Love at First Fish

by Anne Beaudreau & Chris Sergeant

Editor’s Note: The University of Washington’s School of Aquatic and Fishery Sciences (UW-SAFS) will celebrate its centennial year in 2019. As alumni, my husband Chris Sergeant and I were asked to write an article for a series about partners who met each other at UW-SAFS. Our article below was published as part of the Centennial Story series, along with other contributions from our friends and colleagues: https://fish.uw.edu/2018/08/centennial-story-24/. We have lots of great memories from that time and enjoyed reminiscing about the early days of our relationship as graduate students in Seattle.

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“Hey, what does your Leslie matrix look like?”

During my final quarter as a Master’s student in 2004, Anne and I had already become good friends and regular study buddies. We shared mutual embarrassment when Dr. Don Gunderson looked over our shoulders and could barely hold back his disappointment as we struggled to fill in an age-structured Leslie matrix. Our early days as friends shaped our future together. Anne likes to believe she shifted my dreams of semi-pro bass fishing and lure testing to PhD fisheries researcher. In turn, I honed Anne’s research acumen by increasing her acceptance of salmon and freshwater ecosystems as legitimate and interesting study subjects. –Chris

“Have you ever tried a drop-shot rig for lingcod?”

This was said during Chris’ intensive bass fishing phase, when he tried to bring his warmwater recreational sensibilities to a marine reserve in the San Juan Islands. It turns out that the drop-shot rig worked great, as did sight fishing for aggressive lingcod in the kelp canopy. I had many volunteers help me fish for science over the years – around 60 in total – but Chris was the cream of the crop. He had the highest catch per unit effort of any volunteer (yes, I kept track) and also picked the best snacks. We wrote a rap together about the life and times of Jethro, one of my acoustically tagged lingcod, as we tracked his stealthy movements through the night. It was in the field where we really got to know each other. Chris helped me hook lingcod in the San Juans, I helped him pull gillnets on Lake Washington. In the early days, we debated (only half-jokingly) about the merits of fresh- versus saltwater ecosystems; in the end, we have found shared curiosity and wonder in both places. –Anne

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Safety first for Anne and Chris at Friday Harbor Labs, circa 2004. Photo by Danny Garrett.

“We can move wherever you want, except to an island.”

It was time for Anne to realize her years of hard work and find a fulfilling faculty position. I did my best to keep an open mind about potential locations. Juneau – with no connection to a continental road-system and surrounded by impassable icefields (i.e., basically an island) – was pushing the limits of my comfort zone. But we did it, and seven years have flown by. Anne is an associate professor of fisheries at University of Alaska Fairbanks and I am an ecologist with the National Park Service. We still go fishing and even write the occasional paper together. In 2014, we welcomed James Neil Sergeant to the world and have enjoyed watching him become a resilient, puddle-loving Alaskan kid with an intense interest in everything around him. –Chris

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Fishing is a family affair now. Photo by Eric Ward.

“Hey Dad, the velcro star has a lot of pedicellariae.”

Our stomachs dropped. Was our only child going to become an invertebrate biologist? Until recently, our almost-four-year-old was not a big fan of boats and we would have to lure him (pun intended) onto ours with donuts. Fortunately, young James seems to enjoy all manner of aquatic creatures – the finned, the spiny, the squishy, and the slimy. Chris and I both still do a lot of fieldwork, so James is often parented by one of us at a time in the summer while the other is off doing “fishy work.” It’s just a matter of time before he’ll be right alongside us in the field, teaching us how to identify sea stars and reminding us of the joy we felt when we held our first fish. –Anne

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With fish nerds for parents, James is already learning the tools of fisheries ecology. Photo by Cheryl Barnes.

 

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.

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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.

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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.