A Summer of Discovery

Posted on December 17, 2018 by abeaudreau

by Willa Johnson

Biking through the Safeway parking lot in the pouring rain, my first week in Juneau, I heard someone yell at me from their truck window. I was outraged; someone was catcalling me. As the truck drove off, I looked down and saw my sodden mitten on the ground. The person who I thought was catcalling me was actually just kindly letting me know I had dropped my mitten. My time in Juneau was full of surprises like this.

Over the summer, I had the opportunity to work in the Coastal Fisheries Ecology Lab as a research intern and NOAA Hollings Scholar. I’m from Seattle and currently a senior at Whitman College in Walla Walla, Washington, majoring in biology with a minor in gender studies. After spending the previous summer in the dry 100+ degree Walla Walla heat, I was overjoyed to be living near the ocean in Juneau’s temperate climate.

I spent my days working with MS student Matt Callahan on a study of juvenile sablefish ecology. This meant that I spent a lot of time looking at stomach contents. One of the surprises of my summer was discovering how interesting sorting through fish vomit can be! Sablefish are generalists, meaning they consume a wide variety of prey, so there was always something new and interesting in their stomachs. We found salmon bones, herring, mysid shrimp, shiner perch, and numerous amphipods – small crustaceans that are a favorite food of many fish.

Days at the dissecting scope (left) and on the water (right) can be a mix of monotonous and amazing. Photos by Willa Johnson (left) and Anne Beaudreau (right).

Sablefish are voracious. One day, Matt and I spent the entire morning counting 439 amphipods in the stomach of a single sablefish. As I became better at identifying prey, the work was more exciting. Each time I picked otoliths (ear bones) out of heavily digested fish remains, I would think, “Yes! It is another Pacific herring!” We also used heavy duty blenders to homogenize fish and measure their energy content. This will help us understand what types of prey contribute most to sablefish growth. For my project, I analyzed the differences in diet composition between age-0 and age-1 sablefish. It was cool to experience all the different aspects of the research and to learn what it would be like to go to graduate school.

I also had the opportunity to join Matt, Anne Beaudreau (CFE Lab PI), and Katy Echave (NOAA scientist) in Sitka for a week of fieldwork. This was, by far, the highlight of my summer. Each morning we would wake up, put on many layers of rain gear, and drive our small boat out to Saint John Baptist Bay, a nursery habitat for juvenile sablefish. Except for fishing in small creeks when I was little, I was new to fishing. Sometimes I hooked multiple sablefish at once, sometimes we waited a long time for a bite. I spent many hours sitting on the corner of the boat contemplating what all the little sablefish were doing down there. I even tried talking to them to coax the sablefish into biting. I don’t think they heard me! But even on days when I caught only a few sablefish, there was some interesting bycatch, including a ratfish, a crab, and a quillback rockfish. We were also excited to see brown bears from the boat. Other highlights of the trip included many delicious dinners cooked by Rhea, a recent graduate from the CFE Lab, and picking big bowls of salmon berries on sunny days.

Jesse and Willa went on many hikes to explore Juneau’s varied landscapes.

Thanks to the Hollings Scholarship, I had the opportunity to present my research results at the NOAA headquarters in Silver Spring, Maryland, at the end of the summer. While I was there I went to museums, ran into Elizabeth Warren in a vegan restaurant, and got to see the other Hollings Scholars from all around the U.S. present their fascinating projects. It was a wonderful science nerd convention. However, traveling to humid, metropolitan Silver Spring from Southeast Alaska made me realize that Juneau might be the place for me.

From Pride events to Audubon bird walks to lab potlucks, everyone in Juneau made me feel so welcome. When it wasn’t pouring rain I would bike into work past a rainbow of wildflowers on the side of the road. On the way home I could stop for a walk or a quick jump in the ocean. I spent most of my weekends hiking with friends, including current CFE Lab member, Jesse Gordon. Everywhere in Juneau, there are beautiful views of the mountains, the ocean, glaciers, or all three. Now I’m back at Whitman, halfway through my senior year, and I’m already thinking about how I can find my way back to Alaska.

What a view! Willa is dreaming up ways to get back to Alaska. Photo by Hillary Behrman.

