Ask us anything: how to keep up with the literature

A while back we invited readers to ask us anything. Here are our answers to the next question. We’ve paraphrased for brevity, click through to see the original.

How do you stay up to date with new papers and books in your field? Also, how do you store your references? (from Karin)

Jeremy: Re: keeping up with the literature, it varies, everyone does what works for them. Which for most people is some mix of traditional methods, like skimming journal ToCs, and newer methods like Google Scholar recommendations, recommendations from people on Twitter, etc. My advice is do what works for you. By all means try out different methods, especially if you feel like your current methods aren’t working for you any more. Ignore anyone who overgeneralizes from their own example and tells you you’re Doing It Wrong if you don’t filter the literature as they do. (Unfortunately, people will tell you this. More than one person has gotten weirdly upset with me on old comment threads for still using traditional filters like “keep an eye on what’s been published in leading selective journals”.)

Maybe also think about what it means to “keep up with the literature” or “stay up to date”. Think about why you read–what you’re looking to get out of it. For instance, I’m a community ecologist, but I make no attempt to keep up with all community ecology! Nor do I try to read all and only those papers on the topics on which I currently happen to work (spatial synchrony, the Price equation…). Rather, I read to keep the flow of new ideas coming into my head, and maintain my sense of where the field of ecology is going. Given the purposes for which I read, it makes sense for me to stay up to date mostly by skimming the ToCs of leading journals in general science, biology, ecology, evolution, and philosophy of science. I read the abstracts of papers that strike my fancy because of their titles and/or authors. Those papers include but definitely aren’t limited to papers on topics on which I currently work. And then if the paper sounds really interesting/important/up my alley, I read the whole thing, carefully (I rarely skim papers). I supplement this by looking at Google Scholar recommendations, by occasionally following up interesting-sounding references I happen across by chance, and by serving as a reviewer. I’m sure I miss some things that I would’ve wanted to read had I known about them. But that’d be true for any filtering method, so there’s no point worrying about it. As I said, all this works for me, but your mileage may vary.

Lately I’ve found myself getting antsy about how much time it takes me to skim journal ToCs, so I’m considering trying to set up some combination of keyword & author searches instead. I’m worried that this will unduly narrow my reading, so I’ll probably try it out in parallel with my existing system before I commit to it.

Possibly, at some point in future the whole idea of “keeping up with the literature” will become obsolete. But I doubt it. Science is a collective enterprise, so scientists will always have an interest in (i) reading the “best” stuff, where “best” is defined according to some criterion more universal than “whatever I personally happen to like”, and (ii) reading what other people are reading. So the methods by which scientists “keep up with the literature” will change, but I think scientists will still “keep up with the literature”. I have some old posts on this.

For books, I mostly browse the publisher booths at the ESA meeting every year and buy whatever strikes my fancy. And then try and mostly fail to get around to reading them.

I’m a terrible person to ask about how to store and organize references, because I do it in my head. I’ve never used reference management software (I twice purchased Endnote and then never used it). I believe I’m unusual in this. I keep waiting for somebody to tell me “I use reference management software X, it’s totally awesome, you should try it”, but I’ve never heard anyone rave about reference management software. Everyone I talk to seems to think of their own reference management software as the least bad option from a bad bunch. So the floor is open: which reference management software should Marin–and I!–use?

Brian: Jeremy covered most of the general issues, so I’ll just add what I specifically do:

  1. Getting electronic table of contents emailed to me from about my 10 favorite journals and skimming them when they come in. I will typically follow links to 3 or 4 articles and open the PDFS. I will skim the abstracts and print out 1-3 and put in my to read pile. I mostly read the to read pile on airplanes and when I have a lunch when I need a break from teaching and admin (since lunch is not exactly prime time for deep research).
  2. Google scholar – I took the time to tell Google Scholar my papers (i.e .created a profile). It now gives me very on target recommendations which I treat like #1
  3. Editing and reviewing – this might sound like cheating, but I do much reading through these routes. And the papers are all hand picked to be relevant to me and I get to say no when I want.
  4. Pick a subset of books (conferences like ESA where all the publishers are showing their wares is a good place) and actually read them. I try to read ~3 graduate/monograph level books a year (although lately I’ve been punching this goal through reviewing as well).

