Answers to reader questions, part 2: our darkest moments, how we read, and more

For part 1 in this series, go here.

What was your darkest moment in ecology and what did you do about it? (from Margaret)

Brian: Hmm, I don’t have that crisis moment during grad school/postdoc like Jeremy and Meg have described. My crisis moment was after working in industry for 9 years (and having fun and intellectual challenge and good colleagues) I woke up and said “I’m helping telephone companies to target their junk mail”. Less than a year later I was back in graduate school. Fifteen years later, I still make half of what I was making then, but I haven’t really looked back. Within ecology, I would probably say it was after my first (and still I think my best) paper which was sort of a unified theory of many aspects of biodiversity science, when I realized Hubbell’s neutral theory had accomplished the same thing. Needless to say I liked my version better. But it made me think long and hard about what makes a successful theory and what makes a successful test of a theory (which resulted in another paper and another) – in short a rather productive crisis. One could say I am going through a bit of a career existential crisis right now. This is rather typical for people in their first year or two post-tenure (nearly everybody in my cohort I talk to is going through it). Figuring out “what I really want to do” instead of “what my P&T committee wants me to do”.  The freedom to blog is one such result. I have interests and at least a modicum of talent in basic macroecology research, applied research and administration. Or even how much time to invest in students vs. my own research. Haven’t really figured out what mix of these I want going forward. It’s kind of jarring to be a Type A personality with a clear goal and then to suddenly be turned loose to “do good work and make us proud (and rich)” which is basically what is expected of a post-tenure professor.

Jeremy: Meg and I have already written about our darkest moments here and here, respectively. Although mine wasn’t nearly as dark as hers; I was more sadly (but not too sadly) resigned. And unlike Brian, I’ve never really had the feeling that there’s no social value to what I’m doing with my life, or felt that it’s all been said and done before, or been seriously uncertain about what I want to do with my life. I’m sure some of that is down to personality. And like the Mighty Mighty Bosstones sang, some of it’s down to rarely having been tested. Through a combination of luck and ability (probably mostly luck), my professional life has rarely thrown at me situations I haven’t been able to handle (same for my personal life, actually…). And I hope some of it is down to me being self-conscious and thoughtful about why I do what I do. Not that I might not wake up one day and change my mind about what I want to do or why it’s worth doing. But if I did, I would be changing my mind, not suddenly becoming self-conscious for the first time about what I’m doing or why I’m doing it.

How much time do you spend per week reading the literature and books? Do you feel like you’re constantly learning and evolving your beliefs, or like you’re implementing your training? Any advice to grad students for balancing learning and doing? (from Sciencepseudonym)

Brian: The joke about a PhD is that you learn more and more about less and less. There is indeed a local optimum at just specializing and being really good at something. However, I think the best scientists find a different global optimum that involves finding some way to carve out time every week to read widely in the literature and be a perpetual learner. I think a grad student should spend close to 10 hours a week doing this in the early days (has to wind down a bit during field seasons, thesis writing time, etc). But I constantly remind my students this is more important than classes. As a postdoc I would say I spent at least 5 hours a week doing this. I still aim for something close although it might be 3-4 hours. I also find that a lot of the papers I read these days are either assigned (e.g. for my lab group or a class) or through my participation as an editor in the peer-review/editorial process. There are pros and cons. It is nice to have some filter that constantly bring papers interesting to me my way, but also restricting. I still spend time every week reading “random” papers from eTOCs. Don’t plan to ever stop. As for advice about how to do it – a) I love reading papers so its always a treat for me – its not that hard to find time, I just have to give myself permission to put some administrative function on the back burner, and b) as you advance in science, you will find time management is a really important skill – it is about putting things that are important like reading on your calendar along with the things you have to do like meetings. If your appointment calendar isn’t a representation of your priorities, then something is out of kilter (but different people have different ways of achieving this).