Tips on Data Management from Someone Who Learned It the Hard Way

Posted on February 4, 2018 by abeaudreau

by Rhea Ehresmann

Experiences in data organization and management

It was 2 AM the week before a fisheries conference, and I was attempting some last-minute analyses. Having added a couple hundred lines of new code for figures, my code would no longer run from the beginning and I had a hunch it was because I hadn’t set everything up correctly initially. Ten hours and 25 Stack Exchange posts later, I had the realization that no researcher wants to have: my data needed to be completely reorganized from the ground up. I should have organized my data months ago (or ideally from the get-go) but instead I ignored it until it became absolutely necessary. Further complicating this issue was that I am a remote student working in Sitka (most of the faculty and students are in Juneau or Fairbanks) so finding the solution was entirely on me. Data organization is like working out or eating healthy: we all know we should do it, but often it is given the “I’ll do that tomorrow” excuse. Out of this minor meltdown, I learned a lot about data organization and management and even how to overcome roadblocks independently.

The message you don’t want to see at 2 AM when you’re trying to finish a presentation. Source.

How things go wrong

It often feels that life as a remote student is all about learning things the hard way. Being on my own in Sitka, I can’t walk down the hall to talk with another student about a problem or spontaneously chat with a professor in passing or after class. Only having my screen in front of me, I don’t have much opportunity to compare other students’ code writing techniques or data management practices. With my complete dataset nearly 4 million lines long, bad habits were started without corrections: developing a “run the code until it’s broke” philosophy, overwriting and deleting code I didn’t think I’d need, and even naming files poorly by just tacking on another number or “new” at the end of the name.

While these are now commonsense practices I avoid, I learned these after much trial and error, as well as after reading other articles on data organization and management using R. There are many other struggles that come along with being a distance student, but I believe it ultimately pushes me to be a better researcher. And the best part of being remote is no one can see your meltdowns! But you don’t have to wait until you are in a panic to start some best practices.

What typically happens when you don’t follow best practices for coding in R. Source: https://imgur.com/gallery/x0ml8

Five data management tips

Careful organization and management of data and code is essential for any analysis. Taking the time and initiative to make clear notations for code, to be consistent with code-writing techniques, and to organize script files in your directory will help with more than data management of the entire project. These steps also protect against data loss and analytical errors while allowing your analyses to run smoothly from one to the next. There are many tips and tricks for data management taught in classes and online, but here are the top five I’ve learned from my solo trek to good data practices with links to more information on each:

Keep raw data as a “flat” table saved in an open data format (like .csv) with records saved in rows, using descriptive and concise names for the data files. Though it is tempting to quickly add in a new column or delete some rows of data in Excel, don’t do it in the raw data file (more here).
Be diligent and consistent with notation, syntax, and commenting lines in script files. Comment often! This will help to remember what/why you did something when revisiting an earlier analysis, as well as helping others make sense of your code if you need to share it. Also, don’t delete code you think you don’t need. I can’t count the number of times I’ve gone back to this “unused code” months later, only to tweak it a bit and make it useable. Keep separate analyses in their own script files. Style guides like Google’s and Hadley’s R Style Guides are great resources.
Use Stack Exchange to solve an issue or google your R questions. I’ve developed a special knack for figuring out how to do obscure things in R by scouring these websites. My philosophy is that anything I’m trying to do in R has already been done, and usually that is the case. It just requires a bit more patience and persistence to identify the search terms needed for finding the solution.
Back up everything and keep your folders organized. Time spent searching folders for an older version of a script or data file is not efficient. I save script files and raw data files on Google drive for ease of access at any computer, along with an external hard drive. Dropbox is commonly used because of its simplicity of automatically backing up files. There are other options for version control and backing up data like Git that I don’t currently use but are worth looking into (more here).
Don’t cut corners to save a few minutes in the short term. It’s so easy to make quick-fixes to get that figure to run or to get to the desired output, but these shortcuts aren’t worth the time you’ll have to spend fixing the code or trying to remember what you did down the road. Take the time to establish a good workflow for yourself, and be consistent with this while working on your analyses. There are great resources for establishing a solid workflow (more here).

As her code now runs flawlessly, Rhea can relax and enjoy tea while finalizing a figure in R over winter break.

