Wednesday, July 29, 2009
Sometimes lab work requires a lot of waiting. Usually it’s a good idea to use that down time to read papers, or go through data (when you have data to go through). Sometimes I like to clean up the lab or do some minor lab tasks like sterilizing pipette tips or replenishing supplies.
But what can sometimes be more important than any of those responsible activities, especially when not everything has been going well, is to leave the lab. Just leave for a couple of hours. Divert yourself and then return later. That’s what I did today.
Summer Fellows at WHOI live in row house apartments that are conveniently located between Woods Hole and Falmouth (picture below). We have easy access to the Shining Sea Bike Path and when it’s not raining, I commute to work on my bike.
We live right near Oyster Pond, one of the Cape’s ubiquitous ponds that lend themselves to scenic walks and expensive property. We’re lucky to live near this particular pond because on it’s shore is a beautifully landscaped garden called the Spohr Gardens.
When I got home from the lab, I jogged down to the gardens with my camera and took a few pictures. Note that I don’t really jog, but I thought it would be a good change of pace.
Tonight, it’s back into the village for a bit of work at the library.
Tuesday, July 28, 2009
Finishing a degree is both a joyous and possibly stressful occasion. This summer, after 6 years of hard work and determination, Kate Buckman, the PhD student in my lab, completed her doctoral work. Yesterday, she gave her public talk and closed-door defense. The public presentation lasted about 45 minutes and was followed by questions. Then there was the scary part (or at least I imagine it was scary for Kate)…
When you complete a PhD, you have a committee of specialists who are meant to keep you and your work on track. When you defend your thesis, you are holed up in a conference room with your committee and they essentially grill you on details about methods and results until they are satisfied that you (a) are 100% comfortable with and confident in the work you’ve done and (b) can stand up to rigorous peer review in the scientific world. After many questions and intense discussion, you leave the room and the committee “deliberates.”
When Kate’s committee was deliberating, we sat around the lab distracting her with mindless internet surfing. (picture below)
When eventually called back into the room, the PhD committee gives you a list of revisions and possibly another list of things they think you still need to complete, including lab assays or statistical analysis. Rarely are the revisions extensive and almost always, the student leaves with the knowledge that he/she has completed the rigors of life as a PhD student.
Kate’s talk was awesome and her closed defense session went really well (I wasn’t there, clearly, but I heard great things)! Now I get to call her “Doc” whenever I ask her questions. =) After the successful presentation and defense, we held a lovely reception for Kate in the lobby of our lab building. Dr. Tim Shank, our adviser, gave a lovely toast to Kate and everyone enjoyed a bit of champagne.
Being present for Kate’s defense really got me thinking about what course I want to take now that I’m navigating the post-college waters. As I think I’ve said before, I am ultimately interested in being involved in marine conservation policy. I am extremely intrigued by the interaction of science and policy and want to find a niche working to bring policy makers and scientists together on common ground.
There are several ways I think someone could end up working to accomplish that goal including any number of policy or science masters degrees, PhD programs, and law school options. The possibilities abound. I have to say, though, it’s pretty inspiring to see people like Kate come out of the Joint Program with many years of hard work and a lot to show for it! Hmmm… Dr. Eleanor Bors has a pretty nice ring to it…
Tuesday, July 21, 2009
My mother recently e-mailed me a NY Times article that highlighted differences in views held by most of the science community and views held by most Americans. You can read the article online at http://www.nytimes.com/2009/07/10/science/10survey.html.
The article reports results of a recent survey that investigated public perception of important scientific issues. Interestingly, “the proportion [of Americans] who name scientific advances as among the United States’ most important achievements has fallen to 27 percent from nearly 50 percent in 1999, the survey found.” Is the US lagging in science or is there a misconception on the part of the public about what we do and accomplish?
I wonder how much governmental respect, or disrespect, for science affects public opinion. For example, cuts in funding and open disregard for scientific advice by policy makers likely gives the impression that science isn’t that important. What is the relationship between science and politics, and how does the political climate affect public perception of science? While answers are rarely straightforward or obvious, we should all ponder such questions.
In addition to the declining opinion of scientific achievement, the article mentions that many people don't believe scientist's assertions about evolution and climate change. As a biologist, it is hard to consider evolution and climate change as things in which you can chose not to believe. That being said, I think differences in opinion about such topics bring up the really important issue of how science should be treated in education.
What we learn in school can really affect our opinions when we enter society. If the general public were more well versed in science, they would be more inclined to dig deeper into issues of evolution and climate change and might research such issues on their own, coming to more informed conclusions.
