Postcards from an intellectual odyssey

hello... is there anybody out there?

2011-02-16T23:48:00.004-06:00

I am still here... surprise, surprise. I have been asked by a few people in the last week if I am still blogging. This makes me feel loved, but also like a slacker. I actually have been blogging a bit over the last few months, but not here. I contribute (more science, much less personal) to a blog called We Beasties that got picked up by ScienceBlogs a few months ago. This has been very exciting because it turns out that a lot of people actually read ScienceBlogs. Yes, this means I am "outing" myself here, but I think I am OK with that. Its not like my identity was particularly well hidden before, or that I wrote anything I mind being public. Anyhow, it's one of the reasons I haven't been writing much here.

I feel much more like a scientist these days than I did 6 months ago. I am beginning to formalize my research plans and goals, and feel generally less clueless. I am in the stages of preparing for this summer's research cruise, and also starting to think about my oral (scary!) qualifying exams that are going to happen some time next September... that reminds me, I need to add "schedule quals" to my ever growing to-do list. Apparently professors schedule's fill up months ahead of time, and getting 4 of them together in a room is quite a scheduling feat.

I got to travel to (sunny!) California last week for a conference on microbial genomics and metagenomics. Basically I spent the week starting at screens (computer and projector) thinking about how to deal with absurdly large data sets that are generated by sequencing DNA from environmental samples.

So that's me in a nutshell (help! im in a nut shell! - sorry couldn't resist). If you are actually reading this consider leaving me a comment... I am debating whether or not to keep this blog going, and that partially depends on whether or not there is actually anybody following me anymore.

and... she's back

2010-08-23T20:26:00.003-05:00

It is hard to believe that August is almost over. I spent three weeks at sea, and it was great. Hard, but also amazing. I expected to be totally worn out by the end of it, and ready to get back, but instead I felt like I could have done more. I think that is a good sign. Now I am trying to settle back into life in the lab. Instead of focusing on one project for 18 hours a day I have 4 or 5 projects that I need to keep making progress on while also doing the whole personal life thing... much more complicated, and easier to get distracted.

The new year starts soon, which is also hard to believe. This is a big one: teaching, analyzing the data from my first set of experiments, and oh yeah... the dreaded qualifying exam. I also need to pick back up the goal setting. I kind of let that go for the summer, but now its time to put the game face back on. I a bit apprehensive, but mostly I feel good about it.

I went hiking this weekend. It was rainy and clammy, but fun. One big goal for this year is make time for being outside. Specifically I want to get up to the White Mountains regularly (is once a month realistic? I think so.) and start getting to know them. It is so easy to fall back on having too much work, but I think ultimately it will keep me happy and sane. I just have to remember to bring my trekking poles, and maybe get some new shoes, because my knees are still hurting!

See you in August!

2010-06-30T14:25:00.002-05:00

I head out to sea tomorrow to try to do some science. I have set up a separate blog for the voyage. If you want to follow along, it can be found here. I would love to hear from readers while I'm out there so comment away if you are so inclined. If not, I will be back at the beginning of August.

Peace out, homies!

Blog Carnival: zomg grad skool carnival!!!1

2010-06-26T21:02:00.001-05:00

I have just completed my first year in a PhD program. I started blogging a little over a year ago when I transitioned from one phase of my life into another. It started as a way for people from the life I was leaving behind to keep up with what I was doing. It has turned into an arena to reflect on the various aspects of grad school life. That is why I was particularly interested in writing for the zomg grad skool carnival!!!1. So, this is my attempt to impart the vast wisdom that I have gained this year (ha!) to the group of folks about to start:

This year has been a big one for me in many ways. I felt dumb much of the time, but am beginning to believe that many of us do… and its kind of the point. When you are studying something that hasn’t been figured out there are no easy answers. Additionally, when you are surrounded by people who have been working on their projects for longer than you it is very easy to fall into the how-will-I-ever-know-as-much-as-they-do mindset. I took something that James Watson (I know, not the best role model, for many reasons) wrote in his autobiography (much of which was incredibly pompous). I don’t remember the exact quote but it went something like, if you surround yourself with people who are smarter than you, you will learn much more than if you are the smartest person in the room. This helped me be ok with not being the top of the class. I learned a huge amount from the people that know more than me, which makes me lucky.

Having people to commiserate with is immensely useful in realizing that you are not alone in these feelings of inadequacy. That being said, I have realized that grad students (myself included) like to bitch, a lot. It is easy to dwell on frustrations, and while venting is important, it is also important to keep things in perspective. I often found myself thinking about how incredibly lucky I was that someone decided it was worth it to pay me to be in school. I earn money for learning stuff, and all the downsides (for me at least) pale in comparison to that.

I will give one piece of advice that might not work for everyone, but has helped me this year. Have a Plan B. Mine is knowing that I would be happy with a career as a middle or high school science teacher, or as an outdoor educator. Whenever things got particularly challenging this year, or I really felt like I was in over my head, I just told myself that no one is forcing me to be here, and if I decide I really hate it, I can always get a job as a science teacher that would be rewarding and probably fulfilling. Obviously Plan B would feel like a let down, and I would undoubtedly be very disappointed in myself if I left my program. I have no plans to do so (that’s why its not Plan A). However, simply having a Plan B takes the pressure off, and allowed me to keep the stress level relatively low this year.

In summary, to survive and even enjoy your first year of grad school you should…

Have a thick skin. Allow yourself to believe you are in the right place. Vent and commiserate, but not too much! Have a plan B.

People doing something to help the Gulf Coast

2010-06-26T12:31:00.004-05:00

I haven’t written about the oil disaster. It’s not really a spill. A spill is what happens when something gets a hole in it, or gets knocked over. This was a blowout and the oil is still pumping out… so spill is not the right term. Anyhow, I haven’t written about it despite it being on my mind because the details of who all is really to blame, what is being hidden from us, how bad things really are are tough to keep on top of and many people in the “blogosphere” are doing a good job. Carl Safina’s blog and Deep Sea News have been doing particularly good jobs of this. These are links to recent posts on each of these sites, but they both have many informative and thoughtful ones of late.

I am writing this because I have a semi-personal connection that I want to share. I did a semester in college with the Williams-Mystic Maritime Studies Program. A key component of this semester’s program are 3 field seminars: one offshore voyage, one west-coast road trip, and a third that has changed since I was in the program. When I was there we spent a weekend on Nantucket to get a taste of island life. In the last few years they have been taking the students to the Gulf Coast. These trips are typically an amazing combination of experiential education (think lecture on salmon farming at a salmon farm), interdisciplinary education (you travel with your science, history, literature, and policy professors), cultural experience, and fun.

Over the last few years through the trips to the Gulf, folks in this program have developed strong personal connections to the community on Grand Isle, which is one of the places that has been hardest hit my this disaster. This community depends on the fishing, oil, and tourism industries for its livelihood, and all three are effectively gone. It has reached the point where the grocery store on the island may not be able to stay open. Because of the personal connections people in this program have built they have had many first hand communications with people on Grand Isle. I recently heard the director of the program (Jim Carlton) speak at a mini-reunion and he described the strange feeling of seeing the people he knows on the evening news over and over again.

People from the Williams-Mystic Program have decided to try to do something to help the folks of Grand Isle directly (very little of the BP money for helping people out of work has actually reached this community). A fund has been set up to allow the grocery store to remain open (therefore allowing people to remain on the island where they live) and establish lines of credit at the store for residents. Two people from the program have been sent down to Grand Isle to help set this up and try to document what is actually happening. They have set up a blog here that provides a nice perspective - that of non-media real people spending extended amounts of time on Grand Isle. If you have been wishing there was something you that would actually help the people affected by this disaster, please consider donating to New Englanders For the Gulf even if you are not from New England. Spread the world.

some welcome R&R

2010-06-20T12:25:00.005-05:00

I am spending this weekend in Maine relaxing. I am justifying this because we leave for the cruise on July 1st and that is when the science-marathon begins. (Funny how I feel I need to justify relaxation to myself. Luckily, I can rationalize just about anything.) Once we set "sail" it will be all science all the time. For the amount of money it costs to do this type of research, you sacrifice sleep and "down time", and I am totally cool with that. After the cruise is over, we will have time-sensitive samples to analyze, so the marathon will continue. I am fine with that also. It is hard to know how I will deal with that type of rigorous schedule, but I like to think I'll do alright. It may be illogical, but I am trying to rest up (physically and emotionally) ahead of time in the hopes of setting myself up for as much endurance as possible. I think the good food (aka mom cooking for me!), sea air, some tide pool time, and general relaxation of my family's place in Maine will be good for this.

Speaking of family, today is both Father's Day, and my big sister's birthday. I made my dad a 3 berry pie. I used to do a lot of baking, but haven't in a long time (one of the many things I have felt too busy to do), so it was really fun to do. It also turned out pretty well. I'll post a photo soon. I love being close to my family. I don't see my sister as much as I would like (and I have historically forgotten her birthday more often than I have remembered it), but its at least more than when I lived in Texas. I also talk to her more often then I did in Texas. I really think that the pace of grad school would be a lot more difficult if I didn't have them all supporting me, and relatively close by. (Just in case they're reading - I love you guys!)

In other news... I just summarized a cool new study that links sperm whale poop to the carbon cycle (and therefore climate change) in the Southern Ocean via microbial metabolism over at MasticatedScience check it out. I used as many different ways as I could think of to say "poo" without cursing (I think I got 7)... did I miss any?

Van packed - check!

2010-06-15T19:42:00.005-05:00

The Van - ready to ship

In about two weeks I head out to the west coast to spend 3 weeks aboard the R/V Atlantis doing research on the hydrothermal vents. Hopefully we will have Alvin with us... but that is not certain (looooooong story).

We have spent the last month preparing for this research cruise. Everything from radiation permits to hiring a crane to load our shipping container/mobile laboratory onto the truck, to labeling hundreds of sampling tubes, to ordering equipment, to fixing broken equipment had to be taken care of... not to mention designing experiments and anticipating everything we might need to carry them out on the ship.

The lab-mate who I have been organizing all of this with described it as if someone who had never baked anything was told to make a cake... its easy just mix the sugar and flour and bake it. That is how we have felt for a good part of the last month... lots of figuring things out along the way... it has been frustrating at times, but as I sit here our shipping container is fully packed and ready to be picked up tomorrow, and that feels good.

Science Blog Post Competition

2010-06-06T16:53:00.003-05:00

For all of you who enjoy science blogs... you might want to check out this link:

http://www.3quarksdaily.com/3quarksdaily/the-nominees-for-the-2010-3qd-prize-in-science-are.html

3 quarks daily is a cool blog that collects some of the most interesting internet-stuff in one place. They are having a competition for the best science blog post of the year. There are 80 nominated posts, and you can vote for your favorite. I have one post on there. However, whether or not you vote for mine, it is a great selection of science writing!

updates

2010-06-06T15:56:00.003-05:00

I have started contributing to another blog (in my spare time... ha). It is called Masticated Science, and the idea is to "chew" interesting research into bite sized bits that can be easily consumed by non-scientists. You can check out a recent post I wrote about a very cool recent study characterizing the life in a Mars-like hypersaline methane seep here.

In other news, the goal setting for the month of may was pretty dismal. My upward trend has taken a dive.

hectic.

2010-05-26T16:36:00.004-05:00

Somehow I assumed that after classes were over my life would open up and I would have free time to do things like read, or scrapbook, or hike, or sit outside and enjoy the sun, or even cook some good meals again. I suppose that any of you who actually know me will not be at all surprised when I say that none of that has happened, and that, somehow, that surprised me. Now that classes are over I have transitioned into finding-testing-fixing-packing-ordering-labeling-organizing-contacting for the upcoming cruise. I have prepared for extended trips before, but I have never had to plan for doing experiments on a boat, especially the kind of experiments that haven't been done before. This is a daunting task - equal parts frustrating, exciting, and confusing. I guess that is what grad school is all about though, figuring out how to do things that no one is going to tell you how to do, and coming up with what other things you should do alongside the ones you will, theoretically, figure out how to do soon... hopefully. Throw in some last minute grant writing and surprise potential structural issues with the sub we are supposed to be using on the ship and this week has already been crazy than most. I fear that the upward trend in monthly goal setting will not continue in May!

April Goals

2010-05-09T22:48:00.002-05:00

In one week I will be completely done with the coursework side of my 1st year back in school! I had one final this past week, wrote 2 papers (turned the second one in today) and have one final final next Saturday. Yes, Saturday... I don't get it either.