Wrapping up

Even though data management ranks up there in fun with tasks such as doing your taxes, folding laundry, and weeding the garden, the short-term pain will save you a lot of headache and time by having a well-organized and accurate end result. As I move onto new analyses for the next chapter of my thesis, I now know how important it is to set things up correctly from the beginning. Being a remote student during all of this has been challenging, but it has ultimately made me a much stronger student and more self-reliant. Meltdowns not included.

♦♦♦

Rhea is a Master’s student in the Coastal Fisheries Ecology Lab and is studying the movement ecology of juvenile sablefish near Sitka, Alaska.

The little ROVs that could

Posted on October 3, 2017 by abeaudreau

by Veronica Padula

I felt like a little kid on Christmas when I opened the white box that said OpenROV. Inside that box was a kit that, when assembled, would become a remotely operated vehicle (ROV). ROVs are little robots that can be driven remotely to explore and capture images of the mysterious underwater world. For those who can’t SCUBA dive but want to see more of what lies beneath the surface, ROVs open the door to that world by capturing photos and video of things that live under the sea.

Plus, there were extra special surprises in the box: a red knit beanie with the OpenROV logo embroidered onto it, which made me feel like we were stepping into a scene from The Life Aquatic, and stickers! The stickers were my favorite part.

ROVs have been used by marine scientists for decades but are now becoming more accessible to the public for exploring the depths of the ocean. Photo credit: http://www.openrov.com

We had actually received two OpenROV kits, and I was tasked with transporting the kits from Anchorage to St. Paul Island in the Bering Sea. They were a generous gift from the manager of the Trident Seafoods plant, Bill Briggs. The new instruments are meant for students to use to collect data as part of citizen science projects. I gave Bill one of the red beanies, which I think looks great on him, but I can’t wait to show him the video and photos that come from driving the ROVs around St. Paul harbor, the salt lagoon, and other unexplored territory.

So many pieces!

Our plan was to host an ROV Builder Club, where people from the St. Paul community could come together one night a week over the course of the summer to construct these ROVs. I was supposed to lead the ROV construction and sincerely wish I could say I have lots of experience with building things like ROVs, but sadly I do not. Luckily, Mr. Mac, Walt, and Jacob came to the rescue, contributing their knowledge and expertise to the ROV construction. Kids joined us too, including Zoe, Kadyn, Til, and Brynn.

Jacob and Zoe work together to make sure we have all the parts we need.

It was wonderful to have folks of all ages joining our builder group, and the kids learned a great deal from the adults in our group, including patience. While kids wanted to just jump in and glue all the pieces together, I wanted to go through the entire kit and match every piece of construction material to the pictures in the manual so we were absolutely certain we had everything. You see, while living on St. Paul Island is amazing, sometimes it takes packages a while to reach us. So, if we had to order any parts for our kit, we definitely had to do it at the beginning of the process, because otherwise we would be stalled in our construction.

This was a team effort!

I had fun watching the kids match the ROV casing’s acrylic shapes to the pictures in the manual. It definitely tested my spatial awareness and likely tested theirs as well. They worked together to identify all the pieces of the kit. Gluing the acrylic pieces together was not an easy task, because we had to make sure the puzzle pieces fit together perfectly. The seals need to be water tight so that seawater doesn’t leak into the ROV and destroy the electronic bits and pieces that make it function. Luckily we had several people on our team who meticulously glued the parts together, so fingers crossed that the seals are water tight!

Kadyn and Walt glue wires down and make sure everything is water tight.

While we have the ROVs mostly built, we are troubleshooting some technical hiccups with the batteries. Thankfully we have a dedicated team of builders that will fix these glitches so they are ready for their maiden voyages. I can’t wait to see the excitement on all the kids’ faces when we drop the little robots in the water for the first time and watch them sink away from us, disappearing into the depths of the ocean. Operating the ROV is a job for video-game aficionados, because we are using a video game controller as the remote driving apparatus for the robot. I just hope that our first mission does not involve donning dry suits to free a stuck ROV underwater. That water is cold!

Almost complete_photo by Veronica Padula

They are almost ready for their maiden voyages!

