and... she's back

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!

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

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

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

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!

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

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

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.

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

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

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

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

rapid rambling reflections

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

a (not so) productive day

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

Procrastination Fun

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

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

Data!

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

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

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

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

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

World Water Day

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

Time well spent out of lab

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

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

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

Wonderfully Wet Windy Woods Walk

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

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

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

An unexpected lesson from a test

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

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

How's that for a silver lining?

Can I be a museum educator when I grow up?

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

Rainy Day Therapy

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

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

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

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)

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

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)!

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

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

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.