I am happy to see that the monthly goal setting seems to be working. Looking at the graph below I just realized that the year is 1/3 over. Where did it go? I am pretty sure it was January yesterday.

Brief Belated Earth Day Post

2010-04-26T08:24:00.003-05:00

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

2010-04-25T22:58:00.000-05:00

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

2010-04-14T21:28:00.003-05:00

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

2010-03-31T21:48:00.005-05:00

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!

2010-03-28T11:44:00.003-05:00

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

2010-03-22T19:04:00.002-05:00

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

2010-03-18T09:47:00.003-05:00

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.

Wonderfully Wet Windy Woods Walk

2010-03-13T20:03:00.004-06:00

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.

An unexpected lesson from a test

2010-03-10T16:51:00.004-06:00

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?

Can I be a museum educator when I grow up?

2010-03-08T15:46:00.003-06:00

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.

Rainy Day Therapy

2010-02-25T20:54:00.003-06:00

If you ask most people around me it is miserable out... cold, rainy, dreary. If it were a bit colder it would be a wonderful snow storm and a good way to end the winter. But, it is raining, raining, raining. The wilderness instructor in me calls this "prime hyperthermia weather". However, I am not in the wilderness, and I do not have to worry about hyperthermia when indoors is always nearby, so I propose a radical notion... it is actually wonderful out. Don't believe me? Follow these steps on your next walk home in the cold rain and enjoy experiencing the elements, the feel of your cold damp skin, and appreciate your warm home when you get there.

1. Walk with a friend

2. Skip until you get warm

3. Stamp in every puddle you pass trying to get your friend wet, make sure they do the same to you

4. Laugh loudly, try to laugh so loudly that people hunched over near you look up and maybe appreciate the experience, just a little bit

Getting ahead of myself

2010-02-21T10:08:00.005-06:00

The pacific ocean.

The view from our "guest office" at MBARI

I have been slacking in blog-land recently, but I have something to report. I want to move to California, at least for a couple of years... like for a post doc. Now all I have to do is finish my PhD. I spent the last week out in the Monteray area working with collaborators at the Monteray Bay Aquarium Research Institute. By "working with" I mean that I was being shown how to use a very complicated instrument that we will eventually get to play with in our lab and bring to sea. I am (mostly) confident that when said instrument arrives I can tinker with it without breaking it. Using this instrument is going to test both my molecular biology skills as well as force me to learn some basic computer programming. As usual, I am looking forward to the challenge.

This was my first school-sponsored trip in this grad program, and it was certainly exciting to learn about this cutting edge technology. I really did try to come up with a less cliche way of saying "cutting edge". My advisor gets serious points for deciding to send my science-partner-in-crime along with me for this training. It cost him some extra money, but the two brains being better than one will certainly hold true when the instrument arrives.

So... back to CA (ah... if only I could go back). The folks at MBARI seemed to really enjoy their work, and why wouldn't you when you got to have the above view from your office each day. I grew up in New England where we like to think that the weather makes us tough, and we are stronger for it. This leads to the mindset that "those Californians can't possibly appreciate all that nice weather, how could they get anything done?". I am certainly willing to go give it a try, and report back!

Molecular Biology Actually Works

2010-02-07T13:39:00.005-06:00

Up until this past Friday I was semi-convinced that molecular biology doesn't really work. Or, at least, that it was never going to work for me. Since I transitioned into biology from the world of Geology and Environmental Science I have been playing catch up in terms of learning lab techniques, some of which are very finicky. I can now say that it is very exciting when these processes actually work.

We have been attempting to increase the volume of our extracted DNA using a Whole Genome Amplification (WGA) kit. In contrast to the more common PCR which amplifies a specific region of the DNA, the WGA process amplifies all of the DNA in a sample. This is great if you have very small amounts of DNA, but the downside is that if there is any non-sample DNA present that will amplify along with your sample.

My science partner and I spend about 2 weeks trying to work with our WGA kit. In order to make sure we were really amplifying our sample DNA and not a contaminant that we inadvertently introduced we used water as a negative control along side our sample. If we did things correctly we should have seen amplified DNA in our sample and no DNA in the water control when we were done. However, time after time we had more DNA in our water control than we did in the actual sample. This was very frustrating. We tried everything we could think of to be more sterile, and kept getting the same result. Finally we contacted the company and they sent us a new kit to work with. The first time we used it we got good results! There was no DNA in our water control, and plenty of DNA in the sample. It is really good to know the process works, and now we might actually be able to send some DNA out for sequencing. I am beginning to believe all the people who have told me that in molecular biology you do something over and over and over and over again... and then, finally, it works.

a new month and a new semester

2010-02-01T18:54:00.002-06:00

One month ago I decided to do monthly goals and self-check-ins rather than make new years resolutions. It is time to see how I did with my January goals.

Overall I would say not too well. Of my 10 goals I partially accomplished 3 of them, partially failed at 2, and totally failed at the rest. As I expected, I did not have nearly as much time for myself as I thought I would. However, this was just month one, and the overall goal was to set more realistic goals. So, now it is time to decide what I will accomplish in February. I have made 7 goals for myself that should be doable. 2 have to do with family. 2 have to do with work. 1 is fitness related (sort of a 3-in-1 goal). 1 is to keep my room clean and organize stacks of papers that have accumulated over the last months, and the last is to write at least 6 blog posts. So far I like the monthly goal setting.

The academic semester has started up and my schedule already seems much busier than last semester. This is primarily because there is lots of lab work to be done before our summer research cruise. I am struggling with the voodoo-like nature of molecular biology, and really hope that things start working out soon! Everyone tells me that this is just the way it goes... you mess up a bunch of times, and then, magically, it works. I am really looking forward to being able to say "it worked!". Some day soon, hopefully...

Super Exciting Microscopy (SEM)

2010-01-24T21:23:00.008-06:00

The scanning electron microscope (SEM) is my new favorite toy. Ok fine, its not really mine, and I guess its not a toy, but I have to admit that I was just as giddy as a chile with a brand new Ticke Me Elmo (or whatever is cool these days) on Friday afternoon, when I got to play with one of these amazing tools. A light microscope is limited in resolution by its optics, but also fundamentally by the properties of light. The microscope uses light reflected off of the subject to see it and then the optics focus and magnify the image generated by that light. Basic physics proves that any object or feature that is smaller than the wavelength of visible light (380-750 nm) will not be detected by a light microscope. That is where the SEM comes in. An electron beam has a much smaller wavelength than visible light, and when it is used to scan an object the resulting image has much higher magnification than is possible with a light microscope.

The image below is the fungus Acremonium strictum.

This next image is a Stibella fungus growing on Manganese.

The next image is from the same sample (Stibella growing on Mn). I think we are looking at bacteria growing next to fungal hyphae (on the right side of the image) but I am not entirely sure. It is interesting that when looking at something familiar under a new level of magnification, it can be difficult to tell what you are actually looking at.

Below is another image of the fungus Acremonium strictum, but at lower magnification.

I am pretty sure that everyone in my group thought I was a total nerd when I excitedly exclaimed "yes!" upon hearing that one of our samples was dinoflagellates. These are some of my favorite marine plankton, and leave behind beautiful shells that accumulate in sediments and allow scientists to reconstruct past climate based on which species (or really morphotypes) are present. Here is one image that I thought was especially nice. The UFO shaped object is a dinoflagellate, but I dont know what species or type.

Here is an image from the same sample that I was able to make into a 3D image by taking a picture of the same thing on a stage tilted 3 degrees in either direction and then merged with a special program. Unfortunately unless you have 3D glasses, it wont be that exciting.

Fun with light microscopes

2010-01-24T14:43:00.004-06:00

Composite image of bovine endothelial cells created with fluorescense microscopy.

I spent three days last week participating in a microscopy workshop organized through a microbial sciences initiative at my school. It was interesting to meet others who different aspect of the micro-world. While I work with specific types of environmental samples, most microbiologists work on a specific model organism trying to figure out a specific process or part of that organism's physiology. Microscopy provided a common tool of interest to all of us!

This is an image of filamentous algae taken out of a Winogradsky Column, which is a great way to grow a lot of bacteria and other microbes in one location with very little work. We looked at many samples (compost, fungi, cultured organisms) under light microscopes but this sample was the most interesting to me to me because it was easy to find lots of cool microbes to take pictures of.

This is another image from the same sample. Here there are at least two different types of organisms, but I don't know what they are. The green is an alga of some sort, and the red could be a colony of purple sulfur bacteria.

After playing around with the basics of light microscopes and trying to perfect our focus, we tried our hand at fluorescence microscopy. This technique uses specific wavelengths of light to excite certain molecules within cells that emit light when they are excited. It is typically used for looking at samples that have been pre-stained with fluorescent dye (like the one at the very beginning of this post), but many of the organisms in the Winogradsky were auto-fluorescent so we were able to get some cool images by looking at them under specific colors of light. This green image is the same image as the one above, but with the red filter on. The organisms absorb red light, and reemit green light.

I looked at this exact part of the sample under red, green, and blue light. Each light excited different organisms, or different parts of the same organism. When you capture an image of each and merge the image you get something pretty cool!

Here is another example, but this time looking at a filamentous algae (shown in red) and a round one (shown in blue).

Stay tuned for even more exciting images from a Scanning Electron Microscope (SEM)!

Have you donated yet?

2010-01-19T23:02:00.001-06:00

On class and race issues, and their relevance to my scientific career, or not.

2010-01-06T11:25:00.012-06:00

This image provides an appropriate setting for the daydream described below.

Warning: the following post contains ramblings and daydreaming. Please comment if anything needs clarification.

I just finished watching a 4 part PBS/BBC documentary called America Beyond the Color Line, by Henry Louis Gates Jr. It brought me back to things I haven't thought about as much as I used to since my current graduate program. This film examines the state of black Americans 100 years after W.E.B. DuBois said that the problem of the 20th century would be "the problem of the color line". Gates travels through black America in this film (from Hollywood to wealthy black neighborhoods in Atlanta, to inner city Chicago housing projects and much more) and elegantly communicates a very complicated situation - race relations in America having come incredibly far since the beginning of the Civil Rights movement, but still having far to go. The film identifies a growing gap between inner city disadvantaged African Americans, and the growing African American middle class (and very wealthy) that have "made it". Much of the film asks questions about where to we go from here and how do we bridge this growing gap. There is no easy answer (obviously) and many interconnected approaches ranging from political changes, to localized mentoring and education programs, to a need for bigger dreams and belief that better is possible are all discussed.

So what does this all possibly have to do with me, a white graduate student studying deep sea microbiology? I am not totally sure, but the segments of this film that interviewed educators and high school age students resonated with me, and reminded me why I went into teaching rather than more grad school 3.5 years ago. It is easy to get sucked in to the world of research and academia and never look out. This is understandable given the amount of work and time required of a career as a professor or even life as a grad student.

I have worked with underprivileged students of various ages in a few different mentoring/inspiring/extra help/outdoor experiential ed programs, and it is something I love doing. I sometimes wonder whether I would have a bigger impact doing the science I am doing now (and whatever comes out of that) or through a career of teaching. I am honestly not sure I could hack it as an inner city teacher, and I sometimes feel guilty about that. I do know that I love working with kids, and really enjoy talking to them about how cool science is, and would like this to be part of what I do when I "grow up" (I like to live in a bit of denial-land where I am not yet an adult). I had so many wonderful opportunities growing up that inspired me to study science, and I would love to be able to provide similar experiences for youth who won't get them otherwise.

Back in October I wrote about a workshop I attended about how scientists communicate with The Public. One of the things that got brought up is how outreach-type activities are typically not valued in academia (at least not when it comes to hiring and/or tenure decisions) and that this is a reality that scientists like me (who think it is our responsibility to communicate not just with peer reviewed scholarly papers) have to deal with. Maybe I am cut out for academia and maybe I am not, but here is a day dream of a program that Future Me has started...

Located in the woods somewhere with water (maybe a lake or a river, but ideally a rocky sea shore) on a large tract of pristine land, but within a couple hours drive from a major metropolitan area (read - bad inner city school system) lies a campus that looks part farm, part school, part summer camp, and part laboratory. There is a ropes course, kayaks and/or canoes, camping equipment, cabins, and maybe a big fire ring. There are lab facilities with plenty of salt water tanks and touch tables housing a rotating selection of organisms and a good set of microscopes, and plenty of room to set up experiments. There is a garden that provides local organic produce and maybe even chickens for out kitchen and also provides educational opportunities. This is a property that I (or some very wealthy and dear friend) own and have built up. Hey, its my day dream so maybe I even built some of the buildings.

