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

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.

R Error Message

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.

Code Confusion

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:

  1. 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).
  2. 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.
  3. 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.
  4. 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).
  5. 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).
Rhea Hard at Work

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.

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

Unexpected Gains

by Natura Richardson

Editor’s Note: Grad school is hard, there’s no question about it. It is a time of immense personal and professional growth, which can be exciting but is also challenging and intense. The process of learning to master a craft – whether in the sciences or arts – requires confronting uncertainty, climbing steep learning curves, and a deep and sometimes uncomfortable examination of one’s own strengths and limitations. It takes perseverance. Natura Richardson, a Coastal Fisheries Ecology Lab alum and author of today’s post, would call it grit. It also takes a support system of peers and mentors, friends and family. (We will discuss the importance of mentorship in an upcoming post.) Even with that support system, many graduate students – and post-graduate professionals – face feelings of inadequacy. The term impostor syndrome was coined in the late 1970s to describe people who feel as though they are a “fraud” despite evidence of high achievement. There have been some excellent articles written about this phenomenon as it applies to early career scientists (e.g., here) and the importance of scientists from all career stages sharing their own stories. In this post, Natura reflects on how she confronted her own feelings of being an imposter and other stresses of grad school, and the strength and resilience she gained from her experiences.

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I officially graduated from the Coastal Fisheries Ecology Lab in May 2016, although that already feels so long ago. How can something that was only a year and a half ago feel like it happened way back during the Jurassic period? I’ll tell you how: because graduate school is HARD and you try to forget it. While in school, I had amazing support from my husband who drew a bath and put me to sleep, an employer that provided field support and reasonable use of work time, an advisor who knew how to encourage, push, and laugh with me, and fellow students and lab mates that would lend a listening ear or help me with analysis or R script. The deck was stacked in my favor, and yet, for me, graduate school was this weird alternate universe, where I worked harder than I ever had, yet I often felt inadequate and irrelevant. After graduation, I was ready to move on and never look back. But the truth is, I do look back. A lot. There are certain experiences and lessons that I continue to positively draw from for my personal and professional growth.

Everyone has a different experience and not all students struggle so hard, but for those of you who are in the throes of grad school and need a little pick me up, here’s what I have to offer for motivation: my unexpected but oh-so-great gains from graduate school.

Out-running the anxious stress monster

Over the years I practiced all the standard graduate student responses to stress and anxiety: crying, complaining, getting frustrated or angry, drinking, and avoiding my advisor and hoping she would somehow forget I existed. Shockingly, none of those worked.

The University of Alaska Fairbanks campus in Juneau is located on Lena Point, with access to forested trails leading to ocean views, right out the front door. One day, rather than break down in the student offices, I put on my sneakers and went for a walk. After a few walks, I started to run (although it was more of a shuffle). Be it walk, shuffle, or run, whenever I did something, I felt better. I tried to be consistent in going outside and getting exercise but with a constant fear of deadlines, it was hard to justify 20-40 minutes away from the computer. So I did something else I feared. I signed up for a 50-mile race. I was not a runner, had never run a marathon in my life, yet somehow I thought running almost double the distance while working on my Master’s thesis was a good idea. Boy, grad school was making me really crazy. But that commitment forced me to take a break, get outside, and do something else every day. From that daily commitment, I improved my mental clarity, physical energy, and perspective, which in turn helped me to become a better student, researcher, and less of an anxious stress monster.

Without the relentless stress of grad school, who knows how long it would have taken me to figure out that doing something for myself everyday would have enormous impacts on my mental and physical health? I’m done with graduate school now, but I am not done with running. If I ever feel the anxious stress monster trying to come out, I pull out my sneakers and run away from her. If you’re familiar with the anxious stress monster, I recommend identifying your stress-relieving, non-school activity and figuring out a way to make it mandatory. Believe me, it will be there for you after you’re done with your thesis.

Natura Kesugi Ridge_photo by Michael Bach.jpg

Natura outruns the anxious stress monster on Kesugi Ridge Trail near Denali National Park, Alaska. Photo by Michael Bach.

Liar, liar, pants on fire

While in grad school, I said to myself over and over, repeated like a broken record “I can’t,” just like a whiny adolescent child. As it turns out, I’m a liar, liar, pants on fire because I could do it. I am capable. Working on my Master’s thesis was the first time that I realized how often I play that broken “I can’t” record and how much wasted energy goes into that. It was also when I discovered how capable I am and that I need to quit lying to myself. So it is from my thesis days that I now frequently draw strength when I start to doubt my abilities.

