The Journey to Scientific Publication

Setting the mood and diving back into thesis graphs.

Setting the mood and diving back into thesis graphs.

I recently had lunch with one of my graduate school advisors to give her some reprints – hard copies of the paper we had published on my master’s thesis work. The project was years in the making, and had been built up in my mind as something practically unachievable, so it still seems surreal to me that I finally published my thesis in a scientific journal. It’s something that I think deserves more than a little reflection here in this space where I am charting my journey in science and writing and fish. This paper’s path to publication was certainly a circuitous and intermittent journey, with many fits and starts.

The paper was published in September 2015, four years and three months after I defended my thesis and completed my master’s degree at Moss Landing Marine Labs in the summer of 2011. The path to graduation was a challenging three-and-a-half-year journey in its own right that pushed and tested me on so many fronts. In the home stretch, it took everything in me just to finish my thesis presentation and format the final manuscript for San Jose State University, my home campus. By the time that was done, I was so ready to move on, so ready for something different – like diving headfirst into the world of science journalism. Almost immediately after finishing at Moss Landing, I went straight into a one-year science communication program at UC Santa Cruz. There I used every ounce of brainpower to learn how to translate science into popular writing. Between the crazy schedule of classes and internships and deadlines, the thought of picking up my thesis just seemed like too much. As far as I was concerned, I still needed a mental break from it. And that need for a break continued even as I finished the science writing program and started my current job.

Throughout my graduate career, I had heard many a cautionary tale of students who invested years into rigorous scientific work for their theses, studies worthy of publication, and who maybe came very close to publishing, but never did. What a shame, I would think. I vowed to myself that I would not become one of those cautionary tales. But the other take-home message was: do it soon. Don’t let too much time pass before you submit your manuscript for publication, or it may never happen. This is where I hit my obstacles in the seductive guise of “taking a break” –   break that became increasingly harder to return from. My housemates are currently Ph.D. students at UC Santa Cruz, where their advisor will not sign off on their dissertation until every chapter has been submitted to a journal. I watched how this requirement pushed my housemate in the grueling final stretch of her dissertation – and she did it, she submitted every chapter. Because publishing is optional at MLML, the responsibility usually falls on the student to make it happen. Some advisors are more involved than others as far as prodding their students towards publication. One of my advisors once told me, “I know I don’t need to nag you since I’m sure that you’ll get this done.”

Collecting gopher rockfish for my thesis in grad school.

Collecting gopher rockfish for my thesis in grad school.

As the months and then years went by, I sometimes wished someone would nag me about publishing my thesis – just to have some proof that this undertaking mattered to anyone besides me. I eventually realized that no one was going to do this for me. Just like finishing the research had been a grueling test of my own perseverance, getting the publication over the finish line would be the same – if it was something I really wanted, I was then one who had to find a way to make it happen. But this looming responsibility was a hard one to face. Every once in a while, the guilt and weight and fear of submission would rear up in me – sometimes while I was out for a jog on West Cliff Drive and caught sight of the smokestacks in Moss Landing across the bay. I would eventually put those nagging fears aside, and one day I realized with a sensation of panic that it was getting easier and easier to quiet my internal nagging, to live with the fact that my thesis wasn’t published. My window of opportunity was closing. The scales were tipping more towards me not publishing as opposed to publishing. Each day and year that went by would make it even harder to resurrect this work. In the fall of 2014, I attended a friend’s thesis defense that had been a long time in coming, and I received some reassurance from another former student: there was a home for my research out there somewhere. Even if it wasn’t in my first choice of a journal, even if it ended up in some obscure technical publication – as long as the analysis was sound, my paper would find a home.

These were words I needed to hear because they got to the heart of what was setting me back – the fear of rejection. Rejection is just as much a part of the scientific publishing world as it is in the popular science writing world. I had learned to become more familiar with the latter, but the thought of rejection for my first scientific undertaking was hard to bear. Far from the detached scientist, I was emotionally invested in this project. It had been part of my life for more than three years, and it was so difficult to disentangle myself from the manuscript – even though at its heart, science is supposed to be an objective undertaking. And because of everything I had poured into the project and receiving my degree, I realized I also owed it to myself to try to publish it. Because this is something I had promised myself I would do, my biggest failure would be not to try, to let the fear hold me back. So I set myself a deadline: submit by the end of 2014. It just had to happen, or it might never happen.