This campus is home to a variety of programs that have the following goals 1. bring urban youth into the wilderness, 2. get youth excited about science, 3. preach academic excellence, and 4. provide underprivileged kids with role models and connections that last a long time. I can many different types of programs occurring in this facility from a college semester or summer program to weekend or day trips for school groups. The coolest program offered is some type of collaboration with a program in the nearby city that targets a group of youth in elementary school and works with them through their college years on tutoring and mentoring and uses my facility for regular (annual? Monthly?) gatherings or mini-courses… who knows?

There are many programs that do things like this. Someone I know started a program of this type on his own that is particularly impressive. Some day I hope to go visit and learn how he pulled it off. I guess the point is that I am going to eventually want/need to be doing something other than pure science. This film reminded me of things that were definitely a priority at one point in my life that have become more of a passing interests/side project over the last few years.

In some ways it is all about your perspective. Being a geologist taught me to see things in very long time scales, time scales at which global catastrophic climate change might matter, but probably wont change Earth itself all that much. From this perspective, environmental issues are not about saving the planet, but about preserving our ability to live on it, and the environmental issues are the most pressing for humanity to tackle because all the social issues will be irrelevant if we are dead. ON the other hand that type of perspective can allow many of us (ie me) to ignore social issues that just seem too difficult to tackle.

I can’t help comparing two potential contributions that I could make to humanity: one being the creation of a wonderful program that is some fraction of what is described in the day dream above and the other being whatever cool scientific tidbits I might discover along the traditional track lying ahead of me in Academia. Depending on the perspective I look at these options with I can make arguments that either is somehow better. It is hard to know where I would have a greater impact (which is how I like to think of success). I remember as a child having very definitive opinions about just about anything (ask anyone who knew me before I was 18), but much of that certainty has vanished as I have seem a plethora of possible roads to travel (I have written about this before too). Maybe clarity will come, or maybe opportunities will arise, or not, and that will determine where life takes me.

Resolving not to resolve... sort of

2010-01-03T19:02:00.006-06:00

I hate New Year's Resolutions. I never keep them, or even remember what they were. I always feel dumb resolving to do something like "get in shape" or "make more time for me". I am curious what percentage of American women resolve to lose weight each year, and don't do it. That said, I really do like the process of reflecting on the year and trying to consciously make changes to improve the next year. I was thinking that setting goals might be a better thing to do than make a formal, intimidating, year-long RESOLUTION.

I have worked with numerous groups of students on goal-setting. I like to use a quaint little acronym (S.M.A.R.T.) that I became familiar working for NOLS. Good goals are Specific, Measurable, Attainable, Realistic, and Timely. I figured this was a good time to start practicing what I have preached. I sat down this evening with grand plans to make some goals for the year, but had trouble thinking about the whole year. Years that are now past seem to be very short, but the one ahead of me seems very long right now, and therefore hard to plan for or thing about as a unit. However, I did have plenty of things I wanted to accomplish on a shorter time scale. So, I made a list of 10 goals for January, and decided that monthly goal setting would be a pretty good activity. So after my initial decision not to make resolutions this year, I actually have one after all... I hear by resolve to make goals at the beginning of each month, and to revisit them at the end of each month.

For January I have 10 goals. One is to accomplish a lab safety project that I have been avoiding. One is getting to the next phase on a paper I am trying to write. Two have to do with physical fitness, specifically making time for climbing, and getting out on the ice at least once. One is to make sure I see a friend I haven't seen in a while. One is to visit family members a few hours away. One is about sticking with a new hobby of mine (scrap booking). One is to go hear local live music at least once. One is to make at least 6 blog posts.*

Each of these goals is doable, but I don't think I will accomplish all of them. I have a long history of telling myself I am going to do things, and then not doing them. Maybe this process can break me of that habit. I am hoping that thinking about what I get done and what I don't each month will help me figure out my priorities, and whether or not I am allotting them enough time, and, subsequently, better manage my time the following month. Make goals...evaluate...repeat... this might even lead to a spreadsheet and graphs! Now I just need to remember to reevaluate come the end of January, and each month thereafter. Reminders will be greatly appreciated!

*Yes, I know I only described 9 of my 10 goals. The 10th is complicated, personal, and takes place entirely inside by brain, so it stays private.

More holiday ruminations

2009-12-28T22:51:00.005-06:00

Two bloggers that I follow (FSP and Karina) have inspired me to write this post because we all share Christmas time birthdays. I wrote a bit about this before the holidays happened, but now that they are almost over I can say that it really was wonderful. My birthday was great because exams and such were over, and I was able to spend it with a few important people I don't see very often. In the past I have spent my birthday working and hectically trying to finish up before winter holidays, or at college when friends were either taking exams or gone already for break. As a child I celebrated my birthday in the summer because my mom wanted nothing to do with planning a winter party that close to Christmas (quite a brilliant move on her part I must say). This year my housemate threw me a party, I had no work to do, and my advisor told me not to come into work (lab policy: no coming in on your birthday)! These festivities really got me in the spirit for Christmas with the family.

While living away from my family for the last few years, these winter holidays were always a bit stressful because I struggled to fit in seeing everyone I wanted, and doing everything I felt I needed to do during the few days I was there. This year was different. I made the 20 minute trip to my parents house and stayed there for a few days. There were no out of town guests, and no trip to be made out of town. There was no dressing up, and no fake formality with people I am not totally comfortable with. Instead it was really relaxed. This is the first truly stress free holiday that I can remember!

I went back into the very empty lab today for a productive day's work, and now sitting on my couch there is no work to do... it is a strange feeling, and one that I am trying to enjoy and not feel guilty about because I know it wont last long. I had a long meeting with my advisor about my project today, and things are about to get busy! Here's to a cheerful ringing in of 2010!! Bring it on, I am ready to get down to work.

Internet Love (get your mind out of the gutter!)

2009-12-22T04:50:00.004-06:00

I love the internets... I know this is trite, but I really don't know how people functioned before it. I am specifically thinking about how people did science (the whole social aspect of the internet is another issue altogether). Forget how much more difficult it was to create a document (paper, thesis, dissertation) without word processing... I can't imagine trying to do research and find articles without academic search sites like ISI, Science Citation Index, PubMed, or GeoRef. I know that most universities have large paper journal collections for this reason, and that things took longer. Maybe people actually got more out of the articles they looked up because if you took the time to actually go find an article you might do more than just read the abstract, look at the figures, and maybe skim the conclusions. I wonder (and this is something that would be easy to look up... in all my free time) if papers published pre-internet, or even pre- lots of stuff on the internet, had fewer citations. I wonder if there were fewer papers published. If there were fewer papers published I wonder if the average quality was the same, or if all the e-resources have increased, or decreased the average quality of papers. How one would assess average quality of papers, I have no idea. I do wonder about how many new journals have been put out in the last 5, 10, 15 years as compared to the 15 years before that. Clearly, it is too early in the morning for completely comprehensible thought (I had to drop someone off at the airport at 5am), but maybe this January when things are quieter I will look up some of these things.

Thoughts... predictions.. more interesting questions?

Oh, I completely forgot to mention what spurred this: Yesterday I was able to google-chat with a friend who is currently in Antarctica doing research on glacial movements and change over time. She (as I understand it) pours bright red dye into cracks in glaciers and her colleagues, positioned in boats in various bays along the coast, wait to see if they see the dye come out. Sometimes nothing happens and they feel like they have waisted time and resources, but other times they learn incredibly cool stuff about the way water moves through large glaciers (rates, volumes, speeds, distances), which is very difficult to measure any other way. I think this trip is actually taking ice cores, but they may be doing multiple things. Anyhow, the fact that I was able to chat with her while she is in Antarctica doing all this full on burley fieldwork really struck me as amazing which started the "i heart internetz" train of thought.

Semester's end brain dump

2009-12-16T21:29:00.004-06:00

The academic semester has ended. I somehow thought that the pace of things would calm down once classes were over. I feel as busy as ever. Partly it is general holiday time hectic, but it is also the pressure to start cranking out the lab work, now that I have "more time". I find it hard to explain to people out side the university that, unlike in undergrad, I am not actually "off" now that classes are over. I am beginning to understand (although not yet agree with) the advice I have received multiple times - that classes are just a waste of time and get in the way of all your work.

I am not complaining. The fact that I have lots of lab work to do is good. I am getting more comfortable with molecular biology techniques. Now I just need to work some PCR voodoo and start getting some results! I also need to figure out if I will have time to volunteer in a local classroom again next semester. I should clarify... by "figure out if I have time" what I mean is decide whether or not to make time. I am beginning to realize that "when I have time" will never happen, and postponing things until then is pointless. I am the most productive when I decide that things have to happen now, even if there isn't really enough time for all of them. I think that part of being successful in academia (and certainly many other careers as well) is knowing that you are able to do more than you think you have time for.

All of this makes me feel guilty of course for not prioritizing family and friends at this time of year. It has always been my favorite time of year because I get Thanksgiving, My Birthday,Christmas, and New Year's Eve all in succession.

Thanksgiving is my favorite holiday because it is all about family for me. When I was younger and the world was blacker and whiter Thanksgiving represented hypocrisy and white oppression/extermination of native peoples. However, I have come back to truly loving it at its face value... a time to think about how lucky we are, and be with the ones we love, and cook! Cooking is huge in my family, and making thanksgiving dinner with my mom, and recently brother is something I look forward to all year.

The reasons for loving my birthday are obvious... its all about me! While I am feeling a bit of the "OMG I'm almost 30 where has my life run off to", mostly I am excited for a party, a visit from my boyfriend, and more friends and family time.

Christmas, (for me a secular holiday), is like a combination of Thanksgiving and my birthday... good food, family, and of course presents (giving and receiving). It is always a whirlwind, but (at the risk of corny-induced eye rolling) it is the time of year when I feel the most loved, and I when I think the most about how much I love my friends and family.

New Year's Eve is sometimes exciting, some times dramatic, some times disappointing, but always spent with friends. This year I will be spending it with some friends I no longer see regularly, and I am particularly excited about that.

Since classes ended, I have become absorbed in a time consuming, but very fun project that I have a feeling is going to become a hobby. I am making a Christmas/birthday present for a friend, and since they occasionally read this blog, I don't want to spill the beans as to what the project is quite yet!

This year I am feeling the holiday spirit quite a lot for two reasons. One, I have a particularly festive lab-mate who has been playing Christmas carols, baking cookies for the lab, and wearing cute cheesy holiday earrings and somehow pulling it off in a totally endearing way. Second, I am back in the Northeast, and it is cold! Winter never really felt like winter to me when I was living in Texas.

warning: completely random...

2009-12-10T23:53:00.002-06:00

A friend and I were instant messaging (ok fine, procrastinating) today, and somehow we started thinking how amusing it would be if the ocean was made of wine. This conversation turned into a discussion of what a great cartoon this fantasy world could make. Drunken crabs and fishes stumble-swimming all over the place... Yes, I am a biologist, and I realize that this is not actually feasable, but neither are talking sponges or deep sea fast food chains, and that cartoon has managed to take off and might have even taught some kids a bit of science along the way! If only I knew how to animate. This is what happens when exams start turning my brain to mush!

Do any of you readers have suggestions for things you would enjoy seeing on such a cartoon?

The mysterious love child of geology and biology: Hydrothermal Vents - Part 3

2009-12-04T09:01:00.002-06:00

Hydrothermal Vents 101

Hydrothermal Vents are chimney like structure that form along with new sea-floor at divergent plate boundaries in the middle of oceans. They form because an oceanic plate is being pulled from two opposite sides where it meets continental plates and subducts below. The oceanic plate splits apart in the middle, under miles of water. This splitting process allows sea water to come in contact with hot magma from below Earth’s crust. This hot magma forms new sea floor in the form of basalt. Basalt is a rock that is low in silica, unlike granite which makes up the continental crust and is much more buoyant. The water that comes in contact with the magma becomes super-heated and therefore able to dissolve lots of minerals that water doesn’t otherwise contain. Heat adds energy to a system which causes chemical reactions to speed up, and so many reactions happen in the presence of hot water that wouldn’t be noticeable otherwise. These hydrothermal fluids can be up to 350^oC (662^oF), which means that they would be gas (water vapor) under pressures that we are used to on Earth’s surface. However, because pressures at the sea floor bottom can be up to 345 times what they are at sea level, these liquids remain just that. As soon as the heated fluid comes in contact with cold seawater (2^oC, 36^oF) the minerals it was holding on to immediately precipitate out of solution (in a process that is the opposite of dissolving) and form solid rock structures. These sulfides make up the chimney-like structures that are characteristic of these environments. Minerals such as pyrite (fool’s gold) and chalcopyrite (a crusting mineral often confused with fool’s gold) coat the inside of these chimneys with shimmering golden crystals. Hollow tubes remain in the center of these structures, and the chimneys grow taller as more hydrothermal fluid flows through them adding its minerals as it is suddenly chilled by the surrounding seawater. Eventually the cracks in the underlying rocks fill in with new rock, or small earthquakes occur forming new cracks. When this happens one chimney “dies” and others begin to form. A single chimney might last 20 years.