Remember that 50 miler I signed up for? At mile 35 the “I can’t” record started playing, but then I thought, “If I can finish that thesis, I can do this!” I bucked up and finished that race…then puked.

I have accomplished other goals, big, small, professional, and personal. I applied for a competitive job that I didn’t think I could get, and then got it. I busted out written management plans and fishery summaries in very short time frames. I painted the exterior of my house by myself, when I was certain I couldn’t without my 6’6” tall husband or hired help. Don’t get me wrong, I do not believe that because I finished a Master’s thesis I am now Superwoman in disguise, but I do remind myself to quit wasting time lying to myself with the “I can’t” talk and get cracking on whatever it is I want to accomplish.

Go through the grits

Many individuals are capable, smart, and maybe they are Superwoman in disguise. But just because someone is Superwoman and she can do something difficult, doesn’t mean she will.

My thesis did not happen overnight, over a month, over a semester, or even over a couple years. It took several years of field work, lab work, data analysis, writing, re-processing lab samples, re-running data analysis, re-writing chapters, incorporating edits. Did I mention re-writing? There were feelings of failure, adversity, and frustration that came with what felt like only minor victories or successes. But for some reason, I just kept going. And going. And going. Relentless. Forward. Progress.

Post-graduate school, and thanks to psychologist Angela Duckworth, I have put a name to this determined behavior: Grit. Angela Duckworth says grit is passion and perseverance for long term goals. Having grit means maintaining determination and motivation over long periods of time despite experiences with failure and adversity. How many folks actually hold to their new year’s resolutions? Or lose those 20 pounds? Or write the peer-reviewed journal article after the committee has signed off on the thesis? Not that many. It takes some serious will-power to turn down chocolate cake, or put on your running shoes, or close your web browser. Pick a goal that cannot be achieved in a few days (or even just a few hours), throw in a lack of willpower and some tough challenges, and I bet that goal is likely to sit by the wayside, especially when the new season of [insert popular TV show] is released.

Sandpaper grit is measured as the number of particles per square inch. Wood can start out rough, scratched, and blemished but sanding with increasing levels of grit removes the scratches from the previous grit until the scratches are so fine that the wood is smooth as a baby’s bottom. Like a woodworker, I had to “go through the grits,” starting with a stripping 80-grit, to a smoothing 150-grit, and finishing with a 360- to 600-grit. In hindsight, I recognize that all those perceived failures or setbacks actually gave me grit. Now when I get a report back from a colleague that is bleeding red with edits, instead of crawling into bed and hiding, I don’t think anything of it. That’s just the first stripping grit; I want to get to the polishing grit. When it gets hard and you want to quit, just remember to go through the grits.

Graduate school is arduous, but for all your sleepless nights and caffeinated days, you do gain some great skills. You might graduate with fluency in computer programs like ArcGIS or R, you might become a stock assessment modeling genius, or you might be the expert on Pacific staghorn sculpin reproductive strategies (a highly coveted title, by the way). But for me, it has been the unexpected gains of healthy life habits and recognizing my capabilities and grit, where I have found the greatest value.

CFE Lab Oct 2014.png

It takes a village to raise a child…and to get through grad school. Natura (3rd from left) gives her advisor a break from parenting duties and enjoys the camaraderie of labmates.

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Natura Richardson received her M.S. in Fisheries from UAF in 2016 and is a groundfish and shellfish management biologist at the Alaska Department of Fish and Game in Kodiak, Alaska.

Critters

by Nina Lundstrom

Editor’s Note: Nina Lundstrom has been working with us since July 2017 and was a core member of our beach seining team over the summer. She arrived in Alaska already a seasoned seiner, having learned the tools of the trade during her internship in the San Juan Islands, Washington, the summer after graduating with a degree in biology and ecology from Colorado College. In this post, Nina writes about her work with the Kwiaht Center for the Historical Ecology of the Salish Sea and the people and places she got to know. Incidentally, I (Anne) also worked with Kwiaht nearly a decade earlier and helped train volunteers in the delicate art of inducing fish to regurgitate their meals (for science!). I was proud to be there at the start of the wonderful citizen science monitoring program that continues today. Nina’s story perfectly captures the feeling of working in the islands.

