COMBIO 2010

Yesterday evening I returned from COMBIO 2010 in Christchurch. There were several hundred participants, mostly from New Zealand and Australia but some from the U.S., Europe, and Asia. There were talks on protein structure and function, microbiology, genetics, signal transduction, plant biology, agriculture, and medical science. The keynote speaker on Sunday evening was Sir John Walker, who solved the structure of ATP synthetase. Monday through Thursday were jam packed with talks and poster sessions. One topic that I learned a particularly large amount about and became very interested in is drug design. There were some very neat ideas presented, such as designing compounds that mimick the transition state of the substrate-->product reaction and high-throughput crystallography to screen for small compounds that bind the active site of an enzyme. I also went to some talks on biofilms and plant-microbe interactions, the carbon and nitrogen cycles, protein kinases, mammalian development, and more. Most evenings there were drinks and social functions, and on Wednesday there was a gala dinner at an old air force base turned into museum. It was neat to see a bunch or scientists on the dance floor, including Sir John Walker.

On Tuesday evening after the talks I took a walk up into the Port Hills to the west of Christchurch. There were many hiking and mountain biking tracks to explore and good views of the city and Canterbury plain. I'm glad I discovered this playground of Christchurch because in previous visits to Christchurch I hadn't been particularly impressed by the city.

My talk on Wednesday afternoon, as part of the New Zealand Society for Biochemistry and Molecular Biology student speaker competition, went well. I got several questions at the end including one from Sir John Walker! There were five speakers total from the various regions and they all gave good talks. So far my masters project has been entirely in developing a method, so the other students all had more biologically relevant results than I did. The winner of the competition found a link between ascorbate and cancer.

Today has been very busy as I cleaned up my flat for inspection by the landlord, organized my cycling supplies, moved all my things to a storage unit down the road, and got things sorted in lab. Tomorrow I depart on my bicycle for the West Coast and on up to Hokitika, where I'm flying home from. It will be an 11-day trip, between 700-800 kms. No day is super long as I've planned it, so I'll have plenty of time to enjoy the scenery. Sigurd may join me for a day on the Otago Rail Trail!

Caples Greenstone

Last week I rented a car and drove to Fiordland with Sunmi, who was visiting for a few days. I picked her up from the airport Wednesday afternoon and we drove to Te Anau, a sleepy town that serves as a base for exploring further into Fiordland. We took a short walk around Lake Te Anau and visited the Wildlife Park, then crashed in a backpackers. We woke up early the next morning and bought hut passes and picked up provisions for our trek. The Kepler track still had snow covering the alpine section, so we decided to walk on the Caples and Greenstone tracks instead. We started the walk from the "Divide," a car park on the road to Milford Sound, as opposed to the carpark on Gleenstone Road where most trampers begin at the other end of the circuit. This allowed us to walk for an hour on the famous Routebourn track before bearing off on the Caples track. We encountered some deep mud pools and then a steep and rocky climb to the McKellar Saddle, where we had excellent views. We descended to Upper Caples hut, cooked up our first dinner of couscous and courgettes, then hit the hay. The next day we finished off the Caples track, following the river gradually downhill to the convergence of the Greenstone and Caples rivers. We had a great lunch at the convergence, with an awesome view of the long valley we had just walked down. In the afternoon we headed up along the Greenstone River. The track was a bit of a roller coaster, going up and down the side of the gorge carved by the river. There were some neat places to stop and gaze at the turquoise water. When we reached the Greenstone Hut in the late afternoon, the sun was out in full force and we sat on the porch of the hut, taking in the rays and the views and chatting to some students from Auckland who had just finished their studies. For our second dinner we had some rice pilaf and chocolate, and at dusk I did a little poi surrounded by snow-capped peaks, which was pretty awesome. It rained during the night and all the next day for our walk to the McKellar hut further up the Greenstone Valley. Stomping through mud, wading through streams, and in general moving at a brisk pace, we arrived at McKellar just about as the rain was ending. We changed into dry clothes, ate a lot of tortillas and pita, and played gin rummy into the evening, when two guys and a girl from Purdue arrived and claimed they were going to reach the Glenorchy car park, 30k away, that night. Crazy Americans--I wonder if they made it. In the evening the sunset was spectacular, and the old adage proved true as the next day dawned a sailor's delight, with clear skies and a crispness in the air. On our walk back to the carpark we met an Argentinian man who had cycled from Auckland and was attempting to reach Glenorchy by the next day to catch a bus. He was traveling on the Greenstone track, as it was the shortest route as the crow flies, but I imagine the track was a real challenge with his bicycle. We took a short side trip to the top of Key Summit, where we had breathtaking views of glaciers, valleys, and jagged peaks.