The mysterious producers referenced above that were found to inhabit this extraordinary window into the deeper Earth are microscopic bacteria and archaea. Archaea are a relatively recently defined ancient group of microscopic organisms as genetically different from bacteria as animals or plants. These microrganisms, referred to as microbes or “bugs” (affectionately by microbiologists) garner energy from the dissolved minerals in the hydrothermal fluids described above. Some of these microbes thrive in the pore space of the sulfide rocks and are constantly bathed by incredibly hot, mineral-rich water.

The rocks that make up the chimneys, as well as the basalt crustal rocks that they grow on top of, provide a network of cracks and pore spaces in which the heated, mineral-rich waters mix with cold overlying seawater. The result is a warm and hospitable area called a diffuse flow zone that supports most of the life (animal and microscopic) in these ecosystems. The microscopic producers that convert this geological energy into energy that other organisms can use are called chemosynthesizers, chemoautotrophs or sometimes chemoautolithotrophs! While the terminology can seem like jargon it is actually very specific and explanatory. Chemo- means chemical, auto- means self, litho- means rock, and troph- has to do with feeding. By the same naming conventions plants and certain plankton are considered photoautotrophs, while we are considered heterotrophs, because we require organisms other than our self (hetero means different) for food.

Scientists do not know how life appears seemingly out of nowhere at new vents. Some have proposed that the carcasses of dead whales (whale falls) or sunken logs (wood falls) provide an intermediate nutrient source. Others have found evidence that there is an underground reservoir of microbes (the Deep Subsurface Biosphere) that survive in mantle material and come up as new vents are formed. Scientists have identified seven different biogeographical provinces of vents that all share similar species assemblages. Two of these provinces are dominated by the charismatic white and red tubeworms, but the others are dominated by various combinations of giant mussels, enormous clams, amphipods, shrimp, crabs, polychaete worms, huge barnacles, snails and anemones.

The mysterious love child of geology and biology: Hydrothermal Vents - Part 2

2009-12-02T20:45:00.001-06:00

A Discovery of Significance

In 1977 geologists made a discovery that changed the way we think about life on this planet. On a geologic research cruise to find places on the deep sea floor where the Earth’s crust was pulling apart (divergent plate boundaries) and study newly formed sea floor they found unbelievable assemblages of species. In this environment, thought to be devoid of life due to the lack of sunlight, they found diversity and richness that rivaled the tropical rain forests. There had been previous indications of life in these deep wastelands, but no one had expected that a significant amount of life could exist in the deep. Huge clamshells had appeared on videos of the deep taken by a robotic camera guided. This camera was attached to a Remotely Operated Vehicle (ROV) but the footage was dismissed as an anomaly. It wasn’t until scientists themselves physically went down to the deep in mini-submarines called submersibles, and saw thriving communities with their own eyes, that the concept of significant life on the sea floor became a reality.

People who have been down to see the vents in submersibles describe it as a totally surreal experience. A slow and erie descent through darkness punctuated by layers of neon light shows, much of which can not be caught on film. Dr. Bob Ballard was one of the scientists on the 1977 expedition that discovered the vents. He described it as follows

“We didn’t know we were going to make this discovery. I mean, my god, thats what makes it so amazing. We thought we’d find a crack in the ocean with water coming out. Big deal: that’s what surprised us. We didn’t know this was going to be as gigantic a deal as it was.”

These communities were something people had to experience in order to believe because it was contrary to what we thought we knew about life. The vast majority of exciting Eureka! moments in science happen in a lab. This discovery was so fundamental that it happened out at sea on a ship, rather than after samples had been processes and analyzed. The thrill the geologists on board felt at encountering something so novel, must have been something like what Charles Darwin felt when he came across creatures in the “new world” unlike anything he had seen before. There are few places on land where this type of encounter can still being had. The deep sea represents one of the last environments on Earth where the scientists can still be considered Explorers.

Prior to the discovery of deep sea hydrothermal vents, it was understood that all life on Earth was dependent on the sun, and could not survive without it. Period. It may seem that the existence of these verdant deep sea communities is little more than a bizarre exception to this rule. However, their existence forced a scientific re-evaluation of life and its evolutionary history on this planet (and potentially others) on par with the re-evaluation of the planet that occurred when early scientists realized that the world was not flat.

Living things are primarily divided up into producers (who make their own food), consumers (who eat other organisms), and decomposers (who break down dead organisms). It had been assumed and taken for granted that all producers made their food by converting the sun’s energy into sugars such as glucose through photosynthesis. Maple tree sap that becomes maple syrup is a clear example of this process. Producers form the base of all food chains and they tend to be present in ecosystems in far greater amounts (either in terms of numbers or overall volume of organisms) than the consumers. In a simplified view we can think about a single carnivore like a bald eagle. It feeds on animals such as snakes or fish which in turn might feed primarily on insects. If all of those insects fed only on grasses, you could imagine that a huge grassy field would be necessary to form the base of the food pyramid supporting a singe eagle. In the ocean it is much the same except instead of plants the surface waters are full of microscopic plankton that perform photosynthesis (phytoplankton) as well as slightly larger animal-like plankton (zooplankton) that eat the plant-like phytophankton and in turn feed smaller fish who feed larger fish and so on and so on. The one glaring exception to this is can be seen in the largest organisms on the planet. The baleen whales (such as Humpbacks) who filter unimaginable numbers of krill (shrimp-like invertebrates who feed on plankton) from the ocean on a daily basis. The blue whale is the largest animal that has ever lived on the planet, and it is able to grow as large as it does because it feeds low down on the food chain on organisms that are found in great abundances. If it had to swim quickly after fish it would not be able to eat enough to meet its energy demands.

The sun’s light energy does not penetrate more than a few hundred meters below the ocean’s surface, and because of this it was assumed that producers would not be found in any abundance at depth in the ocean. Up until the early 1980’s it was thought that the only creatures in the dark mysterious world covering most of our planet’s surface were solitary strange fishes that feed on each other or the organic debris that continuously rains down from the upper layers of the ocean where it was generated (directly or indirectly) from the sun’s energy. These alien organisms (and they really do look like aliens!) with their own lights to lure in prey, or jaws able to open far wider than their head to consume large prey were known, but they are few and far between. The world that people imagined at the bottom of the sea was a desolate one inhabited by rare monsters, completely dependent on nutrients from above.

The discovery of dense communities of tubeworms, crabs, snails, mussles, clams, shrimp and even fishes at these vents in concentrations that rivaled the rain forests meant that there had to be a totally new class of producer forming the basis of these bizarre ecosystems. There simply couldn’t be enough organic matter drifting down from above to support them otherwise. A fundamentally new type of energy pyramid had to be understood! The organism forming the basis of that pyramid had to be using a source of energy other than the sun to create sugars that in turn provided energy for the rest of the animals that otherwise would never be able to exist in such high numbers. It turned out that geology was the key. These perplexing organisms were tapping into energy from inside the earth, rather than 93 million miles away from it, in a process that remained undiscovered for the first 10,000 years of human civilization.

Stay tuned for Part 3: Hydrothermal Vents 101

The mysterious love child of geology and biology: Hydrothermal Vents - Part 1

2009-12-02T08:44:00.005-06:00

I have been working on an essay for a writing contest for the last few weeks, and thinking about it for a month or so prior. Last night I realized that I had been looking at last year's submission deadlines, which means that I completely missed the deadline for this year. D'oh! Needles to say, I was very frustrated with myself for this. I suppose it is better than missing the deadline for something important like the fellowship applications I have also been working on. I am going to post the unpolished essay, in sections, here. My overall goal was to express to a wide audience how exciting it is to study the oceans, and in particular hydrothermal vents.

The Mysterious Ocean

From space Earth is a glass marble swirled blue and white. The white cloud cover shows change and active weather processes, while the blue announces to onlookers million miles away the single most important defining characteristic of our home planet: it is covered with water. The seas cover roughly three quarters of Earth’s surface. The oceans also contain the majority of places on the planet where things can live. This is because the depth combined with the area covered provides a much more three dimensional habitat than the land. Rain forests have three dimensionality in the various layers of tree canopy, but the scale of that (tens of meters) is minor compared to the ocean depths. 80% of the biosphere (the portion of the planet where living things are found) is actually in the ocean below 1000 meters.

These deep sea environments are very challenging to study because we can't see them. The Hubble space telescope can see galaxies 15 billion light years away, but satellites can not take pictures of the bottom of the ocean because “seeing” through the water is difficult, since light only penetrates the top 50 meters. We have ways of sensing the topography of the ocean floor using satellites and sonar aboard ships, but we can not see whats there without sending down a some type of camera. This means that there are many snapshots, and make guesses about what’s between them. How many photographs would you need to understand what it was like on another planet? How many would you need to see before you felt like you had seen it all? We have more detailed maps of the surface of the Moon or even Mars than we do the sea floor. Anyone with internet connection can go to Google Mars and see images of individual craters canyons and mountains on Mars, but Google Earth can only take us under water in specific areas that have been well documented.

One way to think of how well we know what’s at the bottom of the ocean is this: If aliens found earth and wanted to see what it was like without leaving their space ship, they might take a sample from the surface but lowering some sort of bucket or jar and seeing what they pulled up. If they sampled somewhere over the United States and pulled up a bucket of corn, their best guess might be that the whole U.S. is one big cornfield. That is a silly analogy, but roughly illustrates how well we understand the deep ocean know. We know where the major under sea mountain ranges are, and we know that 80% of the worlds volcanic activity happens underwater, but the specific details are few and far between, literally. Scientists are constantly discovering new species in the deep sea, and they regularly find types of organisms that are very unique and that we know almost nothing about (this type of discovery happens only rarely on land). They are still discovering dramatically different types of ecosystems that were unimaginable only a few years ago. One discovery in particular stands out...

Stay tuned for Part 2: A Discovery of Significance

Who knew I would like 1st graders?

2009-11-30T18:46:00.002-06:00

I have been volunteering in a local 1st grade classroom once a week for the last couple of months. I run a weekly "science club" for the girls in two classes, while the boys have their club with male mentors in an adjacent room. I have to admit that I was not really all that into it at first. These kids are so young that it really felt more like babysitting than teaching. Also, a few of the girls are very clingy, and I just don't have the patience for that. The last two weeks I started to have a change of heart. I think part of it was learning how to keep the attention of a 7 year old, and part was my allowing myself to be a bit more enthusiastic. I remember one day walking over telling myself that I was going to enjoy it this time, and it worked. Anyhow, today was our last meeting, and I realized that I had gotten through to them. I had come up with some questions based on what we had been doing that I was going to make a game out of. I fully expected to have to lead them to the answers. Many of the questions were about vocabulary words I had mentioned a few times, and some were more abstract questions trying to get to the point of the experiments we had been doing. I was so impressed because not only were the girls attentive and not calling out (I told them I got points when they called out, and they got points when anyone got a question right) the got probably 85% of the questions correct on the first or second try! It was a very tangible way of showing them (and me) that they had learned a lot. Even better was the enthusiasm they showed when I asked them if they thought science was cool... all hands shot up and the squirms were basically uncontrollable. It was completely adorable. I realized that I haven't been wasting my time, and that some of these girls might actually benefit from being introduced to science in a fun way at such a young age. The dry ice fog was just the icing on the cake that made it a really great end to the semester. Part of me is worried that I really don't have time to volunteer, and that I should wait until I get more settled into grad school. However, when I think about it, I'm not sure I'll ever be less busy, and if outreach/teaching/volunteering is important to me I need to make it a priority starting now!

Trying on my rose colored glasses

2009-11-23T18:30:00.005-06:00

It has been brought to my attention that my last blog may have been a tad melodramatic. (What... me!) Just to clarify, my world is not coming to an end, and my thoughts of dropping out of grad school were mostly (I'd say 92.3%) in jest. I will chalk it up to my first real ride on the emotional roller coaster (please forgive the cliche, it really is a good image) that is, by all accounts, graduate school. I suppose I could institute a 24 hour waiting period before posting any emotionally charged blog post. But then, where is the fun in that?

