I am, among other things, a conservation geneticist. What that means is that I use the tools of molecular ecology and population genetics to make observations about species and populations in at-risk ecosystems, assess the status of anthropogenically disturbed populations, and generate data that has direct applications to conservation and management issues. Essentially, the only difference between what I do and what a population geneticist or molecular ecologist does is the motivation—I select systems to work in that have a high conservation priority.
This motivation leads to a constant intellectual conflict at the bench. The tools of molecular ecology—PCR, gene sequencing, and, more frequently, high-throughput sequencing—are waste intensive. In order to avoid cross-contamination and practice precise, clean, technique, we use thousands of tiny plastic consumables every day. These come in the form of pipette tips, sterile packaging material, micro-centrifuge tubes, and numerous other plastic widgets. Often, because of the biohazard potential, these consumable cannot be recycled.
So we have a problem. As a conservation geneticist, we need these tools to produce the data necessary to make wise conservation and management decisions. As a sustainability minded individual, I find the massive daily accumulation of plastic waste inexcusable. Do we just accept this waste as the cost of conservation genetics? I believe that the answer is no. I think we can and should develop best practices to minimize the amount of plastic waste produced by a molecular lab while maintaining good, sterile technique. I would like to propose four guidelines, based off the principles of Reduce, Reuse, and Recycle, for minimizing waste in a conservation genetics lab.
Continue reading Establishing Best Practices to Minimize Waste in a Conservation Genetics Lab
Cartographers of old produced maps that now hang in art galleries, living rooms, and libraries. They were works of art, embellished with the cartographer’s personality – from their handwriting to the fanciful borders of the page and sometimes even sea creatures. Peruse for a moment this map of North Carolina (then part of the Virginia Colony) from 1636 – the ocean comes complete with ships and large toothy fish, the land depicts the western border of our country back then (the Appalachian mountains) and each tribal territory is nicely color-coded. The map not only gets its message across but says something about the mapmaker. Today’s cartography looks very different.
map from 1636 documenting tribal territories, courtesy of the NC Map Collection in the UNC library
Modern geographers are trained in geographic information systems, highly reliant on software and abundant data to make the required maps. GIS careers are in high demand from both sides – employer and employee – following the adage that a picture speaks 1000 words. Maps talk. But with this technological shift, much of the art is gone from cartography – but it doesn’t have to be. Continue reading How to Make A Pretty Map
Shannon is a student who participated in my blogging workshop as part of her Science and Nature Writing class earlier this semester. He she recounts her experience conducting independent research at the Duke University Marine Lab.
This past semester I was simply enjoying my life and doing what college students do when it happened: I got crabs. Sixty-four of them, to be exact. Never before had I experienced such prolonged irritation; before long I was just itching to get rid of them. For weeks I was sure that I had made a foolish mistake, vowing to be more careful in the future. Now, I’m not talking about Pthirus pubis, the sexually transmitted disease—get your mind out of the gutter! The crabs I’m referring to are Clibanarius vitattus, the striped hermit crabs that haunted my dreams and terrorized my every waking moment for the duration of my first ever independent study experiment.
Continue reading Guest Post: The Semester I Got Crabs
Megumi Shimizu is a graduate student aboard the RVIB Nathaniel B. Palmer to collect sediment samples near Antarctic Peninsula as a part of the LARISSA project. She is interested in microorganisms and biogeochemistry of marine sediments; how the metabolism of microorganisms interact with the surrounding environment and the chemical components in sediments. See her first update here.
Are you playing with mud on the research vessel?
Some people on the ship joked when they saw me processing my sediment core. Yes, I’m playing with mud in Antarctica. Sampling sediments can tell us a lot, not only what happened across geologic time scales, but also what kind of organisms are living in the sediment, microbiology, and the geochemical conditions. We are serious about collecting mud and playing with mud.
upper panel: the entire view of glove box, lower panel: Liz Bucceri working on sediment sample processing in glove box. Photo by Megumi Shimizu
Nathaniel B. Palmer has three pieces of equipment to collect sediment; the megacore, kasten core, and jumbo piston core. The length you can reach below seafloor is different, 40cm, 1.5 to 6m and 24m respectively. Megacore is more suitable for biological studies since it preserves the sediment-water interface better than kasten core and jumbo piston core. Geological studies prefer Kasten core and jumbo piston core so that they can get older data from the sediment.
