Friday, December 30, 2011

Tubulin Prep and Meeting My Meat. 

Most of what I do in the lab involves manipulating DNA in little tubes, growing cells in culture dishes, and taking images of them with fancy microscopes.   The most striking images are inevitably those where microtubules are labelled (in the image below in white).

These filamentous structures are not only beautiful but extremely functional in the cell, and myself and thousands of other scientists around the world spend a lot of time studying how the cell uses them to carry out a variety of essential functions.

Several people I work with use purified microtubules outside the cell to study how other proteins interact with them and modulate their physical characteristics.   Microtubules are made of small proteins called 'tubulin', which stick together in an ordered way to eventually generate the long skinny structure.  Getting reasonably pure tubulin is not trivial.  It's just not as easy to generate and purify as some other proteins.  So the best way to get lots of tubulin has been to get it out of cells that have already made it naturally.  The most tubulin is in nerve cells, and the most nerve cells are in the brain.    So the best way to get tubulin is from brains.  And the best way to get lots of tubulin is from lots of brains, and the bigger the better. 

My friends Simone and Per, who are expert tubulin biochemists, recently decided to organize a large tubulin purification.  And until some brilliant person comes up with a way to purify large usable amounts of tubulin without brains, this means acquiring lots of brains.  Of course I jumped at the opportunity to help.  This sounds like real science. 

Now, it turns out that tubulin in brains doesn't freeze well, so the best way to get tubulin is actually from lots of big fresh brains.   It also turns out that thousands of big fresh brains are simply trashed in these parts each day in an effort to satisfy the German craving for Schwein.    The mission, then, was to go to a slaughterhouse in the wee hours of the morning, and get 100 fresh, warm pig brains, right out of the pigs.  

Coincidentally, at that time I was going pseudo-vegetarian, after reading the moving book 'Eating Animals' by Jonathan Safran Foer, and felt this would be a good opportunity to see the inner workings of a slaughterhouse.  Since I knew I would not realistically be able to cut out all meat forever, I thought I should at least know first-hand how it got to my plate. And who knows, maybe it would have some sort of impact.  I was starting to fall of the wagon. 

So Per and I got up one morning before sunrise to drive to the slaughterhouse, collect brains, and be back in the lab with enough time for all the biochemical processing to get the tubulin.  I think we were in the lab around 5am to get the supplies, where we found a friendly note from Simone:

She had arranged a chocolate basket and note for us to bring all the guys down at the slaughterhouse as a thank-you for all the brains.   

I don't have any photos from the slaughterhouse, I didn't even bother trying to take my camera in there.  As Per and I arrived in the dark the entrance looked like the registration lobby of a hospital: clean, white, cold, sparse, open.  After we explained we were the scientists there for the brains, our contact guy came out to greet us wearing a full body lab coat.  He then gave us each protective wear, including shoe-covers and hair nets.  We had several heavy containers of ice that the three of us then had to carry all the way to the slaughterhouse floor, which was a long trip though a maze of cool, white, fluorescently lighted corridors and locked doors, even more emphasizing the hospital feel.  Except that at with each door we crossed, a distinct scent registered stronger in my nose, undetectable at first, and overbearing by the last door.    At the last room before the slaughter floor, we passed over a machine that scrubbed our feet, and then through a door, where we were instantly confronted with a large, loud, crowded room with a thick suffocating stench, and absolutely buzzing with activity.  Dozens of workers, men and women, and hundreds of pig carcasses where whizzing around.  There was a long assembly line, which came in the room beyond our vision, twisted throughout, and back on itself, and then exited on the opposite side.  Our contact, probably younger than both of us, very matter-of-factly took us to the place on the line where the brains were removed, and then asked me a question.  With all the noise, and the guy's thick Saxon accent, I could just not understand what he was asking, but eventually gathered he wanted me to follow him to the other side of the room.  He very adeptly navigated across assembly lines of hanging carcasses being whisked through stations.  I had to pause often to get the timing right for fear of getting whacked with a carcass, but more so of somehow screwing up the whole operation.   Eventually he took me to another guy, high up on a metal grating, seemingly overseeing all the operations of the floor with a panel of knobs and phones. I was to come back to this guy when we were finished getting brains so that we could be led out of the floor.  

Once back at the de-braining station Per and I decided to dive into collecting.  We then realized that with all this protective gear, we were never given any gloves.  As we glanced around, we only then noticed that in fact nobody on the floor had gloves.   To ask for gloves would mean bothering three more people, interrupting the whole operation, and potentially receiving the scorn of the people in the room that were already looking at us with annoyance.  So we dug in with bare hands.   From our position, pigs came by cut in half.  They were whole about 30 meters to the left of us, where a guy stood with what essentially looked like a giant chainsaw with a firehose integrated. He cut the pigs, hung by their forelegs, perfectly in half, head to tail.  When the half pigs came by us, a woman was grabbing the brains and kidneys, and tossing them into separated cartons.  We then grabbed the half-brains, about 3 seconds out of the pig, and still quite warm, and tossed them into an ice-cold saline solution.   Occasionally a kidney would accidentally fly into our carton.  It probably took us 15 minutes to collect 200 half-brains. 
After we had packed all the brains in the car and ready to go, we were blocked in for several minutes by a huge semi truck - with a trailer containing dozens of pigs sticking their little snouts out through grates in the side of the truck, eyeing us in confusion.  If we had come 30 minutes later we would have had their brains in the trunk. 