In the spirit of Thanksgiving, I would like to end this brief post by stating how lucky I consider myself (for many reasons, but here referring to my student-ness). In a time when many are without jobs, or worried about security, my research has been deemed worthy of 6 years of support, and my responsibility is to learn as much as I can, and try to discover exciting new things. It really doesn't get much cooler than that!

A(nother) big 'ol piece of (wicked) humble pie

2009-11-18T20:57:00.004-06:00

Today I got the lowest grade that I have ever earned on a test. It made me feel like crap. Because of this, I may or may not get the grade for the course that I need in order for this course to "count". Everyone keeps telling me not to worry, and that it will work out, and that grades don't matter in grad school, but none of that really helps much. I have decided to work my butt off in this last section of the course, so that (for the first time all semester) I really feel like I understand the material. There is one more test left, and if I do well everything will be ok. I am not exactly sure how "well" I have to do to make everything ok, but hopefully I can do it.

I really don't care about the grade itself. This is a very challenging class, and I have some issues with the way it was organized, and I now realize it was not a good choice for an intro course in my new field. I am, however, stubborn, and in possession of a decent sized ego (fine, I admit it). So, this somewhat arbitrary grade that I need to earn is a matter of pride as well as practicality. Things will get complicated (in terms of requirements and such) if this course does not "count".

If it doesn't work out there is always plan B. In Plan B I go back to teaching middle school science. Plan B has started to look pretty appealing lately. If it weren't for that pesky feeling like a failure for the rest of my life thing, I might seriously consider it. Now its time to stop blogging and go type up my notes from class, actually do the readings (I should probably even take notes on them), and throughout all this I need to write down questions to ask the TA about everything I don't understand. Interestingly, this is more or less the advice I gave my students when they were struggling in a class.

A (hopefully) comprehensible explanation of something complicated or... why DNA is hard to read

2009-11-17T19:32:00.009-06:00

Before I became a biologist (ok fine, I'm not a biologist yet, but I'm getting there), I didn't think very much about methodology. I knew what type of information genetics could provide, and how that information could be used, but I had no idea how that information was gathered. I hadn't really considered how scientists got DNA out of cells, how they figured out what that DNA said, or how they actually determined, using genetics, how closely related various species are. I think I had a vague idea that biologists took samples from organisms, sent them somewhere, and got a genetic code back, which told them what they wanted to know. What I have learned is that this process (like most things in science) is complicated. I am still learning all of these techniques, so this is not a technical explanation (you're welcome), and I might even have a few of the steps not quite right, but I think it is interesting to visualize all the steps involved in a process that we might think just sort of happens in a lab.

In the type of work that we do, just getting the cells out of the rock or sediment where they were living can be difficult. Many of these organisms are adapted to live at high temperatures and pressures, and live deeply embedded in rock and aren't going to detach just because we scientists want them to. There are chemicals that help with this step as well as various regimes of shaking, spinning, heating and cooling. From there the next step is to lyse (burst) the cells so that they release their DNA (or RNA depending on what you are interested in). This can be accomplished with freezing and thawing as well as sonication (using sound to move particles), and more chemicals. When a cell bursts it releases more than just DNA, and so the next step is to use other chemicals to make sure that the cells' own enzymes don't break down the DNA (or RNA) that we are interested in. If there are lots of metals present in the sample they need to be removed with still other chemicals. Eventually you have (hopefully) isolated your DNA and you are ready to make copies of it so that you have enough to "read". One way this is done is with a PCR (polymerase chain reaction). In a tiny tube goes your DNA, loose nucleotides (raw material to make more DNA), an enzyme (does the actual assembly), primers (tell the enzyme where to start and stop building), water and buffer. Then the tubes are placed in a machine that runs them through cycles of heat and cold to (hopefully) stimulate the enzyme to make copies of the DNA by assembling the nucleotides in the same order they are assembled in the original DNA.

Lots of things can (and do) go wrong in this process. If you didn't have DNA to begin with, you will get no DNA after the PCR (obviously). If you use the wrong primers they won't match up with the DNA, and the process can't start. If the temperature is too hot or too cold, the enzyme makes mistakes and copies the DNA incorrectly or doesn't work at all. If there are too many metals in the solution left over from the sediment, the reaction will not work. If your enzyme has been stored incorrectly it will not work. When it doesn't work you simply try again, and again, and again until you figure out which step went wrong. Keep in mind that this has to happen for each sample you are dealing with.

Once you have your PCR product (amplified segments of DNA selected by your primers), it gets run on an electrophoresis gel. Basically you use electricity to move the DNA segments through a gel (kind of like gelatin). The smallest fragments will be pushed the farthest along the gel by the electricity and the largest fragments will move the least. If all goes according to plans, you see bands in the gel corresponding to different-sized fragments of DNA. Each band represents millions of copies of that specific fragment. At that point you use a gel extraction kit to remove the now-purified (all the same segment) DNA from the gel. At this point the DNA gets sent off for sequencing where various technologies that are too technical for this blog (maybe I'll try explaining when I understand them better... on the other hand, maybe I'll spare you that) are used to read the pattern of A's, C's, T's, and G's of each fragment. The code then gets sent back to the scientists who have to figure out how to assemble the various fragments of DNA into something that can be useful.

The final step is analysis. Depending on the question asked, this might be trying to use the genetic code to figure out how closely related two species are, or what organisms were in your sample, or what genes were present, or any one of a number of different questions. For each question there are multiple ways to search for an answer and in some cases different methods will provide different answers. Scientists need to understand the (often new) technologies used for the various steps so that they can properly interpret the data. It is not enough to simple know the code. A question as simple as "is species A more closely related to species B or species C?" can have different answers depending on what part of the DNA was amplified. Sometimes one gene can tell one evolutionary story, where a whole genome (all the DNA in an organism) can tell a very different one. If you only look at the one gene, you might never know. This is why scientists still argue about how certain species evolved and why phylogenetic trees (think family tree of species based on genetics) can be very controversial.

The point is not that science is hard (duh!), or even to make you think I am crazy for wanting to do all of this. However, maybe next time you watch CSI or Law and Order and the crime lab instantaneously delivers that key DNA evidence, you will realize that science doesn't actually work that fast, and you will know that it really is quite complicated!

Science that looks like magic!

2009-11-12T19:48:00.003-06:00

Image from: http://farm3.static.flickr.com/2013/1818381113_3ea6eeca57.jpg

I dont have much time tonight, because I have 8 papers to read for my 9:30am class. However, I had a good day and wanted to share part of it. Some folks in my lab and I are working on a project that involves trying to get DNA out of rocks that microbes are (presumably) living in. The rocks have been frozen, and the first step is to grind the rocks into a powder so that we can get at all the microbes that might be present within the rock's pores. The way we did this was very basic - mortar, pestle, and elbow grease. However, the key was not to let the rocks thaw out because we wanted to preserve the microbes as they were when the rocks were collected. In order to accomplish this we were pouring liquid nitrogen over the samples as we were crushing them in the stainless steel. Nitrogen is a gas at room temperature (~80% of what you breath in with each breath is dinitrogen, or N2). Nitrogen is a liquid at very cold temperatures, so when you put something in it, it freezes almost instantly. This makes it great for biology because you can freeze tissue samples before molecules start to react and change. LN2 (as liquid nitrogen is called) boils at -196 C (-321 F). When you pour it over something at room temperature it immediately starts to boil. I will bring my camera in next time I do this type of work (the above image is not mine, but gives the general idea) because it looked like a witches brew with nitrogen steam spilling over and down onto the floor as we worked. This is a similar (but more pronounced) effect to that created by dry ice (frozen N2). I really felt like I was in a Hogwarts potions class rather than a microbiology lab... awesome!

I just can't help myself, and I blame my mother

2009-11-10T21:15:00.004-06:00

My mother is terrible at saying no. I admit that I used this to my advantage many times growing up (I don't manipulate her any more, I swear!). I don't really believe in karma, but if I did I would say that my similar inability to decline interesting opportunities or requests is what I deserve for all the times I didn't allowing her to say no to me.

I volunteered my lab for something this evening, and I don't regret it... yet. I went to a meeting tonight at the nearby museum of natural history to discuss ways to engage students on campus more with the museum. At this meeting I learned that they have a series of family programs on weekends where professors, post-docs, or lowly grad students give presentations based on their research to a family audience. I was not really interested in spending my time and energy to engage the undergrads in the museum, but the idea of presenting out work to kids and their parents... totally exciting! I think I have gauged the personality of my lab well enough to know that I will not be doing this on my own, but I also think it is something I can handle if no one else is interested. The challenge will be to bring in enough of what we are actually studying to supplement a basic talk about how cool hydrothermal vents and the deep sea are.

I can see the presentation starting off with an image depicting how much of the planet is covered with water, then talking about how most life that we think about gets its energy directly or indirectly from the sun, and then moving in to how different things are in the deep sea and contrasting the barren abyssal plains with hydrothermal vents. Enter here all sorts of cool preserved vent organisms that our lab has, and maybe even some vent sulfide (rocks that make up the chimneys) samples to pass around. From here I could go into some of the specifics of what our lab does, but the challenge will be to present microbial metabolism to middle schoolers in an engaging, but not too oversimplistic way. Maybe I can just do the basic microbes are awesome shpeel.

I am excited about this, especially because the museum administrator I was talking about it with said that he has a lot of trouble finding people to present. The problem is, this could become a huge time-suck, because I know how much time I can spend putting together an interesting slideshow. I think that this kind of communication and outreach is important, and under-valued in academia, but I also know that my priority needs to be my research, and that I have to guard my time. I don't think this will put me over the threshold, but I am realizing that I am going to have to start thinking before I volunteer for this type of thing. I did stop myself from volunteering at the aquarium last night when I realized that 4 hours per week plus travel time really was a bit much. I just want to do it all, which has always been my problem, like I said I blame my mom, who is only now at age beginning to guard her time to keep her sanity and prioritize things like gardening and weekend trips to Maine.

An inspirational class... finally!

2009-11-09T22:29:00.006-06:00

The class that I have been frustrated with just got better! We have moved on to our third and final professor, and I am excited and motivated once again. I felt guilty for not really caring about the last section, the professor was an incredibly impressive scientist, who had been teaching this course for decades. I wanted to be the mature grad student who grasped fully how lucky we were to learn from this legend, and take in all I could. Instead, I was frustrated that he was no longer an effective educator, and his past accomplishments didn't seem all that relevant. When a class takes up half a day (commuting to a different school) it is frustrating when it doesn't seem like you're getting much out of it.

Today, however was different, and I think it came down to the craft of the educator. I sort of thought when I left teaching that making things fun and exciting was an important skill for a middle school (and high school) teacher, but that college professors were sort of above that, especially when it came to graduate level classes. Today I changed my mind. It could be that I have the bias of someone who is new to the subject, and that while my classmates have more background this particular style really resonated with me because of the novelty. The main thing I came away with was that this specific topic (prokaryotic cellular membranes) is important, interesting, and maybe even... fun? I keep coming back to my teaching experience, because more than anything that was what I wanted my students to think at the end of my classes; that science = cool.

This professor used analogy, talking about our classroom as if it were a cell to illustrate size and scales that are difficult to conceptualize and telling us he was going to try to get us to thing like a bacteria. He ran across the room, did little dances, and at the same time kept me frantically taking notes the whole time because he was teaching fairly complicated material. I know that this was his introduction, and I am betting that things will get more "serious" next class, but I am enthralled... at least for now.

Lesson of the day: Effective teaching methods apply at all levels, "higher" ed is no exception.

and the science begins!

2009-11-07T08:42:00.003-06:00

After a long week of finishing up a National Science Foundation grant application and tackling another take home exam on material I don't really understand, it looks like i'm actually going to start doing some research starting next week. I am excited because this is (obviously) what its all about. I really do enjoy taking classes, and I have a huge amount still to learn from classes, but original research is really what matters. The grant application was a valuable experience (even if I don't get the grant) because it forced me to write concisely what I am interested in, and how I intend to investigate it. Since this is a new field for me, and I am not yet familiar with all of the methods and instruments it was a challenging process. In the end I described a project that I am excited about and eager to dive into. I am about to start on two different projects in the lab each working with a different person. This will be great because the idea of figuring out all the methodology on my own is certainly intimidating.