For my microbial lipid biomarker study, I’m taking samples from the megacore and kasten core. Along with microbial lipid and DNA, our team is collecting sediment and porewater (the water in pore spaces of sediments) to analyze geochemical properties of sediments, such as methane, sulfate, sulfide, and dissolved inorganic carbon. To maintain the condition of the sediments as close as the real environment, the sediment cores are processed under the condition of cold (~0C degree) and anoxic (no oxygen). How to make that condition? We have a special room called “The Little Antarctica”, on the ship, which is a big refrigerator containing glove box. A glove box is the transparent container with two pairs of gloves. The inside of the box is kept practically anoxic (less than 1% of oxygen. Atmospheric oxygen is ~20%).
Continue reading Beneath the Broken Ice: Playing with Mud
The last few weeks have seen a groundswell of support for Kevin Zelnio’s #IamScience movement, what began as a single, incredibly heartfelt post and twitter hashtag evolved into a series of personal reflections, a somber music video, and a tumbler and Facebook page, all with the unifying message that there is no traditional path through science, only your path through science. In the spirit of the #IamScience and This is What a Scientist looks like movement, I’d like to present two photographs, taken more than fifty years apart, of the Duke University Marine Lab’s Marine Invertebrate Zoology class.
The first photograph, taken sometime in the mid-1950′s, features legendary marine biologist and director of the Marine Laboratory Cazlyn Green ‘Bookie’ Bookhout teaching his Marine Invertebrate Zoology class.
Marine Invertebrate Zoology Class, circa 1950
The second photograph*, taken in 2009, features legendary marine biologist and directory of the Marine Laboratory Cindy Lee ‘first scientist to pilot the DSV Alvin‘ Van Dover teaching her Marine Invertebrate Zoology class.
Marine Invertebrate Zoology Class, circa 2009. photo by Katie Wood
This is what a scientist looks like. These are what future marine biologists look like.
*Obviously we staged the second photograph to look like the first photograph (and I’m pretty sure that ring stand hasn’t left the lab in 60 years). We did bring in a few ringers (notably myself, Kevin Zelnio, William Saleu, and another lab tech) to match the 1950′s photo.
Here at SFS, we seem to have an affinity for cyborgs. I recently had a dream in which I envisioned my future as such a creature. I had aged, achieved a professorship, and was teaching an introductory geography class. Contrary to the current classroom, however, there was not a learned scholar standing in front of pupils transferring information from my brain to theirs through lecture and leading discussions. Instead, there was a flurry of multimedia flying around the room and the “lecture” was really a snippet of a semester-long conversation involving the entire class intended to immerse them in geographic thinking, in and out of class. My thoughts and the in-person conversation was immediately digitized and encoded to be connected to parallel tweets, emails, blogs, and other online content.
Continue reading The Connected Professor
How do you declare your undying love for science? How do you immortalize your doctoral dissertation? How can you let the world know about your eternal love affair with tardigrades, Euler’s Identity, caffeine, or the voyager spacecraft? If you answered any of these with “get a tattoo!” than you’ve probably already heard about Science Ink: Tattoo’s of the Science Obsessed, by Carl Zimmer.
Over the last several years, Zimmer has been compiling scientists’ tattoos at the Science Tattoo Emporium, which now contains 255 pieces of ink. In Science Ink, Zimmer has selected the best looking, most memorable tattoos from his online collection and published them in a beautiful book featuring both artwork and insight into each piece.
Zimmer is among the best of the “science communicators”, those who distill the essence of important concepts into comprehensible units. Each tattoo come with either a description of the story behind its origin, its meaning to the canvas, or the fundamentals of the concept it represents. The book covers an extensive range of topics, from mathematics to natural history to physics and astronomy. When I first heard about this project, I was expecting a coffee-table style book of tattoo photographs, but it is much more than that. The tattoos are simply prompts for a deeper exploration into the meaning of science to society, as well as a delightful collection of (very) short stories about individuals experience in science.
Continue reading The indelible stamp — Scientists and their tattoos
It’s the moment we’ve all been waiting for, the single most misunderstood marine creature that calls our oceans its home: the rare, elusive, often smelly, occasionally employable, Marine Biologist!