Back in Dresden the sun had come up and a small team had assembled to process the brains as fast as possible.  The first step was to clean them up.  A cold room was set up to process them.

It was a cheerful environment as the team whistles while they work:

Ultimately the brains were liquified in a giant blender for further processing.  The official protocol says they should be blended until the consistency of a nice strawberry milkshake. 

More milkshake action, in the 4 degrees C room.  10 liters of brains in the end.

The rest of the purification consisted mostly of hours and hours of centrifugation steps and running protein over columns until reasonably pure tubulin was isolated.  One thing I did not foresee was that the incredible penetrating stench of the slaughterhouse would stay in in my clothes and skin.

Here Per and I had changed clothes from the slaughterhouse, but the stench of the worn clothes were so great we had to wrap them in plastic bags.  And were only in there for 30 minutes!  My skin even smelled for a day.  I can't imagine working 40 hours a week in that place.  I guess you get used to it, but that smell must be permanently attached to you. 

In the end the prep was a success, but we slightly underestimated our brain capacity and could have collected more in the beginning.  By making tubulin ourselves, we saved literally tens to hundreds of thousands of euros compared to buying it pure. 

As for the experience of seeing a slaughterhouse in action, and my newly found pseudo-vegetarianism, I was glad for the opportunity to visit.  It wasn't really all that disturbing to me while inside, as the pigs were already partially processed by the time they came in our room (dead, with no hair or skin, more like being in a giant meat locker).  It did kind put some things in perspective when the truckload of live ones showed up as we were leaving.  These are intelligent fully-aware individuals being processed.  And the sheer number was astounding.  

Our expectations for having meat for every meal really doesn't make sense when you sit down and think about it.  It's not sustainable, it's not in anyway necessary for health reasons, and as I've found out, meat actually tastes a whole lot better when you eat it on rare occasions, and when it's of the highest quality. I've gone from about 10 meals a week containing meat, to less than one a week on average.  I don't miss it, because if I really have a craving, or if I'm in a nice restaurant, or traveling, I go ahead and have some, preferably of free-range origin.   I'll never give up an occasional BBQ brisket or fresh homemade bratwurst, but I'm happy to give up cold-cut turkey (I cut out turkey, cold-turkey, so to speak, going from 4 sandwiches a week for the last 10 years to zero since I stopped), low grade hamburgers, canned tuna, and tasteless steaks that you just stuff in your face to make you full. 

Sunday, December 04, 2011

December in Germany

Okay, 9 months since my last post.  Anybody who read this blog regularly is long gone.  December is here, and along comes the wonderful Christmas season in Germany.  This winter so far has been unseasonably warm, and while I really can't complain, I do hope we get a good snowfall at least once before the holidays are over.  Two years ago I posted a round-up of the Christmas markets around Dresden with photos.  Last year I posted a time-lapse movie over-looking the Striezelmarkt.

Last year I got a few nice photos when there was some snow on the ground, and I'll post them now since it hasn't snowed this year.  The first is from the Neumarkt Christmas market, currently the best in Dresden:

Last year I went down to Nürnberg during the season, too, and luckily it snowed.  What a beautiful town.  

And the year ended with fireworks in Dresden


Wednesday, March 09, 2011

Cell Phone Camera Dump

About a year since the last one, random images and observations accumulating on my phone:

If you live in Germany, sometimes, even if you're leaning vegetarian lately, you just have to go for big hearty German meal, like Haxe, Saurkraut, Knödel, and Bier.

This is a photo of the sleeping situation I've encountered multiple times in hotels. This bed is two mattresses. There is a space in the middle. The frame of the bed is once piece. Who is this for?? If you want to sleep two together, or spread out alone over the bed, somebody falls in the crack. If you want to sleep two separately, you cannot separate the mattresses. On the other hand, I HAVE gotten used to the whole no covering sheet thing in Germany. Just a mattress covering sheet and a duvet.

This vuvuzela has been in our lab for years. It is not used anymore, but at one time it was the bane of my existence, and so I wrote "Use only in case of emergency" on it. And somebody got smart with an extra comment.

Speaking of vuvuzelas, last summer was of course the world cup. I happened to be traveling while Germany was playing, along with several other unfortunate souls. I think this was the Frankfurt airport, where not only was the gave live all over the airport, not only did they even pipe it in on planes, but the buses that took us to the planes had a live feed over the speakers. What you hear here is the drone of vuvuzelas over the radio.

This photo is also from the summer. I was at a conference in Heidelberg, and as I was leaving a full cafeteria of people on the last day after saying goodbyes to catch the train home, I walked smack straight into a clear glass door. I did not look back to see people staring, but walked straight on to catch a cab, pausing only to reflect on the pain and take a photograph of the welt developing on my forehead.

Flohmarkt on the Elbe. Cliff and Sarah rented a stand to get rid of their wares in preparation for moving back to the States. I joined and sold a shirt and a headset!

