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PLOS Ecology Community | Researchers dis.. by Caitlin Mcdonough Mackenzie - 4d ago

This post is a short attempt to peel back the curtain on my “bad at pollen” process. Since my very first pollen clinic in the BEAST Lab at University of Maine I’ve been instructed to sketch the pollen as I see it on reference slides and create my own kind of visual library. This approach makes sense — I remember drawing carex perigynia and fern pinnae in my first field botany course, filling my Rite-in-the-Rain notebook with pages of half-erased sepals and efforts to capture anther angles. I’m not a practicing sketch-book type of scientist — my field books from my PhD research are mostly long tables dotted with squashed mosquitos and lists of taxa — but I don’t vehemently claim that “I just can’t draw”. When I was a master’s student, I took at print-making class at Burlington City Arts and got off campus and out of my head for a couple hours each week. I couldn’t completely stop thinking about my research, but I could redirect that energy towards creating screen prints of my study species. I poured over my photographs from my field season and sketched each of the six flowers over and over again.

My Lillstreet Art Center alpine six screenprinted t-shirt and a detail from the original screen.

And after I graduated, and moved to Chicago, I took at class at the Lillstreet Art Center and did it again — creating a new alpine plant screen from a new series of sketches of the same six species. But, I knew those plants (even if, as it turns out, our volunteers maybe didn’t know them?), and drawing familiar flowers repeatedly is perhaps a different game from sketching pollen grains and lining the margins with notes like “cute tennis ball” (Fraxinus) and “I think this is a margo” (Acer).

A recent paper in Journal of Biological Education reinforces the idea that drawing plants — or in my case, pollen — can help us develop botanical knowledge. The paper, “A comparison of descriptive writing and drawing of plants for the development of adult novices’ botanical knowledge,” presents a case study that supports the sketch-to-learn model, or at least the sketch-to-better-capture-the-details-in-your-notes model. Drs. Bethan C. Stagg and Michael F. Verde led half-day wildflower events where students filled notebooks with either descriptive writing or labelled drawing for a suite of plants. Later, the students were given an identification test (labeling plants from the learning activities with their common name or noting ‘look-alike’ for trick question species that were not a part of the learning activities) and a morphology test (true/false questions about diagnostic characters of the study species). These were all self-described novice botanists — “the event announcement stated that participants should not be able to identify more than twenty common native plants.” The writers and drawers scored equally well on the tests, but Stagg and Verde found that the sketches captured more recognizable diagnostic characters for each species than the written descriptions.

“Drawing in biology develops students’ observational skills by engaging the learner in close, detailed study of the focal organism,” Stagg and Verde write in the Introduction. They reel off a list of citations, but this connection between drawing and observing in biology has a long tradition in natural history training. In the classic essay “Look at Your Fish,” a prospective entomology student joins Louis Agassiz’s lab in the 19th century and is given a jarred haemulon fish specimen and instructed to study it.

Slowly I drew forth that hideous fish, and with a feeling of desperation again looked at it. I might not use a magnifying glass; instruments of all kinds were interdicted. My two hands, my two eyes, and the fish: it seemed a most limited field. I pushed my finger down its throat to feel how sharp the teeth were. I began to count the scales in the different rows until I was convinced that that was nonsense. At last a happy thought struck me—I would draw the fish, and now with surprise, I began to discover new features in the creature. Just then the professor returned.

“That is right,” said he; “a pencil is one of the best of eyes.”

Ultimately the student spends three days observing this fish and sporadically fielding questions from Professor Agassiz in what sounds like one of the most stressful and bewildering orientation exercises. Agassiz is never satisfied and leaves every interaction cryptically instructing him to “look at your fish” before disappearing for an unspecified period of time. The pedagogical style is outdated, kind of. While none of my PIs pulled a straight Agassiz on me, the essay has been assigned as a reading in natural history courses twice in my career.

My fish is a box of pollen slides. But my fish is also a stack of literature, palynology and conservation paleobiology papers in a field where I am very much still sketching the outlines and learning the vocabulary. Is it possible to bring that pencil-is-one-of-the-best-of-eyes attention to detail to reading indoors instead of botanizing outdoors or pollen-counting under a microscope? The amazing botanical illustrator and comic artist Liz Anna Kozik inspired me to think about this last month.

Liz Anna Kozik draws her response to the academic paper Stemen, M. (2003). Keeping the Academics in Service Learning Projects, or Teaching Environmental History to Tree Planters. The History Teacher, 37(1), 73-78. doi:10.2307/1555600 https://www.jstor.org/stable/1555600

She tweeted, “I’m going to do quick TLDRs for the articles I read~!” and posted a handwritten summary of the 2003 paper Keeping the Academics in Service Learning Projects, or Teaching Environmental History to Tree Planters with an illustration of a student sitting by a freshly-planted seedling asking “What did I just do + what does it mean?” Liz usually creates artwork that centers the prairie plants she studies, but here, she’s sharing digital sketches of the academic literature. She beautifully distills the papers into these concise take-away nuggets framed by her simple, striking art. Each TLDR page is inviting and memorable —and the process creates so much more meaning than my haphazardly highlighted pdf pages and marginalia from my folder of #365papers.

Liz Anna Kozik draws her response to the academic paper Larson, B. M. (2005), The war of the roses: demilitarizing invasion biology. Frontiers in Ecology and the Environment, 3: 495-500. doi:10.1890/1540-9295(2005)

I love exploring prairie ecosystems through Kozik’s eyes, but now I can’t wait to see more of her TLDR and follow her reading!

To circle back, I’ve been trying to apply Stagg and Verde’s advice to my pollen sketches — “Participants were encouraged to be undeterred by drawing ability or botanical knowledge and were advised to create their own terms for unknown morphological features.” I’m not quite at the level of sketching paleoecology papers, but my “light freckles, three-cornered popcorn kernel” is slowly becoming “surface psilate, exine indistinctly tectate, sub-triangular to spherical, pores aspidate.”

Banner image: sketch of Kalmia angustifolia on the back of a datasheet by Caitlin McDonough MacKenzie, summer 2016.

Reference:

Stagg, B. C., & Verde, M. F. (2018). A comparison of descriptive writing and drawing of plants for the development of adult novices’ botanical knowledge. Journal of Biological Education, 28(2), 1–16. http://doi.org/10.1080/00219266.2017.1420683

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PLOS Ecology Community | Researchers dis.. by Caitlin Mcdonough Mackenzie - 3w ago

I’m in the middle — the frustrating, slow, and muddy middle — of learning how to be bad at science. How to be bad at one very specific part of a subdiscipline of a scientific field that I love, in theory, but currently suck at.

On my CV I’ve worked very hard to present myself as someone who is good at science. I am, academically, good on paper: I’ve got the advanced degrees to prove it. I’ve been a “fellow” more than once. And while I wasn’t born, Athena-style, a fully-formed botanist, I don’t remember the beginning, the part of my education where I learned how to be bad at plants. I think my plant ecology skills were honed so slowly — from gardening with my mom as a kid, hiking at summer camp, working in outdoor education in college — that I became good at plants imperceptibly, and by the time I took a field botany course in grad school, the taxonomy and morphology were at least familiar, if not already labeled correctly, in my mental map. I grounded my PhD research in field sites that supported the same plant communities I studied as a master’s student. When I began, I bought a new field guide, but I honestly could have just carried the old dichotomous keys across state lines.