So began a push that lasted about two months. It was amazing how any minor obstacle threatened to become a major setback at every turn. Although San Jose State required me to format my thesis manuscript according to a journal’s guidelines so that it would in theory be ready for submission, I ran into my first stumbling block soon after graduation: I realized my manuscript was nearly 50% too long compared to the suggested word limit for the journal I had in mind. Rather than trying to parse my thesis into chapters, I had combined everything into one long manuscript, since everything was related. Figuring out how to pare it down was enough to discourage me for six months, a year, two years. Finally I got down to the business of cutting things out, only to put them back in. My final draft was still over the suggested word limit, but at that point I needed an editor to tell me what else to take out.

Other little things loomed large before me. I needed to change the font on one graph; I needed to change the depth units from feet to meters in another. It’s incredible how these things became monolithic in my mind, an insurmountable molehill turned mountain. The thought of tackling these problems filled me with anxiety because I wasn’t sure where to start. But with my deadline before me, I made a list and started carving out time in the evenings, trying to cross things off. I lit candles, I drank tea, trying to quiet the raging fears in my mind. Finding the right data files for the graphs in question took a fair amount of digging, but once I found them, the actual changes were straightforward and simple. I remember laughing to myself as I looked at the finished graph on my computer screen, feet having successfully been replaced with meters. This is what has been holding me up for months and years? Was it really that hard?

Analyzing gopher rockfish guts

Analyzing gopher rockfish guts

It was that hard because each little thing required digging deep into my emotional reserves. I agonized over the cover letter to the journal, worried that even the slightest misstep would be grounds for rejection. But at last, with everything in order, I submitted the paper from my parents’ dining room table on December 30, 2014 – a whole day ahead of schedule! The succinct online message that confirmed my submission hardly seemed worthy of the momentous occasion, but there it was – proof. Then the waiting game began.

The reviewer comments arrived in March while I was traveling in Vietnam with my family. I opened up my computer at our quaint lodge in Da Lat and stared at the email, slightly terrified to open it. As I skimmed through it, I saw the email provided the reviewer’s comments, but said nothing about the paper being officially accepted. My advisers later assured me this was implied, but I still felt uneasy without the paper’s acceptance spelled out explicitly. One reviewer had provided extensive comments, and the other had written a mere two sentences, saying that the manuscript needed work on the flow. For better or worse, I had just the one set of comments to work through. Some changes were small, but others seemed substantial: my paper was analyzing the diet of the gopher rockfish, and the reviewer questioned how I had grouped the prey items, saying the classification was too broad. S/he suggested running the analysis with new prey groupings.

Panic rose in my heart: if any additional analyses were required, that might set me back to the point of derailing the whole endeavor. I consulted with my advisers, who were all coauthors on the paper, and they felt confident I could defend why I chose the prey groupings I did. We went line by line through each of the comments, and I typed notes furiously. Having published dozens, probably hundreds, of papers among them, my coauthors seemed much less worried about the whole process than I did – they assured me that all of the comments I received were constructive, that they weren’t pointing out big holes or flaws with the paper. They felt confident that the paper would be accepted once I addressed each point, but I stuck by my conviction that I would believe it when I saw it.

Various prey found in the stomachs of gopher rockfish.

Various prey found in the stomachs of gopher rockfish.

One of my fears was that I would be asked for some piece of information that I could no longer find or remember, given all the time that had passed. For this reason, I was scared to delete a single computer file or recycle a single paper related to my thesis for years. Then, during the second round of comments I received from the managing editor, I was asked about the percent of variability in the dataset explained by a particular analysis. This would be a single number on the output of a single analysis – but which one? I had run dozens of versions of that analysis, and of course the one that I needed I couldn’t find. I had been very good about labeling and organizing some of my results, but not all – and this particular analysis was in the “not” pile. I began a deep search through my computer files. I no longer had a license for the software I had used for the analysis in grad school, but mercifully I still seemed able to open the output files I had generated – although they threatened to freeze my computer each time they loaded. I combed through file after file, and finally found that one little number I was looking for. Five percent! It was only five percent! The smallness of the number was a sharp contrast to the immense relief I felt being able to insert it into the manuscript.

