The A-frame shuddered as the box core, heavy with mud and reeking of sulfur, emerged from the water. We knew that it had found its mark 2300 meters below. Soft sediment from the seafloor oozed out the sides as I slid the safety pins into the spade arm. There was nothing visibly special about this mud. No ancient arthropods or primeval polychaetes crawled through this muck. It was a cubic meter of sticky, stinking glop. My first sample.
We were in the middle of the Gulf of Mexico, aboard the R/V Cape Hatteras. Our cruise objectives were to characterize the pelagic and benthic fauna associated with deep-sea methane seeps. For me, it was a ship of opportunity. In exchange for and extra set of hands to work the gear and process samples, I could add my own small research project to the cruise objectives. My goal was to collect sediment cores from multiple sites and survey the diversity of fungi associated with these methane seeps.
The 12 hour shifts rarely left me enough time to eat meals. Though I had never seen the equipment before we left port I became the acoustic tracking technician, out of necessity. Things consistently went wrong. Nets tore, gear broke, a misfired box core almost crushed my leg. Two hurricanes, one a category 5, hit the Gulf of Mexico while we were at sea. Work was exhausting and rest was brief, when existent. I loved every minute of it.
The end of that cruise was the high point of a 4 year project that began with unbridled optimism and early, exciting results, only to decay into drudgery, failure, desperation, and collapse. In the end, it would rise from the past for one small victory. In hindsight, so much of those four years seems painfully trivial, but this story is really about how much of a human being is poured into a scientific manuscript.
Last week, volunteers monitoring a sea turtle nesting beach on Virginia Key came across a beached lemon shark. They called in scientists from the University of Miami’s RJ Dunlap Marine Conservation program, including myself . Dunlap program director Dr. Neil Hammerschlag decided to film the necropsy to use as an online teaching tool. The end result, edited together by Dunlap program multimedia specialist Christine Shepard, is below. Check it out to learn about the internal anatomy of a shark, as well as the process that scientists use to determine causes of death in marine organisms. If you have any questions about the process or about the animal, please leave them as comments below.
Meagan Dunphy-Daly is a graduate student at the Duke University Marine Lab studying the effectiveness of marine reserves in protecting apex predators. She also has ongoing research examining bullshark/dolphin interactions in the Neuse River, NC, where she recently caught an 8 foot bullshark.
Well, it’s Shark Week and instead of heading up to the Neuse River to try to track bull sharks, I’m sitting in front of my computer staring at the marine forecast. Right now, we’re under a small craft advisory until tomorrow night and we’re all keeping our eyes on what Tropical Storm Emily is going to do over the weekend. Such is the ever-exciting life of a field biologist. Although there are a fair number of days spent in an office in front of a computer (be it checking the weather, entering data, or hoping that a manuscript will write itself), the days in the field are what make this job so sweet. I’m a graduate student in Dr. Andy Read’s Lab at Duke University and, in addition to my dissertation interest in the effectiveness of marine reserves for apex predators (think sharks, tuna, and billfish), I have the chance to carry out and participate in many other research projects in North Carolina and elsewhere (check out Reny Tyson’s previous posts on our trip to Antarctica). This summer, I’m studying bull shark habitat use in the Neuse River. Andrew joined us for a day of fieldwork last week and, although we didn’t catch a shark on this trip, we caught a big bull shark on the first day of our season the week before.
While cleaning out our lab the other day, we discovered this mysterious piece of equipment buried deep within a cabinet. After querying several dozen scientists of different eras, we have determined only that it was manufactured in the early 20th century and no one has any idea what it is. The optics were made by Bausch and Lomb, the motor was made by Dunmore. We have a few guesses about its intended purpose.
This machine is massive, it weighs about 50 pounds and is forged from Bakelite and steel. The drum is clearly some kind of centrifuge and the optics point into the center of the spinning drum. No one has yet been willing to plug it in and turn it on. There are two patent numbers listed on the plate – patent # 1,648,369 and patent # 1,907,803.
As search algorithms are getting better and better, some scientific papers are getting more difficult to access. Journal subscriptions are expensive and many institutions are foregoing all but the highest impact journals. For those working outside of academia, only open access journals are a viable option. I’m fortunate that my university subscribes to most scientific journals, which means that many of my colleagues will drop me an e-mail, tweet, or phone call along the lines of “Hey, I don’t have access to this article. Can you send me a copy?”
The answer is, without hesitation, always yes. Science can only progress when we have access to the literature. At this point, I’m fielding 4 or 5 paper requests per week, and I imagine many other scientists are doing the same. Most of the time the requests are simple and straight forward. Sometimes they’re so cryptic that it takes another round of e-mails before I even know it’s a paper request. I thought it would be helpful to compile a short list of advice for how to make it all just a little easier.
It’s the end of a long a productive field season abroad. You’ve collected, processed, and packed thousands of precious samples. These samples are your life-blood. They will be the foundation of not only your thesis, but dozens of theses to follow, the cornerstone of a long and prosperous scientific career. There’s only one barrier left between you and scientific glory – you have to get those samples home.
Traveling with samples, especially internationally, carries with it a bit of diplomacy, some tact, confidence, and a huge amount of (often undue) stress. Even if you’re completely on the level, there are horror stories about overzealous security guards, irate customs agents, suspicious packages, and the risk of being detained, having a visa revoked, being stuck on the next plane out of the country, or, worst of all, losing your samples. As you pack up your gear and prepare to board your flight home, take a step back and remember the immortal words of Douglas Adams – don’t panic.
A few weeks ago, I listed several common mistakes that people make when applying for a job in the field of shark science. This led to a lot of laughs and commiseration. It also led to a series of e-mails asking me how to apply for a shark science job. These e-mails came from people in various stages of their lives, all the way from children to adults who already have another career. Since I had some laughs at the expense of people who apply for jobs incorrectly, it seems only fair that I offer my advice on how to do it correctly.
This photo of me with a sandbar shark was taken while working for the South Carolina coastal shark survey
It is important to note that I am describing the path that worked for me. There are many other paths, though there are likely lots of similarities with mine. Some may seem pretty straightforward, but what seems obvious to some can be a life-changing revelation for others. Most are applicable to science in general and not just sharks. Similar advice can be found on this excellent website from the Love lab.
The dissemination of science follows the conventional route of rigorous peer-review followed by publication in an accredited scientific journal. This process has been the standard foundation from which the general public can trust that the science is, at the very least, valid and honest. Of course this system is not without its flaws. Scientific papers of questionable authority, dishonest methodology, or simply flawed design frequently make it through the gates of peer-review. Politically charged papers possess strong biases and many high impact journals favor sexy or controversial topics.
Beyond the conventional route of peer-review, there exist a vast accumulation of gray literature – conference reports, technical notes, institutional papers, various articles written for specific entities that enter into general circulation without the filter of peer-review. Much of gray literature is valid, robust science, but much of it is not. The challenge is that sometimes gray literature is the only science available.