Show me the data!

I read some sad news on Twitter recently. The Ecological Society of America has decided to publish its journals with Wiley:

Whilst I think the decision to move away from their old, unloved publishing platform is a good one. The move to publish their journals with Wiley is a strategically poor one. In this post I shall explain my reasoning and some of the widespread dissatisfaction with the direction of this change.

Society journals should not be a profit-driven business

The stated goals of The Ecological Society of America (ESA) are noble and I reproduce them here below to help you understand what the society in theory aims to do:

  • * promote ecological science by improving communication among ecologists;
  • * raise the public’s level of awareness of the importance of ecological science;
  • * increase the resources available for the conduct of ecological science;
  • * ensure the appropriate use of ecological science in environmental decision making by enhancing communication between the ecological community and policy-makers


Reading those four bullet points, it strikes me that a society with this stated mission should be a vanguard of the open access movement. An efficient, well-implemented open access publishing system, supported (and thus empowered) by the ESA would positively address all four of those goals.

Do I need to explain how open access would improve communication among ecologists? It should be obvious to most. Some facts:

Universities around the world do not have access to all subscription journals, not even Harvard. Wiley’s big journal bundle of subscriptions is no exception to this rule. Brock University in Canada is one such notable example. ‘Ecology and Evolution’ is one of two “main themes” of Brock’s Biology Department yet it does not have access to the Wiley bundle of subscription journals.

Furthermore, as the above tweet demonstrates many ecologists are not based at universities. Not all uses or readership of ecology journals is by ecologists, it’s absolutely not sufficient to just provide access to ecologists (alone). It’s vital that policymakers and the public have access to the latest research, no embargoes. Want evidence that policymakers lack access to research? Look no further than this blog post from a recent intern at the UK Parliamentary Office for Science & Technology (POST):

The level of access to journals was far lower than I had expected (it was actually shocking) – I ended up using my academic access throughout my placement.

Source: (2015-01-12)

If the ESA seriously wants to “ensure the appropriate use of ecological science in environmental decision making by enhancing communication between the ecological community and policy-makers” then making it easier for policymakers like those at POST to access research published in ESA journals would surely be a great way of doing that. How does the ESA expect to “raise the public’s level of awareness of the importance of ecological science” if most of the science that they themselves publish in their own journals is behind an expensive paywall? $20 for 30 day access to one article? Admittedly that’s cheaper than many but it’s simply not supportive of ESA’s mission.

Does this help raise the awareness of ecological science?

Does this unnecessary paywall help raise the awareness of ecological science?


Lastly, with respect to increasing “resources available for the conduct of ecological science” the ESA urgently needs to consider the big picture here. Wiley, Springer Nature, Elsevier and other legacy publishers are a major drain on the financial resources available for research. With their big bundle deals they ransom/rent access to libraries for sums that can be up to many millions of dollars, every year, per institution. Money should instead be diverted into efficient, high-quality publishing systems like JMLR, Open Library of Humanities, PeerJ, Pensoft and Ubiquity Press to name but a few. All of these not only provide open access, but also high-quality publishing services at a significantly lower cost. Many provide added extras such as semantically-enhanced full-text XML which would make synthesis of ecological science easier. Wiley does not provide direct access to per article full-text XML even to its paying subscribers! They do half the job for thrice the price. Why would ESA want to help to sustain and enhance Wiley’s famous 42% profit margin? These legacy publishers are strategically merging, and acquiring journals in order to make it harder for libraries to cancel their dross-laden ‘big bundle’ subscription packages. It doesn’t seem like a logical decision to me or others.

Comparing this to other recent journal publishing changes

To put into context the ESA move to Wiley, let’s look at three other recent examples of academic societies changing publisher:

1.) Museum für Naturkunde Berlin journals (flipping to open access)

In 2014 all of their journals moved away from being published with Wiley. Their two zoological journals which have been around since before the ESA was even formed(!) transferred to open access publishing with Pensoft. Their Earth Science journal Fossil Record also moved away from Wiley, to open access publishing with Copernicus Publications. Guess what? The sky didn’t fall. I predict the articles in these journals will start being read, downloaded and cited more now that they are open access to everyone.

2.) Paleontology Society journals (switching to arguably a more benign, less profit-driven legacy publisher)

In 2015 PalSoc journals switched to be published with Cambridge University Press (CUP). I’m not super enthusiastic about CUP but if a society really wants to do legacy publishing, without worsening the stranglehold of the big publishing companies over libraries then CUP, or other university presses (Oxford, John Hopkins, Chicago) seem like safer custodians of academic intellectual property to me.