Finally, on July 10, 2015, after two rounds of comments and edits, I received the email from the journal I had been waiting for. The subject line said, “Final acceptance,” and the message read, in part, “All the comments and suggestions have been thoroughly addressed and the manuscript is ready for publication. I believe the readers of MEPS will by very interested in reading this excellent paper and learning from the results of your efforts…Congratulations.” A month later, we received a set of proofs with the paper laid out as it would appear in the journal. And on September 29, my paper made its debut in Issue 539 of the journal Marine Ecology Progress Series. It was done.

Erin Thesis paper

In print at last!

But not quite done – at last I could do all of the little celebratory things related to publishing this paper. I had received a stipend during my final year of grad school from California Sea Grant (after two unsuccessful attempts at applying for the funding – so really I was no stranger to scientific rejection after all). The program periodically sent emails to their mailing list reminding former grantees to share any publications that had resulted from their work. One of the first things I did after the paper was published was proudly send an email to the Sea Grant office with the journal manuscript attached. I had fulfilled my obligation to the funder, to the project, and most importantly, too myself. I wrote a post on Facebook about the paper that I had been dreaming of crafting for years, and also shared the paper on the Facebook page of the collaborative fishing program that had helped me collect my samples. I sent an email to my family, added the publication to my resume, and at last I could unceremoniously part with the piles of notes and data sheets associated with my thesis – especially timely, since my parents had sold my childhood home, and I needed to do some serious purging of my “archives.” Months later, I have finally delivered the paper copies to all of my coauthors. All the loose ends had been finally tied up and tucked away.

As part of this celebratory sharing process, I also uploaded my publication to a few academic sharing sites: ResearchGate and Academia.edu. When I recently signed up for a Google Scholar citation alert, I realized that my paper even received its first citation in February of this year! It probably doesn’t hurt that one of my coauthors is also a coauthor on this citing paper. I downloaded the manuscript and eagerly scanned it – there was my name in the list of references, there it was cited in the text – as an example of how a species that is considered a “generalist” may actually consist of several differing “specialists.” It was like when I saw my name in print in the Los Angeles Times, quite unbelievable, and not fully real. But there it is – I am a published, cited scientist.

From start to finish to publication, my master’s thesis has been my biggest test to date of how to take responsibility for a project and see it through, how to self-motivate through the difficult stretches. The final push to publish took many winter evenings, and many glasses of wine. It took me three and a half years from the time I graduated to actually submit my thesis to the journal, and it was published nine months after I submitted it – more than four years in total, but now it is out in the world for anyone to read. One of my advisors fortunately had funding to pay for the hefty publication fees, including paying extra to make the work Open Access. After all the effort it took to make the research happen, and finally get it into publication, I really wanted to make sure that anyone who wanted to read the study could easily access it, free of charge.

The research can now take on a life of its own – who knows, maybe someone will dig it up in 20 years and decide to repeat my study, to see what gopher rockfish are eating in marine protected areas, and whether anything has changed. I may publish other scientific papers over the course of my career, but I doubt if any will be as satisfying. This journey has been my first true test as a scientist. They say that closure is something you have to make for yourself. Now that my work is out in the world, and I have thoroughly marked and reflected upon its journey, at last I can say I can close the books on this project – and can move on to the next chapter.

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To Market, to Market

Forget the mall. My favorite kind of shopping is visiting the farmer’s market.  Or here in Laos, it’s simply “the market.” There are no big chain stores for produce here in Vientiane where I’m visiting the FISHBIO office. So for fresh food, including fish, head to the sprawling maze of vendors under tarps or umbrellas in one of the city’s many outdoor markets.

Luckily, I’m in “window shopping” mode only on my visit—even for an open-air market fan like me, the selection is overwhelming. Piles of bright, colorful food usually tempt me into buying way more than I need. And next to the food there are stalls and stalls of clothes, jewelry, incense, toys and other things for sale. How anyone does their shopping here without getting lost is beyond me.