Reaching the car around noon, we stuffed ourselves with our remaining provisions and headed west along the Milford road. The weather was amazing for Fiordland, warm and sunny, and we took advantage by stopping often to gawk at our surroundings. We got a decent view of Milford Sound at the end of the road but to really experience the Sound you definitely need to go kayaking, take a cruise, or do the Milford track. Satisfied with our survey of Fiordland for this trip, we drove back through the Milford tunnel to Te Anau and then Dunedin on Sunday evening. Sunmi stayed until Wednesday, so she had a couple days to check out Dunedin while I worked in the lab. Tuesday evening we walked up Mt Cargill and flew my kite from the summit. It got stuck in the radio tower when we were trying to reel it in, but I was able to rescue it by climbing over the barbed wire and a short ways up a metal ladder.

The next few weeks will be filled with work as well as adventures. I have one week to get the results I need for the COMBIO meeting Dec 6-10 in Christchurch, where I am giving a presentation in the student speaker competition. When I return from the meeting I'll have to find a place to store my stuff for the next couple months, as I'll be in the U.S. for the holidays and med school interviews. Then it will be off on my bicycle journey from Dunedin to at least Hokitika on the West Coast. I've got to make it at least that far because that's where my flight leaves to go back to Maryland.

Happy Thanksgiving!

One year in New Zealand

I've now been in New Zealand for one year. It's been a great growing experience for me. In the lab I've learned an incredible amount and decided on a path to pursue in my biomedical research career. I've tried new hobbies, explored new places, made some good friends. I've even begun to embrace the Kiwi culture, despite trying my best to maintain my American-ness during my first several months here.

Next month is the Combio Meeting in Christchurch, the largest biology/biochemistry meeting in New Zealand. I've been selected as the Otago representative for the student speaker competition, which is very exciting. There were only two candidates in the Otago competition on Friday (the other was a PhD student working on honeybee genetics), but I came away with the W. Should be a fun and informative meeting, and when I return I will embark on an approximately 11-day cycle journey from Dunedin to Hokitika, where I'll fly home from. More details on that later, but I now have the necessary mountain bike, purchased for NZ$350 on TradeMe. The more immediate adventure is that Sunmi (Williams '08) is visiting New Zealand this coming week and we are planning a hiking trip on the Kepler track in Fiordland, possibly followed by exploration of Milford Sound.

Taking my geekiness to the next level

Halloween--another holiday that Kiwis have failed to appreciate completely. I saw a couple kids out trick-or-treating, but most people don't have candy ready by the door. Moms coordinate with each other and drive their kids around to the few homes with lollies available. The kids are definitely not going to get hundreds of pieces of candy per hour like I did. When Halloween rolled around each year, I was usually still working on the candy from last year's stash. This year in NZ I celebrated Halloween by attending a horror movie night. We watched Seven, Halloween, and Candyman, of which I though Seven was the best.

Also on Halloween I worked on the Habitat House, this time hanging gib (drywall). This is my favorite part of house construction because it requires a fair amount of spacial awareness to cut the pieces so that they fit to the walls and ceiling. It can be frustrating when a piece doesn't quite fit into place and you have to shave it off a few millimeters.

