Brief Belated Earth Day Post

I have noticed recently that a few "evil" corporations have started to put forth an eco-friendly message. When empired, er... organizations, like Fox (with their new "Green it, Mean it" add campaign) and Walmart (with their recent focus on organic produce and doing well in taste tests against Whole Paycheck, er... Foods) start being "green" I have two simultaneous reactions. The first is to call bullshit. My uber-liberal educational background makes it hard for me not to assume it is just for show. My second reaction, however, is that even if it is just posturing due to mounting public concern about the environment it is a good thing. It means that all the bad press about being eco-terrible has worn off, or that they realize being green is something people actually care about. While I wish we would all just start cherishing nature and being better stewards of the planet because it is the right thing to do, I know that is not going to happen. It is going to take large corporations with big capital to actually make meaningful change, but they certainly wont do it out of the goodness of their "hearts" we need to keep their feet to the fire and make sure they are not just posturing. So here is a tentative cheers to Fox and Walmart, even though it makes me choke a little to say it.

Also, for some awesome science-art-earth inspiration check out what is happening at one amazingly awesome small uber-liberal arts college: Feet to the Fire

rapid rambling reflections

It is hard to believe that my first year back in school is almost at its end. 3 days of classes, 2 exams, and 1 paper stand between me and the relative relaxation of simply being a scientist rather than juggling doing science alongside taking science classes. I am looking forward to being able to focus on my research and getting ready for summer field work. I have really felt like classes were slowing down the research this semester. I also have a good feeling for what material I need to read up on to increase my background knowledge directly relevant to my research, and I haven't been able to make much progress in that while focusing on my classwork. I have 3 textbooks that I would like to read this summer. I am hoping I can get other students to read them with me. It is funny how much more likely I am to stick to something (be it reading a textbook or going to the climbing gym regularly) when I set a schedule with a friend. Somehow it is easier to come up short on promises to myself than to others (I wonder what a psychologist would say about that). I think I am finally getting over my inferiority complex and beginning to feel like I actually belong in this program, and have (or will eventually have) something meaningful (albeit probably small) to contribute to the general body of knowledge that is science.

a (not so) productive day

Things have been hectic lately. The lab work is ramping up, and finals and papers are rapidly approaching. I decided to be extra productive today. I got to lab early and got one reaction going and did some sampling for someone in the lab who is out all before my morning class. I came back from class and looked at my samples and did the next round of lab work before lunch. After lunch I set up another reaction and finished sampling for the person who is out before the whole lab went over to a nearby school for a particularly relevant talk. I came back looked at my reaction, and did the final bit of lab work in time to go meet with my cohort to discuss Darwin's Origin of Species that we have been reading in monthly installments. I was busy all day, and was all ready to feel like I had accomplished something... except that the reactions I was trying were not working. The DNA refuses to amplify, and I keep returning to square one. I will keep trying, but it kind of feels like all my efforts to be super-productive today were a waste. Sigh.

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)!

Data!

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.

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!

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.