Chickens spin on spits, fish flop in vats of water, workers push carts of ice through the narrow aisles. Vendors, mostly women, swish sticks with air-puffed plastic bags over their tables to keep the flies at bay. And they scrape fish scales and yield cleavers with deadly efficiency.

My co-worker Mout and I meandered through three different markets so I could film the different species of fish for sale.  And I have to say, some of these fish from the Mekong are huge!  Catfishes two and a half feet long. Granted, that’s nothing compared to the true Mekong giant catfish, a species that can grow more than ten feet long. Still, these big guys are far larger than anything I’ve seen at any grocery store. It’s impressive to think how many of these hefty fish are swimming around in the river­—and how there were probably even more, even bigger fish in the past.

And what do the vendors do with the fish they can’t sell? Dry them or ferment them. Nothing goes to waste. Although based on the smell, I’m guessing that fermented fish is probably an acquired taste…

A Familiar (Fish) Face and the Language of Science

Why hello, Chaunacops coloratus!

It’s always comforting to see a familiar face in a foreign country—especially when the face belongs to a deep-sea fish. I had the surreal experience of “bumping into” an anglerfish from the Monterey Bay area while visiting some fish researchers at Can Tho University.  One scientist had the latest copy of a Vietnamese aquaculture and fisheries magazine on his desk, and the front cover bore the mug shot of a fish that resembles an adorable pink grapefruit.

I’d know that whimsical tilt and “smiling” face anywhere. I passed it many times on a scientific poster hanging on the way to my graduate advisor’s office at Moss Landing Marine Labs. My advisor, ichthyologist Greg Cailliet, recently co-authored a research paper about the first live observations of this anglerfish, called Chaunacops coloratus, with researchers from the Monterey Bay Aquarium Research Institute. (I’m guessing this paper is why the little angler is now a Vietnamese cover model. )Thanks to the technology of underwater robots and cameras, they were able to describe this fish going about its business in its natural habitat at an incredible depth of 3,300 meters (11,000 feet). The MBARI website has a great story about the fish, and even video of it swimming around and hanging out.

Needless to say, there was something so comforting in seeing my culture and my field of study intersect in this unexpected way. I don’t know if I adequately conveyed to the Vietnamese researcher why I was so excited about this fish, but he gamely let me photograph his magazine.

In my first post, I mentioned how I wanted to cultivate a relationship with Vietnam through the lens of science and the environment. My Vietnamese is rudimentary at best, but once we start speaking the language of science, I feel right at home.  Getting a tour of the facilities at the university’s school of Aquaculture and Fisheries was a chance for me to comfortably lapse into full geek-out mode.

Bubble bubble…vials of algae soon to become shrimp food.

I learned that students and faculty at the university study diseases and parasites that afflict farmed shrimp and catfish. That they isolate and culture different species of algae to feed baby shrimp and mud crabs. That they are researching methods of integrated aquaculture, using plants to filter the waste from catfish farms. All very cool.

An experiment to see if these plants can clean up farmed catfish waste water.

A highlight: the researchers invited me to check out some tiny planktonic animals called rotifers—both marine and freshwater varieties— that they grow for aquaculture feed.  As I sat down at the scope and adjusted the eyepiece, suddenly all the barriers of this foreign country dissolved. For my graduate work, I spent more hours at a microscope than I care to count, trying to identify bits of fish guts. Suffice it to say: a microscope is familiar territory.

We’re on home turf now… Photo by Bao Quan Nguyen.

Staring at the little critters zooming about tapped into a deep-seated feeling of wonder and appreciation that usually bubbles up when I’m reminded about the incredible diversity of life. Another time this happened was in the seventh grade when I, also seated at a microscope, first watched a paramecium ambling around a drop of water.  My thirteen-year-old self had no way of knowing what direction my future would take me, but I knew I wanted some connection to that experience of awe, as the natural world opened up to me under the lens of science. It’s humbling to think how all the paths I’ve taken and connections I’ve made have overlapped and intersected to bring me to this point.

Amazon Catfish in the Mekong: First FISHBIO blog post

Sailfin armored catfish, far from its native South America.

I’m lucky enough to be blogging for FISHBIO while traveling in Southeast Asia, and my first post went online today! Please check it out!