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“You have to see this picture I just took of the most gorgeous little earwig, sipping on some Yarro nectar!” My boss, Russel Barsh, had just come pounding down the trail towards me, brandishing his camera and looking nothing short of gleeful. This was undoubtedly the first time in my life anyone had ever used the words gorgeous and earwig sequentially. I stood up, brushing dirt off the knees of my pants, and took the camera, Russel still gazing lovingly at the photo. Through the course of the summer, I would get used to these reverential descriptions of some arguably repulsive creatures. It takes a special kind of person to see the beauty in something like a clam worm: a sickly pink annelid that moves like a cross between a snake and a centipede and can administer a nasty bite to the unsuspecting clam digger, but Russel had a gift for recognizing the nuances and charm in just about every living thing.

I was living and working on Lopez Island off the coast of Washington, and there was no difficulty in recognizing the nuances and charm of the place itself. The island was small, only 15 miles long and 8 miles wide. One main road ran from end to end, appropriately named Center Road. The island was covered in thick forests of douglas fir, some of which were over 500 years old, and each edge of the island looked out on Mount Baker, or the Olympic Mountains, or the Cascades, depending on where you stood. I was a research apprentice for Russel and his partner Madrona Murphy, the directors of a non-profit research organization, Kwiaht. I worked seven days a week, between six and twelve hours a day, split evenly between the field and the lab. My primary project involved fish genetics, but my daily tasks ranged from digging up square meters of frozen muck and determining the species and ages of the clams living in said muck, to monitoring the comings and goings of the bees on wild blackberries. Russel and Madrona had an unparalleled love for their jobs and for the natural world, and I never got the impression that the hours we spent collecting data felt like work to them.

The best days were the “seining days” on Waldron and Lopez islands. Russel, Madrona, several buckets of equipment, and I would load up into a 20 foot boat driven by the designated boatman of the day, my favorite of whom was Tom*. Tom was a middle-aged man who always wore Wrangler jeans tucked into his Wellingtons and cheerfully passed his time on the boat, fishing for lingcod while we worked. He loved to rant about the fishing industry and “the bureaucracy,” and he shared his freshly trapped Dungeness crabs with me. He would motor us to Waldron Island or the south side of Lopez, where we would set up the net, a contraption 120 feet long and six feet deep, with floats on the top and weights on the bottom. The boat would pull one end in an arc through the bay and back to shallow water. There, someone on each end would swim out and grab it and pull it in with the somewhat unwilling help of strangers who had unknowingly picked our research spot on the beach as their relaxation location. The minutes following the pull were nothing short of chaotic, as we held the net in the water and sifted through its occupants. I grew accustomed to blindly plunging my hand into the depths of the submerged net to grab a jellyfish, a crab, or a sculpin that could harm one of the smaller fish or, consequently, my fingers. These predators were casually tossed over our shoulders and swam happily away. Russel and Madrona both possessed an incredible ability to snatch swimming fish out of the water with their bare hands and identify them with a single glance. We counted and released gunnels, sticklebacks, perch, flounder, snake pricklebacks, pipefish, pink salmon and chum salmon, but temporarily kept the king salmon to extract their stomach contents.

*name changed for this story

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Beach seining on Lopez Island. Photo by Chris Sergeant.

It was easy to fall in love with king salmon, or Chinooks, as a species. The fish we studied were only about five days out of the river in which they were born, and they were charming and beautiful babies. Their glowing green backs sported cheetah-like black spots, and they swam less with their tails than with their tiny pectoral fins, alternating strokes. Most of them still had their par marks, perfectly spaced oval spots running down their sides, signifying their young age. We cheered for the fish whose stomach contents were full of smaller fish, and gently encouraged the ones who had only eaten an insect or two. I have never seen a pair of people so connected to and invested in fish vomit, but Russel and Madrona’s love for the Chinooks was infectious. Russel cooed to each individual fish, practically cuddling it as he plunged a blunt ended syringe down its throat to collect stomach contents. I was taught to perform “fish CPR” if any began to float, and someone was always closely watching the “recovery bucket” to ensure the well-being of the salmon. We didn’t have a single fatality all summer.

Chinook salmon_photo courtesy of Nina Lundstrom

Performing gastric lavage (left) and taking a small fin clip (right) from a juvenile Chinook salmon. Photos courtesy of Nina Lundstrom.