According to the NY Times article, “the report said 85 percent of science association members surveyed said public ignorance of science was a major problem. And by large margins they deride as only “fair” or “poor” the coverage of science by newspapers and television. Only 3 percent of the scientists said they “often” spoke to reporters.”
To be sure, the news fixates on sensational stories: explosions, car chases, murders, sad stories about neglected dogs, women who birth 8 children in one go. Okay, those things can be important, but why is science so infrequently in the news?
Why is a 1-hour special focused on a possible pickle-pricing scam at the local supermarket more important for the average American to read/hear/see than a story about climate change, coral reef decline, or deforestation?
The simple truth is that people don’t think science is pertinent to their everyday lives. They don’t think that environmental issues affect them nearly as much as the local pickle-pricing scandal. And while I contend that drinking clean water, breathing clean air, and preserving global ecosystems is MORE important than what is usually on the news, the onus is on us to convince people that they need to pay attention.
We could blame the public for not being interested in our science, but ultimately it’s our job to make them listen, right?
There are two sides of every coin.
Wednesday, July 15, 2009
I’m working on a longer entry to be posted soon about communicating science to the press and to the public. It’ll focus on the discrepancies between beliefs held by the science and the non-science communities. In the meantime, however, I am going to cave in under some pressure from my friends to do a follow-up on the 4th of July, the Barn Olympics, and some other goings-on around WHOI.
Fourth of July Parade
Woods Hole has a 4th of July parade every year. Most of the participants, I’m led to believe, are form the Marine Biological Laboratory (MBL), which is down the street from my Lab (Redfield Laboratory). The parade route goes right through the heart of the village (see aerial view of the village below, from www.whoi.edu).
This year, many of the parade groups featured depictions of marine animals (see the jellyfish and the blue lobster below)…
…while others focused on smaller biological agents, like viruses (below is an image of the virus group).
In one of my previous entries I told you about the Barn Olympics, but I never told you how they went. For those of you just joining us, the Barn Olympics is a day-long, fun-filled event that is organized by Joint Program graduate students at WHOI.
This year, many grad students and summer student fellows partook in the activities, which included a photo scavenger hunt. Our team did okay in the rankings (we weren’t last) and we had a blast! I’ll share with you some of our scavenger hunt picture.
Below you’ll see my team—“the interweb”—each with a different species of flower.
Some of the more interesting tasks included interacting with tourists. Here’s our very own Sam with a tourist family in Woods Hole:
Fish for Everyone!
One of the summer student fellows is an avid fisherman. He fishes more than anyone I have ever met in my life (and my dad’s side of the family is from Alaska, so that’s really saying something)! The quality of his fishing experiences seems to match the quantity because last week he brought home part of a 100-something pound bluefin tuna caught up in Cape Cod Bay.
This, of course, meant sushi for everyone last Friday night when the boys dorm hosted a surf ‘n turf dinner party!
On Saturday, I was lucky enough to join fisherman Willy on the WHOI dock for a little bit of relaxed, casual fishing. I caught a very small sea bass (picture of me brimming with excitement below). We threw everything back that we caught.
Fishing was fun, but our trip to the dock was sweetened when I made a couple of new friends: the autonomous underwater vehicles (AUVs) ABE and Sentry! They are both WHOI submersibles and I’d never seen either vehicle in person. I took the opportunity to snap a picture of ABE:
Until next time,
Friday, July 10, 2009
Yesterday the summer students gathered in the Clark building (above) for a workshop about ethics in science. While I think many went into the 3+ hour meeting emanating what might be called less than positive vibes—or at least mild skepticism—everyone I’ve talked to came out of it feeling more conscientious about ethical issues in science and happy that we’d spent that time discussing such issues.
We talked about intellectual contribution, teamwork in a lab, authorship on scientific papers, presenting data in an accurate and transparent way, the role of the lab adviser in overseeing his/her students’ work, the responsibility of scientists to the greater community, conflicts of interest, secrecy surrounding lab techniques and results, and many other topics.
The workshop focused on a series of scenarios, or case studies that presented situations in which there was ethical grey-area. Often, people would have an immediate visceral reaction to each scenario—“Sandra shouldn’t have gone behind her colleague’s back,” or “Bill shouldn’t have told John about his friend’s research,” etc.—but through group discussion everyone noticed nuances about each scenario that often changed initial impressions about the ethical issues involved.