3.) American Society of Limnology and Oceanography (moving to Wiley)

To provide a fair comparison it’s important to look at what happens when a society journal joins Wiley. I know of one such case recently: ASLO journals. The transfer to Wiley was far from smooth or professional. In the few months that Wiley had the ASLO journals, they managed to ‘accidentally’ paywall thousands of articles that should have been available for free (as per ASLO’s wishes) and charged actual readers for reading these older should-be-free articles.  I paid $45.60 for access to one such ASLO article at Wiley – it should have been made available to all for free. Both Springer and Elsevier have also been caught doing this. The ESA currently makes some articles in its subscription journals ‘free to read’ to all, so I shall be closely monitoring the new Wiley-ESA journal websites when they launch, to see if they make the same conveniently profit-generating ‘mistakes’ again.

How did this happen? Who was consulted? Why was this choice made?

I for one was completely unaware that ESA were looking for a new publisher. I would have tried to help if I had known. I have many unanswered questions over the consultation process. For example, the ESA has an Open Science section and mailing list, its members are extremely knowledgeable about the academic publishing landscape and publishing technology.

Was the ESA membership in it’s entirety specifically and clearly asked which publisher they would like the ESA to publish with? Did they ask their membership what features they wanted from their new publishing platform? I would have requested a platform that provides access to semantically-enriched full text XML – Wiley does not provide this. Given a choice, and the vital context and information given above I think few ESA members, policymakers, or members of the public would choose Wiley as ESA’s new publisher.

I gather from Twitter that “any and all” were invited to submit a proposal to publish ESA journals and that Elsevier submitted a proposal. But having a lazy tendering process only biases decisions towards major conglomerates who have the time, energy and resources to make slick proposals – I wonder if smaller but high-quality publishing companies were pro-actively approached by ESA to submit a proposal? In the public interest, I think the ESA should publish the names of all organisations who submitted proposals to publish ESA journals – I think just that data alone might potentially reveal flaws in the tendering process. I’m finding it really hard to reconcile the goals of ESA and shareholder-profits motivation of Wiley. I genuinely think the leadership of ESA is out of touch with its membership and that they may not have been properly consulted about this major change to the society.

This is a long post, and I’ve said enough, so I’ll leave it to a professional scholarly communications expert (Kevin Smith, Duke University), to have the last word about Wiley, and the recent trend towards cancelling Wiley subscriptions:

I don’t know if Wiley is the worst offender amongst the large commercial publishers, or whether there is a real trend toward cancelling Wiley packages.  But I know the future of scholarship lies elsewhere than with these large legacy corporations.



But perhaps we can turn this negative into positive by creating resources and impartial educational guides for academic societies on how to negotiate better publishing deals, and how to start a tendering process with an eye towards the inevitable future of open access? If SPARC or SPARC Europe already provides these resources please do point me at them!

With a first commit to github not so long ago (2015-04-13), getpapers is one of the newest tools in the ContentMine toolchain.

It’s also the most readily accessible and perhaps most immediately exciting – it does exactly what it says on the tin: it gets papers for you en masse without having to click around all those different publisher websites. A superb time-saver.

It kinda reminds me of mps-youtube: a handy CLI application for watching/listening to youtube.

Installation is super simple and usage is well documented at the source code repository on github, and of course it’s available under an OSI-approved open source MIT license.

An example usage querying Europe PubMedCentral

Currently you can search 3 different aggregators of academic papers: Europe PubMedCentral, arXiv, and IEEE. Copyright restrictions unfortunately mean that full text article download with getpapers is restricted to only freely accessible or open access papers. The development team plans to add more sources that provide API access in future, although it should be noted that many research aggregators simply don’t appear to have an API at the moment e.g. bioRxiv.

The speed of the overall process is very impressive. I ran the below search & download command and it executed it all in 32 seconds, including the download of 50 full text PDFs of the search-relevant articles!

You can choose to download different file formats of the search results: PDF, XML or even the supplementary data. Furthermore, getpapers integrates extremely well with the rest of the ContentMine toolchain, so it’s an ideal starting point for content mining.

getpapers is one of many tools in the ContentMine toolchain that I’ll be demonstrating to early career biologists at a FREE registration, one-day workshop at the University of Bath, Tuesday 28th July. If you’re interested in learning more about fully utilizing the research literature in scalable, reproducible ways, come along! We still have some places left. See the flyer below for more details or follow this link to the official workshop registration page:


Wiley & Readcube have done something rather sneaky recently, and it’s not escaped the attention of diligent readers of the scientific literature.

excellent facebook comment

On the article landing page for some, if not all(?) journal articles at Wiley, in JavaScript enabled web browsers they’ve replaced all links to download the PDF file of the article with links that direct you to Readcube instead.

