Wednesday, March 31, 2010

Procrastination Fun

It is the end of March, which means it is time to revisit my March goals (for background on this see here and here). It also means that I have been doing this goal setting process for 1/4 of a year now! I think this means its time to share how I'm doing so far. I made a graph for this purpose. For each month "n" is the total number of goals that I set for each month. The blue represents the portion of those goals that I successfully completed, the yellow represents the portion of goals that were not completed, and the green represents the portion of my goals that I made some progress on, but did not complete. I am glad to see such a positive trend in my successes, however, I am disappointed that my "failures" rate is not decreasing. I am hoping by the end of the year to have a large enough data set to do some statistics with. I do like checking in at the end of each month with myself and seeing how I am going. Maybe I should add to the analysis types of goals (ie fitness, academic, relaxation, life maintenence, friends/family). It would be interesting to see if I am better at certain types of goals than other.

Ok... thats enough procrastination for now. Stay tuned for more super-nerdy analysis of my goals (or SNAMG for short)!

Sunday, March 28, 2010


I have data. We sent off one of my samples for sequencing and got the results back a couple of days ago. Now I need to start learning what to do with this type of data. It is really exciting to have this data because, while it is still very preliminary, it means that I have a springboard to start thinking about what might be going on in the environments that I am studying. It also means that our process of DNA extraction and amplification (from very difficult samples) worked, at least for this sample.

I like that scientific research comes in phases. First you have to plan out your experiments or your sample analyses. This often involves a lot of background research to figure out what other people have done to ask similar questions, and how they did it. Then you have to do the actual lab or field work. In the case of the lab work I have been doing, a lot of this feels like one step forward two steps backward because each time we figure one thing out in our procedure, there is another issue to deal with. We spend a lot of time trying to figure out why our extractions or DNA amplification isn't working, and deciding which of the 20 factors to tweak the next time around. If we get luck and pick the right one, things progress fast. If not, we can spend weeks or even months trying to navigate around some road block that is standing between us and the data we seek. Once samples have been collected, experiments have been carried out, experimental samples have been preserved or analyzed we are ready to proceed to the next phase... data analysis.

Once there is data in the picture the game changes. A new set of challenges arise because the goal in this phase is to figure out what the data are telling you. Sometimes this is frustrating because there is no clear story, and sometimes you realize you need to back up and get more data or slightly different data in order to really understand what is going on. In the world of genetic sequences that task becomes figuring out what hundreds of thousands of A's, C's, T's, and G's mean. There are databases to help you figure out what organisms are in your samples, but in environments like hydrothermal vents where so many of the microbes are uncultured and unknown these databases are of limited use. So now it falls to me to learn a new set of skills that involve computer savvy (using new programs and platforms), a thorough understanding of genetics, and I'm not sure what else. Bioinformatics... here I come!

After preliminary data typically comes more experiments and additional data collection. Eventually you decide you have enough data to tell a compelling story and then the next phase begins... writing. That one is a long way off, but it is the ultimate goal: to write up your results and get them published. In reality these phases often co-occur if you are working on various projects or various aspects of the same project. The way people do science very rarely occurs in the way that middle school science text books describe the "scientific method", but to me these phases represent different mindsets, and the transition from one to the next makes me feel like I have accomplished something.

I am excited because this data provides a peak into the next phase of my science... data analysis. It will be fun to not just be doing lab work for a while. It is intimidating and exciting to have a whole new set of skills (bioinformatics) to begin learning. This whole process has been one steep learning curve after another. It keeps you busy, and transition between phases prevents boredom.

Monday, March 22, 2010

World Water Day

In honor of world water day, take a few minutes and check out Annie Leonard's new film "the story of bottled water". If you don't already, skip buying bottled water and carry a reusable bottle...every little bit helps!

Thursday, March 18, 2010

Time well spent out of lab

On Tuesday I was walking to the middle school where I lead a weekly afterschool club for a group of girls on the broad topic of "ocean science". I was feeling a bit torn and overextended because this takes away an afternoon per week from lab work, which has been piling up lately. Additionally, the first few weeks of this club were a bit chaotic, and I wasn't sure how engaged some of the girls were. I was wrestling with whether or not I was actually doing something important, or whether I was just wasting time that should be spent trying to get DNA out of rocks that don't feel particularly like giving it up.

I arrived at the school to learn that my co-mentor had to quit the program, and that I was flying solo. I am a bit embarrassed to admit that I actually like it better this way... not because I didn't like working with her (I actually did), but because I am a bit of a control freak, and not having to cooperate and compromise with someone else is often easier for me. I was given a second high school student helper, and set off to do an exciting dissection activity with the girls. I started club by talking with them about how I had been frustrated not feeling like I was being listened to, and asked them for a bit more respect since the only reason I am there is for them to have fun learning about what I think are some of the coolest topics in the world.