And then I decided to become a paleoecologist.

There are 99 glass slides of pollen in a box that represent my postdoc work. They cover 408 cm of sediment from the bottom of a pond in Acadia National Park. As a PhD student, I spent four years monitoring the plants on the ridge above this pond — I know every stem that grows there now; the slides should tell me what used to grow there, the pollen like a fingerprint of past vegetation communities. If you gave me the lace of veins left behind from a decomposing leaf on that ridge, if you handed me an empty fruit stalk, I could identify the plant to species, almost carelessly. But when I look at my slides, I feel like I am drowning in unknowns. Under the microscope, my plants become anonymous. Pollen, it turns out, is not intrinsically identifiable. When I look at a birch tree, for example, I don’t need to think about how to parse it, the identification is reflexive. When I look at birch pollen, I see shapes, kind of rounded-triangles or triangular-balls, with nubbins at the corners, and nothing about it screams birch. Not yet.

I am 35, and I am a beginner, learning plants again and for the first time. I say for the first time because last time around, I was not cognizant of the learning process. I didn’t know I was ever bad at plants. But I am definitely bad at pollen.

Pollen is humbling me. I’m learning how to tell tricolpate grains from tricolporate grains, making Pinus v Picea lists to remember which one has an indistinct transition zone between its rugulate bladders and stippled body, and assigning the keys on my keyboard in the program PolyCounter, so that when I tap ‘k’ it counts one Fagus. But, I’m also learning how to inhabit this research: when is my best time to count pollen, how do I increase my daily hours at the microscope without burning out, and when I see improvement in how quickly I count a slide, how do I know if I’m getting better at pollen, or just getting sloppy. I’m still so bad at pollen, that I don’t know the difference between feeling genuinely stuck on a hard identification or just seeing a common grain from an uncommon angle. It’s hard to see a way out.

I’ve been bad at pollen for a couple months now. I was so afraid of being bad, so stuck in this feeling, that I stalled in the learning phase. I stuck to my box of reference slides — each one a simple collection of a single pollen type, labelled with the genus or species it holds — and tentatively shuffled through. When I would peek at a real slide, a slide from my project, the chaos of unknowns would overwhelm me. I dragged my feet; I didn’t feel qualified to start counting. I knew that I would, someday, probably be good at pollen because at some point in the future the 99 slides would be identified and counted, I just didn’t feel connected to that process.

I still haven’t gracefully learned how to be bad at science. But, I have started collecting advice, and noticing my stumbling blocks, and I think that eventually these reflections will help me empathize with students in a way that I couldn’t before because I didn’t know what it felt like to be bad at plants. I love the Tall Heights song, Learn Again. Full disclosure: I knew those guys in high school, and so I might have been there in the study halls in the song. However, high school me was probably dutifully doing her homework, and generally learning how to be good at academic things and would not have identified with the lyrics on this level. Postdoc me is all about learning again. Occasionally I rewrite the lyrics and sing them to my pollen. “Sometimes I forget to do, the things that paleoecologists do…”

The most meaningful advice I’ve found about being bad at something you love is from Ira Glass. I didn’t go to high school with Ira Glass and so this is slightly less personal, and on top of that he is speaking to creatives, and not necessarily scientists, but this resonates. This American Life superfans can listen to this recording of Ira’s advice; it’s slightly different from the quote as transcribed on GoodReads (below):

“Nobody tells this to people who are beginners, I wish someone told me. All of us who do creative work, we get into it because we have good taste. But there is this gap. For the first couple years you make stuff, it’s just not that good. It’s trying to be good, it has potential, but it’s not. But your taste, the thing that got you into the game, is still killer. And your taste is why your work disappoints you. A lot of people never get past this phase, they quit. Most people I know who do interesting, creative work went through years of this. We know our work doesn’t have this special thing that we want it to have. We all go through this. And if you are just starting out or you are still in this phase, you gotta know its normal and the most important thing you can do is do a lot of work. Put yourself on a deadline so that every week you will finish one story. It is only by going through a volume of work that you will close that gap, and your work will be as good as your ambitions. And I took longer to figure out how to do this than anyone I’ve ever met. It’s gonna take awhile. It’s normal to take awhile. You’ve just gotta fight your way through.”

My pollen is my story here. And I just need to start counting pollen. And if I have to come back and recount the first five or ten slides, the first twenty slides, I will do that. I will fight my way through. I will learn again how to be bad, so that I can eventually become not a static good, but a growing better.

Banner image: Anna Bahnweg, Creative Commons. (This is a scanning electron microscope image of buttercup pollen grains; my compound microscope pollen counting experience is significantly less fancy)

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There is something magical about reading a well-written, remarkable paper from outside of your sub-discipline — the echoes of familiarity in methodology, the unpredictable overlaps, the serendipity of finding the research in the first place. I recently found this magic in Vertical foraging shifts in Hawaiian forest birds in response to invasive rat removal, published in PLoS ONE in September 2018. Co-first-authors Dr. Erin E. Wilson Rankin and Dr. Jessie L. Knowlton transported me to the northeast slope of Mauna Loa Volcano for a bird-watching and bug-counting adventure through a network of half rat-eradicated kīpuka — a jigsaw puzzle of fragmented forest pieces dissected by lava flows.

By most measures, I should never have read this paper. It came out while I was staggering though the first weeks of parental leave last fall. My invasive species are plants (not rats); there’s really no vertical space available (the trees are too short!) for shifts in arthropods or their predators in my plant communities at treeline; my island study site (downeast Maine) hasn’t seen volcanic activity for hundreds of millions of years (Hawaii’s kīpuka are created when volcanic lava flows move through native forests). For reasons I can’t explain, earlier this month I clicked on a link to The Wildlife Society’s — a society I’m not a part of and don’t actually follow on social media — Wildlife Publication Awards 2019 shortlist announcement. At the end of the Journal Paper category, this Hawaii study caught my eye, because I’m planning a trip there in the fall and recently spent three early morning hours driving through Iowa and Minnesota with my friend who is a postdoc at the University of Hawaii, Hilo. Despite the winding the path to get this paper into my To Read Folder, there was a straight line from my final scroll through the Conclusions to the “compose” button on my email. I had to hear more from Drs. Wilson Rankin and Knowlton.

Photos by Erin Wilson Rankin. Top a happy face spiders taken under a scope and nocturnal spider in the kipuka. bottom: a sticky trap for sampling arthropods, a native bee on the ohia flower.

Here is what my initial google searches turned up: stunning photographs of kīpuka; and the discovery that the two first authors, now faculty at UC Riverside and Wheaton College, were postdocs on this project who first came to the kīpuka from the subfields of entomology (Dr. Wilson Rankin) and ornithology (Dr. Knowlton) back in 2011. The invasive rat removal efforts in their paper was a part of a larger study: 16 kīpuka fragments were methodically outfitted with trapping grids and compared to another 18 kīpuka without rat traps. “The larger study has examined how impacts by invasive predators (rats) change across a gradient of ecosystem size,” Wilson Rankin and Knowlton explained to me. “The kīpuka are a patchwork of forest fragments that were created when volcanic lava flows moved through native forests. The result is a landscape dotted with naturally fragmented forest patches that range in size from very small (<0.1 ha) to very large (>12 ha). This study system allowed us to tease apart the effects of invasive rats and the effects of ecosystem (or forest patch size) in order to better understand the forces that shape communities.”