For something so incredibly popular, articulate, good-looking, and revered, there sure are a lot of misconceptions about who marine biologists are and what they do.
Myth # 1 – All Marine Biologists have beards.
Yes, if you look through a history of marine scientists, you’ll find many pictures of old, bearded men. But that’s true if you look through the history of any science and reflects a long cultural history of gender discrimination and outright misogyny. Couple that with a long standing tradition among maritime cultures that women don’t belong on boats, and you might be led to believe that most marine biologists are men. That fact becomes futhur from the truth every day. Among the pioneers in marine science are Mary Rathburn, Julia Platt, and Rachel Carson, while modern barrier breakers range from Ruth Turner, the first woman to use the DSV Alvin for research, to Cindy Lee Van Dover, the first to pilot it (incidentally, no one has a beard on the Alvin, since it would interfere with the emergency respirator should the oxygen system fail).
The website Women Oceanographers (http://www.womenoceanographers.org/) has a spectacular series highlighting the contribution of women to marine sciences.
Myth # 2 – Marine Biologists all study whales and dolphins.
No, we don’t. Some of us don’t even particularly like whales or dolphins. For that matter, we don’t want to work at Sea World.
Myth # 3 – Marine Biologists hate fishermen.
Perhaps one of the most insidious rumors is that we have it out for fishermen. In retrospect, it’s not hard to see where this would come from. Any catch limit, fishery closure, or fishing regulation is going to track back somehow to the work of a marine biologist. And there are some marine biologists who are opposed to fishing, just like there are members of the general public opposed to fishing. But Marine Biologist and fishermen have the same goals – we both want a healthy, productive ocean (that both our livelihoods depend on). Most marine biologist that I know fish, eat fish, and support our local fishermen. In fact, if I didn’t screw up the schedule, I’ll be out fishing when this post is published. Unfortunately, as overfishing is one of the biggest problems facing the ocean, conflicts are unavoidable and we’re going to butt heads on important issues.
Even so, most Marine Biologists would love to see the ocean return to a state of abundance where fishermen can harvest without regulations. Dare to dream.
Myth # 4 – Marine Biologists spend their lives on the water.
This myth is more prevalent among aspiring Marine Biologists. The job looks glamorous, with trips to tropical islands, extended cruises, and life on the beach. While I hate to burst the bubble of the next generation, Marine Biology is mostly lab work and sitting in front of your computer. If I’m lucky, I’ll get maybe 3 months of field work every 2 years. The rest is endlessly freezing and thawing samples, pipetting clear liquids into other clear liquids, and typing, typing, typing. Don’t get me wrong, I love (almost) every minute of it, but it’s a far different lifestyle from what Jacques Cousteau led me to believe.
Myth # 5 – Marine Biologist are all just like Jacques Cousteau.
Milton Love said it best when he wrote ”We really like Jacques Cousteau, too. But, drinking thousands of gallons of red wine while scuba diving around the world does not make you a marine biologist. It makes you a wonderful and effective spokesperson for the sea, and gives you a liver with the consistency of a chocolate necco wafer, but it does not make you a marine biologist.” Most research cruises are more akin to the Life Aquatic, anyway, but with more disasters and less research turtles surviving. A personal submarine would be nice, though.
The National Science Foundation has recently announced the NSF Career-Life Balance Initiative largely in hopes of retaining women in the sciences past their the dissertation years. Most notably, the Initiative allows a year long pause in awarded grants to new parents. This pause matches the pause in the tenure process that most universities offer (but few faculty know about). In addition, parents can apply for supplemental funds to keep their labs running while on leave. In addition, NSF promises to advertise its new help for families, continue researching new methods of keeping women in the sciences, and continue to promote tenure pauses and spousal hires in its partner academic institutions.
Thinking about ways to make the academic environment more friendly to families is a topic that fascinates me both as a sociologist and as a person who will likely benefit from this initiative. According to the White House announcement for the program, the Initiative emphasizes the need for women in the sciences in order to maintain creativity and leadership. Language like “parental leave” instead of maternity leave also signifies that NSF is leading the way to a new kind of workplace, recognizing both men and women’s desires to balance work and family in an equitable way – not to put the burden of that balancing act on the mother. Kudos to NSF.