I was pleasantly surprised at how club went. By no means were they all behaved perfectly, but when I asked for attention I got it, and more importantly, they were totally engaged in the activity. Mostly I think this is because it was a particularly exciting activity (dissecting sea stars - we don't call them star fish in our club), but it might have had a bit to do with the fact that I laid out for them ahead of time how I wanted things to progress. I told them we were going to walk through a few questions slowly together, and then they would be free to investigate on their own. My high school helpers were awesome, and everyone had a good time. I walked back to lab confident that the past 3 hours had been a worthwhile investment in these young women, and reminded that this aspect of science (call it outreach, teaching, or hanging out with kids) is not something I am willing to give up just because I don't have time for everything.

Saturday, March 13, 2010

Wonderfully Wet Windy Woods Walk

Saturday was cold, rainy, and windy. It was certainly a day to hunker down inside, but I was determined to spend some time in the woods... it has been far too long, and I had my mind set on some solitary thinking time. I do my best thinking outside in beautiful places; sitting on a dock looking over a lake, on a rocky beach, on a mountain top, in my kayak, or wandering amongst evergreen trees. I almost gave up on the idea of Saturday tree time, but decided it was silly to let a little rain keep me inside. I broke out the waterproof gear and hiking boots that I rarely wear these days and set off in search of a local park that I had heard about.

I didn't have a trail map, or even know where to park, but thanks to the maps feature on my iPhone I was able to find the place and start walking without taking too many wrong turns. I was prepared with water, snacks, more layers of clothes, a mini first aid kit, and a headlamp... just in case. Just in case what, i'm not exactly sure, but just in case.

As I started walking I was chilly, and began to doubt the sanity of my plan. However, I was determined not to let the rain get me down and I moved quickly and soon warmed up. I found a pond and stood watching sheets of rain dance across the water. I scampered over wet rock, moss, and lichen, squelched through mud and pine needles, and got off the trail to do a bit of exploring. It felt like I was the only person in the park, and I don't think I could have enjoyed if more if it was bright and sunny because I felt like I was experiencing a side of these woods that most people don't bother to get to know, and somehow that meant I knew them in a different way even though it was my first time there. I look forward to many more trips to this little oasis only 15 minutes from my house. Knowing that I can be in the woods in 15 minutes if I need to makes life a little bit better.

Wednesday, March 10, 2010

An unexpected lesson from a test

I had another experience today that offered insight into my experiences teaching. I took a test, the first timed math test that I have taken in 11 year (with the exception of the GRE). I came from yoga and tried to keep the mantra " bright, calm" going through my head, but the panic was hard to keep at bay. I could feel my heart begin to race as I skipped over question after question that I did not immediately know the answer to. Things that I knew were in my brain only minutes before the test were gone, and it appeared that they had taken with the the calm that I had intentionally cultivated in my yoga practice before the exam. Eventually I got to the last question of the test and the answer came right away. I second guessed myself, but then came back to the original, simple answer. With that came a bit of peace of mind. As I worked backwards through the questions I had skipped I was able to retrieve some information that had been missing upon my first read. Eventually I worked through the whole test, and at the last minute remembered something that allowed me to answer a big question that I had through I was going to have to skip.

Big deal. The point of my sharing this is not to complain about my stressful day, or even whine about how math is hard. Up until this year school has always been very easy for me, and as a teacher it was sometimes challenging to relate to my students who were struggling with the material or had test anxiety. This test taking experience, and the experience of being in a very challenging academic setting has shown me what it feels like to know the material, but not confidently, and has helped me understand why testing is a good educational tool for some and not others. I can see how easy it would be for a young student to give up on school relatively early if they had never know how good it feels to ace a test, or feel that you really understand something.

How's that for a silver lining?

Monday, March 8, 2010

Can I be a museum educator when I grow up?

I spent most of Saturday volunteering at the nearby museum of natural history. There was a geology festival and I got to spend the day talking to people about the differences between rocks and minerals, and talking about different types of volcanoes and volcanic rocks. I realized (or maybe remembered) that communicating cool information to other people really is one of my favorite things to do. It occurred to me that museum education would be a pretty ideal job for someone who really loves teaching. You get to plan curricula, spend time one on one with people who are genuinely interested in learning from you, and you get school groups who are excited about being on a field trip. Most importantly you don't have any grading to do, and you don't need to worry about teaching to a standardized test. Now clearly there are some downsides as well, specifically not forming relationships with your students, but from my one day it seems pretty idea. Now, I should stop daydreaming and start studying for that pesky statistics midterm that I have on Wednesday.