I wrote about one of the Mekong’s more unusual inhabitants: an ornamental fish imported from South America. Here’s an excerpt:

The last thing you might expect to catch in the Mekong River is a fish from the Amazon—but that’s exactly what can happen now. Researchers from Can Tho University in Vietnam use trawl nets and gills nets to survey fish diversity in the Hau River, a tributary of the Mekong, every other month. A recent survey pulled up two different species of sailfin armored catfishes in the genus Pterygoplichthys. Thanks to the aquarium trade, these natives of South America are now comfortably at home in Southeast Asia, North and Central America, and the Pacific Islands.

Read the full story here!

It’s really quite sobering to see how people can change the species composition and ecology of a natural system by transporting fish all around the world.

First Fish

Since a focus of my trip is, after all, fish, I thought it was worth backtracking to describe my first fish encounter—not at swim, but on a plate. Which is pretty fitting, since mealtime is how I imagine most people associate with fish. Eating is the last link in the chain that truly connects fish, people, and the ocean or rivers.  For better or worse.

On my second day in Saigon, my cousin took me to get some Vietnamese comfort food. Rice, sautéed greens, pickled onions, pork and egg cooked in a clay pot—and salty cooked fish. It was all delicious, but I couldn’t help but wonder what kind of fish I was eating, and where and how it was caught. The little guys had more identifying characteristics than your typical fish fillet, but the salient features I remember were the crunchy skin and the sharp tiny bones. Hopefully my fish ID will improve when I hit the field…more observing, less eating.

A first for me was drinking starfruit juice. It’s so sour, you get a little jar of sugar water to mix in to taste. Quite puckerlicious. And I enjoy the concept of drinking through a reed!

I’ve had a few other gastronomic encounters with fish since then, including at my family’s house. My mom’s cousin put it exactly as I have imagined: “Vietnam has such a long coastline that the people here are used to eating many different types of fish.”

Fish in the river, fish in the sea.  And so much for me to learn.

The “before” shot—straight from the market.

And “after”—cooked with herbs.

Claypot fish—one of my favorite dishes, but this one was only so-so. My grandma’s is better!

A pomfret, or butterfly fish–known as “ca chim” or “bird fish” in Vietnamese for its long pectoral fins (missing here). A special dinner with researchers from Can Tho University. Photo by BảoQuân Nguyễn.

The Dragon Fish Path

This is the origin story.

All plans of action start with an idea. My plan, in short, is this: Spend one month in Vietnam. Write. Learn. Absorb. Document. Oh sure, and Eat, Pray, Love, as appropriate. Pay particular attention to fish.

The idea for this plan, such as it is, goes back to the time when I first started writing. As an undergraduate working at the UC Davis News Service, I interviewed a professor who studied the economics of sustainable agriculture development in the Amazon. He told me about a “critical triangle,” the intersection between poverty, the environment, and economic development. Trying to address any one point of the triangle required tradeoffs from the other two points. But was there a way to strike a balance, one that could benefit both people and the natural world they depend on for survival?

Something about that question spoke to the core of what I believed in. I kept circling back to it while wondering what to dedicate my life to. I took the story of the Amazon, filtered it through my values, and came out with…fish. Because of all the world’s amazing ecosystems and habitats, the one I care most deeply about is the ocean. And nowhere is the relationship between people and the ocean more tangible than the fish they catch to eat, sell and survive.

Fish brought me to graduate school at Moss Landing Marine Laboratories. I learned to catch them and dissect them, learned how they lived and what they ate, learned different approaches to managing them.  And it was at a graduate student workshop (sponsored by the excellent MARINE program), where I started thinking about what how to turn fish, the ocean, and the critical triangle into a life plan. What would be my Amazon?

One of the many exercises of this “Designing the Professional” workshop was to map out three different possible life paths immediately following graduate school. Three different tracks we could envision our lives taking. The workshop host, Stanford instructor Dave Evans, called it our personal odyssey. I took the exercise to heart, and concluded that for one of my paths, my Amazon would be Vietnam.

Here it is worth mentioning two things: 1) My mom is Vietnamese, making me half Vietnamese. 2) I don’t speak Vietnamese, but wish I did.