On one exhausting day, the first pull of the net yielded only smelt, a silvery fish that is a popular food source for island residents. A second net pull brought in herring, their rainbow scales flashing in the sunlight. A third pull seemed pointless and time-consuming on an already long day, but we did it anyway. Much to our surprise, thirty sizeable Chinooks were brought in, and we set up our “lavage station.” As we started our machine-like process of measurement, fin clip, scale collection, gut lavage, and recovery bucket, Russel whispered lovingly to one particularly large fish, “Oh, you are a little fatty aren’t you?” I did my best to disguise my laughter as a coughing fit.

My job was to sift through the stomach contents of each salmon and collect the sand lance, a small needle-nosed fish often eaten by juvenile Chinooks. I then extracted their DNA, amplified it with a set of primers (known gene sequences), and ran it through the genetic sequencer to try to formulate a population structure. It initially sounded like a straightforward process, and I dove in enthusiastically. Eight weeks of viciously whispered profanities followed. The monstrous machine had daily malfunctions, and as soon as things seemed to be running smoothly, some outside factor would throw the data off, forcing me to start over. Twice during the summer, all of the power in the school went out because of ongoing construction, and the whole machine crashed. All of the frozen polymers, buffers, and primers defrosted, became useless, and had to be reordered. While we waited for them to be shipped, I got the pleasant task of sorting through bags of poorly preserved dead fish, some of which had been partially decaying for three years. Oh, how I longed to work on the horrible machine in those days.

Seining on Waldron_photo by Nina Lundstrom

Setting up the beach seine on Waldron Island, a northern neighbor of Lopez Island in the San Juan Archipelago, Washington. Photo by Nina Lundstrom.

Near the end of my time on Lopez, Russel, Madrona, and I went out to the spit to check on some oysters that had been planted there the year before. We were knee deep in mud, cutting into the oyster bags to count the living and the dead. In the span of a year, the bags had become tiny ecosystems, kelp growing on the outsides and critters making their homes among the oyster colonies. Several crabs had crawled through the plastic mesh when they were small, made their homes, and grew too large to ever leave. They showed their appreciation for our rescue mission by vigorously pinching us as we returned them to the ocean. Russel opened one shell to find a spaghetti worm camping out in the enclosed space. Spaghetti worms are small and dark pink, with seemingly endless tentacle feelers that closely resemble angel hair pasta. They are the stuff of Fear Factor, the antithesis of charming. Russel beamed down at the worm. “You wonderful, smart spaghetti worm, how innovative of you to make your home in that shell,” he crooned. I turned back to my oysters, grinning.

Several hours later, hands caked in mud, and feet sunk fully and permanently into the mud, I found another shell housing a spaghetti worm. I released the worm into the water and watched it sink to the bottom and crawl away. “Good little spaghetti worm,” I whispered, in spite of myself.

Nina Lundstrom with sculpin_photo by Doug Duncan

Nina with one of the critters we love in Juneau, Alaska. Photo by Doug Duncan.

Things we’re thankful for

In honor of Thanksgiving, the Coastal Fisheries Ecology Lab took a moment to reflect on the many things we are thankful for.

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We are thankful for the scientific adventures waiting right outside our door and the people we get to share them with. ♦ We are thankful for the new experiences and amazing opportunities that Alaska has to offer. ♦ We’re thankful for the absolutely wonderful people that we’ve gotten to know while working with Juneau’s fishing community. The generosity they’ve shown with their time, knowledge, and resources have greatly improved our research. ♦ We are grateful to share our love of science with students of all ages, who make us feel forever young at heart with their endless energy, curiosity, wonder, and joy. ♦ We’re thankful for the continued enthusiasm of research assistants who have helped out in field and lab. ♦ We are thankful for the wonderful group of people we’ve had the chance to work with in the course of our research. ♦ We’re thankful that we get to live in a pristine place with such a presence of wilderness. ♦ We are thankful for the hospitality and warmth of Alaska and its people. ♦ We are thankful for the kind and generous people and breathtaking landscapes that make Juneau home. ♦ We are thankful for the wonderful people and beautiful places that fill our lives with happiness.

Happy Thanksgiving to all of our colleagues, friends, and family across the world!

-Anne, Cheryl, Doug, Joe, Maggie, Matt, Nina, Rhea, and Veronica

A 5-star field extravaganza!

by Anne Beaudreau

There are many measures of success in fieldwork. The first, and most obvious, is whether you catch fish. They can’t just be any fish; they have to be the right fish to meet your study objectives. A second measure of success is whether the crew gets along. Luckily, most everyone I know in the field of fisheries loves to be outdoors. But you never know how personalities and expectations will mesh when everyone is wet and cold. Of course, the most important measure of success is whether everyone stays safe (and staying safe also means protecting the boat!).

