Student Research at Duke

Sorry about the hiatus…I blame a busy week coupled with minor blogging technical difficulties. Anyhow, there’s a lot of catching up to do:

Last week, the program focused on Responsible Conduct in Research. As a beginner lab-rat, a lot of the goings-on in the lab flew right over my head at first. Procedures, customs, protocols, and common courtesies had to be learned or inferred. Luckily, there are people who study lab conduct and devote their careers to encouraging researchers to abide by a common set of ethics and rules.

As part of the week’s focus on RCR, we heard from Colleen Denny and Dr. David McClay on bioethics. We also viewed And the Band Played On, a film released in 1993 about the AIDS epidemic. I found both speakers extremely interesting, but I enjoyed the film the most. I left impassioned, motivated, and charged to continue my foray into the science world with a new vision.

The film revolved around the scientists at the Center for Disease Control, who were working furiously to discover what was causing an epidemic among gay men. A major part of the film also concerned the scandal between the main (albeit young) scientist at the CDC, Dr. Don Francis, and a world-renowned scientists, Dr. Robert Gallo. The film portrayed Dr. Gallo as an overly competitive and manipulative scientist, thirsty for fame and glory. He committed egregious offenses as he tried to falsely claim full credit for the discovery of the retrovirus, taking down anyone in his way (and this part fits in well with the week’s theme, highlighting clearly irresponsible conduct in research).

Dr. Gallo’s clout and reputation in the world of science ultimately rewarded him with partial credit for the retrovirus (shared with the French). While the film’s negative portrayal of Dr. Gallo left me with an ominous feeling about the competitive world of science, I was extremely motivated by other parts of the film.

I’ll admit, science isn’t my only interest. I’ve always been intrigued by politics, and I’ve been wondering how these two fields intersect. In addition to the struggle between competing scientists, the film also captured the struggle between scientists and government officials, both trying to contain a deadly disease quickly and effectively.

When AIDS was first identified, it was actually called GRID, short for Gay Related Immunodeficiency Disease. During the era of the “moral majority” and the Reagen administration, a disease that seems to affect only gay men was getting very little press coverage and virtually no funding for research. None of the blood banks or pharmaceutical companies wanted to lose or waste money by testing for HIV, and as a result hundreds of thousands of people were unknowingly affected. The scientists’ desperate search for funding and acknowledgment of this deadly emerging epidemic– for years to no avail– truly moved me.

Even today, I see such a struggle between scientists, ever hoping to improve living conditions and our understanding of life, and the government, trying to regulate and maintain order. Both institutions, science and government, have the good of society in mind…but who’s view really wins? I don’t know if there’s any good answer, but I remain interested in the overlap between these two worlds.

FINALLY, the moment I have been waiting for…the tomato frog samples came in today!!

Alas, they are packaged in a giant cardboard box with hundreds of other reptile and amphibian samples. Maybe “packaged” isn’t quite the best word…apparently throwing all the little tubes in a box and taping it up is adequate for shipping rare frog samples halfway across the world. Shockingly, the box opened mid-trip, and an undetermined number of little tubes may/may not have spilled out.

Anyways, the frogs are here, but first the samples have to be sorted. There are lots and lots and LOTS of tubes. So today, I discovered the tedious side of lab work: sorting and organization. Luckily, everyone tells me I’m anal retentive when it comes to organization, so I seem to have a leg up on this kind of work.

Once the samples are sorted, though, the fun begins…isolating, amplifying, and sequencing the DNA. Lots to do next week!

So I’m starting to see a trend with my lab work…

The past week, I’ve had a LOT of really awesome stuff to do. Sequences, DNA extractions, gels, PCRs, nanodrop machines…tons of cool things to try out. Except for the fact that nothing really seems to work out for me.

I’ll admit, I’m not exactly the amazingly perfect scientist I’d hoped I would be (yet). I don’t really have a natural-born talent to repeatedly pipet single microliters of liquid without fail, and apparently I have some trouble reading directions from a protocol. Like when the book clearly says “add 4 microliters of buffer” and I somehow decide to add 5 microliters. Or when I fail to notice that the vial of DNA-grade water is actually ethanol. Oops. [A note to my lab: don’t worry, I caught my mistakes. Eventually.]

Anyways, I’ve discovered that frequently (and in my case, more often than not) things don’t work out. And sometimes, it’s not because I forgot a step or added the wrong buffer. Thank God.

For example: yesterday, I did a whole-genome amplification on some DNA samples. I managed to follow every single one of the directions, which I thought was a pretty big improvement from my previous week’s performance in the lab. Except that today, I ran out the amplified samples on a gel to gage my success….and I was sorely disappointed. There was almost NOTHING to be seen on that gel.