As for reference management, I have been using Endnote since my graduate student days. Its so easy. Find the paper in Google Scholar. Click on the Citation/Endnote link and its into Endnote permanently. Then hit Alt+2 and wham its in my paper and the bibliography is automatically formatted. There are plenty of other packages out there that are equally good or better. I’m not going to argue Mendeley vs Endnote vs etc. I use the one I have familiarity with. But unlike Jeremy, to me it is inconceivable not to use some reference manager. It saves me hours of a job that I would find incredibly unpleasant (typing bibliographies). That said, when I was in grad school I typed in every paper I read into endnote. Now I wait until I need to actually cite a paper and then just pull it in.

And just a note on what it means to keep up with the literature. For me you have to do several distinct things:

  1. Expose yourself to things outside your field
  2. Skim broadly within your field
  3. Read deeply a subset of papers (and books) (primarily within your field)

It seems to me a lot of people are over focused on #2 these days but I strongly believe #1 and #3 are very important.

30 thoughts on “Ask us anything: how to keep up with the literature

  1. All good advice. Glad to see that Jeremy doesn’t use a reference manager; – neither do I, so we’re both unusual. I started using Endnote years ago and then lost a whole database and never got back into it. I quite like re-formatting references for specific journals, I find it relaxing (that may make me sound even odder…)

    Two other ways that I keep up with the literature (though clearly this is not going to be so relevant for early career researchers):

    1. Don’t turn down opportunities to examine research theses; research students are always going to be more up to date (or at least they ought to be) and this is a good way to see what the latest ideas are in a field.

    2. Keep track of who is citing your work. It always amazes me when an active researcher tells me that they don’t bother to regularly check their citations. Why wouldn’t you? It’s not (just) ego – it’s a way of finding out how the work that you are publishing is being received and used in more recent literature.

    • ” I quite like re-formatting references for specific journals, I find it relaxing (that may make me sound even odder…)”

      It makes you sound odd because it is odd. 😉 But fear not; odd and unique are not synonyms:

      • I have been hand-formatting my references, but I have recently migrated to Endnote; it’s a lot easier and helps to save a lot of time!

      • Hand-formatting references sounds like a type of medieval torture to me. I’m solidly in the reference manager camp.

      • So you’re saying Jeff is a masochist? And that I’m more willing than I should be to keep doing things the way I’ve always done them?

        You might be right on both counts. 🙂

      • Hey, I’m still listening! That’s me and at least two others….

        As I said earlier I find re-formatting quite relaxing and I think (though I may be wrong) that it develops attention-to-detail and accuracy skills that are useful in other contexts.

        Also, somewhere on this blog I made a comment that I thought reference management software was responsible for perpetuating errors in references that then result in mis-citations on Web of Knowledge, etc. My suspicion is that this has got worse over time as people rely more and more on reference management software rather than their brains. By coincidence yesterday I spotted a great example of that:

        Ollerton, J., Cranmer, L. (2002) xxxxxxx Oikos xxxxxx

        was rendered in the reference list of a paper as:

        Ollerton, J., Cranmer, L., Northampton, U.C., Campus, P. (2002) xxxxxxx Oikos xxxxxx

        The last two “authors” are actually from our institutional address – University College Northampton, Park Campus! [UCN is the old name for University of Northampton].

        Now in theory that shouldn’t happen if an author’s reference management software is doing its job properly, but it does happen: errors are not uncommon, but (it seems to me) people often don’t check their reference lists after they have been produced by the reference management software. It also shouldn’t happen at the editorial production end of things, because references are usually cross-checked for accuracy, but again it does, even for top-end journals (in this case from the Royal Society’s stable!)