Suffice it to say, trying to learn Vietnamese has been one of the greatest personal challenges of my life. It’s the result of garden variety multicultural identity issues, and a highly Westernized tongue mangling the nuances of a tonal language. Was there a way  I could integrate my longing for a key cultural connection into the study of fish? I threw it all in the mix, and came out with a timeline with different “seasons” for my path that looks like this:

How I originally imagined the Dragon Fish PlanI hung this on my wall for the past few years as a sort of personal compass. As a result of the workshop, my crazy pipe dream seemed less crazy and almost, well, doable. Three different seasons building up my knowledge of language and culture, of people and nature.

And suddenly, I now find myself racing through Season 1, about to hopscotch through Season 2, and ready to land in Season 3. This trip, which starts today, is turning my plan into action.

I admit, my intensive Vietnamese-study-as-preparation hasn’t been quite as intensive as it could be, although Mom has been inserting more Vietnamese into our conversations of late, which is nice. Hopefully I will be learning a lot on the go. Which reminds me to pack my pocket dictionary.

I’ve also skipped over the whole teaching thing, but with any luck there will be kids and schools on this path yet. My inner elementary school teacher will be scoping out the possibilities. Extended family and language immersion are still part of the plan, since I’ll be staying with my Mom’s cousin and his family. And Season 3 will come about largely thanks to my new job – but more on that later.

As part of the personal odyssey exercise, Dave Evans also instructed us to design a talisman, something to remind us of our favorite path. Hence, I created this stunning piece of Clip Art:

Dragons, fish, you get the ideaI wrote this about it:

This is my talisman. I’m calling this plan the Dragon Fish path because the dragon is an important figure in Vietnamese mythology, and the country itself is said to look like a dragon. I also think I will need to draw on some of that mythological strength and determination to actually carry this plan out. Fish are my area of study and I was drawn to them because they embody the intersection between people and the ocean. So this plan is a bit of melding between my personal background and my educational path.

Fast forward to my most recent round of schooling, a year at the UC Santa Cruz Science Communication program. Enter another assignment, this time to write a book proposal – something I could see myself writing in the next five or ten years. With the Dragon Fish path still on my brain, I again took the assignment to heart.  My proposal starts like this:

The country of Vietnam curves like a dragon sleeping at the edge of the sea. Green, jungle-covered mountains armor its head and spine, and the fertile fan of the Mekong delta spreads across its tail. This slender country and the great ocean it borders host a lush richness of tropical flora and fauna. However, Vietnam’s natural heritage remains obscure to the western world, overshadowed by the human tragedy of war that ripped the country apart, and defined it for a generation of Americans. Nearly four decades later, Vietnam has one of the fastest growing economies in the world, and the country’s environmental resources are under siege. I propose to write an ecological travel book that highlights the country’s threatened natural diversity in its ocean, rivers, and jungles, and examines the relationships between the Vietnamese people and their natural environment.

And why should I be the one to write this book?

This book is a subject of great personal and professional interest to me, one that draws on my cultural heritage and scientific training. Vietnam is my mother’s lost country: she and her family fled at the end of the Vietnam War. Growing up, my relationship with Vietnam has been colored predominantly by this loss. I am also trained as a biologist and marine scientist, with a particular interest in fish. I am fascinated by the relationship between people and their natural environment. This rare combination of characteristics makes me well poised to write the book I have proposed. I have met few other marine or environmental scientists of Vietnamese heritage in the United States. The book’s exploration of nature, culture, and conservation will offer a new perspective of Vietnam not just for readers, but also for myself. I have struggled to improve my rudimentary Vietnamese for years, but as a science writer, I can approach the country through the language of fish and oceans, of mountains and trees.

I originally started planning my upcoming trip primarily with this book in mind. But since then, my path has crossed with the company FISHBIO. With them, I will have the opportunity to immerse myself in the critical triangle of the Mekong Basin, both as a writer and as a scientist. My journey over the coming month, part personal, part professional, will be my first foray into acting out my plan. A book is very much part of my end goal, and this blog will be one way of encouraging me to write in the coming weeks. Thank you for reading – I welcome you to take this journey with me. I hope this is only the beginning.