Luckily, not everything has to be blamed on the scientist (and in this case, that would be me). There is a possibility that it is actually not my wrongdoing at all, and really the horrible amplification is the fault of the company that made the whole-genome amplification kit. At first I thought everyone in the lab was lying and just trying to make me feel better about screwing up so many procedures…but apparently it’s somewhat common for things to just not work out. Unfortunate, but common.

In any case, I’m still crossing my fingers for the shift-blame-from-Sam-to-the-company deal.

A little more information about the Yoder lab…

Basically, all of the research that is conducted in Dr. Yoder’s lab concerns the island of Madagascar. The cool thing about Madagascar is the incredible amount of biodiversity: there are already hundreds of thousands of observed species, and new species are being discovered as I type. The REALLY cool thing is the fact that more than 95% of all these species are endemic and can be found only in Madagascar. Like these cute little guys:

So anyways, everyone in the lab is studying a different Malagasy species to see how they’ve evolved, or how physical barriers (ie rivers, mountains) have affected their evolution. My main project looks at a few different species of Tomato frogs, which are not as cute as mouse lemurs but still pretty funky looking:

.

As of right now I’m still waiting for the samples to arrive from Paris, but then I’ll be off isolating, amplifying, and sequencing till my hands fall off from overpipetting.

On a side note, today Steve Goodman came all the way from Madagascar for a visit. According to Dr. Yoder, Steve has done more to study the biota in Madagascar than any living human…and after hearing him speak at the Lemur Center this afternoon, I definitely believe her. He’s spent over 19 years exploring the island and discovering new species. I found this article about him online: “Madagascar Tames the Bohemian of Biology”…he’s had quite a career. I’ve never been to Madagascar and knew absolutely nothing about it until a week ago, but his presentation was great and really makes me want to spend time there myself.

After the speech, the lab and I went on a tour of the Lemur Center (thanks to Aaron, who happened to be at Dr. Goodman’s speech as well). Unfortunately, I forgot my camera today, but hopefully I’ll go back and take some pictures because lemurs are so darn cute. There are some weird kinds though…like the ones with the anal-genital scent glands and therefore rub their butt on every surface to claim their territory. Thank god lemurs and humans evolved differently.

Myth #1: Scientists are crazed workhorses

I mentioned before that I had (still have?) a pretty skewed idea of what “lab life” is like…but today, I realized something monumental: scientists don’t work all the time, 24/7. There IS such a thing as “down time” (thank god!). No one is expected to survive 7 straight hours of micropipetting (unless you have ridiculous forearm muscles).

So to honor my downtime, I snapped some pictures of the Yoder lab. The lab is bright and shiny and brand new; they just relocated this past February. Hopefully I won’t break anything new and expensive in the next eight weeks…

Entrance to the Yoder Lab

a pretty nifty lab bench

the conference room (notice the flowers in the flask…scientists are crafty, too!)

…and my best attempt at a self portrait with some gels

Back to work!

Hi! My name is Samantha Pearlman, and this is my very first blog post. I’ve written a little about me in my profile, and I may update it from time to time so feel free to check that out. I’m not really too sure how to start writing this (blogging beginner here), but here it goes…

I’m currently participating in the Howard Hughes Research Fellowship, which is a group of about 30 rising sophomores (and Jose, the odd one out…but don’t worry, we still love you Jose) who are interested in biological research. We’ve all been matched up with labs and paired with mentors, with whom we will be working for the next eight weeks. In the lab, we are all doing different things, but out of the lab, we attend biweekly lectures, get together to discuss our research (hows that for academic collaboration?), and try to pass time in hot and humid Durham.

The program has decided that blogging is the new frontier of science research. At first, I was a tad bit incredulous. I’m an avid facebook user (okay, user isn’t the best word. Maybe addict) so I’m no stranger to the post-your-life-story-on-the-internet deal, but I can’t say I’ve ever entertained the idea of writing in a blog for public scrutiny and consumption. I mean, really, we are all science people here…not your stereotypical F.Scott Fitzgerald/write-the-great-American-novel type. But after hearing it explained in full, I started to warm up to the idea. There are a lot of misconceptions about science and about people who devote their lives to science. While I’ve always loved the crazy mad scientist character with the ubiquitous white lab coat, I’m not so sure which stereotypes are actually true and which are fictional (Do researchers have social lives or are they confined to lab-intramural softball leagues? Does anyone actually use that dingy shower in the women’s restroom on the third floor of BioSci?), but I’m planning to find out this summer. And, hopefully, this blog will be a way for the outside world to see what really happens in a lab.

So, stay tuned for riveting updates from the lab. I’ll let you know when I find my first mad scientist.