All I Really Need to Know I Learned From Peer-Reviewed Papers (Part 1)
I remember feeling a spark of urgent curiosity when I found a copy of All I Really Need to Know I Learned in Kindergarten on a shelf in the guest bedroom. I was 11. And though I had made it to middle school, I had never attended kindergarten. This book contained information that I lacked and needed. I hid under the guest bed and read it cover-to-cover.
This character trait — this drive to read my way into knowledge — is still going strong in my life as an early career ecologist. Recently, I turned to Dr. Marieke Frassl’s 2018 Ten simple rules for collaboratively writing a multi-authored paper as I took on a leadership role writing a paper with my postdoc cohort. Reading this guide for collaborative writing gave me a new sense of focus and energized me for the ensuing work of organizing notes, framing our paper, and planning for an upcoming writing retreat. I’m a reader, and so it shouldn’t be surprising that I seek paper-based advice in the stacks of my #365papers To Read Pile. Reflecting on the helpful scaffolding that I found in Ten simple rules for collaboratively writing a multi-authored paper, I pulled out my favorite Advice Papers from the last year. Flipping through the pdfs, I wondered, Why do we publish advice in journals? Why did these papers, which often echo advice I’ve already received in person or on twitter, resonate so much for me? What does it mean to offer your advice via peer-reviewed papers? One of the major perks of writing for PLoS Ecology is the opportunity to cold-email scientists (or work-email scientist-friends) and pick their brains about their papers on exploding pollen, unexpected biodiversity hotspots on historic battlefields, and epic fieldwork roadtrips. So, I started writing to the authors of my favorite Advice Papers. This exercise took on a life of its own as Advice authors shared their stories, and their advice, with me. At the same time, I started collaborating on my own Advice Paper with coauthors. The project of selecting the year’s top Advice Papers has expanded beyond my initial curiosity and grown way too long for a single blog post. Here is the first of a two-part series on the best recent Advice Papers in ecology — Part One: How to Do the Science.
The two best papers I read on doing science were Broman and Woo’s 2018 Data Organization in Spreadsheets in The American Statistician and Dyson et al’s 2019 Conducting urban ecology research on private property: advice for new urban ecologists in Journal of Urban Ecology. I ranked Data Organization in Spreadsheets as one of my top-ten Summer 2018 papers, and I continue to stan this lovely guide to foundational data management. While my research is largely National Parks-based and urban ecology on private property seems to fall outside of my wheelhouse, I appreciate the framework for planning urban fieldwork in Dyson’s paper, and my friend Carly Ziter is a coauthor. When the paper came out, Carly tweeted “A few of us ECR urban ecologists got together and wrote the paper we wish we had been able to read before starting private property research.” At the time, I was hip-deep in revisions with a few alpine ECR ecologists on the paper that we wished we had been able to read before starting common garden research. I had to read someone else’s version of the paper they’d wished they’d been able to read and see that this process could be completed.
Dr. Karen Dyson explained, “During my first (urban) field season I realized very quickly that I had had no idea what I was getting myself into.” She was surprised by the time commitment needed for communicating with private property owners to set up site visits and experienced the gamut of hospitality from having security called on her to being subject to overly-friendly non-stop talkers. “Basic things like bathroom breaks required more planning than you would expect. If I recall correctly, it was this last point that I was commiserating with my co-author Tracy about when the first idea for this paper came about.” Second author Dr. Carly Ziter agreed, “Like Karen, I didn’t know many people working on private land when I started my PhD fieldwork, and I really just muddled through it pretty naively.” Private property is an important part of the urban ecological landscape, but the challenges of working on private property mean that urban ecology research is often conducted through remote sensing or from a sidewalk. Dyson wrote, “You’re never going to understand ecology in cities if you don’t engage with people—and not just park administrators, but the individuals who make myriad decisions each day on every parcel about what trees to cut down, what shrubs to plant, etc. All this is critical to furthering the field, and we wanted to see more of it, done well, with sensitivity to the people whose lives we’re intruding on.” Dyson put together a workshop on the topic for ESA 2016, and Ziter attended. She remembers thinking, “finally, other people who get what this is like!” Dyson interviewed Ziter for the paper, and as Ziter remembers, “at some point, I think I more or less invited myself onto the team (thanks Karen et al!). I started out thinking this is the paper I wish I had been able to read as a graduate student, and of course by the time the paper came out I was starting my own lab, so now I think I’m so excited that MY grad students will be able to read this before they start fieldwork.”
I asked Ziter and Dyson why they decided that this advice needed to be presented in a peer-reviewed paper. Ziter notes that “Urban ecology is growing really quickly right now. And as the field grows, there are more and more students collecting urban data whose advisors/labmates are not trained in urban ecology or urban field methods (e.g. in my case, I was the only urban-focused grad student in my lab). So there isn’t that passed-down or institutionalized knowledge present within research groups to help students get started.” And, as Dyson recognizes, “Peer-review is more permanent and has gravitas, and can be cited as a reason for doing something. We also wanted open source, since it’s accessible to those without library connections. Also, this is a serious subject that needs to be treated seriously, and often isn’t… which is also why we interviewed almost 30 people from as many countries as we could and went searching outside the discipline for role models.” There’s definitely some field site pride on the line. Carly explains the exasperation of hearing, “oh you do urban ecology? Your fieldwork must be so easy.” “Really the logistics are often more challenging than working in traditional field sites. So it was personally really rewarding to be able to help Karen and the team articulate in a more formal way that hey, this isn’t just in our heads, there really are unique and pervasive challenges inherent in this kind of work (just as there are challenges inherent in more remote field ecology that we don’t face!)”
