Dissecting rock scallops

Scientific research, especially with live animals, is inherently high-risk. It turns out it’s really hard to care for a species you know almost nothing about, let alone get them healthy and happy enough to spawn. Very little is published on the Purple-hinged rock scallop, Crassadoma gigantea, and folks are just now developing methods for commercial production. Although my research team had good reasons to believe we would be able to spawn our animals for a larval common garden experiment with a low pH treatment, it never really happened. Sometimes one population would spawn, but others wouldn’t. Sometimes a few would spawn on a Friday afternoon when everyone had left the hatchery. But alas, they never spawned the way we needed them to and we finally cut our losses this summer. A year of of my PhD preparing for an experiment ended without any data. But out of the flames came a tiny, beautiful phoenix…

Crassadoma gigantea, photo from soundwaterstewards.org

We decided to use the adult scallops we’ve kept alive to do a similar experiment. I have four populations of scallops, one from Alaska, one from California, and two from Washington, and I split them between ambient pH and low pH treatments, with four replicate tubs each.


This week, we dissected some at Time Zero, before the low pH treatment was turned on, and then at Time One, after half of the animals were exposed to low pH for 48 hours to look at the physiological response to short-term exposure to low pH. In about 6 weeks, we’ll sample them one last time at Time Two, for long-term exposure. Hopefully we’ll be able to make population comparisons. But at the very least, we’ll get some insight into the species’ physiology and what might be coming with ocean acidification.

We collected samples for SO many things. First, we sampled five tissue types for RNA and two for proteins to look at RNA and protein expression. Those are the most time-sensitive and needed to be quickly immersed in RNALater or flash-frozen in the first couple of minutes. Then, we sampled other tissue types for lipid analysis, and others for microbial community. We weighed the scallop, took slivers of the gonad for histology, and classified the color of the mantle.


And getting inside these animals is not easy. Fortunately, we had a room full of experienced shellfish shuckers. And a LOT of shucking knives.

Alongside the biological sampling we are sampling seawater chemistry. Our water treatment system that makes low-pH seawater has Durafet pH sensors to manage the pH of the water by adding CO2 to drop the pH to a target. One of the four replicate tubs per treatment also has a Durafet, so that we can ballpark what pH our treatments are at. Then, on a daily basis, we collect discrete seawater samples from all the tubs in each treatment and the water header tanks to measure pH, salinity, and temperature. At the same time, we collect a water sample to measure total alkalinity later in the lab. Altogether, this gives us a clear picture of the carbonate chemistry experienced by the scallops.

Sampling days for most projects are often chaotic and strenuous. Everyone’s frantic and tired, and you have to provide cupcakes and donut holes to keep the calm. Somehow, these sampling days went off without a hitch. I should have known, since I have an amazing team of collaborators and many experienced shellfishy peers that are always ready to volunteer their skills.

And moreover, I had legit good omens from the universe. On our way out to sample at Time Zero, we saw the whole J Pod of resident killer whales right off the beach at the Fauntleroy ferry terminal.


And right after finishing the sampling at Time One, we had 45 minutes to kill at the ferry with Buster the 12-week-old border terrier.


What a rush to finally have samples in the freezer. Now, I just need to monitor the seawater chemistry and make sure the system stays stable until our last sampling day sometime in November. Fingers crossed nothing explodes!


Salish Sea Ecosystem Conference, 2016


Two weeks ago, I attended the Salish Sea Conference in Vancouver, British Columbia, and by the third and final day I was already looking forward to two years from now when I could attend all over again. Sleeping poorly on a firm chaise in a closet of an Air BnB and riding a caffeine roller coaster did not dampen my spirits. I was too stoked from three days of strong native presence, interdisciplinary research, and a wonderful community passionate about our Salish Sea.

The local tribes had a powerful voice. The session on clam gardens was particularly moving, as it started and ended with traditional drumming and dance, and was filled with story-telling –stories of ecological research by scientists and traditional stories passed down by elders. And clam gardens are just so cool! In case you are as unfamiliar with clam gardens as I was, people roll rocks down the beach to form a small sea wall parallel to the coast, and the little pocket of beach accumulates sediment over time making a perfect habitat for dense clam populations. There are plenty of historic clam gardens in the Salish Sea, and some are being restored today. The research presented in the session suggests that clam biomass in the clam gardens is four or five times as great as in the unmodified beach. And the little sea walls themselves are coated in diverse life, much of which is delicious. Clam gardens also serve as a way to bring people together and teach lessons through stories – a rich resource all around.