Since 2012, the Coastal Fisheries Ecology lab has been studying the ecology of juvenile sablefish. Two weeks ago, before our team left for Sitka to begin a new phase of our sablefish field research, we were facing a lot of unknowns: Would we catch fish? NOAA researchers had caught juvenile sablefish in October during the 1980s and 1990s, but that was a while ago and every year is different. Would the weather hold up? This was fall in Southeast Alaska after all. Wind could be a real threat. Would there be any issues with the rental boat? We were pretty sure that the 22-foot Hewescraft would be just what we needed to get the work done, but hadn’t worked with the company before.

Pre-fieldwork uncertainty can be stressful. But uncertainty brings with it the promise of discovery, of seeing something new even in a place you have visited countless times, of learning something about the system you are studying. So, how did we do? Were we successful? If you read the title of this post, you’ll probably guess the answer: a 5-star week on all counts! Here’s a recap of the highlights, with reflections from the whole crew.

SJBB Scenery_courtesy of CFE Lab.JPG

The quest for sablefish begins. Even when it’s overcast, raining, or sleeting, St. John Baptist Bay is an idyllic place.

Catching the right fish and learning on the job

We were hoping to catch a range of ages and sizes, to understand whether young sablefish at different life stages store energy differently before they enter the lean winter months. Matt Callahan, the lead MS student on the project, and I had been planning this work for months and were eager to find out if, in fact, we would catch the “right fish.” Within the first moments of fishing we had our answer. As Matt said,

The most memorable aspect for me was the first day, or really the first thirty seconds of fishing. After months of planning and uncertainty as to whether we’d even catch fish, we finally put our hooks in the water and BAM! Our hooks barely hit bottom before getting swarmed with hungry, hungry sablefish.

Triple Sablefish_courtesy of CFE Lab

It was so exciting to reel in 3 or 4 sablefish at once! We caught nearly 300 all together.

Joe Krieger, a postdoc and collaborator on the project, was amazed to see the behavior of the fish in the wild. He said,

I’ve been feeding young-of-the-year sablefish in the lab so I had some appreciation for their lustful appetite and piranha-like feeding displays, but that was nothing compared to looking over the boat and seeing a swarm of 20-30 sablefish streaming to the surface in pursuit of my jig. Their voracious appetite and apparent generalist feeding strategy certainly help to explain why these fish are able to grow as quickly as they do.

Justin Priest, a MS student studying Arctic fish ecology, agreed:

The way that the fish were so clustered really surprised me. Fishing 100 feet in either direction yielded almost no fish, but when on top of them, there were a lot down there…how voracious they were really surprised me.

We retrieved the stomach contents of the ravenous sablefish using gastric lavage, a non-lethal technique that involves flushing out the stomach of a sedated fish with a gentle stream of water. I have lavaged thousands of fish, from 30-pound lingcod to baby salmon no longer than my pinky finger. Yet, I am still excited each time to see what ecological clues lie inside the stomach of a fish. Luckily, Matt, who will be doing a lot of gastric lavage over the next couple years, found it fun too:

I learned how to perform gastric lavage, and enjoyed seeing the stomach contents pour into the sieve. It’s like a box of gross fishy chocolates, you never know what you’re going to get.

Matt Lavaging_photos by Justin Priest and CFE Lab

Matt retrieves the stomach contents of a juvenile sablefish using gastric lavage. Have you ever seen someone so happy to be holding a sieve full of fish vomit? Left image by Justin Priest.

As with all fieldwork, there were unexpected challenges. One of our goals was to measure the energy content of the main food types being eaten by sablefish in the fall. Sablefish were primarily consuming juvenile herring, amphipods, euphausiids (krill), and jellies. For most prey groups, we were able to salvage intact, minimally digested prey from the stomachs. As Cheryl Barnes (PhD student) noted, “sablefish eat tiny euphausiids,” so we tried to supplement euphausiid samples from stomach contents with field collections of more intact prey. Our attempts to catch euphausiids using light traps was unsuccessful, but we have some ideas about how to improve the process next time.