While I’m still no master ROV builder, I am so grateful for the community members that came together to mentor the students, and champion the ROV construction. Their work and dedication means the ROVs will come to life soon. The best part of the process is yet to come, when the kids can partake in ROV voyages and discover the underwater world that surrounds their home. This amazing technology will bring that world closer to them. Who knows, maybe they will discover new species of invertebrates or fish never seen before in the St. Paul ecosystem (or find someone’s glasses that fell off while paddle boarding). I can’t wait to share that joy and wonder with them. Even if the waters are murky, the kids will be able to experience something extremely special using these ROVs—the excitement of exploration. And the best part is that we can have countless ROV explorations over the years. Imagine all the amazing images we can capture, and the stories we can tell over many years through those images.

Kadyn will captain one of our ROVs.

We hope to test the ROVs in October. Zoe will captain one of our ROVs, and Kadyn will captain the other. We haven’t named our ROVs yet, but are open to suggestions. Stay tuned for pictures from their maiden voyage. Can’t wait to see what these little robots will find!

—

To see an example of some underwater ROV video, check out this vintage highlights reel that Anne put together in 2004 from an ROV survey in the San Juan Islands, Washington: www.vimeo.com/236496491

For more about Veronica’s graduate research, read her article on the impacts of plastics in the marine environment: https://krakenandfriends.wordpress.com/2017/05/10/guest-blog-the-plastics-problem/

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All photos in this post were taken by Veronica Padula unless otherwise noted.

From the beltway to the icefield: An East Coaster’s experience in Juneau

Posted on September 25, 2017 by abeaudreau

by Willem Klajbor

What does the ideal summer vacation sound like to you? The image that pops into most people’s heads probably resembles an island resort somewhere, fully stocked with colorful drinks, and white sand as far as the eye can see. The average person probably wouldn’t come close to thinking about wading into the frigid ocean at 4 am, wearing a rain jacket every day, or evading bears on a hike. And the average person definitely wouldn’t want to be working in those conditions!

Let me back up – my name is Will, and I was lucky enough to spend last summer as a research intern in the Coastal Fisheries Ecology Lab. My hometown is in suburban western New York and I’m currently a senior at the University of Maryland, College Park, studying Marine and Coastal Management, Economics, and GIS. When I was a sophomore, I received the NOAA Ernest F. Hollings Undergraduate Scholarship, which gave me the opportunity to assist with research on any NOAA-funded project between my junior and senior years. The good news for me was that it led to ten weeks in the 49^th state, where rain, cold, and bears are plentiful.

Will models “Juneau business casual.”

Specifically, I was working with Ph.D. candidate Maggie Chan to evaluate subsistence harvesters’ responses to a relatively new set of halibut fishing regulations. There are a lot of different terms for what I was: intern, research assistant, apprentice. But for me, all of that just meant working as a Swiss Army knife for the project – sometimes doing background research, other times managing and organizing our data, and even making maps. This was my first experience doing real research of any kind, so I was nervous going in, but Anne and Maggie made me feel at home right away and always kept me challenged with new tasks.

I also got to do some beach seining with Doug Duncan, another graduate student in the lab. There’s a great blog post about what that’s like here (link), and though there were some very early mornings and some very drowsy afternoons as a result, I was grateful that I had the opportunity to get in the water and do some field work while I was up north.

Sharing a moment with a starry flounder. Photo by Phallon Tullis-Joyce.

I was also lucky enough to be living with a group of other interns from around the country who were in Juneau working on projects at UAF. On top of that, we all grew close to the graduate students we were working with, so there was no shortage of people to show us new things about Juneau. And don’t get me started about Juneau – the city really is a hidden gem. Nearly every minute of my free time in Alaska was spent outside trying to find another hidden bike path or spot another bear. If you’re into leg workouts, I can tell you that I got a chance to hike some of the major day trails around the city, and those were usually enough to put us on our butts for the 12 hours that followed. But the view from the top was always worth it.

Building a fire in the pouring rain is one of the important life skills you learn in Southeast Alaska. Coastal Fisheries Ecology Lab members, pictured from left: Cheryl, Doug, Aiden, Phallon, Madison, Will, and Nina. Photo by Maggie Chan.