  2. Great ideas! For those who wants to receive updates from specific journals, I personnaly love RSS feeds. You can set-up the RSS feed in your email manager, like Outlook or Thunderbird. The great thing is that you can also receive feeds from your favorite blogs like Dynamic Ecology.
    Since my institution has Web of Science, I set-up an alert with my PhD keywords. Once a week, I receive new articles

    • I use ATOM/RSS heavily, too, but it’s limited depending upon the field. I principally subscribe to the feeds. I find it good for statistics (mine) and quantitative population/ecological biology (also somewhat mine). But I can imagine it might not be good for other fields.

    • I love using RSS feeds to keep up with new papers. I use feedly for most of the journals i read. It is a good way of reviewing multiple journals simultaneously as you just get updates on new papers. Regretfully many new journals do not add an RSS feed to their TOC

  3. My methods line up closely with Brian’s. Just a few addenda.
    1) Google Scholar Citations is great. One flaw is with seriously huge multi-author papers. It appears to concatenation the list to the first 20 authors or so.
    2) Keep a folder for new papers readily available on your desktop to minimize the effort it takes to save a PDF there. I make a new folder every year (Literature 2016, Literature 2015). When you read the paper is strangely important to memory.
    3) There at least 3 levels of reading, equally valid:
    –Read the title and download. This is a big one. Why let something potentially interesting swim away into the ocean of literature when with a few keystrokes you can put it where it can be found with a few more keystrokes?
    –Read the abstract. An hour spent reading abstracts is a good approximation of reading for breadth.
    –Read the paper (sort of). If something really gets me interested, it’s the Results, then Methods, first and last paragraph of Intro, first and last paragraph of Discussion. And of course the acknowledgements, which occasionally contain the seeds of a good academic soap opera.

  4. I’m in agreement with all of these approaches! As for reference management, I would recommend Zotero. I’ve worked with Mendeley, EndNote and Zotero. Zotero is free, only requires copying/pasting a DOI into it to get full reference details, and has plugins that work great for word (at least on mac). Works well enough that I’ve stopped looking for alternatives.

    • I like Zotero, as well. I add references via the browser plugin that lets me just press a button rather than via the DOI. The Cite While You Write plugin works well for Word on Mac, as mentioned, and also for OpenOffice. Another benefit is that you can create a free Zotero account and back up all your citations to their server. I set mine to sync automatically.

      I used EndNote in the past, and like Zotero much better. The only minor issue I occasionally have is that if you are adding a long list of citations it may take a minute or two to process.

      Jeff and company, you could still use Zotero to manage your citations but format each reference yourself. (You can also code a new format if the one for your journal is not in their database, although I have found the database to be pretty extensive.)

  5. I just read this on my phone while waiting for my computer to unfreeze itself, after it hung when I tried to install an EndNote update. Make of that what you will. 🙂

  6. Even if I never wrote a manuscript, I’d use a reference manager. I download far more PDFs than I actually read. So I use Zotero to organize these by topic and subtopic and subsubtopic. It never fails that after I peak into one of these subfolders I rediscover a paper and think “huh, I didn’t know that existed, I need to read it”. Any paper can be in multiple folders so it is easy to find these (unlike brick and mortar papers which can only physically be in one topic folder). I have folders for each research project and even potential projects. This way I don’t forget a citation when I’m writing a manuscript.

    A reference manager is especially critical if your (1) research has zero focus but is wildly diverse across disciplines, or (2) you teach introductory biology courses at a primarily teaching university, or (3) #1 and #2 combined.

    I use Zotero because it’s free. And I keep all my pdfs on the Zotero cloud so I can read these papers using my ipad, my iphone or any computer in the world that has internet access and a web browser. I do pay for the Zotero cloud (they give you some bit free but if you are a hoarder of pdfs you will quickly fill this).