Camaraderie and teamwork

Science is fun when you’re working with fun people. And this crew sure was fun! In between the serious work of research – navigating to the study site, catching fish, recording data, keeping fish alive – we did a whole lot of laughing and snacking (see below). Rhea Ehresmann, a MS student studying sablefish movement ecology, said it best:

The most memorable aspect of the fieldwork was getting to know everyone better. Fieldwork provides an opportunity to disconnect from phones and email, and focus on the project together. We were able to spend more time in person working and talking together as a team.

Rhea & Cheryl_courtesy of CFE Lab

Rhea (left) drops her line in the still waters of St. John Baptist Bay, while Cheryl (right) moves a newly captured sablefish to the holding tank.

As far as safety goes, the owner of the boat rental company had set a low bar as he handed us the keys: “Just don’t sink the boat!” I’m happy to say that not only did we not sink the boat, but we got our crew safely to St. John Baptist Bay and back every day. Yes, we got soaked with rain and sleet, but the wind was kind and I saw more rainbows in the span of one week than I thought possible (outside of Hawaii). Joe summed it up perfectly:

Having just moved to Southeast Alaska I am still awed by the natural beauty of the Inside Passage: snow covered mountains, endless forests, sunlight glistening off the ocean surface, sea otters, bears. I could go on and on. We were extremely fortunate to have several excellent days of weather, which really was the cherry on top of an all-around great trip.

We also did a lot more singing than I expected. Wednesday was Alaska Day, and Matt serenaded us with the Alaska state song on the way to the boat. We topped off the week with karaoke and an impromptu dance party at Ernie’s Saloon, in celebration of Joe’s birthday. A sign of a good week in the field indeed.

Happy Team_courtesy of CFE Lab

Joe, Justin, Matt, and Anne (left to right) celebrate the end of a successful trip.

 

Our favorite field snacks

Joe: Definitely the dark chocolate covered dried mango. I probably ate over half of the bag. Dark chocolate and fruit are healthy right?

Rhea: My go-to favorite field snack is cheddar and caramel popcorn mix. It makes a great snack because it satisfies salty and sweet cravings at once!

Cheryl: duplex cookies 🙂

Justin: Of course Grandma Tillie’s. And I’m not even a sweets guy!

Matt: Grandma Tillie’s blueberry donuts with lemon glaze narrowly edged out her pumpkin rolls. Mmm, so good.

Anne: I gotta agree with Matt and Justin!

In a future post, I will talk more about the research itself and why we think sablefish are so interesting. For now, you can find more information about the sablefish studies on our current research page.

All photos in this post are courtesy of the Coastal Fisheries Ecology Lab unless otherwise noted.

The little ROVs that could

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.

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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.

ROV pieces_photo by Veronica Padula

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.

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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.

Team effort_photo by Veronica Padula

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!

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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!

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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.

Captain Kadyn_photo by Veronica Padula

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/

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

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 49th state, where rain, cold, and bears are plentiful.

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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.

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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.

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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.

Glacier view_photo by Dana Flerchinger

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

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.

Sunset_photo by Matt Callahan
“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.

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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.

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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.”

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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.

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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.

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.

Why I love sculpins (and why you should too)

by Anne Beaudreau

Sculpins get a bad rap. Scorned by anglers and scoffed at by scientists, these bottom-dwellers have a host of unflattering nicknames, from “bullheads” to “double uglies.” The array of adjectives used to describe them is reliably disparaging: ugly, useless, homely, drab, and a nuisance.

All that trash talk is pretty unfair, if you ask me. Sculpins are not only a fascinating group of abundant, ubiquitous fishes but they may very well be the silent rulers of coastal marine ecosystems. To show you why, I bring you three vignettes about the wonderful world of sculpins.

The red Irish lord is a real beauty.

One. A Thing of Beauty

Sculpins come in all shapes, sizes, and colors. They have lovely and bizarre names, like Myoxocephalus polyacanthocephalus, the scientific name for great sculpin that roughly translates to “muscle-head spiny-head.” Most have spines protruding from their cheeks—shaped like antlers, spikes, combs, and clubs—to protect them from the mouths of predators. They need that protection because, truth be told, most sculpins are less than a foot long. But a few can give anglers a run for their money. The biggest sculpin – the cabezon – can reach sizes of 3 feet and 30 pounds1. I have heard stories of aggressive cabezon head-butting divers who came too close to the egg masses they were guarding. Some sculpins are quite beautiful and lavishly decorated with colorful designs, like the red Irish lord, and others are adorable squat little creatures, like the buffalo sculpin. Sculpins have been inspiration for both art and beer.

