Run and Tumble

Spending the afternoon reminding myself that the excitement of reading through faculty research interests on candidate school websites is, fortunately, not indicative of the excitement felt when actually working on the research interests.

It’s going pretty well in the class I was worried about. There was a slightly rocky period for a few days where I retooled my brain to study for an engineering course (more drills, fewer lecture reviews). The first wave of practice problems really helped me dust off my algebra skills.  Barring mistakes made when I rush or try to cram too much math on too little paper, I’m doing ok.

The course is turning out to be excellent background. So far I’ve learned about hydrology, mass budgets, reactor design, and risk assessment. I’ve also re-learned chemical equilibrium, but in the context of environmental chemistry.

I’ve figured out what I’ve got to do each week to keep on top of the material. I’m rather proud that the list is pretty different and more comprehensive than what I would’ve come up with in my early undergrad days. I’m taking it as more proof that a lot of my problem back then was more about attitude than aptitude.

The biggest downside has turned out to be time. While engineering courses require about the same amount of things to study as other courses, each ‘thing’ takes much longer.  Compare going through a 10 card flash deck with a 10-20 min example problem. I’m not spending every waking moment on the course or anything like that, but if I don’t spend a significant amount of time each day on it, I quickly fall behind my schedule.

Just a few weeks until I get to visit the wastewater treatment plant. Is it weird that I’m looking forward to that?

I’m starting Intro to Environmental Engineering Science today. It’s a bit like a quantitative sequel to the Env. Sci. course I just finished. The previous course emphasized the effects of oxygen sag downstream from a wastewater outflow. This course talks more about how much organic matter in a waste stream causes a dissolved oxygen decrease of n% x meters downstream, but doesn’t go as much into the effects. I think they complement each other nicely.

One of the issues I’m dealing with in picking out a graduate program is if I want to lean more towards science or engineering. I’ve got strong urges to both learn and create. I won’t be happy building yet another bog-standard anaerobic digester, but I also won’t be happy determining the ratio of micronutrients that triple nitrate reduction if it is never used in the real world. There are plenty of programs that offer opportunities for both, but they are generally lopsided in their mix. This course will help me figure out which side I’d rather have emphasized.

I do have a little anxiety. I am fine with math, and agree with Lord Kelvin that if you can’t measure something, you can’t improve it. However, this is the first course I’ve taken since graduation that flexes my mathematical, rather than conceptual, reasoning abilities.

Remember when I mentioned that bugs in the genus Pseudomonas are the Br’er Rabbit of the microbial world, renowned for eating stuff that’s meant to kill them? Well, guess what they found in some mouthwash.

Do you know how sometimes you read good news, and know it was real, but were so excited you feel like your eyes played tricks on you and you need external proof? That’s how I feel about the GRE. I’m looking forward to getting the official score in the mail so that I know I’m not misremembering the score on the machine and did, indeed, kick its butt.

You can find a list of GRE Tips anywhere, but here’s a few I didn’t see anywhere, some of them are meta-tips.

• GRE practice books are incredibly useful, and can be expensive. However, any library near you is sure to have one.
• GRE practice books from years ago are still very helpful, but make sure the test hasn’t introduced new types of questions.
• I ended up choosing two books. One had really good review sections and test tips. The tips included specific GRE strategies. The other book was light on strategies, but separated practice questions not only by topic, but also by difficulty. An ideal book would have both.
• Don’t just read the explanations of the practice problems you got wrong. As you practice, note any questions that seemed really hard or took a long time. The explanations will often reveal a much easier approach. Recognizing common GRE math shortcuts will give you valuable time savings.
• Make sure you do the entire test at least once in one sitting. Near the end, the GRE is harder just because you’re exhausted.
• Exhaustion is exacerbated by the experimental sections you may get. Mentally prepare yourself to take yet another verbal or quantitative or both. Practice tests don’t prepare you for it and I nearly screamed when I thankfully ended what I thought was the last section only to be greeted by 30 more minutes of intense thinking.
• Work on your intuitive skills. I didn’t try this, but think it would’ve helped.  Try doing sets of practice questions in under 30s per question. This helps with both intuition and dealing with the inevitable moment you must guess to answer a question.

