Downsides of writing harder: musings on the need to pace myself

When I was thinking about whether to try to be more social about how I write, I thought about how I can run harder and further and faster and without it seeming so hard if I run with a friend. That was one of the things that led me to start a writing accountability group with some friends and to set up a write-on-site session once a week, as I described in Monday’s blog post. I think these changes have led me to write more. That’s a good thing, right?

In the weeks since adopting these new approaches, I’ve started to wonder about possible downsides. To go back to my running analogy: I can run further and faster and harder with a friend – but might end up getting hurt in the process if I push myself too much. Last week, I ran with a friend and was so distracted by our conversation that I didn’t notice that I had forgotten to put on a brace that I’m supposed to wear while I run. My back noticed, though, and that night it let me know that I had overdone it. I had to take a few days off from running afterwards to recover.

Clearly pushing myself harder while running can backfire – could the same be true of writing?

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Journals have a responsibility to ensure ethical oversight of mental health research (and we do not currently have evidence that grad students are 6x as likely as the general population to have depression and anxiety)

I care deeply about mental health in academia (and have blogged about it in the past, including here and here and here). Given that, I was really interested when a recent paper by Evans et al. came out on graduate student mental health. However, when I read it, two things stood out to me: it didn’t mention IRB approval, and the most striking conclusion – that graduate students experience anxiety and depression at 6x the rate of the general population – is not supported by the study. The key messages of this blog post are:

  1. the authors did have IRB approval to do this work, but Nature Biotechnology did not know that when they published the study. The editor of Nature Biotechnology claims that, since they published this in their Career & Recruitment section, it is not a research article and therefore didn’t require peer review or questions about IRB. This is problematic, as the study is clearly written and presented as presenting new findings, and journals have a responsibility to ensure ethical oversight of work they publish.
  2. While the Evans et al. paper claims “Our results show that graduate students are more than six times as likely to experience depression and anxiety as compared to the general population,” that claim is not supported by their study. Their survey was not a representative sample of the graduate student body (it was a voluntary survey, distributed via social media and email), but they compare it to a representative survey of the general population to get the 6x statistic.

Again, I want to be clear: the authors did have IRB approval for the work, but I only know that because I wrote the authors directly (after being dissatisfied with the responsiveness at Nature Biotechnology), and Nature Biotechnology did not know they had IRB approval when they published the study. In addition, this study does not provide evidence that grad students are six times as likely as the general population to experience depression and anxiety.

Graduate student mental health is really important, so we need to get as accurate a picture as we can of the current situation regarding graduate student mental health. As discussed below, a study (by Levecque et al.) with a more carefully controlled comparison group found a 2.4 increase in risk in graduate students compared to the highly educated general population. This is definitely something that is still a problem and that still needs to be addressed, but it’s not a 6 times greater risk.

To expand on these points more:

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New paper on science community blogging!

I really don’t want the blog to turn into a platform for announcing personal papers, but this is another case that seems worthy of an exception. I am a coauthor on a paper that just appeared in Royal Society Open Science that focuses on science community blogging as an important type of blog. In the paper, we make the distinction between two types of blogging: science communication blogging and science community blogging. Science communication blogging is traditional scicomm: communicating science broadly, with non-scientists as a typical audience. Science community blogging, on the other hand, focuses on the process and culture of academia, with other scientists being the primary audience. Dynamic Ecology is pretty much entirely science community blogging. Some other blogs mix the two, and some are solidly on the science communication side of things. One of our arguments is that science community blogging is valuable, even though it often gets overlooked in discussions of science blogging. One piece of evidence supporting the assertion that science community blogs are overlooked: the Wilcox et al. book, Science Blogging: The essential guide, does not mention science community blogs, despite aiming to provide a comprehensive overview of science blogging.

Our new paper (which is open access so available to everyone!) discusses the reach of science community blogs and their value to the scientific community, including as a means of diffuse mentorship and as a means of contributing to scholarly discourse. The diffuse mentorship aspect of blogging is a key reason I blog. I think science community blogs are a great way of ensuring broader access to information that some people have but others do not (such as my post on how to format a CV for a faculty job application or Jeremy’s on how North American search committees work or Brian’s post on the five pivotal paragraphs in a paper). I also think science community blogging is a great way to raise issues that I think are important to consider (such as my posts on not needing to work 80 hours a week to succeed in academia or on being a scientist with an anxiety disorder). At this year’s ESA meeting, a surprising (to me) number of people thanked me for talking about these issues; my favorite may have been the person who stopped me and said “Thank you for being a real person!” This feedback meant a lot to me.