On Sunday I went to the movie theater to see Food, Inc. The main adviser to the filmmakers was Michael Pollan, and I've read a lot of stuff by him, so most of the information wasn't new. However, it was good to see pictures of industrial farming; in particular chicken coups. Farmers house thousands of chickens in one fully enclosed, dark,and remarkably unsanitary building. The chickens are so crowded they can barely move. But even if they weren't crowded, the chickens have been selected for to have massive breasts so they can only take a few steps before toppling over. Once the chickens are taken to the processing plant, you can see that the floor is covered with faeces and dead chickens. The movie also talked about beef processing and E. coli 0157:H7 outbreaks. There are only a dozen beef processing plants in the U.S. owned by four of five major corporations, and they are massive factory/assembly line operations. The workers have just one specific job like in an auto factory and are treated poorly and underpaid. When you eat a hamburger, you're literally eating meat from a thousand different cows, so it's now wonder that disease spreads quickly and it's tough to track down the origin of an outbreak.

I really like meat, but the number of reasons not to eat meat from factory farming are really overwhelming. If someone offers me meat at a dinner party I'll eat it, but I'm definitely not going to buy any from the supermarket on my own. I'm going to focus on fish and the occasional grass-fed organic beef and chicken you can get at a farmer's market.

I've made a DnaK rap and posted it on Youtube. Watch at your own risk.

My birthday and International Day of Climate Action

Friday was my birthday, and to celebrate I went bowling with a few folks from the lab. Saturday was the 350.org International Day of Climate Action. 350 ppm is the maximum amount of CO2 in the atmosphere that is compatible with life on Earth as we know it, according to American climate expert Jim Hansen. The idea is for people around the world to create elaborate displays of the number 350 and take pictures, which are distributed throughout the media. Hopefully those pictures will convince world leaders attending the climate conference in Copenhagen in December to agree on a powerful carbon tax.

An article in the New York Times mentioned that 350 ppm is an impossible goal to achieve, and so by publicizing 350 this movement is actually telling people that we've already blown it, so might as well enjoy life while we can. I think this is a valid point, but on the other hand the role of the 350 number was mostly to create a common rallying call for people who speak many different languages and provide a simple symbol of the climate change movement. The actual numerical value of 350 is not as important as what it symbolizes: a coordinated and passionate movement among people of all cultures on earth demanding action from world leaders to avoid catastrophic climate change.

I started Saturday by participating in a human thermometer on Baldwin Street to depict 350 ppm CO2. Somewhere between 50 and 100 people showed up for this morning event. Then I rode into town to the Dunedin train station, the site of the 350 food festival. I had only a few minutes to do a preliminary walk-around before the 350 riders bike ride began. We rode about 5k out to the Vauxhall boat club, snapped a few pictures with all the riders arranged in a 350, and then rode back to the food festival. There were hundreds of riders participating.

The food festival was similar to the usual Dunedin Farmer's Market, except there were additional workshops and a live band. I attended a workshop on beekeeping. At midday hundreds of people gathered in the garden in front of the train station for a photo taken by a guy in the bucket of a fire truck.

Here's a link to pictures on the 350 website. And here are a few I got myself.

Put the champagne on ice

This week I completed preparation of a variant of the DnaK protein doubly labeled with two fluorophores for FRET experiments. Unfortunately, I could not detect any FRET--reasons for this are 1) the so-called Forster distance for the fluorophores is too small for energy exchange at the positions they are located 2) the protein is not actually labeled with two active fluorophores 3) the protein is in too low concentration, a probable possibility since I lost most of it during troubleshooting of the preparative process. Disappointing, but I'm still optimistic I'll have it ready soon.