I asked how an entomologist and an ornithologist from different universities on the US mainland ended up working together in Hawaii. “The kīpuka project was a highly collaborative project among PIs at Stanford University, University of Maryland, Michigan Tech, and the US Forest Service that integrated multiple research fields to examine the effects of an invader on native communities.” They confirmed what google had hinted about their origin story. “We both joined this project early on as post-docs, one focusing on quantifying invasion impacts on the arthropod communities and the other focusing on the responses of native forest birds. By bringing together a research team with diverse backgrounds and expertise, the kīpuka project was able to develop a broad and in-depth understanding of how rats shape the invaded communities and alter the interactions among native species.” They ultimately found that the presence of invasive rats altered the foraging behavior of native birds — in rat-filled fragments the birds foraged higher in the canopy. The rats are not found above 6 m in the forest, but they seem to control the arthropod biomass below 6 m, suppressing the resources available for birds, especially insectivores and frugivores. In sites without rats, there was more arthropod biomass below 6 m and birds foraged at lower mean heights compared to higher foraging heights in control kīpuka.

birds of kīpuka fieldwork photos by Jessie Knowlton

These kīpuka are like the matryoshka dolls of island biogeography, a model system in a model system. The forest fragments are islands of habitat, and these in turn are contained within the island of Hawai‘i. I asked Wilson Rankin and Knowlton what they hoped managers in other systems could learn from this work. They write, “The fact that the kīpuka are fragments of habitat within a less hospitable matrix makes them comparable to other fragmented systems, which, as we all know, are increasingly common as human development continues to expand through natural habitats.” The kīpuka islands within islands system is special, but can still contribute to our understanding about invasive species in general. “While Hawaii is unique because of its high number of endemic species and long isolation from mammalian predators, many fragmented habitats are having to contend with extinctions of native species and invasions of nonnative species, even on the mainland. Our work shows that these invaders can alter whole trophic systems, either directly or via shifts in species’ behavior. This work helps to highlight the importance of considering the synergistic and sometimes unpredictable effects that habitat fragmentation and invasive species together can have on native food webs. We hope that both factors will be taken into account when planning restoration or conservation actions.”

Finally, I just loved the opportunity to write about two women in STEM and their postdoc work. And I told Wilson Rankin and Knowlton that I appreciated reading a new paper covering fieldwork that concluded six years ago. My own dissertation research from 2011-2013 is just reaching publication now too. As they write, “Patience and persistence are the two key words when it comes to getting your research published.” Wilson Rankin and Knowlton shared this reflection on the triumphs and low points of the journey from fieldwork to award-winning publication: “We both came onto this project as postdocs, and supervised the data collection for the three years of field research. After that we both went on to other positions, and thus had to balance writing up manuscripts from this research with the demands of new positions. Once submitted, this manuscript went through the revision process, which took some time but we are all pleased with the end product. In general, our advice to others would be to not be discouraged during the review process or its pace, as you can always improve a manuscript and the reviews are meant to help you improve your work.” Somehow, this magical paper also brought some timely advice into my email inbox as I head into a summer of writing up first drafts of my own postdoc papers. I welcome this nice reminder to keep grinding, and to keep working with some of my fabulous peer-collaborators as they embark on new adventures and new jobs in the coming years. And of course, I am now more excited than ever to spend some time in Hawaii with conservation researchers this fall!

Reference:

Wilson Rankin EE, Knowlton JL, Gruner DS, Flaspohler DJ, Giardina CP, Leopold DR, et al. (2018) Vertical foraging shifts in Hawaiian forest birds in response to invasive rat removal. PLoS ONE 13(9): e0202869. https://doi.org/10.1371/journal.pone.0202869

Banner image: photo by Jessie Knowlton.

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In 1953, ichthyologist Kay Lawrence joined a research expedition searching for fossils in the Amazon Basin. This was the same year that Rosalind Franklin left King’s College in London, after she created the X-ray diffraction image of DNA that was shown to Watson and Crick without her approval or knowledge. Lawrence was the only woman in a team of five scientists, and the only one without a PhD, or at least the only one who was not referred to as “Dr.” in the publicity materials for the expedition. Her fieldwork hit some snags — not the least of which was a foreboding black lagoon and an amphibious monster that fell in love with her and her extremely scientific white bathing suit.

Yes — Kay is actress Julia Adams and the amphibious monster is the Creature from the Black Lagoon. But there’s also a Rosalind Franklin figure in Creature from the Black Lagoon, and like Franklin, her contributions were obscured, overshadowed, and openly questioned for decades. Mallory O’Meara brings the story of Milicent Patrick, the makeup artist and special effects designer behind the Creature, to life in a fun and funny new biography, The Lady from the Black Lagoon: Hollywood Monsters and the Lost Legacy of Milicent Patrick.

Creature movie poster: flickr, Creative Commons

O’Meara grew up loving horror films and she was over the moon when she learned that her favorite movie monster, the Creature, was designed by a woman named Milicent Patrick. The world of horror is dominated by men, and so even though O’Meara only knew the barest details, she clung to Patrick as a patron saint of representation. In her introduction, O’Meara writes:

“Milicent was holding a door open for me that I never realized I had considered closed. Come on, she said. We belong here, too.
I accepted her invitation. I make monster movies for a living. I produce them, I write them. Over the years, I searched for information, for anything that could tell me more about her. For all of my adult life and film career, Milicent Patrick has been a guiding light, a silent friend, a beacon reminding me that I belonged.”

O’Meara’s book is wonderful and engaging. She pieces together the lost legacy of her horror icon and takes the reader along on the research journey. I listened to the audiobook and fell in love with O’Meara’s voice which is somehow both welcoming and acerbic, irreverent and admiring. And, from the beginning, I was struck by how well the world of science mapped onto The Lady from the Black Lagoon’s world of science fiction. The story of why Milicent Patrick’s legacy was lost turns out to be completely banal, standard issue sexism and O’Meara deftly places this history in the context of the #MeToo movement.

“So many women share this experience, women in every profession. We’re ignored, sexually harassed, talked down to, plagiarized and insulted in and out of the workplace. It’s worse if you’re a woman of color, a queer woman, a disable woman, a transwoman and worse still if you’re a combination of any of these. I don’t know a single woman working in my field, or any creative field, or any field at all, who cannot relate to Milicent Patrick. It’s not just her story. It’s mine, too.”

I love O’Meara’s description of Patrick’s process during the design of the Creature: “for inspiration, Milicent researched prehistoric animals: reptiles, amphibians, fish. She specifically looked for illustrations of animals from the Devonian period, which is when the Creature claw fossil in the film is from. The Devonian period, about four hundred million years ago, was the time period when life began to adapt to dry land from the sea. She spent weeks sketching out designs.” I had no idea The Creature from the Black Lagoon built a myth from this core kernel of scientific truth. Aside from this deep dive into a specific monster origin story, O’Meara’s book is not a science story*. But, I spent much of the book’s treatment of women in the film industry thinking about women in STEM.