Our blogging paper was led by Manu Saunders of Ecology is Not a Dirty Word; she deserves a lot of the credit for this paper seeing the light of day! The other authors on the paper are Amy Parachnowitsch and Terry McGlynn from Small Pond Science, Margaret Kosmala of Ecology Bits, Simon Leather of Don’t Forget the Roundabouts, Jeff Ollerton of Jeff Ollerton’s Biodiversity Blog, and Stephen Heard of Scientist Sees Squirrel. Simon, Jeff, and Steve were the ones who had the idea for the paper in the first place.

The abstract of our paper is below the break, as are links to posts at the other blogs:

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Last and corresponding authorship in ecology: a series of blog posts turns into a paper

My paper on last and corresponding authorship appeared in the journal Ecology & Evolution today. Normally I don’t plug my papers on the blog, but this one is different: this paper arose out of a poll and a series of blog posts on the site, so it seems appropriate to wrap things up with a quick post today.

I suppose it’s actually not quite accurate to say the paper arose out of a poll. Before that, I had a tweet storm as I thought through issues, and that, in turn, was motivated by needing to decide on author order for a manuscript. When I was at Georgia Tech, I was told that I should be last author on all papers coming out of my lab as a sign of having driven the work. But I have a paper from work I did as a grad student where I am the last author (with my advisor as a middle author) because I did the least work on the project (Cáceres et al. 2008 Freshwater Biology), so the advice I got at Georgia Tech surprised me at first. At Georgia Tech, I was also told that I needed to be corresponding author on papers out of my lab; when I first got to Michigan, I never heard anyone mention corresponding authorship as something that mattered (and that included when I directly asked a couple of people about it). Notably, though, in the past year I did hear colleagues bring it up a couple of times.

I almost gave up on this paper multiple times, because I wasn’t sure it was worth the time. But I kept hearing comments from colleagues at various institutions about author order or corresponding authorship coming up as an issue, especially related to tenure & promotion discussions, so it seemed important to get this information out there in a format where it could easily be shared.

What did I find? This is the abstract of the paper:

Authorship is intended to convey information regarding credit and responsibility for manuscripts. However, while there is general agreement within ecology that the first author is the person who contributed the most to a particular project, there is less agreement regarding whether being last author is a position of significance and regarding what is indicated by someone being the corresponding author on a manuscript. Using an analysis of papers published in American Naturalist, Ecology, Evolution, and Oikos, I found that: 1) the number of authors on papers is increasing over time; 2) the proportion of first authors as corresponding author has increased over time, as has the proportion of last authors as corresponding author; 3) 84% of papers published in 2016 had the first author as corresponding author; and 4) geographic regions differed in the likelihood of having the first (or last) author as corresponding author. I also carried out an online survey to better understand views on last and corresponding authorship. This survey revealed that most ecologists view the last author as the “senior” author on a paper (that is, the person who runs the research group in which most of the work was carried out), and most ecologists view the corresponding author as the person taking full responsibility for a paper. However, there was substantial variation in views on authorship, especially corresponding authorship. Given these results, I suggest that discussions of authorship have as their starting point that the first author will be corresponding author and the senior author will be last author. I also suggest ways of deciding author order in cases where two senior authors contributed equally.

If you’re interested in finding out more, the paper is open access. Something that is fun is that this is the first paper to appear in Ecology & Evolution’s new paper category, Academic Practice in Ecology and Evolution. Also fun is that, after acceptance, the production staff required that I add an author contribution statement to my sole-authored paper. So, I wrote: {continues below the break}

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Is my latest paper a super-cool result? Or merely a “cute” curiosity? You tell me!

My collaborators and I just published “Population extinctions can increase metapopulation persistence“. New Scientist did a piece on it, which is the first time any media outlet other than my local newspaper has written up my work. I’m chuffed about this, because I think this is the coolest paper I’ve ever done by some distance.

Or, maybe it’s just a cute result–a fun curiosity. I could even imagine someone arguing that it’s oversold fluff. So why do I think it’s so cool? And what’s the difference between “cool” and “cute”?