I’m going to be taking the GRE tomorrow. I’m satisfied with my performance on the practice tests and the amount of studying I’ve done. There was an initial increase in practice scores as I got used to the test format and dusted off various geometry and algebra facts, but they’ve now stabilized.

I’m still not sure if the GRE is complete bullshit, if it’s an idiot filter analagous to FizzBuzz in programming interviews, or if it is truly a good gauge of reasoning ability. I’m not even going to consider whether or not it’s a predictor of graduate school success.  ETS says yes, but ETS makes 160 USD per test and lots more on related services. One of the smaller reasons I want a high score is to be able decide if the test is useless, without worrying about having a case of sour grapes.

T-21 Hours until a sample size of 1 determines, in part, the next few years of my life. Wish me luck.

I finished some much needed yardwork over the weekend. My compost bin is now topped off with the copious spoils of a battle with overgrown straw and overambitious blackberry vines. That’s enough mass to get the compost into the thermophilic stage; I’m looking forward to seeing it steam in the mornings.

What’s really cool is that the heat is the waste energy from microbes metabolizing my kitchen and lawn scraps. Hot compost is essentially the same as a warm toilet seat (or, less icky, a cat resting on your lap). A bug’s tiny size, and therefore tiny energy output, compared with how hot compost can get (around 60 C) gives some idea of just how many guys are living in that 1/2 cubic meter. There are billions of bugs in a handful of compost and about a hundred handfuls of compost in my bin. It’s like I’ve created an environment which generates heat using a population that is equivalent in number, albeit not in heat generation, to 50 Earth’s worth of humans.  Matrix, eat your heart out.

No long excuses, the Holidays got me out of the update habit, but I’m back.

The good news is that I wasn’t out of the growing bugs habit. Look forward to reading about my new scope, the fate of my Winogradsky columns, exploding canning jars, adventures in labware, ballistic fungal spores scaring the crap the out of me, weird junk from my fridge, and darkfield microscopy on the cheap.

Also, I got a fancy polymer-walled eukaryotic fermentation chamber for Christmas. I’ve used it a bit and have performed  (repeatedly, very large n) bionuerological assays on samples which indicate successful metabolization of the substrate  to the desired product.

Academically, I got an A in the microbio course and lab. I’m currently taking environmental science.

It took me a few months, but I’ve also gotten over my fear of change and have actively started talking to some grad schools and signed up to take the GRE. I should’ve done it sooner. If anyone else out there is a) a nerd and b) needs some inspiration, here’s two sci-fi things that I’m not ashamed to admit helped me get my butt in gear. The Tapestry episode of Star Trek: TNG and Duke Leto’s speech to Paul about change, from Dune: “I’ll miss the sea, but a person needs new experiences. They jar something deep inside, allowing him to grow. Without change something sleeps inside us, and seldom awakens. The sleeper must awaken.”

The most credit, however, goes to my wife, who seems to know the right times to gently nudge and the right times to be patiently supportive.

Lab was the pick-me-up I had hoped for. The lab manager accidentally made the Pseudomonas stock broth way too concentrated, so our plates came back covered in the stuff.  They looked like giant, corroded pennies. The pigment was definitely neat. I took a whiff (and even convinced some lab mates to do the same), and while the odor of Pseudomonas aeruginosa is distinct andI can see how people describe it is a grape-smelling, from now on I’ll say that P. aeruginosa smells like P. aeruginosa. Interested students even stayed after lab to turn off the lights and watch it glow. It was not glo-stick awesome, but it was still nifty to see a flourescing bacterial pigment.

As a bonus, we actually got to use E-Tubes and API-20 kits (aka watercolors of pipetting hell) for enteric identification. We can’t use them for the unknown ID final exam, but they’re still way cool to play with.

I was busy figuring out weird ways to make a cheap, safe manual centrifuge.  The awesome wife said, “We have one of those, it’s called a salad spinner.”   I’m a lucky guy!

Update: This will be for separating, say, milk curds, not making pellets of Vibrio cholerae, so don’t worry, it’s still safe to eat at our house.