My uncle, who’s a commercial fisherman in Homer, Alaska, warned me before I left that a lot of people catch “Alaska Fever” when they visit. And honestly, I really did think he was exaggerating. Now, I’m back in College Park, and it’s often difficult to go more than a couple of hours without daydreaming about the mountains or the whales that liked to hang out just outside the lab. Even though it rained nearly every day I was there (I’m not exaggerating, I could count the sunny days on one hand) and it never really got above 65°F, Juneau really left its mark on me. I really do love it here in Maryland too, but I can’t ignore the symptoms – I went up north and caught the bug, and now I’m stuck with “Alaska Fever.” Check it out for yourself and you’ll see what I mean.

On rare sunny days, Juneau spoils you with amazing views of mountains, glaciers, and the sea. Photo by Dana Flerchinger.

Fishing for science—A landlubber’s journal

Posted on September 17, 2017 by abeaudreau

by Matt Callahan

I recently had the opportunity to participate in the final leg of NOAA’s sablefish stock assessment longline survey. I’m starting a Master’s program focused on juvenile sablefish, so taking part in this survey and observing some of the ins and outs of longlining will provide a valuable perspective as I conduct my research. That said, thriving at sea was an adjustment that this landlubber never quite made.

Before boarding the plane to Kodiak, I bought a jump rope at Second Wind Sports so I could keep training for the Klondike road relay on the boat. It turned out to be a kid’s jump rope and since I’m well over four feet tall it didn’t work. “That’s ok,” I thought, “there will be plenty of line on a longliner to make my own jump rope.” This turned out to be a lost cause. Between queasiness and boat rocking that was incompatible with jumping I never got a chance. Fortunately, the Klondike is as much about fun, cheering, and sleep deprivation as running fast.

: “Just think, you could be selling insurance in Detroit for a living, Matt.” –Captain Sam. Photo by Matt Callahan.

Our vessel was a 150-foot longliner, the Ocean Prowler. Captain Sam was a soft spoken, kind, confidence-inspiring seaman who always had a smile on his face. The chief engineer, Frank, counterbalanced Sam’s sometimes reserved manner with a story or opinion for every occasion. Josh joined the crew last minute as the cook and impressed all of us with high-end, restaurant quality food. He can also cut apples so they look like swans, or possibly albatross. The rest of the crew were either deckhands who operated the longlining gear or processors who packaged fish after it was brought on board. There were four biologists on board: chief scientist Karson, Sabrina, Denis, and me.

A juvenile sablefish that was tagged on a different survey near Sitka, Alaska. Photo by Kari Fenske.

The survey samples the same stations annually throughout the Gulf of Alaska over the course of the summer. At each station, we set two lines and a set is divided into 80 skates (lengths of groundline) with 45 circle hooks, each separated by a cannonball weight. We counted and identified every fish caught. Sabrina or Denis stood in a phone booth-sized box on the upper deck, above the roller that pulls in the line, with tablets to record their observations. Whoever was not on deck duty noted the sex of the sablefish and measured all fish with a fancy electronic fish measuring board. Karson and I collected otoliths, which are bones in a fish’s head with annual growth rings that indicate its age. The sablefish otoliths were sent to Seattle for analysis after the survey. (Dear analyst: We tried to clean off the otolith vials and boxes well, but if they’re still foul with fish gore, I’m really sorry!) We also tagged and released some of the sablefish. The deckhand would flick each fish off its hook into a net and we would insert a small numbered tag into its back muscle then release it. Rewards are offered for recaptured fish and the data allows us to track sablefish movement and growth.

A baby Pacific octopus (later released alive) and me. Photo by Karson Coutré.

Our most exciting catches were two sleeper sharks on shallow, gully stations. These massive predators thrashed around on the bottom and created horrible tangles in the lines. We also caught a lot of giant grenadier, which dominate biomass at the deeper end of the sablefish habitat. Apparently, considerable effort to try to do something useful with their meat has been fruitless.

Seas up to twelve feet tossed us around for much of the leg. I started off taking the king of seasickness medication—the coastguard cocktail. It’s supposed to prevent nausea while keeping you alert, but I still felt like a tired, duller version of myself and slept eleven hours each night at first. I never got violently seasick but never felt fully well either.

Despite the internal malaise, I enjoyed many aspects of the trip. We saw spectacular sunsets, though the weather would often return to gloom by day. Sperm whales swam close to our boat before diving to pluck fish off the longline. These huge, weird, ocean monsters are known to steal commercially caught fish from longlines in an act called “depredation.”