The Book! Cover illustration by tattoo artist Matt Buck

When O’Meara compares Patrick’s Hollywood to her own experiences in film in the 21st century, the resemblance of these narratives to the past and present in STEM fields is eerie. O’Meara began her project because the idea of Milicent Patrick — a woman working behind the scenes in horror films — embodied such an important possibility to her in a field where otherwise she did not see herself represented. But, as she uncovered uncomfortable truths about Patrick as a person, she had to grapple with how to portray an imperfect personal hero. “The problem with being the only woman to ever do something is that you have to be perfect,” she laments. “When I found out about her as a teenager, I thought that for Milicent to be the first and only woman to ever design a famous monster, to be one of the first female animators, she had to be superhuman. She had to have been better than any other woman who ever wanted to design a monster. She had to have been the only one worthy enough to enter that boys’ club. This way of thinking is a mal-adaptation women have developed over the years to be able to deal with the fact that we’re getting passed on for jobs because we’re female. You force yourself to believe that there just haven’t been any women good enough for the job, rather than accept the fact that the entire system just doesn’t want you in it.” This is the hip, feminist-forward biographer’s way of saying that the water is not responsible for fixing the leaky pipeline.

I have my own Milicent Patrick, only her name is Annie Sawyer Downs. She left behind just enough of a scientific legacy that I’m awed by her botanical prowess and totally frustrated by the blanks in her life story. Like O’Meara, I’ve considered this woman to be “a guiding light, a silent friend, a beacon reminding me that I belonged.” O’Meara opens her book with the story of her Milicent Patrick tattoo — and, even before you read Chapter 1, you see the beautiful cover art for the book, which was created by her tattoo artist. On the Literary Disco podcast in March O’Meara explained: “When you get a tattoo of someone, you become a sort of information kiosk.” O’Meara later describes an exchange with a librarian at USC’s Cinematic Arts Library: “I even sheepishly rolled up my left sleeve to show him the tattoo of Milicent and the Creature. I’m so deeply invested in this project that asking me about it is like asking a new parent to show you pictures of their baby.”

Me and my Milicent, Annie Sawyer Downs, photo by Kate & Keith photography

I don’t have a tattoo of Annie Sawyer Downs, but I did name my kid after her. Asking me to show you pictures of my baby is literally asking me to dive into the story of my Milicent Patrick. I loved following O’Meara’s journey as she tracked down the pieces of Patrick’s life because I’ve done that too — I finagled an invitation to the Maine summer house that Annie Sawyer Downs’ built, I found her herbarium specimens at Harvard, I read through her collaborator’s field notes and could not help but notice that after she mentored him for the better part of a decade he went on to found a botanical club that did not admit women as members. I’m so happy that O’Meara got to write the book on Patrick — and I really did love this book — but I found the whole experience of listening to it to be bittersweet, and not just because the misogyny that ended Patrick’s career still hangs over Hollywood — and everywhere else. It was bittersweet for me to watch someone else find their Annie Sawyer Downs, tie up the loose ends, and bring a full story to light because I don’t think I’ll ever be able to do that for Annie. Annie died almost a century before Milicent Patrick, her trail is colder, her work is less renowned, there is no cult following of Rhododendron canadense forma albiflora like there is for the Creature**. And, as much as I feel Annie deserves a book like The Lady from the Black Lagoon, I know there are countless fully erased BIWOC in my field who didn’t even get to leave behind a name, let alone a trail of breadcrumbs, for future historians to follow. And so, once again Milicent Patrick is a kind of singular woman — a stand in for a whole suite of women who have given the faintest glimmer of representation to my generation, a small hope that we could see ourselves in them, even if we couldn’t read their full story in a book or Wikipedia page. Maybe I can’t have that for Annie, but I’d love to read the story of another ecologist’s Milicent Patrick figure next — write that book and/or send me your recommendation!

Banner image: Mike Souza, Creative Commons

*Still, some science creeps in to the science fiction, for example in O’Meara’s footnote on page 19: “Sally Ride became the first American woman in space in 1983. Kathryn Bigelow became the first woman to win an Oscar for Best Directory in 2010, the first and only. Sixty women have been to space. It’s harder for women to get into Hollywood than it is for us to get to space.”

**There definitely should be more botanical cult classics.

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How to Write About the Science You (and Others) Did.

I bought Stephen B. Heard’s The Scientist’s Guide to Writing at ESA in 2016. I was a soon-to-be sixth year PhD student with one publication (my master’s thesis) and zero written dissertation chapters. Maybe not exactly zero — there were chunks of methods paragraphs from grant proposals, and a super-rough-draft of chapter 1 shared with collaborators from another university — but close enough that my plans to defend in the spring were borderline comical. I needed writing advice and a structured plan: The Scientist’s Guide to Writing was my magical guidebook, my used Potions textbook annotated by the Half-Blood Prince. I read it methodically, one chapter at a time, and it worked — by March I had four chapters and a viable defense date. I received other lucky breaks besides the perfect reading material: a postdoc fellowship provided motivation to finish the PhD, my parents hosted a writing retreat for my last chapter; there were awesome babysitters, baristas who slipped me extra shots of espresso, and committee members who provided prompt and constructive feedback along the way. But, I still turn to reading when I need help writing.

Earlier this month I covered my favorite new advice papers on How to Do the Science. This week — my favorite recent papers on How to Write About the Science You (and Others) Did: Dr. Scott Hotaling’s Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience and Dr. Emma Sayer’s The anatomy of an excellent review paper. I like the contrasting perspectives here: Hotaling as a newly minted PhD explains the context for getting the writing done — creating a habit of writing and organizing tasks — while Sayer provides critical advice for the writing that must be accomplished once you have achieved Hotaling’s headspace and you are deep into drafting a review paper. Hotaling’s system will get you to the desk; Sayer’s will polish the word document that’s languishing in your Review Paper file.

Hotaling’s Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience began as an informal pep talk: he was a postdoc with a good publishing record and grad students in his new department turned to him for advice. “I realized that, like me in graduate school, the students knew they needed to be writing papers (or their thesis) but they didn’t know where to start from a practical standpoint,” he explains. “So, I decided to write down my approach to working to at least give students a jumping off point. When I started looking in the literature, I realized that much of the existing advice came for more senior academics and was often much more cynical than I felt was necessary. Ultimately, I felt I could fill a need by offering my own positive, but realistic, take on how to be productive in graduate school. Once I began writing it, I realized that it should really be a more holistic perspective with advice for being productive mixed with good practices for developing (and maintaining!) collaborations, taking care of your mental health, etc.”

Though Hotaling offers advice that seems more universal and traditional (journals have been publishing writing advice to grad students for a long time) than how to do urban ecology work on private property, I wondered if he ran into the same resistance (3x rejected) from journal editors that Dyson had experienced. “It was difficult!” Hotaling agreed. “I reached out to a number of journal editors and received replies that varied from encouraging rejections to one editor who essentially asked why I wasted my time writing something so useless. Ideas in Ecology & Evolution was the first journal I formally submitted the manuscript to and it wound up being a great home for it.”