The origin story behind Data Organization in Spreadsheets is a bit different from Dyson’s work to build a coalition dedicated to capturing and publishing best practices for field work on private property. Dr. Karl Broman’s website on organizing data in spreadsheets — “largely a response to a particularly badly organized set of data from a collaborator” — already existed when Jenny Bryan and Hadley Wickham were organizing a special issue on Data Science for the journal The American Statistician. He admits that, “it seemed unnecessary to write an article when I could already point people to the website,” and he backed out of his promise to contribute to the special issue. But, he reports, “Jenny didn’t want me to back out and asked several friends if they’d help me to write the article, and Kara Woo agreed to do that and did the bulk of the work of rearranging the content in the form of an article and adding an introduction citing relevant literature.”
The peer review process for Data Organization in Spreadsheets was fairly straightforward. Broman writes, “every article solicited for the issue was assigned two reviewers from among the authors of other articles. The reviews were constructive and helpful. After the review, the article was published at PeerJ Preprints and also formally submitted to American Statistician…American Statistician is paywalled; available to most statisticians but not many others. I paid some huge fee (like $3500) to make it open access, since the target audience for the paper is much broader. I hemmed and hawed about whether to pay to make it OA; the fee seemed way too high, and the material was already available both at PeerJ Preprints and as a website. But I did pay and I’m glad I did, because I think way more people have read the paper, as a consequence of it being free. If people find the paper and it’s available, they’ll read it, but I think if they get a paywall, they’re not likely to look further to find a free version.”
In contrast, the urban ecology peer review process was long and winding, though it also included a PeerJ Preprint. When it was finally published, Dyson shared the journey in a twitter thread. “It was desk rejected from Landscape and Urban Planning and Methods in Ecology and Evolution and rejected after review from Urban Ecosystems.” She remained dedicated to the paper throughout: “Since I ran the workshop at ESA 2016 and a well-attended poster at ESA 2107, we knew there was a need for it among students…We also put it in PeerJ preprints and it was one of the top five read/visited papers of 2018. So despite getting very frustrated with the process, we didn’t really lose faith in the manuscript—though we did give it complete reorganization after the rejection from Urban Ecosystems. We saw Journal of Urban Ecology was doing a free open access as they got started and decided ‘why not?’ since they’d also published Pickett and McDonnell’s The art and science of writing a publishable article. They’ve been lovely throughout the process—and have been great about re-tweeting and promoting the paper. It’s now one of their most read articles.” Here, Ziter chimed in to say, “I should disclose that I am sometimes the thumbs behind that twitter account. So that’s why it got good twitter press ;). But I have no other role in the journal decisions or review process – so the rest of the loveliness is on them!”
Finally, I asked Broman and Dyson if they had any favorite Advice Papers. Dyson answered with an enthusiastic “Yes! In general, I love advice papers and papers that compare methodology, so I enjoyed putting this one together and hope to do more!” (I agree — we should write an urban-alpine ecology crossover!). She highlighted, “Hilty and Merenlender’s 2003 paper that deals with many of these issues (though not as in depth) on rural private property… [and] we used a few papers as models when we were writing (and re-writing) our manuscript, including Harrison’s Getting started with meta‐analysis; Goldberg et al’s Critical considerations for the application of environmental DNA methods to detect aquatic species; and particularly Clancy et al’s Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault.”
Broman writes that he didn’t seek out any advice papers for guidance/structure while writing Spreadsheets. He muses, “I think the main advice papers I’m familiar with are those “ten tips for …” [sic] at PLoS Computational Biology, which have been really useful though I think the formula has become a bit grating. I also really like Bill Noble’s paper on organizing projects.”
Thanks to Broman, Dyson and Ziter for sharing their advice and adding to my reading list. Both of these papers are well-written and offer tangible, useful advice. I’ve found myself ruminating on them as I plan future fieldwork, and definitely wishing I could have read them much earlier as I wrap up old projects and wrestle with my old data.
Stay tuned for Part Two: How to Write About the Science You (and Others) Did.
Dyson, K., Ziter, C., Fuentes, T. L., & Patterson, M. S. (2019). Conducting urban ecology research on private property: advice for new urban ecologists. Journal of Urban Ecology, 5(1), 48–10. http://doi.org/10.1093/jue/juz001
Broman, K. W., & Woo, K. H. (2018). Data Organization in Spreadsheets. The American Statistician, 72(1), 1–10. http://doi.org/10.1080/00031305.2017.1375989
Banner image: photo by Glenn Strong, Creative Commons