Scientific Communication

2009-10-31T20:32:00.005-05:00

I attended a day long workshop today with Cornelia Dean (science writer for the NYTimes). She has recently written a book called "Am I Making Myself Clear?". It is a guide for scientists about communicating with non-scientists. The book is an easy read and definitely kept my attention. The workshop was definitely a productive way to spend a Saturday!

It was really interesting to hear a group of 12 PhD students struggle to explain to a "normal person" what they study in one minute without using jargon. I actually consider myself pretty good at talking to non-scientists (I did teach middle school for three years after all), and I struggled to come up with a coherent message. The idea that this is something we should think about before hand and have ready had not occurred to me.

It is interesting to think about how universities typically do not encourage or reward scientists who make an effort to communicate with the public or participate in policy discussions. In fact scientists who do make this a priority are often looked down upon by their peers. I suppose this is because that type of communication is not advancing their research, and therefore represents time not spent on that research. It would seem to me that this represents a somewhat flawed values system within the scientific community. I agree that our priority needs to be research, but I think that for the good of the world communication of that research (other than in peer reviewed journals) to the general public needs to be a priority as well. I think this is especially true for scientists funded by taxpayer dollars. Our discoveries belong in the public domain, and the idea that they somehow trickle out of our scientific publications and into the "real world" is inaccurate. This workshop made me realize that it isn't the job of the media to do this communication for us.

When I think about some of the scientists I most admire (Ed Wilson, Jane Goodall, Rachel Carson being the first few who came to mind) I think less about their discoveries and focus more on the books they wrote for general audiences, as well as the activism they dedicate(d) themselves to. I think I admire them in large part because they are/were truly gifted communicators and their writings possess the ability to make people care. As I move forward in my research I look forward to finding ways to share my stories. I hope I have stories to share! Stay tuned...

describing myself

2009-10-27T21:54:00.004-05:00

I had to write a blurb about myself today for our lab's website. It was challenging because I haven't started doing my own research yet, and I am not totally sure what I want to focus on, although I am beginning to develop some ideas. It ended up being pretty vague and not as technical as I would like, but I think this is as good as I can do for now...

I am interested in deep-sea microbial ecology, specifically in extreme environments (ie hydrothermal vents). I am working to constrain rates of microbially mediated metabolic processes that occur in vent chimney walls through the use of flow-through bioreactors in the lab. I hope to be able to extend these experiments into the field. I am interested in how these types of reactions may influence broader marine biogeochemical cycles. I am particularly interested in the role that vent ecosystems may play in the carbon cycle. I am also interested in the insights that high-temperature microbial life can bring to the search for life elsewhere in our solar system. I come from a geology/environmental science background, and I am fascinated by environmental overlap of geology and biology. It is my long term goal to increase our understanding of how biological and geological process interact in the deep sea.

Fall colors, and other things New England

2009-10-19T00:02:00.004-05:00

I spent a day this weekend in the woods of north-central Massachusetts. It was cold and crisp... perfect end of fall weather. I looked for bugs and found very few. I flipped over rocks in a small (freezing!) stream and didn't find any, and was equally unsuccessful under bark of a rotting log, and digging in the soil. I suppose it is to cold for them, but I am curious where they go to. I was reminded that fall is my favorite time in New England, and that (even though it is currently snowing... in mid-October) I am thrilled to be back living in the land of the wonderful Fall.

I learned something about Fall colors this weekend too. The yellow and orange pigments seen in leaves are there all the time, but are normally obscured by the dominant chlorophyll pigments. The gorgeous red, however, are a different story. The red pigments (phycocyanins, if I remember correctly) are made by the plant as it begins to dismantle its chlorophyll and retrieve valuable Nitrogen from the leaves before they fall off. You tend to see red pigments on the top and outermost leaves, and this is because it is triggered by light (so it doesn't occur as much in the shade). This red pigment (the supermodel of all New England fall foliage photo shoots) acts as an umbrella for the leaf cells that are doing the equivalent of removing parts from a power plant without being able to turn off the power source.

I also learned how to stitch photos together and create panoramic images. Here is one that is the opposite of a panorama, but I am not sure what you call that!

lessons learned about teaching

2009-10-10T13:21:00.005-05:00

In my daily classes and lectures I have been learning a huge amount, but not just about the scientific content being discussed. I frequently find myself thinking about whether the lecturer's style and presentation are effective, and what specific things I can hold on to to make my future talks better. I have started keeping a seminar notebook that I bring to all the out-of-class talks that I go to, and more often that not I write down hints about how to make powerpoint presentations engaging (for example start out by giving the audience a puzzle and offer a prize at the end for someone who figures it out), or things to avoid (for example, giving your presentation to the board and not noticing a question in the audience because your back is turned). I have even come up with a set of symbols for these notes so that I can flip through and immediately find all of the powerpoint hints, or all of the references I meant to look up, or all of the ideas about my own research that have come out of these talks. Yes, I am an organizational nerd for doing this, but I don't care! Flipping through my notebook and seeing the symbols I have created for myself makes me feel on top of things... and I'll take that in whatever small ways I can.

I have also been thinking about teaching methodology. This week I had a take home exam, and I can't decide whether I want to avoid giving this type of assignment because the professor created an absurdly frustrating test that was so open-ended that it sucked up as much time as you were willing to give to it (I spend about 15 hours before giving up), or if I think the professor actually created a really valuable assignment because it was a learning experience in itself rather than simply being an exercise in regurgitating details provided to us during lecture.

In one class this week we had a guest teacher who did a great job mixing powerpoint slides with posing questions to his audience, and writing things on the board. I have typically either done a powerpoint lecture, or done an interactive activity, but seeing this professor do both was very cool. The powerpoint had images and figures that would have been too difficult to draw on the board, but it also kept the professor from going too far off track. Simultaneously he was asking us questions (how would you test for X in this case?) and using the answers pulled from the group to guide the outline of notes he was writing on the board. While I was totally bored by the topic (experiments testing genetic controls on bacterial cell division) I was very engaged in trying to pick apart his methods. Hopefully I will be able to emulate them in the future! Unfortunately this was a class and not a seminar, so I was not taking notes in my seminar notebook... I guess this exposes a flaw in my elegant organizational system. :(

The idea of teaching students to think critically and providing them with the tools to teach themselves rather than teaching them facts is one that seems like an enlightened strategy in theory, but in practice I think is very difficult to pull off. Any thoughts on this from all you educators out there?

The Road Not Taken

2009-10-03T10:16:00.008-05:00

2 of my students scout for tent sites in the Wind River Mountains, Wyoming. June, 2007

Being relatively new to blogging, I am taking my first stab and writing for a Blog Carnival. Here goes...

The Road Not Taken

While I am fairly, ok very, early on in my “career” (having just started graduate school) the idea of alternate paths is one that I have mulled over quite a lot in the last year. I often feel torn between science and wilderness. While these are obviously not mutually exclusive, and often (wonderfully) go hand in hand, for me science had meant less wilderness. Specifically, it has meant no more teaching in the wilderness... at least not for a while. I used to lead backpacking trips for students of various ages, and the idea of being a hands on experiential educator is one that I toyed around with for a long time. When I was a classroom teacher I was very involved with our school’s wilderness program, and had I continued down that path I might have had the opportunity to craft new ways for young men of Dallas to connect with the natural world. I think this is incredibly important given our increasing disconnect with Nature (PLEASE read "Last Child in the Woods" by Richard Louv) and as the climate and conservation issues become more and more profound.

I remember as a NOLS (National Outdoor Leadership School) leading my group of 10 16-18 year olds down a steep rocky slope in the Wind River Mountains after an arduous 12 day of day of traversing a 3 mile (yes, 3 miles in 12 hours = immense frustration) scree slope full of house-sized boulders. We were rushing to beat a building storm. Our group got into camp and set up tents just in time for us to tell our students to get out of their tents and assume lightning position in the rain and hail (to avoid proximity to metal poles). Then, as hypothermia became a greater risk than the lightening (roughly 30 minutes later) telling our students to get back in the tents. It was a very difficult day physically, and emotionally. Clearly, my memories of wilderness education are not all wonderful, but after spending a month taking care of themselves and each other in the wilderness those students were more confident, more capable, better leaders, and were certainly Wilderness advocates for life. I learned more about myself, and my leadership style working for that organization group than i will in any other job... I’m certain. The flip side is that I was not doing science, and I missed it.

I decided to leave both classroom teaching (middle school life and earth/space science and high school marine science) and wilderness education behind when I applied to graduate school. I loved teaching about science, and especially talking about what scientists that I knew were up to, but I really missed actually doing science. The classroom teaching had allowed me the schedule to do wilderness based experiential education in the summers, but I am fairly certain graduate school will not.

There are things I already miss... now that I am a whopping 2 months in. Primarily I miss my my colleagues and students. I miss coaching, and watching skills and confidence grow outside of the classroom. I miss my former students running into my room to say hi (or possibly trying to disrupt my classes). I miss having a wonderful group of educators around to collaborate or commiserate with. I miss the fun and silliness that comes with middle school. I miss my after school climbing club.

However, I am somewhere that is almost overwhelming in its vibrancy. The almost tangible swirling energy and idea make it an incredibly exciting and energizing place to be. I had missed doing research while I was teaching, and now I am picking projects and taking classes, and learning a huge amount. Getting paid to learn is quite the luxury, and I consider myself very lucky for the opportunity! I don’t know where exactly the PhD route will take me, but I know that I will always be an educator of some sort. In some foggy crystal ball vision I can almost see the path not taken and the chosen route converging down the line a ways where I create a wilderness-based science school in some beautiful location, maybe overlooking the sea on the Maine coast.

fun found file

2009-09-21T18:35:00.002-05:00

I found this today while going through old files looking for something. It is clearly out of season, but since I have been missing teaching this week it is appropriate. Just a bit of background... the school where I used to teach had chapel twice a week for the middle school. Teachers were required to be there. This was my least favorite part of the job, but it really wasn't all that bad... usually.

A beautiful moment (winter 07?)

As the chapel doors opened out to the main green after the service today, one of the most wonderful moments of my thus far very short teaching career occurred. There door I was looking through framed the lit Christmas tree, and as the chilly air rushed in, we all saw the first snow flurries swirling around the tree. This was accompanied by the excited gasps of about 250 thrilled young men all in unison while trying to maintain the composure required of chapel. The older ones forgot for a second that they are no longer little boys. I hate to admit it but I almost teared up. Maybe it was because a teacher had just finished talking about his son who passed away 10 years ago. There was just something about the tangible kid energy and the visual expression of innocence and enthusiasm that really was beautiful. A colleague also noticed this, and said that it was a moment you would never experience if you weren’t a teacher, and that you couldn’t really explain it. I guess this was my attempt.

On missing Texas, and lobsters

2009-09-20T22:11:00.005-05:00

This is my parents and I at the beach by their new house in Maine. I promise that the navy blue theme was NOT on purpose.

This weekend I caught up with a few friends I left behind in Texas. Some former co-workers had a get together and they thought enough about me to give me a call! It meant a lot to feel remembered and missed, because I have certainly been missing them. I promised one friend a new blog post this weekend. I was psyched to hear that someone was actually reading my blog down there, but now there is pressure to write something interesting... thanks Nick!

I have started having Sunday night dinners at my parent's house. I have to admit that I really look forward to these evenings. Maybe because I was living far away from "home" for 3 years, or maybe because I have become a poor graduate student, but it is wonderful to be able to go back to the house that has always been home and have dinner with my parents. Tonight we had lobsters that my mom brought back from Maine. Lobster is something that has always been a special treat in my family. I remember learning how to eat lobster the right way when I was very young, and how my older brother used to try to trick me out of the best parts of my lobster. I remember having to "earn" my own lobster by showing my dad that I knew how to eat it without wasting any. At my old summer camp they had a lobster dinner on the last night, and I loved being able to teach people the proper technique. Yes, I can hear some of you now... I just like telling people what to do. I guess that might be part of it, but I also love sharing what I know with others... its a fine line though between that and being bossy. I've been working on walking that line years! Anyhow, now that my parents have this amazing house in Maine, I have somewhere just a few hours away where I can kayak, play around in tide pools (one of my all time favorite activities!), and eat lots of lobster.

More science next time... right now I have some Microbial Physiology reading that has been calling my name all weekend!

a comic to share

2009-09-13T14:18:00.003-05:00

title: "Drinking from a fire hose" - originally published 2/5/2007

I have found a new way to procrastinate (just what I needed). This website (www.phdcomics.com) is a hilarious look into the life of a grad student. I thought this one was especially appropriate given my post yesterday!

lots to learn and loving it!