Today was a nice, relaxing Sunday. I began with a walk through the rhododendron dell in the Dunedin Botanical Garden. This week is the Dunedin rhododendron festival. I saw many pretty flowers and some really neat New Zealand parrots as well. I got a few pictures:



Then I continued on to the Otago Museum to see a special exhibition on West African art, music, food, and spirituality. An expert weaver was demonstrating his craft. The loom was a rather complex machine and it took me about fifteen minutes to get to the point where I thought I had an idea of how it worked. There was also an exhibit on how clay pots are made, and there was one interesting video showing a group of women making a pile of pots, covering them with dry grass, and lighting the whole pile ablaze to harden the pots.

From the museum I went to Kmart and bought a kite. The wind wasn't so strong today though, so I didn't get it flying for more than a couple minutes.

It is now exam season at Otago Uni, and most of the honors biochemistry students are really freaking out. The thing is that the exam period runs from last Friday until the middle of November. Some students have one exam now and another four weeks later. This seems incredibly inconvenient if you want to go home for the summer, yet most don't seem to mind. Apparently they intend on studying steadily for one class for weeks on end. And they're still going nuts! Some of them incessantly complain about how stressed out they are, yet they don't take any study breaks. All of this just boggles the mind because back home we had four days of reading period, then one solid week of exams. Having two exams in one day was not uncommon. A good 48 hours of intense studying interspersed with a naked mile or a polar bear swim was usually sufficient for one class. Students here are severely lacking in study skills and studying efficiency, and I think the Uni exacerbates the problem by giving them over a month to prepare. One week was plenty of exams--get it over with and go home.

This Saturday is the 350 international day of climate action. I will begin the day by participating in some sort of giant human scale at Baldwin Street, the World's Steepest Street which is a 1/4 mile from my house. Then I will cycle down to the Dunedin railway station to participate in the Spring Food Festival featuring Otago's best produce, beer, cheese, music, beekeeping, etc. At 10:30 cyclists in Otago are having a short 10k ride around the waterfront to rally the troops. In the evening is a showing of the film Food Inc. I'll give a full report next week.

In a shocking development last week, a student who I know in the biochemistry department was beaten unconscious by an intruder in her own home. She has no memory of anything in the past few years, including the biochemistry department, her studies, and her friends here. It's too early to say whether her memory will come back. Our thoughts are with her and her family.

Robo Rally

Last week I had a lab presentation, which has been posted here. If anything, you'll get the sense that I've been running many SDS-PAGE gels.

This weekend was the lab walk, dinner, and game night at Sigurd's house on the peninsula to celebrate three people's birthdays in October. We walked to Sandfly Bay, which I had visited a few months ago. There was quite a strong gale and so we learned why it's called Sandfly Bay--I was still grinding sand through my mouth on the drive back to Sigurd's place. The track down to the beach is a steep downhill through sand dunes, and when Sigurd started sprinting down we all joined him, which was super fun. At the beach we saw several sea lions and penguins; I got some dodgy pictures of the penguins using digital zoom. After hanging out at the beach for a while we trudged back up through the dunes and back to Sigurd's. I made pad thai which turned out quite well using this recipe. I had been practicing all week. We also had chicken casserole, sweet and sour pork, pizza, salad, and carrot cake. After dinner we all played Robo Rally, an obscure board game that Malcolm brought (He's a fan of many geeky board games and frequently travels to Cleveland, Ohio to participate in tournaments for the game "Advanced Squadleader," which is also a favorite of baseball pitcher Curt Schilling). Robo Rally is a very frustrating game in which you program a robot to turn and move along the board towards checkpoints, but are usually thwarted in your plans by conveyor belts, pits, crushers, and laser beams. Here are some pictures from the walk.



Here are pictures of some dishes I made last week. First is spaghetti--the sauce has mince, tomato paste, sugar, salt, garlic, oregano, and basil, then topped with parmesan. The sauce needed some white wine. Second is chipsi mayai rogo-style, which means fried potatoes, eggs, cheese, and tomatoes. Last is pad thai. I learned in my practice rounds that it is important to boil the rice noodles before you fry them, contrary to advice from the website linked above.