Time for lunch! Photo by Karson Coutré.

We saw albatross and several other offshore birds. Sabrina is a major bird enthusiast and helped me learn to identify them all. She has a powerful camera and got good pictures of brown and masked boobies, which are among the few confirmed sightings in Alaska of those species. Unfortunately, I missed them but still got to share in her excitement. Thick clouds denied us a view of the much anticipated solar eclipse and made for a very anticlimactic dramatic countdown. It only would have been a partial eclipse up here anyway and apparently no one could see it in Juneau either.

Some of the Albatross have identification bands on their legs. Sabrina, one of the biologists, took pictures of the numbers when possible. Photo by Matt Callahan.

After two weeks at sea we finally pulled into Dutch Harbor. The crew were grateful for the amenities of shore. Some of them would go home to see their families, others would re-embark on the Ocean Prowler in a couple of days to fish for Pacific cod (“P-cod”). Karson wished the trip lasted longer—she feels most alive at sea and fieldwork is a major highlight of her job. When I stepped off the boat and felt the ground unmoving under my feet, an irrepressible grin took over my face. I hadn’t transformed into a salty mariner, but I’m still glad I went.

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To learn more about what it’s like out on the longline survey, please check out this video made by former fisheries student and first rate human being Phil Ganz: https://vimeo.com/144235708.

Read more about the sablefish research being done by the Coastal Fisheries Ecology Lab, including current graduate students Matt and Rhea and alumna Karson, on our current projects page.

Three weeks at sea: Life aboard a catcher-processor

Posted on August 23, 2017 by abeaudreau

by Cheryl Barnes

As a PhD student, I spend a lot of time at the computer, analyzing data on fish predators and their prey in the Gulf of Alaska. The decades of data on fish abundance and diets collected by Alaska Fisheries Science Center, one of NOAA’s research labs, is a wealth of information. For my research, the data are a window into understanding the impacts of predation on walleye pollock, which support the largest single species fishery in the world.

Because it’s generally considered good practice to get out of the office and experience the data collection process, I decided to volunteer for this year’s groundfish survey. The entire Gulf of Alaska bottom trawl survey takes place between May and August every other year and stretches from the U.S.-Canada border in Southeast Alaska to the Aleutians. This summer, I participated in the fourth and final leg of the cruise, which lasted three weeks and ranged from Seward to Ketchikan.

Being slightly claustrophobic and having only experienced day trips at sea, I was a bit concerned about how I might fare on this particular excursion. Whatever happened though, it was going to be quite the learning experience! I was pleasantly surprised when we pulled up to the dock and I set eyes on what would be my home for the next 19 days. The F/V Ocean Explorer was an incredibly spacious 155-foot catcher-processor vessel with lots of room to move about.

F/V Ocean Explorer at the dock in Seward, AK
Photo Credit: Cheryl Barnes

As you might expect, this commercial pollock fishing boat was equipped with a considerably large and open-style trawl alley necessary to accommodate vast amounts of net mesh, bulbous floats, and heavy lead. The deck also provided ample space to sort, weigh, and measure fish after each haul had been brought in. The factory (usually used to process and freeze the catch) was located below deck, but because the vessel was chartered exclusively for scientific purposes, fish were not kept or sold. Instead, we used the area as prep space and dry storage.

Trawl alley and upper deck on the F/V Ocean Explorer
Photo Credit: Cheryl Barnes

On continuing to explore my floating residence, I found a hallway with sizeable staterooms just below the wheelhouse. I’d heard horror stories of five people being packed into a single room where only one of them could get out of their rack at a time. As luck would have it, we were afforded two-person units with roomy bunks, plenty of storage, and enough space to stand…two at a time. Conveniently, I also ended up with the only other woman onboard as my roommate, who happened to be one of the nicest and most considerate people I’ve ever met.