Sayer’s advice paper zooms in on writing an excellent review paper. She wrote to me: “To give you a bit of background – I’m a big advocate for the importance of effective science communication. I do a lot of work with early-career researchers on presenting science in various formats to different audiences.” Sayer’s advice paper is built on a deep history of this work. “I started creating guides for the British Ecological Society when I was a postdoc – I’ve written guides on giving talks at conferences and designing science posters (the latter is now used as the society’s guidelines). Within a couple of years of starting my own research group, I had students and postdocs from 7 different countries and many of them struggled with the same aspects of science writing. I compiled a short guide for them, which turned into The British Ecological Society Short Guide to Scientific Writing (and will be published formally in Functional Ecology this year). In the meantime, I had taken on the role of reviews editor for Functional Ecology. Based on the success of the “Short Guide” and my experience in handling review papers from different subdisciplines, the other editors asked if I would try to write a guide for review papers…”

Most of the authors I talked with for this blog post wrote their advice papers as grad students — they were writing the paper they wanted to read early in their careers — but Sayer writes from a more established point in her career. I asked if she thought writing review papers is just a topic that requires more experience. “In this case, yes, having greater experience certainly helped. I’ve always preferred reviews that synthesise information and create something new from the published literature, but it wasn’t until I became Reviews Editor for Functional Ecology that I realised how useful a set of guidelines would be. We learn to summarise information but synthesising it is much harder and is quite an abstract concept to explain to someone.” I too have noticed this steep learning curve between being able to summarize the literature, and being able to add something to the conversation. I first read the short and sweet (three pages!) The anatomy of an excellent review paper early in the group-writing phase of my own review paper (Berend et al. 2019, accepted!). I found myself returning to our google doc with new eyes (which, in an inside joke to myself, I named “Box 1-tinted glasses”) and re-structured our outline around central concepts.

In Part 1 of this series Dr. Ziter had reflected, “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.” Similarly, Sayer wrote The anatomy of an excellent review paper from the perspective of a PI reminiscing on resources she wished she could have had earlier. “I initially wrote the Short Guide to Scientific Writing for my research group – partly because it described the kind of research papers I wanted to read, but also because I would have loved something like that when I started writing.”

Both Hotaling and Sayer felt that the peer-review process added value and reach to their advice. Hotaling writes, “I chose to publish it as a peer-reviewed paper for two reasons. First, I wanted reviewer input on the paper. I received extensive feedback from my lab and academic friends, but it was important that it also be reviewed by people outside of my day-to-day sphere. It’s a very a personal paper and I needed to know that people who didn’t know me personally still found value in the paper. I’d like to add that the reviewers of the paper (Drs. Meryl Mims and Robert Denton) were exceptional and their feedback greatly strengthened the final paper. And second, from a more practical perspective, it was better for my own career that it be published as a peer-reviewed article.” Sayer echoes, “First and foremost, [peer review] ensures quality – the content has been scrutinised and improved in response to feedback, which gives the reader more confidence in the advice. Then there’s the question of recognition – a lot of work goes into writing guidelines, and thousands of authors have downloaded the paper. It may not attract citations, but it’s still important that the contribution is acknowledged. Last but not least, publishing guidelines as a peer-reviewed paper or editorial makes them much easier to find.”

Since Sayer’s advice emphasizes how to structure a paper, I asked if she had leaned on other advice papers for guidance on structure or tone — essentially, what peer-reviewed advice influenced her presentation of peer-reviewed advice. “There are quite a few papers about writing reviews in other subject areas that I cited in the guidelines.” Here, I need to point out that the short references section in Sayer’s paper is an excellent resource for nerds like me that strive to read their way into better writing. Sayer notes that all of the references contain great advice, but no single paper contained all the information she wanted — that’s why she wrote hers! Her own favorite/favourite advice paper is subject-specific: “I give all my students the 1991 paper by Eberhardt and Thomas on Designing Environmental Field Studies (Ecological Monographs 61:53-73) – it gives a great overview of experimental design and introduces lots of important considerations for developing field work. My other favourite is a book, rather than a paper, but it’s a great read and incredibly useful for communicating research: Made to Stick by Heath and Heath (Random House).”

I asked Hotaling about his favorite advice papers too. We have similar learning styles — he says, “I read a lot of similar papers while writing my own. I particular enjoyed John Smol’s 2016 Some advice to early career scientists: Personal perspectives on surviving in a complex world for its clear, conversational perspective and that paper was a big reason why I ultimately submitted my article to the same journal (Ideas in Ecology and Evolution). Beyond academia, I also drew inspiration from Stephen King’s 2000 memoir “On Writing” and specifically his approach to a regular, ritualistic writing routine. If there’s one takeaway from my paper that I hope early career scientists will try out, it would be developing a regular, daily writing habitat. It’s staggering what such a simple practice can yield in terms of productivity and, at least for me, satisfaction with my work. By writing every day, I feel far less stressed about finishing things and more able to balance my work and life in a healthy way.”

I’m drawn to advice papers, in part, because they can ameliorate imposter syndrome; they say, of course you don’t know this yet, but here, I have given you a guide and you can quietly take this pdf to your favorite chair, curl up with a mug of tea, and have an introvert’s field day. Good advice papers can be a kind of pensieve — the instrument in Dumbledore’s office that allowed wizards in Harry Potter to share their memories, and immerse themselves in each others’ past experiences. I love these particular pensieves and the stories behind their publication — thank you so much to Drs. Dyson, Ziter, Broman, Hotaling, and Sayer!

References:

Sayer, E. J. (2018). The anatomy of an excellent review paper. Functional Ecology, 32(10), 2278–2281. http://doi.org/10.1111/1365-2435.13207

Hotaling, S. (2018). Publishing papers while keeping everything in balance: Practical advice for a productive graduate school experience. Ideas in Ecology and Evolution, 11, 1–12. http://doi.org/10.4033/iee.2018.11.5.f

Banner image: photo by Nic McPhee, Creative Commons

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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.

References:

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

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Recently, I was wrapping up some revisions on a phenology paper and to comply with the journal’s style for taxonomy, I needed to know the authority on a species of white violets that a Maine hunting guide had noted in his diaries in the mid-twentieth century. Obviously, I turned to Wikipedia.

Last minute checks on Latin names and authority are a huge part of my Wikipedia page views

Ecologists who study phenology (or anything!) use Wikipedia all the time, but Dr. John C. Mittermeier and his coauthors take this practice to a whole new level in their paper A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation. This study, published in PLoS Biology earlier this month, uses Wikipedia page views to trace when humans show seasonal interest in the natural world. For over 30,000 species in 245 languages —which amassed 2.33 billion pageviews between July 2015 and June 2018 — they found some strong seasonal signals linking how and when people interact with plants and animals online.

“The idea for this study happened somewhat by chance to be honest,” Dr. Mittermeier confides. “I was collecting Wikipedia pageview data on different animals as part of another study (hopefully this should be published soon!) and on a whim I decided to plot a time-series of daily views to see what it looked like.” As an ornithologist, he was drawn to migratory bird data and his whimsical time-series plot for migratory bird page views peaked near its ecological migration season. This was the prototype for a figure in the PLoS Biology paper. Mittermeier says, “this [plot] made me curious as what other plants and animals might show seasonality in their views and how widespread these patterns might be in general.”

