James and the Giant Corn Genetics: Studying the Source Code of Nature

January 6, 2012

Open Access and Ecologists

Filed under: Uncategorized — James @ 4:22 pm

Jonathan Eisen has a new post up on his blog “The Tree of Life” tearing apart a letter from the Ecological Society of America (link is to a pdf). In the letter, the ESA comes out against the government requiring that papers funded by federal research dollars must be made available for free online after a set amount of time has passed since publication. Jonathan Eisen, one of the strongest voices in the open access movement, naturally finds this position disturbing. But why would a scientific society come out against the open dissemination of information? Here is my — entirely speculative — explanation.

First a little bit of background: right now research funded by the National Institutes of Health must be made freely available online within twelve months of publication. This can either mean publishing in an “open access” journal, or publishing in a traditional journal which allows the authors to deposit their results into a free online archive like PubMed Central after a year (something is pretty much all the biomedical journals do now, since not allowing it would mean almost no researcher should still publish papers in those journals). This mandate has worked out so successfully that it may end up being extended to all federally funded research (which means research funded by agencies like the Department of Energy, the USDA, and the National Science Foundation).

Ecologists who receive federal funding would almost never be funded through NIH, but they certainly might receive grants through DOE (bioenergy), USDA (integrated pest management), and they’d be most likely to receive money from NSF. So the Ecological Society of America, which also publishes a number of ecology focused journals, is confronting the idea that many of the articles it publishes may have to be made freely available online a year after publication. It seems that they fear letting people get access to research papers without paying to subscribe to their journals will mean a lot of universities will stop subscribing and without that money:

…the Society could not continue to provide the peer-review and editorial services needed to produce high quality scientific publications.

Now there is a whole separate argument I’m going to put to the side for now: Would  placing papers online a year after publication would really cause universities to start dropping their subscriptions to ecology journals? (This clearly hasn’t been the case in the biomedical field, but the Ecology Society makes some points about how their field might be different). I honestly don’t know the answer. But for the sake of argument, let us say that the Ecological Society of Americas fear are well founded.

The most common way for journals to offset the loss of income from subscriptions is to implement what is known as the “author pays” open access model, where the authors of the paper pay the journal a set fee if their article is accepted for publication, and the article is freely available online from day one. The arguments for the “author pays” model (as opposed to open access itself which has more good arguments going for it than I can count) go a bit like this:

  • Since universities already take a large cut out of any grants researchers receive as “indirect costs” to pay for — among other things — journal subscription fees, the journals are making money off of the authors’ grants, and at least this way researchers don’t have to continue paying for access to an article once it is published.
  • Many journals already charge hundreds or thousands of dollars for papers that have color figures, too many pages, and/or more than a set number of supplementary materials. So clearly scientists can find the money to pay for having their papers published when they need to.
  • Almost all reputable open access journals have policies in place which waive publication charges for authors who simply cannot pay.
So why does the Ecological Society of America just move its journals to an “author pays” open access model? Well I can only speculate and I’m not even an ecologist. But my best guess is because most ecology labs are incredibly poor. There may be a few rockstar labs out there, but in my experience the vast majority of ecology grad students end up having to work as teaching assistants to pay for being in grad school since their professors have no grant money to fund them. In their “spare time” these students write lots and lots of tiny grant proposals (many to private foundations), picking up a few thousand dollars to fund some experiments here, and a few hundred dollars to fund traveling to a conference there.
If a grad student is particularly lucky she (or he) might win an NSF graduate research fellowship, which will pay for their tuition and salary while they conduct research for three years,** or an NSF Dissertation Improvement Grant (which award tiny amounts of money by the standards of molecular biology but which can be stretched out to fund a significant amount of in ecology research). In both cases though, the funding is won by the graduate student, not the professor, and the the university is not permitted to scoop up any of the money as indirect costs. So it would not surprise me at all if the “journal subscription” portion of the indirect costs from grants that ecology departments bring in do not cover the costs of subscribing to ecology journals.***
So what about the second argument, that clearly authors can find the money to pay for color images and extract pages, so what’s wrong with making them pay simply to publish their article? Well if you’ve ever read ecology literature you will now that figures are without exception in black and white (making papers published yesterday look like something out of the 1970s), and papers always always respect page limits.
And while I agree that the we-only-charge-you-to-publish-if-you-can-afford-it model does a lot to defuse worries about “author pays” models distorting the scientific record, it simply isn’t the solution for journals devoted to a field where almost every lab could make a good case for not having the money to publish.
It’s not clear there is even a problem yet. It wouldn’t surprise me at all if universities aren’t nearly as eager to drop their subscriptions to ecology journals (and make their faculty wait a year to read the latest scientific results) as the Ecological Society of America apparently fears. But I have no trouble at all understanding why the field of ecology isn’t as enthusiastic about implementing “author pays” open access as fields without so many grad students (and whole labs) working with little or no funding.
h/t to @PlantGenetGenom the twitter feed of Frontiers in Plant Genetics and Genomics, the open access (and author pays) journal that published one of my first papers.

*One alternative for-profit conferences (like PAG) already exist, but the atmosphere at these meetings is very different and because registration costs more (and housing since they tend to be held at more expensive locations) many labs can’t afford to send as many people (or anyone) as they can to other meetings.

**It should be noted that some ecology departments have mechanisms in place to punish students who win outside funding to cover their salaries, such as giving them last choice of which courses to teach in the years when their salary is not being covered by outside agencies.

***In which case the cost of subscribing to ecology journals is either being subsidized by other, better funded departments, or offset by the tuition payments of undergraduate students who sign up for ecology and evolutionary biology courses in droves (if only we could get undergrads as excited about plant biology!).