Jeremy: More or less what Brian said. I struggle to find enough time to read. I have a growing folder of pdfs on my hard drive that I want to read. I strongly second Brian that you need to find ways to maintain your breadth and read (not just glance at, read) interesting stuff that’s outside your immediate subfield and that you don’t have an immediate need to read. Brian’s methods–serve as a peer reviewer/editor, get assigned papers for lab group/reading group, scan the eTOCs of lots of journals (very different from filtering by keyword, BTW!)–are all ones I use. I also think it’s important to attend seminars–I always attend my department’s EEB seminars and grad student seminars unless I have a serious scheduling conflict, even if they’re on topics far from my own areas of expertise. I also attend conferences (the ESA every year, other conferences occasionally; wish I could go to more). Reading blogs, including ones way outside ecology, helps me too. A lot of my best ideas–and I’m talking ideas that have or will lead to papers, not just ideas for blog posts–have come from recognizing the relevance to ecology of ideas from outside of ecology. You need to keep the flow of new ideas coming into your head. Not really because you’re consciously looking for ideas for papers or grant proposals you could write. And not even because you’re trying to learn new things or keep up with the literature, although you will and you are. But just because you’re an academic. Ideas are your life! Reading and thinking isn’t a means to an end, at least not entirely–ultimately, it’s an end in itself.

What’s the single most beautiful, elegant, or intuitive piece of ecological theory after Darwin’s theory of evolution? (from Konsta Happonen)

Brian: I’d have to give the nod to the Theory of Island Biogeography. It’s not perfect. It is wrong in some ways. There are some things we still don’t know that really bug me (we never solved SLOSS!). But it arguably changed the whole perspective of what a model is away from the classic deterministic differential equation model to a much broader view allowing for stochasticity and dynamic equilibria. And it has done what a good theory should do – inspire field research and applied management impacts as well as additional theory development.

Jeremy: Am I allowed to say the Price equation, even though it’s just the (not “a”, the) mathematical expression of Darwin’s theory of evolution? And even though it’s not a “theory” in the conventional sense of making some assumptions about how the world might work and then deriving the consequences of those assumptions? If you won’t let me pick the Price equation, I’ll stump for the Lokta-Volterra competition equations. And I’ll also use this as an excuse to (once again) plug one of my favorite old essays, by John Maynard Smith, on the most beautiful and elegant idea in science that turned out to be totally wrong.

I also have a question for Brian, arising from his answer: Brian, the simplest version of the Theory of Island Biogeography most certainly is a classic deterministic differential equation! dS/dt=C(1-S/P)-eS where S is the number of species currently on the island, P is the (constant) number of species on the mainland, C is the total rate at which species from the mainland colonize the island (=cP where c is the per-species colonization rate), and e is the per-species extinction rate from the island. That’s just taking the simplest (and famous) graphical version of the TIB and putting it in equation form. And while you can of course regard this deterministic differential equation as an approximation to an underlying stochastic process, the same is true of every differential equation in ecology, including much older ones like the logistic or the Lotka-Volterra equations or whatever. So while I can totally see why you’d pick TIB, you lost me on the whole stochasticity and dynamic equilibria thing…

How do you organize your background reading for a paper? How do you decide what papers to cite, especially if there are many equally-suitable ones? Do you cite papers not only for their results, but also for speculative stuff in the Discussion? (from harisridhar)

Brian: I’m very old fashioned. I have a manilla folder devoted to each paper I’ve written. As I accumulate papers, I print them out and store them in the folder. And when I read a paper I write 2-3 sentences of the main points at the top of the first page. Aside from killing trees, many papers end up printed out multiple times and in multiple folders (and often with different summaries on them depending on the context). But this gives me one go to place where I can browse and organize. As for how I write – I tend to write without worrying about references. Everytime I come to a place where I know I will need a reference I just type “[REFERENCE]” or if I have a clue of the citation I’ll say “[MACARTHUR WILSON 1972 + MORE]” and keep on rolling without slowing down my train of thought. I only put in real references  in my 2nd or 3rd pass. I still use EndNote to organize my references because I know it well. Others use other packages that work equally well. But the key tip here is to use the “import citation feature” from Web of Science or Google Scholar to get references into these packages – there is no reason to ever type out a bibliographic entry by hand in this day and age.