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Ragga shows off an adorable baby sculpin that was caught in a beach seine near Juneau, Alaska. Photo by Emily Whitney.
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Cabezon were fun to catch in the San Juan Islands, Washington. They put up a fight and are tasty too. Photo by Aaron Dufault.

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Just this week we were fortunate to see this beauty, a crested sculpin that was hanging out in some algae growth on a crab pot line. Photo by Anne Beaudreau.

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I spotted these beautiful Tsimshian dance leggings adorned with sculpins at the Anchorage Museum.

Two. Eat or Be Eaten

Wherever they live, sculpins are leading actors in an ecological drama that unfolds every day, where all creatures must eat or be eaten. They play a central role in nearshore ecosystems as both prey and predators. In my graduate research, I found that sculpins were one of the most common diet items for lingcod, a large toothy predator living in kelp forests of the North Pacific. Some small sculpin species serve another important role for lingcod—they act as cleaners, picking off parasites from inside the open mouth of the lingcod itself! It is a dangerous job and one that sometimes lands the helpful sculpin at the bottom of a predator’s stomach.

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Buffalo sculpins make up for their small stature with intimidating spines that deter predators. Photo by Aaron Dufault.

Sculpins may make a tasty snack for larger creatures, including people, but they are also terrific predators in their own right. Most sculpins are basically a big mouth with a tail attached. One of the species we’ve been studying, Pacific staghorn sculpin, is armed with antler-like spines on either side of its face and can eat other fish that are half of its own length. Can you imagine swallowing a 2- to 3-foot long animal alive and whole? What a beast! Staghorn sculpins are omnivores, feasting on everything from baby mussels the size of a poppy seed to carcasses of spawning adult salmon. Just like toddlers, staghorn sculpins can be picky eaters too, sometimes chomping only the siphons off the tops of unsuspecting clams. Some staghorn sculpins even have an expensive taste for caviar: we once collected a staghorn sculpin that had gorged itself on 85 salmon eggs!

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There is no creature so bold as a hungry sculpin. Photo by Emily Whitney.
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If you’ve ever wondered which intertidal species would win a hotdog eating contest, look no further—it’s the staghorn sculpin.

Three. Abundant and Adaptable

Sculpins are everywhere. They are found throughout the world, in both freshwater and saltwater. There are over 750 species of sculpin and around 300 species in the family Cottidae alone2, which is the group of sculpins that I know best. Here in Juneau, sculpins dominate fish communities in the nearshore. About 40% of the fish we catch beach seining near river deltas are none other than the Pacific staghorn sculpin. Many sculpins live in harsh, dynamic environments like the intertidal. Tidepool sculpins, tiny creatures no longer than your finger, have a strong urge to stay close to home. Some have been observed in a single tidepool for more than a year3. If they are moved from their home pool, these wee sculpins can find their way back, even after being on an extended vacation (i.e., moved to an “unnatural environment” by scientists for 6 months)3. As for staghorn sculpins, there is so much we still don’t know about where they live, how far they move, or how many of them are out there, chowing down on a smorgasbord of salty snacks. Staghorns live in the sea, but can withstand freshwater and can even breath air to some extent4. Given the challenging environment they navigate every day, perhaps sculpins just might be the most equipped of all to deal with our rapidly changing oceans.

While I may not have convinced you that sculpins are at least as cool as salmon, I hope that you have gained a little more appreciation for them. If nothing else, show those bullheads a little respect. They might take over the world someday, in all their air-breathing, spine-wielding glory. Don’t say I didn’t warn you.

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Behold, the glorious Pacific staghorn sculpin. Photo by Doug Duncan.

Froese, R., and D. Pauly, eds. 2017. Scorpaenichthys marmoratus in FishBase. www.fishbase.org. Accessed September 2017.

Mecklenburg, C.W., T.A. Mecklenburg, and L.K. Thorsteinson. 2002. Fishes of Alaska. Am. Fish. Soc., Bethesda, MD.

Green, J.M. 1971. High tide movements and homing behaviour of the tidepool sculpin Oligocottus maculosus. Journal of the Fisheries Research Board of Canada 28(3): 383-389.

Love, M. 1996. Probably More Than You Want to Know About the Fishes of the Pacific Coast. Really Big Press, Santa Barbara, California.

Three weeks at sea: Life aboard a catcher-processor

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.

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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.

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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.

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.

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.

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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.

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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.

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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).

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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.