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On finding errors in one’s published analyses

Dan Bolnick just had a really important – and, yes, brave – post on finding an error in a published study of his that has led him to retract that study. (The retraction isn’t official yet.) In his post, he does a great job of explaining how the mistake happened (a coding error in R), how he found it (someone tried to recreate his analysis and was unsuccessful), what it means for the analysis (what he thought was a weak trend is actually a nonexistent trend), and what he learned from it (among others, that it’s important to own up to one’s failures, and there are risks in using custom code to analyze data).

This is a topic I’ve thought about a lot, largely because I had to correct a paper. It was the most stressful episode of my academic career. During that period, my anxiety was as high as it has ever been. A few people have suggested I should write a blog post about it in the past, but it still felt too raw – just thinking about it was enough to cause an anxiety surge. So, I was a little surprised when my first reaction to reading Dan’s post was that maybe now is the time to write about my similar experience. When Brian wrote a post last year on corrections and retractions in ecology (noting that mistakes will inevitably happen because science is done by humans and humans make mistakes), I still felt like I couldn’t write about it. But now I think I can. Dan and Brian are correct that it’s important to own up to our failures, even though it’s hard. Even though correcting the record is exactly how science is supposed to work (and I did corrected the paper as soon as I discovered the error), it still is something that is very hard for me to talk about.

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Why am I a scientist again? – The concept of a data present

(This is a guest post from Isla Myers-Smith, early-ish career academic at the University of Edinburgh, with a conversation at the end with Gergana Daskalova, an undergraduate in her lab)

data_present

Sometimes I like to worry about why I have chosen a scientific career path and the meaning of life and big esoteric questions that really have no particular answer. I have wondered many times why do I push myself so hard to succeed in science? I know the pipeline is leaky for early career scientists and many choose to leave the Ivory Tower to make different contributions with their careers, but at least for now, I have stuck with the halls of academia and here is why.

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Where do ideas come from, and what counts as “novel”?

Note from Jeremy: this is a guest post from Mark Vellend

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During my very first research experience in ecology (mid-1990s), Graham Bell, a famous evolutionary biologist, talked about the forest plants we were studying as if they were essentially just large and slow versions of the algae multiplying rapidly in the highly simplified test tubes of his lab. The other undergraduate field assistants and I (the “Carex crew”) – all of us thrilled to have paid jobs to tromp about in Wild Nature – felt that this perspective sucked all the beauty and wonder out of the forest that we so loved. But it stuck with me.

This is a second guest post expanding upon thoughts and some personal reflections that arose while I wrote a book on community ecology during sabbatical last year. The first post is here, and I couldn’t help noticing that it was given the tag of “New Ideas” by Jeremy. Hmmm…I wonder how we decide whether an idea is “new”? I think the answer has rather important implications for how we judge papers and the scientists that write them. All the top journals want “novelty”, but what is that exactly? And where do ideas come from in the first place?

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Another attempt to stop or steer the phylogenetic community ecology bandwagon

I’m a bit late to this, which is embarrassing because I was involved in it. Back in May, Functional Ecology published a special feature (well, they call it an “extended spotlight”) on community phylogenetics. I helped edit the special feature, along with Anita Narwani, Patrick Venail, and Blake Matthews. Here’s our introductory editorial, which basically argues that phylogenetic community ecology has gone too far down the well-trodden road dead end of trying to infer process from pattern and that it’s high time for a course correction.

If it sounds rather like some old blog posts of mine (e.g., this and this), well, that’s no accident. It’s because of those old posts that Anita and Patrick invited me to join the team (they were the driving force behind this, having organized the symposium this special feature grew out of). So there’s a tangible benefit of blogging to add to the rather short list–you might get mistaken for an expert and invited to edit a special feature. 🙂 That my involvement in this project grew out of my blogging is my tissue-thin justification for posting about it.

The four papers in the special feature are quite different in terms of the specific topics addressed and the approaches used to address them. But they’re all nice examples of contrarian ecology, pushing back against the current conventional wisdom.