For me, the most interesting question that arose was about authorship on papers and what it means to make a “significant intellectual contribution” on a piece of scholarship.
Science today is rooted in cooperation. Interdisciplinary teams are able to answer more complex questions more thoroughly and accurately. But the involvement of more and more people on a research paper can raise serious issues about who contributes what and how everyone should get credit where credit is due.
Issues highlighted at the workshop spurred further discussion between students later in the day that will hopefully continue throughout the rest of the summer.
Thursday, July 9, 2009
My friends and family often wonder what it is I actually do everyday. Lab work is very much a black box for people who have never been inside a lab or been privy to a friend’s lab tales.
How is it that we’re able to take an animal off the seafloor and eventually end up with genetic sequences that help us understand how that animal evolved and how it’s related to other animals in other ocean habitats?
I’m going to attempt to give you a bit of insight into how gene sequencing works and why it’s important. Hopefully you’ll find this interesting. I’ve inserted some hypertext links to wikipedia sites if you want to read more about a specific term or concept.
If you’ve read my previous entries, you know that I was recently on a research cruise to the Mariana Trench. On that cruise, we pulled up several biological specimens from the bottom of the ocean using HROV Nereus.
When you get an animal on the research vessel’s deck, you want to preserve or freeze it as fast as possible. Sometimes, if it’s in a shell or a tube (for example a clam or a tube worm), we will dissect it out of it’s shell/tube in order to get the most amount of tissue exposed. This helps with preservation in alcohol because it means that more alcohol can reach more tissue right away, saturating all the cells and preserving them. We also want to expose the most tissue for frozen samples because that way we have more to work with when we take a piece off for DNA extraction.
Here's a picture of me dissecting out a specimen on the cruise:
Often times, the animals that scientists collect while at sea don’t immediately get back to the lab. In the case of the Nereus samples, they stayed on the ship until it came into port in Hawaii and then were sent over-night in a cooler to Woods Hole.
Building Blocks (ATCG)
For those of you who haven’t thought about DNA since high school biology, I’ll give a very brief description how it is structured. Basically, DNA consists of two long chains of genetic building blocks called nucleotides lined up next to each other. There are 4 kinds of nucleotides in DNA: adenine, thymine, cytosine, and guanine, also known as A,T,C, and G. Each one is a little different from the others and they form specific pairs that we call base pairs. Meaning that A only likes being across from T and C only likes being across from G.
In all of your cells, DNA lives in the nucleus, a well-protected compartment that keeps all 3 billion of your base pairs organized and accessible to the cellular machinery!!
An animal cell (nucleus labeled), from a website I found on google images:
There are many different methods used to extract DNA. They all have a few things in common, however. First of all, you have to essentially destroy the cells in the sample in order to free the DNA from the cell’s nucleus. As you might imagine, DNA is pretty well protected by the cell. Using chemicals and enzymes, usually mixed with heat and some physical agitation, the first step of any extraction is to free the DNA by digesting the cell around it. You have to disrupt the cell membrane and try to digest proteins in the cell.
What does that mean for me? It means that my first step in a reaction is to put a very small piece of the animal’s tissue in a tube with a specific set of reagents that break up cells. Then, I leave that tube in a warm water bath for a while (usually overnight) to help the reaction go faster.
These are the water baths in our lab:
The next day, I go through a number of steps to isolate the DNA chemically from the other fragments of the exploded cell. Since DNA has a specific structure and is made of certain molecules, it has specific chemical properties that we can exploit to isolate it from other molecules. Each of the different extraction methods exploits these properties in different ways but in the end, you should end up with somewhat pure DNA.
Once you have separated the DNA from other cell parts, you put it through a series of reactions that makes many copies of one specific gene. Essentially, you selectively copy the gene you want to study by using enzymes that link nucleotides together in the same way that enzymes copy DNA inside a live cell. This process is called a polymerase chain reaction, or PCR.
After we’ve made many copies of the one gene we want, we run a sequencing reaction. A sequencing reaction is somewhat similar to PCR with a really amazing twist. In PCR, you add a mixture of nucleotide bases for the enzymes to use as building blocks. In a sequencing reaction, some of those nucleotides force the termination of the DNA strand because they are chemically different from normal nucleotides and don’t allow other nucleotides to latch onto them. These special building blocks are also labeled, or tagged with molecules that glow specific colors under certain conditions.