2009-09-12T21:30:00.006-05:00

Bacteria are unicellular microorganisms that have, despite their extremely small size, significant beneficial and harmful effects on humans. This scanning electron micrograph shows the bacteria known as Streptococcus pyogenes, which causes strep throat, a common illness in humans.

In my first weeks in grad school I have felt like a sponge, learning new things just about everywhere I go... from just about everyone I talk to. Part of this is due to the fact that I have signed up to study microbiology knowing just about nothing about that subject. I am more of a geologist by training. I really feel like the proverbial kid in a candy store though. The more I learn about microbes, and their study, the better I feel about my choice of subjects. It also helps that just the other evening I heard my #1 science idol Ed O. Wilson speak and he said that if he were starting out as a scientist now he would study microbes and microbial diversity! Woohoo!

Did you know that your body holds more microorganisms than your own cells? Did you know that crazy drug resistant staph infections killed more people in the US last year than the Aids virus did? Did you know that there are about 5,000,000,000,000,000,000,000,000,000,000 (that’s 50^30) microbes on the planet? Did you know that there is more carbon stored in microbes living deep under the sea floor than there is in all the plant and animal life on land? Did you know that you have an entire ecosystem within your intestines (probably about 500 species of microorganisms) that is key to keeping you healthy, and that we have only begun to investigate how that ecosystem functions, and that your internal ecosystem is very different from that of the person sitting next to you (unless that person is your sibling or mother, then it might be similar)? The vast majority of these species are unknown and many of the ones that we have seen we know virtually nothing about. Talk about drinking from a fire hose! (I know, I am just full of cliches tonight...sorry)

Microorganisms were the only living things on the planet for roughly 2.5 billion (thats 2,500 million) years. Animals have been around for .5 billion (500 million) years, while mammals appeared 220 million years ago. Human beings only showed up roughly 200,000 years ago! I think what gets me the most excited is how little we know about these organisms, other than that they are hugely important for the function of ecosystems (imagine all the trash and dead stuff if there weren’t decomposers!), the function or organisms, and for understanding the evolution of life on Earth. My task for the next 6 years or so... discover something awesome about these organisms... more specifically the ones that live in and around hydrothermal vents! I had better get to work.

Poetic justice... or, why I deserve it

2009-09-11T13:20:00.004-05:00

This one is for my last year's students...

I had my first full week of classes this week. One story in particular is worth sharing: I am taking one class that I know is going to be very difficult, but I am excited to dive into a whole new world (new to me, that is) of microbiology. For each class our homework is to read an assigned published research paper very thoroughly. Part of the grade for the course is class participation. So far this all makes sense. When I learned how our class participation was going to be evaluated I was at first annoyed, but almost immediately welcomed it in the way you might welcome retribution from a friend for forgetting their birthday. The professor is going to call on us randomly and ask us very specific questions about the assigned paper. She is also going to record whether we answered correctly or not, and this becomes part of our participation grade.

This seems incredibly intimidating, but the goal is to force accountability and participation. How am I so sure I know what the goal is? Well, she told us, but also... I did EXACTLY the same thing to my students last year. I called on them randomly and asked them their homework questions, and recorded their answers as a reading quiz grade. Most of my students thought this was unfair. Hopefully they will take some pleasure in knowing that I am going through the same thing now! I can't wait to visit and tell them.

the return to student-hood

2009-09-02T08:17:00.003-05:00

This afternoon I am off to class. It is an interesting feeling, after teaching for three years, to be getting ready to be on the receiving end once again. I have gotten used to planning activities, thinking about the progression of topics, and yes making power point (well, keynote actually... to be a bit snotty) presentations that look just the way I want them to. The job of planning class and how best to teach various topics has been a wonderful challenge. Most importantly, getting students excited about science has been incredibly fun. But, now I have a different job. My new tasks are to figure out what the professor wants us to know for the test (that question I always hated answering as a teacher), stay organized and finish assignments on time, and carve out enough time for my research. The goal is also to have enough time left over to go climbing, hang out with friends and family, and generally stay happy.

Crab training videos!

2009-08-27T10:11:00.003-05:00

I posted yesterday about my student's awesome experiment training crabs. Here are two videos I took of Crab B (Bertha) in the training tank. Note that the crab immediately goes to the hanging metal sinker and earns its reward (a bit of fresh mussel meat... yum!).

summer reflections (part 3)

2009-08-25T12:56:00.003-05:00

Mountain top yoga... it is my new goal to do this as often as possible. I went hiking with friends the other day in New Hampshire. It was a bit overcast, and we were rain soaked on the way down. This was actually a nice break from the heat and humidity of Boston. It was wonderful to be in the White Mountains again. These forests feel familiar and safe to me in a way that the plans, scrubland, and vast open areas of Texas never did. I guess that is part of what makes many of us have such strong attachments to the regions where we grew up.

Reflections on summer adventures as summer comes to a close (part 2)

2009-08-25T12:44:00.003-05:00

I spent some time in Maine with my family before moving in to the new place. I was able to meet one nephew for the first time, and reacquaint myself with my other nephew who I have not seen in about 4 years (they live in Kenya). Taking my nephews into the tide pools was a wonderful experience. We found hermit crabs, green crabs, and even a lobster! At first my nephews were not so into getting wet and sandy, and the crabs were a bit scary. After they got more comfortable, however, they loved it! The above photo is one of my nephews not so sure how he feels about a sea star (Asterias forbesi) that my brother found while we were kayaking.

The unfamiliar is scary, and this is why we need to force young people into it. That should be one of the main goals of education. Not to frighten children, but to expose them to as many things as possible so that less is unfamiliar. If we wait too long prejudices are already established and it takes more than a morning walk through tide pools to expand the world and discover something wonderful.

Reflections on summer adventures as summer comes to a close (part 1)

2009-08-25T12:23:00.005-05:00

The island courses are over, and I have (mostly) moved in to the new place. It is in a wonderful location, and I feel very good about it. A few noteworthy things have happened that you might be interested in...

One of my Marine Environmental Science students who stayed on the island to take another class after ours finished up had an amazing experience that involved her research project from our class and the woman who was her scientific inspiration for the whole project. This woman (Karen Pryor) has written books about clicker training with dogs (among other things) and in one of them she wrote a paragraph about training a hermit crab to ring a bell for food. My student (Lily) had read the book and wanted to see if she could do the same thing. Lily used operant conditioning to train a Green Crab (Carcinus maenus) to interact with a metal sinker in order to earn a food reward. I have to admit that none of the teaching staff of our course really thought it would work, but Lily was so eager to try that we gave her the go-ahead. Anyhow, Karen Pryor just so happened to come out to the island, meet Lily, and hear all about this project. She was very impressed, and Lily was overjoyed! Dr. Pryor wrote about it in her blog and you can read about it here. Most students are not lucky enough to meet their idols when they are in high school. Most high school students probably don't have science idols in high school (I did - E.O. Wilson, still an idol!). I can only imagine what Lily will accomplish in the years to come and how much this experience will be worth in terms of motivation and inspiration! This is an especially wonderful story for me as a teacher. It is pretty rare to see so directly a class activity impact the life and future of a student's life.

Best Whale Watch ever...no, really!

2009-08-07T07:54:00.004-05:00

We went out on a whale watch yesterday with the class. I was excited, but didn’t have many expectations. I figured we might see a few shadowy figures in the distance and be convinced that they were whales. I could not have been more wrong! We must have seen 50 different whales, and we saw some incredibly close. Not only did we see whales up close, but we saw some really amazing behavior.

We blew past some Minke whales on the way out because the captain had been told about Humpbacks a ways out. We stopped to see some Finbacks chowing down on a huge bait ball. This also allowed us to see enormous numbers of Shearwaters and Wilson’s Storm Petrils sharing in the whales feast. After being thoroughly amazed by these examples of the planet’s second largest organism we went off in search of Humpbacks.

We came across a mother and calf and they shocked us by getting right up close to the boat and doing partial breaches. We were able to see the massive head if the young Humpback right next to the boat. We watched the two eat and dive for a while and then went in search of other whales. For a while we were all on sensory overload because in any direction you could see spouting or diving (showing us their tail). There were plenty of Finbacks around as well and even a few Minkes.

The grand climax came just about as we were getting ready to head back. We came across a group of 3 humpbacks that, after gorging themselves on baby herring, were incredibly playful. We were treated to flipper slapping in unison, synchronized dives, and lots of breaching! Seeing a humpback whale come all the way out of the water is not something I will forget, ever. One particularly feisty animal breached 5 times in a row. It really seemed like they were performing just for us. When we finally had to pull ourselves away two of the whales began to tail-slap the water repeatedly, as if waving goodbye to us. This continued until we were out of view. Truly amazing!

Check out the video that I put together about the trip: Whale Watch Film

A typical day on the island

2009-08-01T08:10:00.003-05:00

Written at 11:30pm last night...

Time moves fast on the island. The new course has been here for 5 days now, so the course is more than 1/3 over. It was a good, very busy day. We started with a survey lecture about ocean vertebrates, then had time for group project work (students are designing their own experiments in groups). We ate lunch quickly and half of the class went on a seal-viewing boat trip to a nearby island. They saw Harbor Seals and Grey Seals displaying many interesting behaviors. The rest of us did a second round of transects. This involved gathering chemical, biological, and physical data about tide pools on the exposed side of the island for later comparison with similar data collection from the sheltered side. Organisms on the exposed side tend to be dwarfed, and there is less biodiversity. It is a wonderful venue for discussing environmental factors that affect intertidal life. It was pouring rail during this collection, but the intrepid young scientists were not deterred. There were very few complaints despite all of us being thoroughly soaked, and morale was high throughout!

At 4pm the now dry students came to the lab for their lab practical. They had to memorize the Latin names of 30 intertidal organisms as well as different adaptations that each organism had that helps it succeed in the rocky intertidal zone. They also had to key out a mystery algae using a dichotomous key. After this we had a delicious dinner of risotto, Arctic Char, and sauteed spinach. After dinner the class mad a sculpture out of the non-recyclable marine debris that they collected yesterday. They created a “monster” that they “slew” with a lobster buoy sword. I was very impressed. Following this creative time there was a lecture from the other TA about experiments in Cephalopod cognition. During this lecture there was one of the most beautiful sunsets I have ever seen. There were vibrant reds and oranges and some patches of blue right in the middle of it all. The blue patches I don’t understand, and they didn’t come out in the pictures that I snuck out of lecture (I heard it last course) to take. This all ended about 9pm, and the students had their first (and maybe only) real free night. They had nothing to study for, and no major projects to work on so they were free to hang out and watch movies or go to bed as they pleased. This was a relatively relaxing day, believe it or not. Tomorrow we clean up oil spills, echolocate, do more transects and seal viewing, talk about marine fisheries, and watch presentations from students in the Genetics of Marine Diversity class. It should be another good one.

Sunset disrupts class!

2009-07-23T21:07:00.003-05:00

Let me preface this by saying that not only do photos not capture the reality of a beautiful sunset (duh!), but the colors in this image seem dull and muted compared to how they look in my iPhoto.

Anyhow, one of the most amazing sunsets I have ever seen occurred last night. Most evenings here have been cloudy, so last night's show was a real treat. We (the class I am TAing) were in the middle of reviewing for a test when I opened the door for some air. Folks caught a bit of the sherbet colors in the sky and immediately rushed outside. That is the kind of school I like, where gifts from nature need to be appreciated even if there is studying to be done.

I was especially struck by how the circular patterns in the water mirrored those in the clouds. After talking with the class about ocean circulation in the Gulf of Maine and getting a fresh mental picture of the basin somewhat enclosed by George's Bank and the cold northern water funneling in through only a few places, the gyres drawn on the blackboard just inside seemed a wonderful echo to the micro-circulation patterns we were seeing right off our island.

Adventuring in tide pools... Part 2

2009-07-19T16:51:00.004-05:00

Here are some images of what we collected yesterday. The tide pools always amaze me with how many organisms and types of organisms can be crammed into such a small location. These mussel (Mytilus edulus) for example has barnacles (Semibalanous balanoides), encrusting red algae, limpet (Crepidula fornicata, yes that's its latin name), red coraline algae (Corallina officinalis), bits of some red and green algae, and a hydroid all growing on it... and that isn't even thinking about the microbial world!