Fig 1. Daily pageviews in English-language Wikipedia for nine bird species from Mittermeier et al 2019

While searching for migratory birds on Wikipedia seems categorically different from actual birding, Mittermeier and his colleagues found strong correlations between these two activities. They compared trends in Wikipedia page views to eBird records. In this analysis, eBird frequency records are like “outdoor pageviews” of bird species. “It was easy to match the eBird taxonomy to the taxonomy used by Wikipedia,” Mittermeier says, “and the way in which seasonal abundance information was structured in eBird is very accessible.” Birders, like Wikipedia users, are surprisingly great at generating big data.

Just under half of the bird species in the dataset had page view patterns correlated with seasonal eBird records. But, for species that occurred in more than one of the four language/countries (Italy, Germany, Sweden, and the U.S.), just over a third showed a significant positive relationship between eBird frequency and pageviews across multiple languages. All of the countries in this analysis are in the northern hemisphere and experiencing basically the same seasons, so I asked Mittermeier if this result indicated that some birds are more “seasonally famous” in one location? He agreed that “some species do seem to be more “seasonally famous” than others, meaning that certain species may be viewed more as seasonal indicators. This could be a result of the behavior of the species (i.e. something about their seasonality is particularly visible and obvious), some sort of cultural context (maybe the species featured in a well known book or fairy tale and had a seasonal association there, for example), or some sort of combination of both of these. Comparing how seasonal indicator species are similar or different across languages would be a great way to gain insight into what leads to a species acquiring this significance. I think this is a fascinating question and one that would be very interesting to explore further.”

Fig 2. Effects of culture and phenology on the seasonality of interest in species. English-language pageviews (logged) for great white shark Carcharodon carcharias (purple) are relatively stable throughout the year but show a brief spike during the days when “Shark Week” was aired on television by the Discovery Channel (days highlighted in purple). From Mittermeier et al 2019

But, the paper is not limited to birds, and human interest in animal and plant Wikipedia pages is not always aligned with ecological events. Figure 2 shows a spike in shark species page views that aligns with Shark Week. There are cultural drivers to the phenology of when humans search out certain species on Wikipedia. Mittermeier shares that, “The Wild Turkey was actually the first page that I looked at in relation to cultural events. Turkeys have such a powerful association with the Thanksgiving holiday in the United States I was curious as to whether this would impact people’s online searches (it does as we show in the figure!)” When the turkey hunch worked out, Mittermeier started brainstorming other cultural or marketing events associated with plants or animals that could impact online interest. “This was right around the time that Shark Week was going on over the summer and that’s why I decided to check if that had an impact on pageviews for Great Whites.”

While the eBird community is full of self-proclaimed bird nerds, and eBird data has been used in peer-reviewed papers for over a decade, the programming around Shark Week has a decidedly different relationship to science and natural history. Dr. David Shiffman, a Liber Ero Postdoctoral Fellow in Conservation Biology at Simon Fraser University, studying how information related to sharks is spread on the internet, notes, “Shark Week has a well documented problematic relationship with the truth, spreading nonsense to its massive audience that I and other scientists have to spend years correcting.” I asked him what he thought about the Wikipedia-Shark Week connection that Mittermeier and coauthors uncovered. He says, “the temporary spike in public interest in sharks that Shark Week causes is something that the marine biology community takes advantage of to spread actual facts. This paper provides further evidence that scientists wishing to engage in public outreach about their area of expertise need to know their audience, and know that there are times of year when people are more likely to be receptive to learning about that topic!”

Indeed, these seasonal patterns in interest — whether for migratory birds, Thanksgiving turkeys, or sharks — can be leveraged by conservation practitioners to affect policy and outreach. Research into the public attitudes about species, including how they rise and fall seasonally, is important. Mittermeier and his coauthors write: “Seasonal changes in human interest in plants and animals can have an important role in conservation in at least three ways: (a) by identifying species for which phenology forms a component of their “value,” (b) by helping to reveal differences or similarities in how species are valued across cultural groups, and (c) by providing temporal awareness to help maximize the effectiveness of conservation marketing campaigns.” I’ve experienced this myself in a small way: when I publish papers on spring wildflowers in the dead of winter, the press releases don’t get much traction.

And finally, I had to address the paradox of scholarly work based on Wikipedia. I’ve TA-ed intro Biology labs and scrawled “not peer-reviewed” next to many Wikipedia-base citations in lab reports. Mittermeier laughed with me, “My mother used to teach junior high school and was always telling her students not to cite Wikipedia and now here I am using it as the source for my research.”

Reference:

Mittermeier JC, Roll U, Matthews TJ, Grenyer R (2019) A season for all things: Phenological imprints in Wikipedia usage and their relevance to conservation. PLoS Biol 17(3): e3000146. https://doi.org/10.1371/journal.pbio.3000146

Banner image: photo by Steven Zwerink, Creative Commons

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PLOS Ecology Community | Researchers dis.. by Caitlin Mcdonough Mackenzie - 4M ago

This is a deep dive into my own research — the backstory behind a single line in a recently published paper and the data-driven trip down memory lane that was spurred by an innocent question from Reviewer 2.

This research took place on Wabanaki land. I want to respectfully acknowledge the Maliseet, Micmac, Penobscot, and Passamaquoddy tribes, who have stewarded this land throughout the generations. I am certainly not the first person to devote time and energy to tracking seasonal changes on Mount Desert Island.

This week one of my dissertation chapters, ‘Trails-as-transects: phenology monitoring across heterogeneous microclimates in Acadia National Park, Maine’ was published in the journal Ecosphere. In this project, I pulled the space-for-time trick and hiked three mountains repeatedly to collect a lot of phenology observations across diverse microclimates. The mountains in Acadia are not huge — these granite ridges roll up from the Gulf of Maine and top out at 466 m — but my transect hikes were between 4.8 km and 9.7 km each, and I wore out a pair of trail runners each season. I took to heart Richard Nelson’s advice: “There may be more to learn by climbing the same mountain a hundred times than by climbing a hundred different mountains.”

A couple months ago, in our second round of reviews, Reviewer 2 noted, “I think that it would be useful for those wanting to replicate your transect-as-trails approach (especially land managers) to know approximately how many person hours it took to complete a transect observation, here in the main text or in the appendix.”

A screen shot of my fulcrum app data collection

I had a magnet (which is apparently also available as a coaster) hanging next to my desk in grad school: over a silhouette of a golden retriever with three tennis balls in its mouth, it reads: “If it’s worth doing…it’s worth overdoing.” This magnet perfectly describes my response to Reviewer 2. I sent a back-of-the-envelope estimate to my coauthors, but I couldn’t shake the feeling that the precise person hours per transect was a knowable statistic. In addition to my field notes scribbled into weatherproof notebooks, I had collected my data via fulcrum, a smartphone app that automatically recorded the time of each observation. From my cache of fulcrum csv and xlsx files, I should be able to automatically pull the time of the first and last observation of each transect. The 10.7 MB of data in my fulcrum files represented four years of field work, hours and hours on the trails, slogging through rain, snow, and sun, training field assistants, combing through patches of lowbush blueberry and mountain cranberry for the first, hidden open flower. I became obsessed with the idea of seriously calculating person hours per transect, but I was increasingly convinced that a single number would be meaningless. I also realized that I lacked the coding chops to deal with my messy raw data: 171 files, each with 77 columns, usually containing data from a single transect, but occasionally comprising half a transect (when we had to bail due to weather) or more than one transect (when I ran ambitious double-days, or my field assistants and I split up). I turned to Porzana Solutions, and Auriel Fournier expertly helped me unlock my person hours data.