Kraft et al. use modern coexistence theory to rethink and make precise the disturbingly-popular-for-such-a-vague-idea notion of “environmental filtering”. They then review the literature and find that most studies of “environmental filtering” don’t actually present evidence of environmental filtering, properly defined. They argue that current vague usage of the term overstates the importance of abiotic tolerance in determining community composition. A nice example of something I’ve been thinking about a lot lately–how attempts to quantify vague concepts often just paper over the vagueness, leading to confusion rather than insight. One consequence of their argument (which I agree with 100%, btw) is to undermine a recently-proposed method for generating simulated datasets structured by a specified strength of environmental filtering. Which is kind of a funny coincidence, because the lead author of that method also wrote one of the papers in this special feature.

Gerhold et al. challenge the idea that the phylogenetic relatedness of co-occurring species can be used to infer the mechanisms driving community assembly. They point out that this idea depends on numerous strong assumptions that are weakly supported at best. They suggest more useful things that ecologists can do with phylogenies besides trying (futilely) to use them as a convenient shortcut to discovering community assembly mechanisms.

Venail et al. show, contrary to some recent claims, species richness, not phylogenetic diversity, predicts total biomass and temporal stability of total biomass in BDEF experiments with grassland plants.

Finally, Münkemüller et al. use evolutionary simulations to show that commonly-used measures of “phylogenetic niche conservatism”, such as phylogenetic signal, actually are very hard to interpret, and often are highly misleading guides to the underlying evolutionary processes governing niche evolution.

It will be interesting to see if these papers have much impact. I predict that Venail et al. will. It’s a comprehensive review of a purely empirical topic, and so I think it will quickly become the standard reference on that topic. The impact of Münkemüller et al. is harder to predict. My guess is it’ll get cited in passing a lot, but that people will mostly keep doing what they’ve been doing on the (dubious) grounds that there’s no easy alternative. I think Gerhold et al. and Kraft et al. will have little impact, unfortunately. They’re telling community ecologists to abandon an easy-to-follow recipe that purports to allow inference of process from pattern. Community ecologists only reluctantly abandon such recipes. But a minority of ambitious community ecologists will recognize that there’s an opportunity to do really-high impact work by following the lead of Kraft et al. rather than by following the crowd.

The editorial and the papers are open access, so check them out.

Old school literature searches and the fun of reading classic, non-English literature

In my post last week, I pointed out that I haven’t read nearly as much in the past semester as I’d hoped to read. But I did read some things! In fact, as far as I can tell, I think that, during the course of the semester, I read every paper that has been published (and one that hasn’t been) on parasites that attack developing embryos of Daphnia. This has been a lot of fun. First of all: how often can you say that you think you’ve read everything that’s been written on a topic you are studying?* Second, it’s felt like a classic, old school literature hunt, and that’s been a lot of fun.

Since I was a grad student, I’ve seen Daphnia infected with a parasite that attacks the developing embryos. As a grad student, I initially would record it as “scrambled eggs” in my lab notebook, since I tried to use names that were evocative. (This also led to parasites named “scarlet” and “Spiderman”.) Over the years, I started simply referring to it as “the brood parasite”. It was something I was interested in doing more on, but I didn’t have the time and knew I would need to collaborate with a mycologist to do the work well.

Fast forward approximately 10 years to when I arrived at Michigan. Here, I’m fortunate to have a fantastic mycologist colleague, Tim James, who was game for helping me figure out what the parasite is. We recruited a first year undergraduate, Alan Longworth, to help us work on the project. In the end, the parasite has proved to be really interesting. We have our first manuscript on it in review right now.

One of the key things we wanted to do with the initial brood parasite project was figure out what the parasite was. Microscopy and molecular analyses indicated it was an oomycete, but not particularly closely related to anything that had been sequenced previously. We started thinking about what we might name it if we decided it was a novel species (twitter had some great suggestions focusing on mythological characters that killed babies!), but I also wanted to really dig into the literature.

The first two, most obvious sources to consult were Dieter Ebert’s excellent book on parasites of Daphnia, and a classic monograph by Green on the same topic. Dieter’s book has relatively little coverage of brood parasites, though does point out that they are common and highly virulent. The Green monograph mentioned a “fungal”** parasite, Blastulidium paedophthorum. To cut to the chase: all the evidence points to our brood parasite being Blastulidium paedophthorum. That’s a lot to keep typing (or saying!), and it’s too good to pass up on the opportunity to use “Bp” as the abbreviation, as that works for both the scientific name (Blastulidium paedophthorum) and the common name we’d been calling it (brood parasite). So, we’ve declared the parasite Bp.