Screen Shot 2016-04-27 at 9.25.53 AM.png


Screen Shot 2016-04-27 at 9.26.07 AM.png

The conference reminded me of my time at the School of Marine and Environmental Affairs. I was surrounded by SMEA alumni, and a few SMEA faculty too. It was wonderful to reinforce old relationships and chat human dimensions, and be able to make new connections for my current research in the sessions on ocean acidification and shellfish. This is the first conference I’ve been to where I could pursue both my fisheries science and marine affairs interests.

In the ocean acidification sessions, I learned that I am not a chemist despite my love for organic chemistry in college. Before I presented my research plan for a common garden with a low pH treatment on rock scallops, I listened to Dr. Richard Feely’s talk on how pH is simply not a good enough metric for corrosiveness when studying calcifying organisms. Aragonite is what matters, and an aragonite value of 1 can be constant over a pH range of .3. My plan is to collect discrete water samples to send off for a more complete chemistry analysis, ultimately to get a handle on aragonite saturation, but my slides definitely only mentioned pH and pH is all we can measure and adjust in real-time. So that was humbling.

I also learned that there are many proxies for corrosiveness associated with ocean acidification by using other metrics like salinity and dissolved oxygen together. Dr. Simone Alin of NOAA presented on how we can use these proxies to make use of old data sets that do not include carbonate chemistry data. The story of ocean acidification is made more complicated by biogenic factors, so having older data sets makes it easier to demonstrate how the anthropogenic contribution to ocean acidification has changed over time.

I also reaffirmed my love for Twitter at the conference. It’s amazing how much more I pay attention when I’m trying to summarize the main points or catch the funny lines to share in a tweet. I can also hear about what’s going on in other rooms during the session to find out where I should be- I switched to the clam gardens session because Dr. Bonnie Becker of UW Tacoma was tweeting up a storm. Twitter also helped me network. There are only so many people on Twitter at a conference, and you get to know each other just be reading each other’s tweets. It’s like people already know you by the time you shake hands in person. In other words, connecting on Twitter made it so much easier to overcome that pesky grad school imposter syndrome and ask the questions I wanted to people I admire. Ahhh the joys of #scicomm.

And lastly, thanks to my adviser Dr. Lorenz Hauser for pushing me to go to the conference, and to the organizers who made it so fruitful. Best conference I’ve been to yet!


Being a Biologist at Home Depot

Last week I went to an irrigation supply store to buy 12″ irrigation pipe, and I asked the helper if he could cut it down to a size that would fit in my sedan. He got this worried look on his face- “I dunno, ma’am, you know you can’t glue this stuff back together once I cut it. It’s got a belled end and a gasket,” and I replied “Yea, I’m actually not making a sewage system, I’m making sieves for shellfish larvae.”

“You’re making WHAT?”

IMG_1942.JPGcan never tell if my explanations will be a pleasant diversion from their day to day work, or if I’m really just about to ruin their day with my biologist hooliganism.

I am building a system to hold tiny bucket-like homes for scallop larvae in my common garden ocean acidification experiment, and I need everything to be incredibly tolerant to saltwater conditions AND to not leach out gross chemicals that could harm my sweet little larvae. Plus there’s little tricky details, like the bars that the buckets will hang on cannot sag at all, because the scallop eggs don’t do well when they’re all bunched up on each other, as they would if the buckets were tilted. So I’d think rebar, but that could rust. So rebar inside PVC! But then how do I plug the ends and still have the bar pass through the tiny holes in the buckets? A system like this isn’t something you can buy at a store, so instead, I have to make it more or less from scratch from things I find online and, of course, at Home Depot.


Today at Home Depot:

Me: “Do you have silicone caulking without the anti-bacterial, anti-fungal additives?”

Helper: “Why would you want that?”

Me: “Because I’m working with sensitive larvae.”

Helper: Squinty eyes and long, awkward pause “…right.”

Maybe hours in the shop sanding PVC has made me crave human contact, but I must say I’m incredibly thankful for those people who are a lot smarter than me getting on my page and helping me solve a problem. For example, I called a steel company to get some quotes and the helper wanted to know everything about my set up. He even described the rebar I was trying to buy as “noodley” and directed me to a better product for my needs. Thank you Universe for helpful people because inventing as a grad student can be a challenge!



Cookie Experiments

I was lucky enough to conduct cookie experiments with high schoolers this weekend. Saturday Academy’s Food Science class ventured to the Research and Development branch of Continental Mills in Tukwila, WA, and it was incredible! All day long, we learned about the science of developing new recipes, the science of taste, and the process of product development. I’m going to go ahead and say “we” for all of this because even though I was technically just a chaperone and driver, I learned so much and and grew deeply nostalgic for school field trips. I even wore my complimentary hair net all the way back to the UW.

