that lasted for four hours when I slept through my watch alarm. Hmmm. Maybe that alarm clock would have been a good idea. Luckily, I imagine I'll be pretty adjusted to the six-hour time difference tomorrow.

I went to the ISG Hotel restaurant downstairs for dinner, and I sat ouside on the porch because it was nice outside. I looked over the menu and ordered in German, and the waitress chuckled. In perfect English, she flips over my menu and says, "English is on the back, dear." Ouch. I hadn't noticed the English, but I would have ordered in German anyway. Honestly, I was getting bratwurst and french fries -- not too hard to decipher in German. This seems to be indicative of how the German people in this region operate: they all know English, and they like to speak it. Unfortunately, this makes it a little diffcult to practice my German, but I'm sure that with some work I'll pick it up anyway.

Heidelberg is very picturesque in places, though I've only driven through it at this point. EMBL is actually nestled in the woods halfway up a large hill that overlooks the town. I went for a walk this afternoon to explore, but there isn't too much around that I could find, except for an organized soccer league with a bunch of little scary-good German kids. No wonder we never do well in the World Cup.

Thursday, May 28, 2009

Only 48 Hours...

...until I ship out for Heidelberg!  Actually, even less than that now.  Unfortunately, I have only just begun to pack, get Euros, read the lab's papers, learn German, and do all of that other fun stuff that will allow me to survive for the next three months.  But I'm getting ahead of myself.

Let me rewind for a second.  I've just finished my freshman year at Princeton, and this summer I will be interning at the European Molecular Biology Laboratory (EMBL) in the Korbel group.  The only problem is that I've never been out of the USA.  Except to Canada, which doesn't count.  As of two months ago, I spoke zero German, and I'm going it alone -- I'm not travelling with any organized program.  In short, I'm just getting a job in Germany and seeing how it goes.

I decided to call this blog "Ich verstehe nicht," which is German for "I do not understand," or "I understand nothing."  I think this will in all likelihood be a pretty fitting summary of my experience at first.  I hope that will change by the end of the summer, however.  Hopefully, I'll pick up a bit of the German language and culture, along with the science I'll be shoving into my skull on a daily basis.  I'll let you know how it goes, on all of these fronts.  You can follow along at http://jimingermany.blogspot.com/

Wish me luck!