  7. I don’t even try to “keep up”–I’m interested in several disparate topics, some not even ecological, and between the volume of papers coming out (in even one such) and a worrisome sense of a growing ADHD, the attempt just sends my mind into a spinning chaos and I then get depressed and even more non-productive that I already was. I also, quite often, get more out of things published decades ago than recent stuff; there are many important old papers or books that I am still not familiar with that I should be. An example from this week: going back and reading about Tyndall’s original GHG experimental setup (1959-62), due to claims on Twitter (by people who should know better), that someone else discovered the GHG properties of CO2 a few years before he did (wrong!).

    As for content reading, the only thing that works for me is a ruthless prioritization on the methods section. I friggin’ HATE the wordiness, poor construction and generally unimaginative language of most scientific papers; I find the dictionary a much more enjoyable read, seriously I do. After the abstract, I go straight to the methods–if they are not perfectly clear to me, end of exercise, I’m not reading the rest of that paper. Along those lines, I pay much more attention to online data repositories (DRYAD, ITRDB etc) than to papers. I can get my mind around exactly what those data represent, and whether they can address questions I’m interested in, or motivate new ones.

    I also don’t use a reference manager but I think this is probably a fairly large mistake. However, I was the last person I know to get a cell phone, and never did switch from a wood to an aluminum bat or get a “digitally remastered” version of any.

  8. I use a combination of glancing at everything published in my field and, uh, getting a bee in my bonnet and reading everything I can find to answer specific questions to keep up with the lit in my field. Since the questions that occur to me to ask are often weird and off-the-wall, this usually works fairly well for me–as long as I can suss out which keywords different disciplines use to discuss the topic, since I read in a whole bunch of fields when I’m doing that.

    Having used EndNote, Mendeley, and Zotero–I really love Mendeley and sing its praises fairly frequently. Like Zotero, it’s also free, and what I like about it is that I can just save all my papers in a folder and it’ll automatically watch the folder for me and import the PDFs. It also lets me take notes as I’m reading, either on the paper itself or in a text box alongside the paper, which I like because it helps me focus and integrate the paper’s content. (Men deley also has some cloud storage and the option to pay for more.)

    That said, while I know a lot of people with a wide variety of preferences on reference management, opinions on the best software, and intensity of feelings about ref management software…. I’ve never met anyone who loves EndNote. The closest I’ve come is people who use it out of inertia.

  9. I’ve never used Endnote, because it costs money. I use Zotero, which has come a long way in the past five years. There’s not much I don’t like about it. The early career folks I know are about equally split between Zotero and Mendeley. (I’ve never tried Mendeley only because I’m satisfied with Zotero. It might be awesome.)

    “the whole idea of “keeping up with the literature” will become obsolete”

    Ahem, already there:

    • Aaaaand… and in my pleasure reading tonight… if I may quote Vellend 2016:

      “Some rough calculations indicate that no fewer than 10,000 papers (and probably at least twice that many) relevant to the topic of this book [horizontal community ecology] have been published over the past decade. … You would need to read no fewer than four new papers every working day of your life just to be able to claim a comprehensive knowledge of this one subtopic of ecology.”

      So there you have it: “keeping up with the literature” is obsolete.

      • Depends what you mean by keeping up. I’ve never considered “read everything on topic/field X” to be synonymous with “keeping up.” So some of my apparent disagreement with you is probably just semantics.

  10. Pingback: Do reference management systems encourage sloppy referencing practices? | Jeff Ollerton's Biodiversity Blog

  11. One of my frustrations in accessing literature is the number of clicks between seeing a title and actually getting a saved PDF version of a paper. To me, it’s a real roadblock to my reading, though, perhaps because I’m just too lazy to invest the time on clicking. After seeing an interesting title in an emailed Table of Contents, I have to click to get the abstract, click to open the paper, click to convert to PDF, click to save. Often, I do this from home so after viewing the abstract I then have to log-in to my institution, which then requires me to find the paper again within the institutional vpn. I know if I could just get the PDF straight from the Table of Contents, I would probably be reading twice as many papers.

  12. Pingback: Guest post: Coding Club – trying to overcome the fear factor in teaching and learning quantitative skills | Dynamic Ecology

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