As to what to cite – a major hobby horse for me – part of being a scholar is to know the history of the idea and cite the origin of the idea and any major milestones along the way. Absolutely drives me crazy as an editor/reviewer when I see a paper that only cities papers from the last 5 years. Makes me wonder if you’ve ever read a paper besides what you were required to read for classes. In this day and age of journals limiting citations you can’t get carried away. My general formula is to find the original citation, a good review, and if there is a paper that is recent and highly relevant (i.e. more specific than the review to my point), I will cite all three of those or some subset of those three depending on what I can find and the importance of the point.

And yes – if a discussion section of a paper led you to think about something a certain way you absolutely should cite it. Again being a scholar is about giving credit for the lineage of ideas (Newton’s we all stand on the shoulder’s of giants).

Jeremy: My reference database is in my head, mostly. I have a good memory for references. Not the full citation, but that so-and-so once wrote a paper showing such-and-such, back in year X or so. And I supplement that when necessary with the standard sorts of literature search methods–searching databases for papers on a topic, using the reference sections of reviews, seeing what papers have cited some classic paper on the topic, etc.

In terms of deciding what to cite from an over-lengthy list of candidates, I’m basically like Brian. I try to cite the original source, plus classic or key papers, plus papers that I personally happen to like or admire a lot. These days, I’ll often just cite the most recent review, plus maybe a small number of primary sources, rather than the lengthy lists of primary sources I used to prefer to cite. Early in my career, I basically used my citations to prove that I’d read everything, in part because I was a show-off about what I’d read (mistakenly thinking I’d read lots of stuff nobody else had), and in part because I imagined that referees would call me on it if I failed to cite even one relevant paper.

I cite papers for their results, not speculation, or if I do cite them for speculation I make clear that I’m doing so. In general, I am careful about my citations and I try to make very clear exactly what claim I am citing a paper for. In general, I don’t think ecologists are careful enough about this. Miscitations and vague citations are really common in the literature, something like at least 25% of all citations in ecology aren’t clearly correct.

Also, I’d just like to note that it’s possible Newton was being sarcastic when he wrote that line about standing on the shoulders of giants (seriously; Newton was not a man noted for intellectual generosity).😉

4 thoughts on “Answers to reader questions, part 2: our darkest moments, how we read, and more

  1. I’ve got to take issue with what Brian wrote: “there is no reason to ever type out a bibliographic entry by hand in this day and age.”

    Books, government reports, and the like aside, I’ve found that just importing Endnote references from Web of Knowledge (Scopus, etc) results in many different formats – sometimes the authors names are in all caps, sometimes the title. Scientific names have dashes between genus and species, periodical titles can be abbreviated. More often than not, I’d spend as much time fixing the formatting than if I had just opened the PDF and copied/pasted and typed things out.

    But citation / reference management is a whole other post …

  2. Nice post guys!
    For the last question re sorting references, theres a piece of software recently been written called Docear ( which integrates with Bibtex (via JabRef) and uses mindmaps. It scans through your pdfs for comments/highlights and imports them into an “incoming” mindmap from which you can move the note to other maps of your own design. Once the note is one of its monitored maps, Docear is clever enough not to import the note again. Each note is also linked to the bibtex reference so you can see which paper its from regardless of the actual filename. I really do recommend it!
    Its only real downfall is that if you have a lot of old pdfs with highlights, it probably wont detect them as you have to set up the pdf reader to create comments at the same time as highlights. Plus, it would take a long time to set up the mindmaps to your liking if you have loads of old papers.
    A great piece of software all the same, especially if youre just starting a PhD!

  3. Pingback: Answers to reader questions, part 3: what we’d say to Congress, tropical vs. temperate systems, and more | Dynamic Ecology

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