Over 177 the hikes in my fulcrum files, the mean time between first and last observation is 3.51 hours.

Three and a half hours does not even begin to tell the story. This blog post is my second supplemental appendix. Here is the story of person hours per transect — the lead time, the pregnant field season, and the phenology of phenology monitoring.

Before the first observation and after the last
There is a lead time in every transect hike. After rolling out of bed, pulling on the same old running shorts, race tshirt, and powder blue sunglasses, after packing the same handful of granola bars, dried papaya, and sharp cheddar, zipping my phone into its waterproof case, and slinging my backpack into the passenger seat, after driving to the trailhead and placing my research permit on my dashboard, there’s still a gap between the start of the fieldwork and the first official observation of the day. Especially as the summer crowds began arriving in June, I had to get out early to grab a spot at the limited parking by the north or the south end of Pemetic, or else add some extra miles from a spillover lot*. Even at the best parking spot, the approach to the Sargent South Ridge trailhead requires navigating 0.7 miles of carriage roads between the car and the trail on every hike. When I started the project in 2013, the Sequester kept Park Loop Road closed late into the spring season. For the first six weeks of fieldwork, I walked along the empty road to access Cadillac North Ridge, and Pemetic North and South Ridge.

The transect hikes were 4.8 km (Pemetic), 9.2 km (Cadillac), and 9.7 km (Sargent) up the North Ridge and down the South Ridge or vice versa (all of the mountains had uncreatively named north and south ridge trails). So at the end of a transect, I was 4.8, 9.2, or 9.7 km away from my car. I could run the carriage roads to connect the trailheads after Sargent or Pemetic (a 6.6 km run post-Sargent, and 7.2 km run post-Pemetic). From Cadillac South Ridge, a run up Route 3 to park loop road got me back to the north ridge trailhead in 10 km. Sometimes I arranged rides with friends to skip the run, and when I had funding for field assistants in 2015 and 2016 we often carpooled to drop a car at the finish line for each other. (There were some benefits to this running routine — in 2014 I won free ice cream after placing third in my age group in the Acadia Half Marathon.)

Running the half marathon at my field site after a season of the elite plant phenology training program known as, park your car, hike a transect, run back to your car.

The person hours per transect statistic is limited because not every transect was a straight shot. Sometimes we had to bail 3km into a hike due to bad weather and finish the transect another day. Once, one of my field assistants took a wrong turn and recorded phenology observations on the wrong trail down Pemetic, and so I went back, retraced her steps, and picked up the right trail the next day. Once, I did a wild two-a-day and in the middle of Cadillac, I ran down the Canon Brook Trail, looped through the Pemetic transect, and then ran back up the Cadillac West Face Trail to finish Cadillac. Once, I had a friend in town and we caught a ride to the summit of Cadillac and then enjoyed the leisurely hike down the south ridge with my eight-month-old in the baby backpack.

While the time between first and last observation averaged just over 4 hours for Cadillac, 2.5 hours for Pemetic, and 3 hours and 40 minutes for Sargent, those times discount the bookends of the hikes. As much as I’m railing against the answer to my query here, the process of working with Porzana Solutions to calculate these times has been incredibly rewarding. I feel like I’m getting to know my both raw data and the tidyverse in a weirdly intimate way that goes way beyond a standard tutorial.

The pregnant field season
In 2015 I was 17 weeks pregnant at the start of my field season. In addition to my daughter, I was also joined in the field by two field assistants. According to the Porzana analysis, I hiked less than half as many transects in 2015 (15) compared to each of the two previous years (2013: 35** hikes, 2014: 37 hikes). I actually hiked 20 transects that year — my assistants were entering the data (and getting credit for the hike in fulcrum) while we hiked together in the beginning of the season***. On my solo transects in 2015, I felt sloooooow. I averaged thirty minutes slower than 2013 and 2014 on Cadillac, 50 minutes slower on Pemetic, and 22 minutes slower on Sargent. On top of this, I was covering less ground — in 2013 and 2014 I had monitored phenology in off-trail Northeast Temperate Network plots near my transects in an effort to compare trail-side phenology with forested sites that was ultimately cut from my dissertation. In 2015, I stuck to the trails.

I remember feeling pretty terrible at the beginning of most hikes that year. I had one favorite spruce tree on the south ridge of Sargent, and I can picture myself looking up through the needles on more than one occasion from my lie-down-spot while I tried to decide if a bite of granola bar would make me feel more or less nauseous. As I climbed above treeline and into the breeze the fog of morning sickness would lift, and as I hiked downhill, my daughter would do this funny little fetus-roll and kick in a way that I interpreted to be happy.

The last transect of 2015

Hiking while pregnant was hard, but it felt easier than grappling with the looming challenges of becoming a parent. I liked the hard of fieldwork, it was the kind of hard that I felt capable of conquering. I also loved being pregnant in Bar Harbor. It was my fifth field season in Acadia and I had this wonderful community of supportive colleagues and mentors at the park service and in town. I had a favorite yoga class, a favorite milkshake, a favorite iced chai and blueberry muffin spot. I also had two field assistants — my pregnancy fortuitously aligned with NSF funding! — and working with Ella and Natasha that season was great. The person hours per transect figure obscures my field assistants, folding us into each other and masking the time we spent training together on the ridges. It also hides my pregnancy in the averages. I want to recognize those extra 22-50 minutes: they were some of the best worst minutes of my PhD.

The phenology of phenology monitoring
The person hours per transect average doesn’t show the sprint finishes of June. I monitored thirty species (the paper highlights the 9 most common taxa) of spring-flowering plants. On the transect hikes, I recorded leaf out and flowering phenology. In April, this was a bit of a scavenger hunt, and I’d pour over thickets of shrub stems for the first sign of bud break, then in May I’d peek into each curled Canada mayflower leaf for flower buds. By early June, my plants had leafed out, and the flowering season was winding down. I knew the trails by heart, and the location of each focal taxa along the ridge was bright in my mental map; each transect became a point-to-point trail run between the last phenological hold outs. Did the rhodora finish flowering on Cadillac? Had the last sheep’s laurel buds opened on Pemetic? Were the blueberries beginning to ripen below Sargent’s summit?

As I followed the spring phenology, I grew faster, my calf muscles more defined, my appetite more voracious. Acadia’s steep climbs will whip you into shape. I remember in 2013 arriving in the field a month after passing my comps and feeling so sluggish after a winter of studying instead of running. In comparison, I ran hard in the winter of 2013-2014, set a personal best half marathon time in a trail race in March, and just cruised through the early season field work in 2014. Even in 2015, as I grew rounder each week, I also grew more comfortable with the trails. Hiking while pregnant became easier over the season, although I’m happy it ended when it did, because that trend was not sustainable into the third trimester.