This was on odd, uh....snack I found on the shelves in the supermarket. Texas barbeque-flavored Taccos. My impression is that it's some sort of god-awful combination of tacos, texas BBQ, and some sort of shish-kebab. So I went to the Chio website to learn more. You should visit, it has a very cheesy sound intro followed by - and it changes when you reload - either a man or woman essentially having an orgasm. If you navigate to the Taccos page, you learn they "schmecken wie deftiges Texas Barbecue, kross über dem Lagerfeuer geröstet - ganz so, wie's die Cowboys lieben". riiiiiight.

The tortillas chips you can find in stores here are basically terrible, even though I've gotten used to one brand...but the Chio brand are the worst. They taste and have the texture of pure chemicals. And the cheese dip they market, I literally could not eat. Had to throw the whole thing in the trash.

In conclusion, not even the lure of a free trip home can get me to buy this product.

This is my favorite Hefeweizen. It's not super-easy to find in Dresden, you have to know where to go, but when you find it it's 79 cents a bottle I think. This photo was taken in a supermarket back in the States, don't remember if in NY or TX. Excited they had the beer, was subsequently saddened by the price tag. If and when I get back to the States this will be a hard transition.

Last month I went skiing in Austria. This was the view (click to enlarge; taken with cell phone camera - not masterful at panorama stitching) at the top of a lift where we ate lunch a few times. Unreal.

Monday, January 31, 2011

Singing Sinatra

This year's MPI-CBG Christmas party was a bigger hit than usual, and I think most people agreed it was due to a new format, which was basically much more informal, and with lots of live music, spearheaded by Tim Cross. Several months prior, Tim sent out an email calling for anybody with any sort of musical talent to sign up to play at the Christmas party. I sent an email back saying I'd always dreamed of singing Sinatra with a band, but had never sung before an audience, nor had been trained in any way. I did not expect Tim's response, which was "RIGHT FUCKING ON!!!", and a promise to assemble a band. I then attempted to back out several times over the next couple months, thinking I was in over my head, but Tim wouldn't have it. And so a band was assembled, and with a handful of rehearsals, but never with the entire ensemble present, we pulled off a number of tunes that night:

Tim is on bass, Per's on guitar, Coleman on the drums, Guillaume on paino, and Veikko on violin. These guys basically pulled this off without really practicing, and with me asking for stupid things like changing the key up a couple steps cause it was more familiar that way. It was quite impressive.

I don't have videos of any of the many many other acts from the night, but they were
quite phenomenal, sometimes to a jaw-dropping degree. It's amazing to see your colleagues really jam and wail.

Sunday, January 23, 2011

Dresden Neustadt - Old and New

One day in a random web walk I came across some old black and white photos of Neustadt on somebody's flickr page. It appears that they were taken in the early 90s - not long after the wall came down. Several seem to involve some of the first BRN (BunteRepublikNeustadt) festivals. Most of them include what most likely were long neglected and then rapidly abandoned buildings - most of which (but my no means all) have been since restored. I thought it'd be fun to try to identify the same places in Neustadt as a sort of puzzle, and then try to photograph them today, from the same perspective. Some of them were easy to find, some were difficult, and some basically impossible (closeups with little clues). Below are the ones I've found (I've made mine black and white too for better comparison).

The first is of Alaunstrasse, where there are now a couple of crappy bars. What used to be a bricked up part of the facade is now the entrance.

A closer photo nearby shows how another previously bricked-up entrance is transformed into....another soulless bar....

Also on Alaunstrasse, you see how the buildings have been renovated, and right now they are reconstructing the road here.

I like this next one. Böhmischestr., just around the corner from my flat. This was unmistakably Raskolnikov, with the characteristic window shutters (one of the decent bar/restaurants in Neustadt). To be sure I actually was able to find the exact same stones in both photos. Notice the new photo is the one with cobblestones. Those are about a year old. This is still one of the best streets to visit during BunteRepublikNeustadt - it seems maintains some of the original vibe.

This is another photo from Böhmischestr., now between Rothenburgerstr. and Alaunstr.
Notice there's a patch of cement on the new photo where there was some sort of piping in the old photo. It looks like the doors have been totally replaced, but keeping part of the design. Also, you see holes in the wall from an older sign exist on both photos.

Here's the corner of Louisenstr. and Alaunstr. Now mostly vegetation in front of "Katy's Garage". Which is not actually a garage, but.....another crappy bar.

Here are a couple shots from Sebnitzerstr. First, a "Kinderplatz", where the ground seems to be about two feet higher than it was 20 years ago, based on the building.

And a row of seemingly abandoned buildings

Finally a photo I took this month, but could easily have been from 1993, with the Trabant and graffiti....

Monday, January 03, 2011

Albertplatz Time-Lapse

Here's another one of these fun time-lapse movies. This one I shot from the top of the 'Nudel Turm' at Alaunplatz - a decent vantage point.

Albertplatz, Dresden from Alex Bird on Vimeo.

Filmed from the Nudel Turm, Dec 2010, with a NIkon D300S.

Music: "fire cut" by CIRC