Thursday, June 17, 2010

Adventures in microbial ecology

I arrived at my summer course on Saturday. Not sure how many people are interested in microbial diversity, but this is my life for the next 6 weeks. It's odd being back in dorms and eating in a cafeteria again (metabolism is definitely not as intense as when I was 18). Sunday was pretty chill, but since then, things have been pretty swamped. Lectures in the morning, lab in the afternoon and evening, done for the night around 11PM. Almost every minute is planned out with exciting microbiology things. Monday night, the entire class walked out to a nearby swamp with significant methane production, waded in chest deep, and stomped around in the sediments releasing the biogas. The gas was collected in large stoppered upside-down funnels, which we used to make large (as in 5 feet high) flaring infernos. Unfortunately, the experience came with some very unpleasant odors. Tuesday, we went out to some nearby salt marshes and sampled sediment and water. There were a lot of really interesting microbial consortia, including lots of purple-pigmented bacteria.

The lab experience for tonight was making beer from kits. This also involved imbibing for most of the class. My classmates come from diverse academic and societal backgrounds, and are very entertaining to talk to. It's amazing. We do microbiology all day and all night, and when we have free time to talk, we mostly still talk about microbiology. Nerds all.

There is a beach nearby which has bioluminescent dinoflagillates that you can swim with, so that may be the next big adventure.

Tuesday, June 8, 2010


I've been at my summer course for over 4 weeks now. How time flies. We've finished with organized laboratory procedures and have moved on to conducting our own projects as we see fit. Everyone is really energized and the atmosphere is amazing, but the long hours are beginning to wear on me. I feel guilty if I leave the lab before 10PM. Everyone gets along well, and we have entertaining conversations about science and life. It's good to learn that everyone in academia has issues. It's not just me.

There is a "secret" beach near the site that is reached by a long dark path through the woods. If you go on a good night, the path is lit only by fireflies. And in the waves, the bioluminescent dinoflagellates turn the water to stars when you move. The stars in the sky are significantly less obscured by city lights than in most places I've lived, so the double luminescent effect above and below is enchanting.

Cafeteria food is monotonous, but could definitely be worse. Like undergrad dorm food, for example. We go out on weekends, so there's a little bit of variety. My parents and sister were in town for the fourth last weekend, so I got to sample all the local restaurants with them. The town has a fourth of july parade which is largely populated by scientists from the courses in town. Each course has a theme, and participants dress up as nerdy things. I was Acidithiobacillus thiooxidans, the bacteria I might study for my Ph.D. I also helped dress a friend's 3-year old as a phage.

Eggplant Lasagna
  • 1 medium eggplant
  • 2 Tbsp butter
  • 1/2 medium onion, diced
  • 4 cloves garlic, minced
  • 1 28-oz can crushed tomatoes
  • basil and oregano
  • 4 Tbsp butter
  • 4 Tbsp flour
  • 2 cloves garlic, minced
  • 1 cup milk
  • pinch nutmeg
  • 1/2 lb. lasagna noodles
  • 1/2 pound cheese of choice, grated (mozz is classic, but I prefer co-jack)
  1. Preheat oven to 350F. Cut the eggplant in half lengthwise and cut into thin slices. Drizzle with olive oil and season with salt and pepper. Arrange on foil-lined baking sheet and bake for 30 minutes until squishy.
  2. Heat butter over medium heat in a dutch oven. Add onions, and cook until brown, about 10 minutes, stirring frequently. Add garlic and spices and cook together for 30 seconds before mixing in the crushed tomatoes. Stew for 10 minutes and salt to taste.
  3. Melt butter in medium saucepan. Gradually whisk in flour. Cook the roux together for a minutes or two, then slowly whisk in milk. Simmer for 20 minutes until thickened. If you're going to store the white sauce, press plastic wrap on surface so it doesn't get filmy.
  4. Boil noodles according to package directions.
  5. Line a 13x9 pan with foil and spoon 1/4 of the red sauce over the bottom. Place a layer of noodles on top. Scoop on 1/3 of the white sauce and some eggplant then another 1/4 of the red sauce. Continue layering as you see fit, and cover the last layer with red sauce and shredded cheese.
  6. Bake for 40 minutes.
If you can't eat it all in one go, you can store single pieces in ziploc bags with no air bubbles and freeze. Re-heat by placing the bags in boiling water.

Off to summer camp

Lovely Santa Fe adobe architecture

I leave in two days to go to Massachusetts for a summer class. For 7 weeks. No oven. I am excited to learn lots of stuff and work my butt off, but sad that I won't be able to bake. Matt suggested that I make him lasagna for when I'm gone so that he can have easy dinners. So in the past few days, I have stocked the freezer with lasagna, chicken pot pies, enchiladas, cinnamon raisin bread, and sourdough bread. I must be nervous or something.

We spent the weekend visiting with some friends in Santa Fe. They were coming from Switzerland for a conference, so se made the (much shorter) 6 hour trek down I-25. Did you know there is a town called Wootton? And a Watraus. Go New Mexico. Our car does not have AC, which was less of a problem on Friday night that on Sunday afternoon. As engineers, we refused to submit to fate and bought a large styrofoam cooler that we filled with gas station ice and left uncovered to absorb heat in the car. When it got really desperate, the person in the passenger seat could even put their feet on it. Good thing, because it was about 95.

beautiful heirloom tomatoes at the farmer's market

We were supposed to eat amazing food there, but rather failed. The dinner place we went to was mediocre at best (and they wouldn't serve my friend's beer on their Swiss ID cards). We did have decent tamales from a food stand and granola at the B&B, but no huevos rancheros. And no green chile. I know, it's pitiful. I did really love the granola, and decided to try to replicate it at home. The lady said she used a mixture of honey, maple syrup, and molasses to get a dark flavor and winter spices for warmth.
Granola from Casita del Toro B&B. Delicious

So here is how nerdy I am. I used my muffin tin to try out 12 different variations on a basic granola mix. I tested spice mixes in varying amounts (cinnamon+nutmeg and cinnamon+nutmeg+ginger) and four liquid mixtures (1/1/1: oil/honey/maple syrup, 2:1:1, 1:1:1 plus vanilla, and 1:1:1 plus one part tahini). I toasted some oats and almonds and mixed two tablespoons with one teaspoon of whatever liquid mixture I was using.

I had twelve lovely variations on granola. And I am embarrassed to say that they all tasted about the same. Experiment failed. So much for my scientific method. That said, I do make some pretty good granola, so here's a recipe.


  • 3 cups old-fashioned oats
  • 1 cup unsweetened coconut
  • 1 cup sliced almonds
  • 1 tsp salt
  • 1 tsp cinnamon
  • 1/2 tsp nutmeg
  • 1/3 cup vegetable oil
  • 1/4 cup maple syrup
  • 1/4 cup honey
  • 2 T molasses
  • 1 cup dried cranberries
*The ingredients are pretty malleable. Replace almonds with a mixture of other nuts (pepitas?). Try different spices. Use different ratios of the sweet liquids. Replace some of the oil with peanut or apple butter.
  1. Preheat oven to 300. Mix oats, coconut, and almonds on a baking sheet and toast in oven for about 10 minutes, stirring once or twice to prevent burning.
  2. Increase heat to 350.
  3. Mix spices, salt, and liquids in a small bowl. Pour over oat mixture and mix well. Bake for 20 minutes.
  4. Cool the granola completely, then stir in the dried fruit. Cranberries are my favorite, but cherries and raisins also work well. Just make sure you don't bake the fruit, or they'll be bitter.