I think about Reviewer #2 and I want to ask: do you mean the person hours per transect in April? Or at the end of June? What kind of mileage were you averaging before the start of the field season? Do you have any old hamstring injuries? Tell me about your field assistants. Do you like to stop for lunch at the summit or are you an on-the-go-snacker? Did you pack a couple bucks to buy a Harbor Bar at the Cadillac souvenir shop? Are you saving your energy for the 10k run at the end of the transect? Is the National Park Service well-funded in this year’s federal budget? How do you feel about stopping for a swim in Sargent Mountain Pond?

I love these questions because each one pulls on a thread winding through my Acadia memories. I hiked upwards of 125 transects between 2013 and 2016, and now that the paper is done, I’m a little sad to be shelving the fieldnotes for good. The trail runners that I wore are long gone, my field hat fell apart, most of my baggy race tshirts carried me through my second pregnancy and suffered for it. In the end, the idiosyncrasies of the hikes were smoothed and flattened into the sentence, “Each transect could be completed in under 6 person-hours.” This is both true and wildly circumscribed. Not unlike a well done chapter of a PhD dissertation.

The view of spring leaf out from Cadillac, Acadia National Park

*Acadia National Park actually closed the lot by the Pemetic North Ridge trailhead in 2017 and it’s now exclusively a bus stop for the island explorer, the free bus that begins running right as my season wraps up at the end of June.

**This doesn’t include hikes before I had figured out the fulcrum platform. There was “no” data on those hikes (nothing was leafing or blooming, no signs of budburst) and they only exist in my field note books.

***I hired three field assistants for this project and, concurrently, a common garden experiment. In 2014, Paul was my garden guy, but we also hiked two transects together and he hiked two solo. In 2015, Ella, Natasha, and I split the transect and garden work. Ella came back for most of the 2016 season and then I finished the two projects solo in June 2016.

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In this space, I’ve often shared my love for National Park-based research. I count myself among the researchers devoting time and energy to documenting how climate change affects the ecosystems and natural resources in U.S. National Parks; we study everything from pikas to forests, Joshua trees to birds. But, the underlying rate of warming in these National Parks was not on my radar and I had not given much thought to the climate exposure of National Parks versus the rest of the United States. It turns out, the parks are literal hotspots on the landscape.

Last fall, Dr. Patrick Gonzalez and coauthors from the University of Wisconsin published ‘Disproportionate magnitude of climate change in United States national parks’ in Environmental Research Letters. This study looked at historical and projected temperature and precipitation across all 417 U.S. National Parks. Between 1895 and 2010, mean annual temperature of the national park area increased at double the U.S. rate — parks warmed by 1.0°C (±0.2°C) per century, the rest of the U.S. land area by 0.5 °C.

Dr. Gonzalez is a forest ecologist and Associate Adjunct Professor at the University of California, Berkeley. He is also the Principal Climate Change Scientist of the U.S. National Park Service, but he answered my questions here under his Berkeley affiliation, not for the Park Service.

I asked why he wanted to study a spatial analysis of historical and projected climate across all 417 US National Parks. What was the motivation for expanding on the earlier work of researchers who presented similar findings for the 289 large parks in the National Park System system.

poster from Boston Public Library, Dorothy Waugh (artist), 1930-1939 (approximate), Creative Commons license

“Up until our research, the severity of climate change across all the US national parks was unknown.” Gonzalez writes. “The previous work had only looked at subsets of parks. I work at a national level and it is important for me to give national policy-makers scientific information that is robust and comprehensive. The time-consuming parts of the work were the individual analyses by park and the computational tasks of downscaling all available general circulation model output of future climate projections to 800 m spatial resolution, which had not previously been accomplished for the U.S.”

In addition to the climate exposure of National Parks, Gonzalez and his team considered climate velocities. Climate velocity is the speed at which a plant or animal will need to move, migrate, or disperse — usually north or upslope — to “catch up” to their climate as it changes. Gonzalez found an interesting paradox in climate velocities: the park lands have experienced extreme temperature and precipitation shifts, but they also show lower climate velocity than the U.S. as a whole. They point out that this does not mean that plants and animals in National Parks are not in peril: “The lower climate velocities in the national park area are an artifact of that indicator being calculated as horizontal movement of areas of constant climate. Climate velocity can underestimate exposure in mountains.”

The National Parks are more mountainous than the rest of the United States. This is a reflection of our unsystematic history of serendipitous-style protection; we collect the pretty places as national parks, without considering the underlying biophysical diversity, and mountains are very pretty places. So while moving a couple meters upslope might seem easier than moving hundred of meters north to track a suitable climate, this is often an oversimplification. “Despite the computational artifact, our results indicate that projected climate velocities in national parks could exceed maximum natural dispersal capabilities of many trees, small mammals, and herbaceous plants.” Gonzalez elaborates, “Any new protection of natural areas, whether close to or far from national parks, can add to global conservation of ecosystems for biodiversity and human well-being.”

I asked Gonzalez, if he had any thoughts on how your research could be interpreted for park visitors. I wanted to know if there is an effort to get this work not just to park managers on the ground, but to interpretive staff as well. “For national park interpreters, I’ve given many presentations directly to staff in individual parks, including interpreters,” he says. “I encourage all U.S. National Park Service staff to speak about the robust science of climate change and its human cause, which points us to solutions to saving America’s most special places.”

post from Boston Public Library, Dorothy Waugh (artist), 1930-1939 (approximate), Creative Commons license

Finally, I noticed that both this paper and the earlier National Park System climate exposure study, which covered 289 large parks, were published in open access journals. I asked if this was an intentional pattern and these research teams were hoping to reach managers who may not have access to peer-reviewed journal articles.

Gonzalez confirmed that, “the open access of the journal of course enabled a much larger audience to directly download and read the original work. This greatly benefited national park staff and other natural resource managers, to whom we aimed to provide information useful for conservation under climate change. Intense interest immediately developed – people downloaded the pdf file more than once a minute in the first 24 hours of publication.”

But their outreach was not limited to open access journals. Gonzalez points out, “public media published over 40 individual stories, including in the Washington Post, on page 1 of the San Francisco Chronicle, on public radio stations, and on television.” Gonzalez also wrote a concise summary for the website the Conversation. He says that the University of California, Berkeley, has greatly helped in the effort to reach natural resource managers by publicly posting the spatial data, and he directly provided customized analyses and maps for numerous individual national parks. Finally, Gonzalez writes, “I just presented the results to the U.S. Congress in a hearing where I testified on human-caused climate change in U.S. national parks. The open access of the journal was critical, but we engaged a broader effort to widely communicate the science.”

Thank you to Dr. Gonzalez and his colleagues for providing the climate data that underlies so much ecological research across the National Park System! And thank you for modeling effective outreach and impressive science communication*!

References:

Gonzalez, P., Wang, F., Notaro, M., Vimont, D. J., & Williams, J. W. (2018). Disproportionate magnitude of climate change in United States national parks. Environmental Research Letters, 13(10), 104001–13. http://doi.org/10.1088/1748-9326/aade09

Monahan WB, Fisichelli NA (2014) Climate Exposure of US National Parks in a New Era of Change. PLoS ONE 9(7): e101302. https://doi.org/10.1371/journal.pone.0101302

Banner image: photos by Jodi Kurtz, Via Tsuji, and Gabriel Millos, Creative Commons

*if I ever publish a paper that averages one pdf download every minute, I will throw the biggest party and give everyone temporary tattoos of the figures.

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