After our tour of the galley and a series of safety drills, I met each of the crewmembers onboard. Immediately, I could tell that our captain was one of the good ones. He was really outgoing, super approachable, and quite the storyteller! During the three-week voyage, I constantly found myself up in the wheelhouse, listening to tall tales and peculiar superstitions at sea. Our captain also wrote the funniest things in his communications to the first mate, which I checked on a daily basis just for a good laugh (sorry, I was sworn to secrecy). In addition to entertainment in the wheelhouse, we could always count on a good joke—typically of the dirty variety—from our first mate. The crew was always excited for a new batch of scientists because the rotation meant that they could retell stories and land their favorite punch line for the umpteenth time. We (the slightly nerdier bunch) loved it because even when we were all working like dogs, the crew helped keep things light and lively. All in all, I’d say that I couldn’t have been stuck on board with a better group of people.

It was a pretty cool experience seeing what a large commercial fishing vessel looks like, both inside and out. Mostly though, I enjoyed the opportunity to identify a wide variety of Alaskan groundfish species. Some of these fish looked familiar from the years I had spent working in fisheries in California, but others I had never even heard of or had only seen in books.

sablefish, shortspine thornyhead, giant grenadier, tanner crab, scallops, sea whips

primarily rockfishes and thornyheads

Species caught on different tows. Some hauls consisted of a wide range of species (left) while others were much less diverse (right). Photo Credit: Nancy Roberson

Among my favorite items found on the sorting table were the invertebrates. With deepwater tows, we got to see some pretty gnarly looking sponges, molluscs that look like hot dogs (one is actually called the “sandy hot dog” because it quite literally looks like you dropped an uncooked hot dog in the sand), and the sea mouse, a polychaete worm that I once used as inspiration for a very geeky Halloween costume. We also caught some sad-looking flatfish that we morbidly decided to collect eye parasites from.

sponge

arrowtooth flounder with eye parasites

Cool finds: some of the more interesting and rarely captured trawl specimens (left: sponge, right: juvenile arrowtooth flounder with eye parasites). Photo Credit: Cheryl Barnes

But it wasn’t always rainbows and roses. Occasionally, we’d get really “lucky” and bring up a net completely full of super sticky mud that we’d have to struggle through to find its biological inhabitants. One such tow took us four and a half hours to get through. Because we worked well past lunch, it made for a lot of very hangry scientists.

One of three net dumps on the sorting table resulting from a “mud tow”
Photo Credit: Cheryl Barnes

Of the more feel-good moments was when I could immediately release live fish from the haul. This, I loved, probably because I’ve spent so much time using catch and release survey methods. Rockfishes experience barotrauma, where the air in their swim bladder expands as they are brought through the water column, making it difficult for them to swim back to depth after processing. Like flatfishes, it is also difficult to identify their sex without cutting them open to get a good look at their internal organs. However, lingcod and spiny dogfish come up in relatively good condition and their sex can be easily determined from the outside (yes, we love checking out fish junk). This made is possible to quickly collect the data we needed and let them go alive. And even though this meant getting the occasional tail slap to the face, it was well worth it to watch them swim away after we were done with them.

Cheryl Barnes posing with a big lady lingcod just before processing and release
Photo Credit: Nancy Roberson

Though we mostly enjoyed processing fish day in and day out, everyone was pretty stoked when we pulled up the last tow of the survey. It signified our imminent ability to step foot on land, grab a cold beer, and sleep in our own beds. Even without the constant rocking of the boat that lulled me to sleep every night during the survey, I was ready to spread out again, return to my own space, and close my eyes without hearing the ever-present clanking and engine noise.

Science crew celebrating our final tow of the survey
Photo Credit: Nancy Roberson

It’s been two weeks since I got home and I definitely miss the sunshine out on the open ocean. It’s been an exceptionally rainy summer here in Juneau and I am no longer able to simply climb to the upper deck when I want to bask in the glory of blue skies and calm water. I also miss chatting with our gregarious captain and crew, though I hope to stay in touch. And instead of flinging fish, listening to wise crack after wise crack, selecting from unreasonably diverse ice cream flavors, and passing by magically refilled bowls of bite-sized chocolates in the galley, I’ll be staring at a computer screen, reading scientific papers, and writing code for the rest of my days (or the next two years…it’s yet to be determined).

Sunset captured from the F/V Ocean Explorer in Ketchikan, AK.
Photo Credit: Cheryl Barnes

Read more about Cheryl’s research on our current projects page. For more information about NOAA’s research program in Alaska, visit the Resource Assessment and Conservation Engineering Division (RACE) and Resource Ecology and Ecosystem Modeling Division (REEM) online.