Monday, November 30, 2009

Who knew I would like 1st graders?

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!

Monday, November 23, 2009

Trying on my rose colored glasses

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!

Wednesday, November 18, 2009

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

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.

Tuesday, November 17, 2009

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

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!

Thursday, November 12, 2009

Science that looks like magic!

Image from:

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!

Tuesday, November 10, 2009

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

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.

Monday, November 9, 2009

An inspirational class... finally!

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.

Saturday, November 7, 2009

and the science begins!

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.