Backing up again, the description of Bp in Green seemed like a good fit to what we were seeing, so I wanted to read everything I could about the parasite.*** This started me down a path of reading some really old papers, nearly all of which were in foreign languages. Bp was first described by Pérez in 1903, with a follow up paper in 1905. I was kind of blown away that I could easily download these from my dining room! Chatton had a paper on Bp in 1908 (also available from my dining room table!) After that, it was featured by Jírovec in his wonderfully titled 1955 paper. (The title translates to “Parasites of Our Cladocera”. I love the possessive “our”! 🙂 ). And then, crucially, it was the focus of ultrastructure work by Manier, reported in a paper in 1976.

All of the papers in the preceeding paragraph were important to figuring out whether we were working with the same parasite. None of them are in English. That added to the fun “I’m going on an old school literature hunt” feel, but also made it more challenging to read them.**** Reading them involved a combination of trying to remember my high school French, lots of time with Google translate, and, ultimately, seeking out translators. It was relatively easy to find translators for the French papers, thanks to a few people being really generous with their time. The Czech one, by Jírovec, took substantially longer to find a translator for, but a Czech Daphnia colleague, Adam Petrusek, was kind enough to put me in touch with someone who did a great job on the translation.

All semester, I’ve been thinking about how much fun this has been. Indeed, it’s part of why I really want to figure out how to set aside time to read more! But it especially came to mind after reading this recent ESA Bulletin piece by David Inouye on the value of older non-English literature. In that, Inouye talks about his own journeys through the older non-English literature, and concludes with this paragraph:

So my paper trail extends back to some of these early natural historians in Austria and Germany. Their work helped give me a much longer historical perspective than I would have had if I’d relied just on the English literature on ant–plant mutualisms, primarily from the 1960s on. Although as a graduate student I was able to track down the original publications from the 1880s in libraries, I see that some of this literature is now freely available on Web resources such as ReadAnyBook.com, the Biodiversity Heritage Library, or old scientific literature scanned by Google Books. And the translation from Google Translate I just tried with some of von Wettstein’s 1888 papers is certainly sufficient to follow most of the content. So perhaps the only barrier to familiarity with older non-English literature for ecologists now is the time required to find it. Time that might be well spent to broaden your perspective and make sure you’re not re-discovering insights from early natural historians.

I completely agree that the longer historical perspective – especially that provided by the non-English literature – has been essential. If not for those papers, we would think that this parasite hadn’t been described before and was in need of a name. And I clearly agree with the second-to-last sentence, which is very much in line with my post from last week (which I wrote before reading Inouye’s piece). So, here’s hoping we all find the time to really dig into the literature, and that, while doing so, we remember that there’s lots of value in digging into the classic, non-English literature.

 

* Okay, fine, it’s not like there are tons of papers on the topic. But it’s still fun to think I’ve read all of them.

** The parasite is an oomycete, and oomycetes are not fungi. But that wasn’t recognized in the early 1970s when Green published his monograph.

*** The references for this paragraph are: Pérez 1903, 1905, Chatton 1908, Jírovec 1955, Manier 1976; full references are given below.

**** I would absolutely love to be multilingual. Sadly, I am not.

 

References

Chatton, E. 1908. Sur la reproduction et les affinités du Blastulidium paedophtorum Ch. Pérez. Comptes Rendus Des Seances De La Societe De Biologie Et De Ses Filiales 64:34-36.

Jírovec, O. 1955. Cizopasníci našich perlooček II. Československá Parasitologie II 2:95-98.

Manier, J.-F. 1976. Cycle et ultrastructure de Blastulidium poedophthorum Pérez 1903 (Phycomycète Lagénidiale) parasite des oeufs de Simocephalus vetulus (Mull.) Schoedler (Crustacé, Cladocère). Protistologica 12:225-238.

Pérez, C. 1903. Sur un organisme nouveau, Blastulidium paedophthorum, parasite des embryons de Daphnies. Comptes Rendus Des Seances De La Societe De Biologie Et De Ses Filiales 55:715-716.

Pérez, C. 1905. Nouvelles observations sur le Blastulidium paedophthorum. Comptes Rendus Des Seances De La Societe De Biologie Et De Ses Filiales 58:1027-1029.