Since you are essentially making copies of the many PCR-formed copies of your desired gene, and you are using these special nucleotides that stop, you theoretically end up with many different lengths of DNA strands—from one nucleotide to the whole length of the gene in question. (Meaning, you’ll have a mix of the following: A, AT, ATT, ATTG, ATTGC, ATTGCC, ATTTGCC, etc.) Statistically, the nucleotide mix is meant to have enough of each type of nucleotide for this to work.
There’s a really incredible machine that can read these glowing sequences. It goes through and says, “This fragment is 5 nucleotides long and the last one glows red, so we know that the fifth nucleotide is a thymine.” A computer listens to the machine and stores this info. We get the sequence back and can then use software to read it to (first) see if everything worked, and (second) use the sequence to find out interesting things about the animal.
The data comes back to us not only in text files, but also with what’s called a chromatogram that shows how strong each color signal was and if there were conflicting color signals.
A chromatogram looks like this (the top row of this looks like a pretty good sequence; I pulled this off a google images):
What we do with the sequence could take up another really long blog post. So I will refrain from telling you all about that until a later date.
Until next time,
Friday, July 3, 2009
I’d love to give you the impression that all we do is work day and night, completely engrossed in the perpetual search for scientific breakthroughs and the subsequent enlightenment that is sure to follow. Unfortunately, I feel obligated to tell you that we do other fun things, too.
This weekend is a perfect opportunity to sit back, relax, and enjoy the cape. We had the day off from work today (Friday), making it a three-day weekend.
Here are just a few of the things that I’ve been doing and plan to do during this weekend:
Ladies Racing at the Yacht Club
While I was on the Nereus cruise, I had time to chat with my shipmates about what they do on cape during the summer. One of these conversations led to my discovery of ladies racing night at the yacht club. I wouldn’t call myself an extremely experienced sailor, but I would say that I’m an avid sailing enthusiast who would like to be on the water more than I have been over the last five years.
(Cape Cod Knockabouts. Image from flickr.)
One of the other women on the cruise had a friend—also a WHOI employee—who was looking for crew for ladies night. I, being a lady, deemed myself qualified and contacted her once in town.
Last night was the first official race of the season. It was raining hard all day but it cleared up and the sun shone down on Woods Hole for the race. We had a lovely sail and I had a fabulous time. I know you all want to know, so I’ll just go ahead and tell you: we won (which was nice). Still, the part that really mattered was that I had a fun Cape Cod experience in the afternoon sun.
(Above: WH Yacht Club)
Friday Night Lectures
I know I said that I was taking this extended weekend to sit back and relax, so you might wonder why this section’s subheading contains the word “lecture.”
The Marine Biology Laboratory of Woods Hole (MBL) hosts a lecture series in the summer. Each Friday, they have a speaker come and give about an hour-long talk about a variety of biological and/or ocean-related topics. Dr. Susan Avery—the director of WHOI—is giving tonight’s talk. It’s titled “Coastal Cities, Coastal Impacts: The Tides They Are A-Changin.” I’m very excited to hear the talk because I feel that issues surrounding human impacts on the coast and the impacts of climate change on coastal living are pertinent to my life. In fact, such issues are pertinent to all our lives since the majority of the world’s cities are coastal.
The Friday lectures are free and generally accessible to audiences with little or no background knowledge. To learn more about the MBL lecture series, check out the Friday Evening Lecture Series Website. They even have podcasts of the talks so you can listen in wherever you are!
The Barn Olympics
The Barn Olympics is a holy event. Okay, fine—that might be hyperbole. But it is really fun.
Each summer a group of WHOI graduate students plan the Olympics for Summer Fellows, Joint Program Students (the grad program that WHOI has with MIT), MBL students, Sea Education Association affiliates… basically anyone who is around the Hole in the summer and somehow engaged in marine science. Last year it was predominantly WHOI kids, though.
Participants form teams of 4 (preferably 2 women and 2 men) and compete in a series of partly serious/mostly ridiculous games and competitive events. The events last summer included a photo scavenger hunt, an abbreviated triathlon, tug-of-war, trivia, dodge ball…the list goes on. Each team has a theme and dresses up. There are, of course, prizes for best costumes, best team name, etc. Our team is called “The interweb,” and we’re in the process of designing some winning costumes.
The Olympics are this Sunday. I’ll be sure to let you know how they go!
I hope you didn’t mind reading about my goofy weekend plans.
Stay tuned for my next entry—“From Seafloor to Shank Lab: an odyssey of ATC and G”… I’ll attempt to keep you entertained while explaining some pretty sciencey things.
Happy Fourth of July! Have a fun and safe weekend!