The point of our cookie experiment was to test the effect of sugar type on cookie taste and appearance. The control was the sugar blend Continental Mills usually uses for cookies, and the sugar treatments were granulated sugar, brown sugar, and powdered sugar. The kids got into teams and made cookie dough using giant industrial mixers and ovens; I was there for emotional support. After scrambling about and enduring the ten minutes of cookies baking and students wafting, we got a peek at the results. Powdered sugar gave the cookies a crackled, pale appearance. Brown sugar made them plump and malty. White sugar tasted a lot like the control, but was paler in appearance. Man, it would be great to have a photo to share but we weren’t allowed to take pictures. Top secret cookie mixes!

For the next event, we walked into a room with dividers so that each person was isolated at a bench, under red lights. A little window opened and a tray of marshmallows appeared in front of each of us. Because of the red lights, the marshmallows appeared purple and yellow. We had to guess what flavors they were. I guessed lime and strawberry, my friend guessed blueberry and strawberry. Afteward, the regular lights came on and the marshmallows were green and yellow! Then, they tasted like lime and lemon. It turns out they were ALL the same: a citrus blend! I can’t wait to do some of these experiments at home. Like, what does Annie’s Mac n’ Cheese taste like in the dark?

There were a million more tidbits to share, but the most important takeaway for me was that the Research and Development Branch was FULL of great role models. At least 7 or 8 of the researchers that worked for Continental Mills took their Saturday to hang out with kids and get them excited about food science. The career paths of each person were diverse: some folks traveled the world inventing new flavors of chips and frostings, others went because they couldn’t find jobs in other fields. But pretty much everyone seemed hooked on the creativity and curiosity of working there. The director, Stephen Green, even spent a day with us in Seattle for a Saturday Academy earlier this month just to get to know the kids and the program beforehand. His dedication to outreach was so impressive! Looking forward to writing him a thank you letter with the students next month.

Comparing agency science practices for endangered species management

Even if regulatory matters don’t keep YOU up at night, the Endangered Species Act of (ESA) 1973 is fascinating. Let’s be real. The ESA’s history is as juicy as it gets. In the most famous case, where a giant dam was prohibited from being finished to protect a tiny endangered fish, the judge said that we have to preserve endangered species, “whatever the cost.” Those are some BIG words for federal court. Since then, the ESA has had a lot more teeth than other environmental laws and in consequence, has been seriously attacked by conservatives, particularly in the last few decades.

The Endangered Species Act (ESA) is unique in that it mandates agencies to use the “best available science” when making key implementation decisions. This is why I, as a biologist, am so hooked on studying the ESA. As someone who cares a ton about conserving biodiversity, and someone who is familiar with the science of anthropogenic impact on the environment, I see this as a ticket to secure conservation efforts. Golly gee wiz, was I wrong! Not to say that the ESA isn’t effective—it’s prevented extinctions 99% of the time. But how many species have recovered to the point of delisting? Something like 1%. It turns out protecting species from extinction is not the same thing as restoring populations to bountiful levels.

The point is, there’s room for improvement in ESA implementation. Of course, the two agencies in charge know this: the National Oceanic and Atmospheric Administration (NOAA) Fisheries, and the Fish and Wildlife Service (FWS). If they had reliable and substantial budgets, they could achieve a lot more. But what can be done realistically in the mean time to improve endangered species conservation?

An entry point to that really tricky question is seeing what can be done better. If NOAA Fisheries and FWS share the job of managing endangered species, and ones does a better job than the other, maybe they could learn from each other to improve overall. I know, it sounds like a Disney Channel movie. But administrative law scholars recently wondered the same thing. Is it better for agencies that share tasks to coordinate or to compete? The answer was, generally, that they should cooperate. There’s no I in team!

Of course effective agency coordination depends on a lot of factors, but this provided the framing for my thesis. I compared how well NOAA Fisheries and the FWS adhere to hallmarks of scientific quality when abiding by the “best available science mandate.” I did this by building upon previous research and being creative where I had to be, using ESA reports and court cases to test several metrics as proxies for the quality of science. And the outcome? Drum roll please… NOAA Fisheries came out on top.

Let’s be clear: NOAA Fisheries has more $$/species, manages fewer species, and manages some very charismatic species like orca and salmon, meaning they have a lot of resources to work with. In other words, the difference isn’t either agency’s fault. But, knowing that one agency does better than the other provides insight into how the agencies could coordinate to make the best of their implementation strategies and provides a starting point for further research on how to improve science use by agencies under the ESA.

So that’s the boiled down version of my master’s research that was recently published in Biological Conservation with my adviser, Dr. Kelly at the School of Marine and Environmental Affairs, University of Washington. If you’d like to take a look at the article to learn more, here’s a link that will be free to anyone until April 12, 2016!