  1. All very reasonable, but how come (cash strapped) earth sciences (inc. ecology?) lead the league table of open access adoption? These OA adoption statistics really surprised me!

    Comment by Will Spooner — January 6, 2012 @ 6:01 pm

  2. And excellent point William. Also an illustration of the risks of building entirely speculative stories in the absence of data.

    I would guess earth scientists depend more on public shared datasets while the ecology labs I know tend to be doing fewer things where reuse of data is possible. But that is just adding even more anecdote and speculation.

    Comment by James — January 6, 2012 @ 6:09 pm

  3. […] James and the Giant Corn – Open Access and Ecologists […]

    Pingback by Why doesn’t the Ecological Society of America allow their Open Access content to be text mined? « I wish you'd made me angry earlier — January 7, 2012 @ 2:29 am

  4. I take your point that under the current economic models, there may not explicitly be cash for OA in many ecology projects. However, it is a zero-sum game in reality since all publishing costs are ultimately funded by grants and universities. So while economics can be seen as the proximate cause for why OA is not taking off in disciplines like ecology, it cannot be the ultimate cause.

    My view is that the deeper cause is sociological, and related to the role that Learned Societies have evolved to play in academic fields, especially Society’s that are perceived to publish the high-impact journals in a particular field. In fields like Ecology, where there are effectively no OA journals to submit to (besides BMC Ecology & PLoS ONE), Societies can maintain a guaranteed subsidized revenue stream via their stranglehold on the publishing market by rejecting OA.

    Societies fear OA since it disrupts the Society’s economic base, not because it disrupts the Journal’s economic base. PLoS and BMC prove that journals can be economically sustainable under OA. What is at issue here is the potential risk of OA to kill off the classical cash stream that support Societies. And like any bureacratic class in government, universities, etc., Learned Society bureacracies will seek to protect themselves, even at the expense of the hands that feed them.

    What is needed is a broader discussion of alternative economic models for Learned Society’s that are not coupled to subsidies based on publishing closed access journals. If such alternatives are non-viable, then perhaps it is time to ask how Learned Society’s must adapt to the realities of the 21st century or if they are actually necessary at all.

    Comment by Casey Bergman — January 7, 2012 @ 2:47 am

  5. I agree with you that at the level of whole universities publishing/subscription costs are a zero sum game.

    But the point I was trying to make is that may not be true for individual disciplines. It very well could be that the cost of publishing Ecology journals is subsidized by overhead from other departments which are more successful at bringing in external sources of funding. So economic models that explicitly shift the cost of publishing to individual researchers from university libraries might be neutral or beneficial overall, but still bad for disciplines that have been benefiting from these sorts of hidden subsidies.

    In my own field (plant biology), the highest impact journals are published by the American Society of Plant Biologists. These journals haven’t moved to an exclusively open access model yet, however the ASPB (unlike the ESA) opposes the Research Works Act. There is clearly variation between different societies, although whether that is a result of the differences in the fields themselves, or just the views of the people who happened to be in power within different organizations when the OA movement burst on the scene is certainly open to debate.

    Comment by James — January 7, 2012 @ 1:46 pm

  6. Didn’t realize that the poverty of ecologists could hamper their progress towards adopting open access!

    Comment by Kulbhushan — January 7, 2012 @ 2:51 am

  7. И почему же экологические лаборатории такие бедные? Неужели все деньги уходят в генетику и медицину?
    Why is ecologycal labs so poor? Is all money off grants been getting geneyics and medics?

    Comment by Kitaev — January 7, 2012 @ 12:36 pm

  8. Once more I should first say everything I am saying is complete speculation. I’m not an ecologist. But yes, there is less grant funding available for ecology research (relative to genetics or research with medical implications). A second issue is that there are so MANY ecology labs (even small liberal arts colleges can support them) and so many undergraduates who want to study ecological questions in grad school — and are willing to put up with having to TA all the time to get that chance. So the funding for ecology is spread very thin.

    Comment by James — January 7, 2012 @ 1:56 pm

  9. Interesting set of ideas. I would be very curious to see how funding breaks down by field when looking at grant money / number of papers (do ecologist actually have less funding per paper they publish).

    I have discussed this topic with the editor of a subscription based ecology journal, he has an interesting take. When journals are subscription pay based they have incentive to only accept high quality material; they want to attract as many subscribers as possible. With an authors pay journal the incentive is go take in as many papers as possible. Because of this there are fears that the average quality of papers would suffer as a result of a journal going open source. Of course this is more black and white then reality but is one source of resistance to going open access.

    Comment by Greg — January 11, 2012 @ 7:20 pm

  10. Well what I can actually back up with evidence is that ecology labs have less funding per student, and that the students who go on to be hired for tenure track positions in Ecology and Evolution have a ridiculous number of papers by the time they are hired. Based on a 2009 study in an (obscure) Ecology journal, the average tenure track hire in the field already had 12-13 papers (7-8 of them as first author). doi: 10.1560/IJEE.55.4.381 N=119, but it’s better than no data at all. The handful of recent plant genetics hires I’ve been able to track down have ~1/2 those publication stats.

    I’m honestly surprised the issue the editor you were talking to brought up doesn’t get discussed more. Aside from a little amount of discussion about “predatory” for-profit open access journals no one seems to be talking about the change in incentives “author-pays” models bring about. I’m really excited to see how “eLife” does when it launches, since it’ll at least initially be operating under a “philanthropy pays” open access model.

    Now if only we could get enough such funding to cover all of science, we’d really be set… 😉

    Comment by James — January 11, 2012 @ 7:50 pm

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