I am also posting some pictures of the aggregation of species collected when I pulled up the Laminaria digitalis that I wrote about yesterday. I feel the need to note that I realize that the latin names should be italicized, but I haven't yet figured out how to do that through blogger, so... stand by!

Adventuring in tide pools... Part 1

2009-07-18T14:16:00.004-05:00

Tide pools are some of my favorite places to explore. The best ones are teeming with life and ripe for personal disccovery. I have heard many astronomers describe the first time they looked up at the sky and saw Saturn or Mars, feeling a sense of awe as if they were the first person to discover it. I feel this way each time I turn over a rock and find a crab or a sea star. Today I got to spend a couple of hours in tide pools on Appledore Island about 6 miles off the coast of Southern Maine.

At one point I pulled up a large seaweed, Laminaria digitata to be precise (I was collecting for a class, otherwise I wouldn't removed it) and with it came the rock that its holdfast was attached to. On the bottom of the rock were two brittle stars, an urchin (Strongylocentrotus droebachiensis) a mussel shell with a curled up fish inside, and a few snails (Littorina littorea). A whole micro-ecosystem in one tug! I have to admit that this is at the top of my list of tide pool finds.

The image above is where I was collecting. I am heading up to the lab now and I will try to take a pictures of some of what we collected.

Muskoka Ducks

2009-07-15T07:08:00.004-05:00

I recently got to spend a couple of weeks at a cottage on Lake Muskoka in Ontario. The cottage is at the end of a bay and is very well protected from wind and boat traffic. There were a pair of ducks that I saw almost every day (as well as a beautiful Loon) and was able to get quite a bit of video of. I put some clips together (above) for you. I think these are Black Ducks because of the male/female similarity and the coloration, but I know very little about birds so I might be wrong about that. One website I saw suggested that Black Ducks would have a darker body. I would love correction if anyone knows that these are a different species.

What I loved most about getting to watch this pair so close up for so long was how they moved in sync. I don't think I really capture this in the video, but when they were in the water they were synchronized swimmers elegantly moving as one. Another think that struck me was how the duck's webbed foot spread out and contracted again gracefully underwater to minimize drag and maximize power from each stroke. It is hard to see in the low-quality video posted here, but it was something worthy of a dance performance.

The ducks seemed to tolerate our presence as well. I was able to walk up to within 5 feet of them without startling them (if I walked slowly). Any closer than that and they would simply turn and walk towards the water. Normally I am NOT in favor of interacting with wildlife in any way, but wildlife doesn't normally hang out just feet from me!

Plugged in!

2009-07-12T20:07:00.005-05:00

I have recently had the interesting, if painful, experience of having my computer's hard drive perish in a deadly crash. What it crashed into I have no idea, but it needed to be replaced. This meant no computer for the two weeks I was at my family's cottage in Ontario. I had planned to do a lot of work and was not able (I can hear you all... poor me!). I was also without cell phone (iPhone) access, and it all made me realize how plugged in I really am. I have no problem taking off for a month in the woods without being able to communicate, but that is pre-planned. The sudden loss of my technological security blankets (email, journal I keep on my computer, photos, music, access to work I need to get done) definitely stressed me out a bit. I do hate to admit it. I will admit to one more thing. After getting my repaired computer back this afternoon, I have been sitting here downloading, formatting, syncing, browsing, emailing, and even composing music (with GarageBand) for going on 5 hours now, and I am not close to bored yet!

Test fron iPhone

2009-07-12T10:16:00.001-05:00

Trying to see if I can blog via phone...stand by.

Tidbits

2009-06-24T22:57:00.005-05:00

After leaving Mammoth Cave I spent a couple days camping in Shenandoah National Park. It was beautiful. There is something about hiking along a rushing stream, and being able to stop at waterfalls that really can't be beat. I also got to ride an awesome horse named Ginger.

It was wonderful to be back on the east coast yesterday and dip my toes into the Atlantic. I saw my favorite familiar sea weeds and lots of crab shells. Some kids on the beach nearby found a large horse shoe crab!

Driving through a wooded Connecticut road last night I saw a two deer run into the woods. This would not have been particularly remarkable except for the fact that one of them was white. A white deer! Apparently they have a low frequency of albinism... I had no idea.

Mammoth Cave National Park

2009-06-20T14:34:00.004-05:00

Written a few days ago, and posted now that I have the internet at my disposal again...

Mammoth Cave National Park, Kentucky

06/16/09

After about 4 hours on the road today. I arrived at Mammoth Cave park today around 2 pm. It was overcast, but not yet ominous. I negotiated a construction-complicated parking lot, checked in, and found my way to my cabin. The cabins I stayed in are very similar to those of my old summer camp and because of that false familiarity I immediately felt at ease. I headed over to to the visitor center under darkening skies to make sure things were all set for tomorrow’s “Wild Cave Tour” and figure out what to do with the rest of my day. I enjoy traveling on my own because I never have to compromise on what I want to do. The down side is (obviously) that there is no one to share the experience with. Anyhow, I realized that there was a 2 hour tour starting at 4 that I could do for fairly cheap, and figured this was perfect given the weather encouraging me to stay away from hiking. As soon as I had purchased my ticket for the “Historic Tour” we were all told to gather in the ticketing room because there was a Tornado warning. Apparently a tornado had been spotted nearby, and was heading right for us! This certainly made for good people watching. About 15 minutes later, under continuing but dissipating thunder and lightening we were the ok... tornado warning had turned in to severe thunderstorm warning. I went back to my cabin to get ready for the tour.

By the time the tour finally started I was excited. I have been in two other caves before, but none nearly this big. The tour group was very large, but I made my way to the front to get as much information from the guide as possible. The entrance to the cave was beautiful. We walked down a long staircase that cut down through limestone cliffs covered with lush mosses in varying greens. The side of the cliff was a forest in its own right only much smaller and growing out of a vertical surface. From underneath the top layers of limestone thin trees seemed to be squeezing out of cracks and immediately heading straight for the sky. At the back edge of the entrance, to the left of the stairs was a waterfall - halfway between a trickle and a stream - the water fell over the edge and seemed to disappear into the vegetation at the bottom. Once we passed under the that ledge we were in the cave. The first section of the tour took us through enormous spaces. It is hard to imagine the amount of water flowing through bedrock and the time needed to create such open areas. I am fairly certain this is what will come to mind from now on whenever I hear the word cavernous. Other than scale, what made this cave different from the few others I have seen is that it was dry, which means there were no dripstone features. No stalagmites or stalactites, no pillars, icicles or ribbons or calcium carbonate once part of in sedimentary limestone, then dissolved in groundwater, and then re-crystalized into unbelievable works of natural beauty. This is not to say that the cave was devoid of interesting geology or not beautiful. It was easy to see the evidence of other people who had visited or worked in the cave in the last few hundred years. Some mining (slave labor), some tourism, some exploration. There were names and dates all over the walls, some dating back as far as the late 1700’s.

We heard the story of one slave named Stephen Bishop who became famous because he was an excellent cave guide and explorer. He was (supposedly) the first person to find the strange blind fishes that inhabit the rivers that run through the cave. He was able to publish his map of the caves, which was nearly unheard of for a slave at the time. He supposedly learned to read and write, and speak 7 languages just from the visitors to the cave over the 19 years that he lived there. What an amazing story... this man was able to find some degree of independence, fulfillment, and maybe something close to freedom while he was exploring this underground world. This strikes me as a very strange type of leadership - being enslaved, but guiding tourists down below ground into a dark and foreign world. He mysteriously died one year after gaining his freedom and moving away from the cave.

One thing that struck me about the geology of the caverns we traveled through was the varying textures. They call the indentations in the walls and ceilings “Scallops”. Larger scallops are made by slower moving water, and smaller scallops are made by fast moving water. Much like fossilized ripple marks, the shape of the rock preserves a story of its history. On one large open area that had very large scallops in the ceiling I could not help but think that the color and shadows created by the dim lighting on these scallops looked exactly like sunlight passing through water and landing on an uneven sandy bottom. I love finding patterns in nature that resemble - more than resemble, that really feel like - some unrelated feature stored in my brain from a previous observation.

A moment that I really enjoyed during this tour was when all of the lights were intentionally turned out. It is nearly impossible to find true dark if you are not underground or deep in the ocean and it is a very cool feeling. The tour guide was able to get our enormous tour to be silent for a few seconds (surprising given all of the small children in our group) and that silence combined with pure dark was a very powerful experience. It was certainly not something I would want to experience involuntarily! However, without fear of being lost or deserted or in any danger it felt refreshing and cleansing. In yoga you try to let go of all the clutter in your brain... it is like meditation and takes a good deal of effort, but is very relaxing. I found that same feeling of calm in the few seconds of silent dark that I was able to experience in the cave.

It is now almost 8 pm and still light out. This means that I will have plenty of time to hike around tomorrow after my cave tour.

6/17/2009

I just spent 6 hours 200-300 feet below ground walking, crawling, slithering, climbing through passages that ranged from hundreds of feet high to so small my head could only fit to one side. It definitely felt like somewhere people don’t really belong. I can only imagine what it felt like to be one of the early explorers... down there for maybe 24 hours at a time, carrying lamps and oil... Maybe people 100 years in the future will look at the gear we use for climbing and camping and think “wow, how did they do that”, but it feels to me like the early explorers were just a lot more badass... period.

One of the coolest parts of today’s adventure was one area called Cathedral Domes where one section of the limestone has eroded to form fluting. There is a layer about 3 feet wide that has all of these vertical features sticking out like pages. The amazing thing about them is that they can be played like bells. The different sizes creating different tones. I wonder if shape has anything to do with it. Anyhow, that was something pretty magical. A natural, stone musical instrument 274 feet below Earth’s surface. This area was just one of 4 or 5 huge domes that we walked through... we came out of narrow passages maybe 20 inches wide into these huge rooms. I could shine my headlamp directly up and it must have been 100 feet tall.

The first hour or so of the tour was dry. We were crawling through red clay powder and coarser gravel in these passage ways that showed little sign of the water that created them. I suppose all of that powder must have been deposited when the cave system floods, but it is hard to imagine a flood with enough water to fill the passageways that far up in the cave system. We rested at a little food stand... yes there are tables and you can buy lunch and go to an actual bathroom in these caves!

After lunch we went to areas of the cave that had much more water. At one point I was wading through thigh deep muddy water! At this point we did less crawling and slithering (although there was another long crawl right before the end of the tour) and more scrambling. The climbing would have been fine if the rocks were dry, but hiking boots on wet muddy rock is a far cry from the indoor bouldering I have become accustomed to. There were a couple of places that involved stretching your feet across a slot canyon that I really thought I was going to be too short to make. However I made it and didn’t fall like I half way expected to.

Towards the end of our tour we started seeing the dripstone features that I associate with caves: stalactites, stalagmites, ribbons, “bacon”... we also saw more of the beautiful gypsum flowers that seem to bloom from the ceiling. In many parts of the cave today the walls and ceiling sparkled with a microcrystaline gypsum coating that has turned black from human use of the cave (lantern smoke mostly) in the parts I visited yesterday.

I am so glad I visited this place. The size and scale of this cave system (300 miles discovered so far under a 7 by 7 square mile of ground) are something that has to be experienced to be believed. It today’s tour it seemed like everywhere you turned there was another passageway going off in some other direction. Someone described the system as being similar to a pile of spaghetti. I like that image. The geologic formations underground are also quite spectacular. It makes me wonder what else is out (or under) there that is truly magnificent that we simply haven’t found yet!

The First Entry

2009-06-03T22:58:00.000-05:00

As I head out on my journey towards doctorhood lots of folks have expressed interest in keeping tabs on what I am up to. In the past I have not felt like I had much to blog about, but I hope this will be a way take past students and co-workers, friends and family, and who knows who else along for the ride. I will write about life as a grad student in Cambridge, all of the exciting scientific discoveries I am (hopefully) going to make, as well the side tracks I am sure to wander down.

Currently I am trying to pack up my life here in Texas for the big move back east. I am trying to leave my classroom and teaching materials in good shape for my replacement, get everything loaded up at home, make time to hang out with everyone before I leave, and not melt in the summer heat! I accomplished the following today: the road trip back is planned...

1- Nashville, TN

2- Mammoth Cave National Park, KY (6 hour Wild Cave Tour!)

3- Shenandoah National Park, VA

4- Washington DC

5- Middletown, CT

6- back in Boston!

This is exciting because I am going to travel through quite a few states I have not visited. The debate to ponder this evening is whether to ship my kayak back East, or bring it with my on the car so I can Kayak in Mammoth Cave.