This is incredibly annoying – they are literally forcing us to use Readcube. That is not cool.

Some will rush to the defence of Readcube and point out that if they detect you have the rights to, you can download the PDF from within Readcube, but that’s missing the point. No-one need waste their precious time whilst Readcube takes ages to load in your browser tab, when all you wanted in the first place was the PDF.

What Readcube provides IS NOT EVEN PDF. It’s a mishmash of JavaScript, HTML and DRM technology. Thus when Wiley has icons saying “get PDF” they’re lying. Clicking the “get PDF” link does NOT send you to the PDF. It sends you to Readcube’s proprietary, rights-restricted mock-up of a PDF.

It doesn’t even render the figure images properly, sometimes missing important bits e.g. this figure (below):

Luckily there’s a simple solution: you can block Readcube in your browser settings and get simple, direct one-click access to PDF files again by selectively disabling JavaScript on all Readcube-infected websites e.g., and

Firefox users

Install the add-on called YesScript and ‘blacklist’ all Readcube-tainted websites.

Google Chrome / Chromium users

Use Vince Buffalo’s ‘Get Me the F**king PDF‘ Chrome plugin. It’s really good.
This browser is so clever you don’t even need to install anything new. Selective JavaScript blacklisting of websites is an in-built function:

A) Click the menu button in the top right hand corner of your browser
B) Select Settings
C) (scroll to bottom) Click Show advanced settings
D) Underneath the “Privacy” section, click the “Content settings” button.
E) Under the “Javascript” section, click “Manage Exceptions” and add at least these three Readcube-infected websites:, and (example screenshot below)


Safari users

I haven’t tested this but the JavaScript Blocker extension looks like it should do the job.

Internet Explorer users

I’m tempted to say: install Chrome or Firefox but I’m well aware that some unfortunate academics have ‘university-managed’ computers on which they can’t easily install things. If so try the instructions for IE here. Let me know if you have better solutions for unfortunate IE users.

Before (left) and After (right) disabling JavaScript on the page.

Before (left) and After (right) disabling JavaScript on the page.

Added bonus function – extra privacy!

Would you want advertisers to be collecting data on you, knowing what you’ve been reading? It’s possible, though not proven AFAIK that the journal publishers themselves, or the advertisers they use are recording information about what articles you’re reading. They might know you read that article about average penis length three times last week for instance… Eric Hellman wrote quite an alarming post about the extent of this tracking at publisher websites recently. Thus blocking JavaScript at publisher websites provides extra privacy, not just protection against Readcube!

Above all I think we should #BlockReadcube not just for our own utility (easier access to the real PDF), but to send them a powerful message: we do not want the literature to be assimilated and enclosed in rights-restrictions by new technology. We do not want non-consenting ‘cubification of the research literature. We are Starfleet, and as far as I’m concerned: Readcube is the Borg.


PS If you like some of the features of Readcube, try Utopia Docs – it’s free and it’s released under an Open Source license, and it doesn’t force you to use it!

Update 2015-03-20: This post does not indicate I’m suddenly ‘in favour’ of PDF’s by the way, as some seem to have interpreted. If Wiley wanted to do something good, they should publish their full text XML on site like other good publishers do e.g. PLOS, eLife, Hindawi, MDPI, Pensoft, BMC, Copernicus… If they did this then readers could choose to use innovative open source viewing software such the eLife Lens. That kind of change would add value & choice, rather than subtract value (& rights) as they have in this case.

Further discussion of Readcube and rights-restrictions:

Last Friday, I genuinely thought Elsevier had illegally sold me an article that should have been open access. This post is to update you all on what we’ve found out since:

The Scale of the Problem

No one really knows how many articles are wrongly paywalled at all of Elsevier’s various different sales websites. So far, Alicia Wise (Elsevier’s Director of ‘Universal Access’) has admitted that 27 articles were wrongly paywalled in this latest incident and that “a handful” of these were sold to readers for $31.50 per article (source).

This wrong paywalling of paid-for ‘open access’ content also happened in 2014. I have a feeling it will happen in 2016 too…

Do we have the time and resources to keep checking all articles, at all providers of ‘hybrid OA’, to see if they are wrongly or illegally on sale?

Can we trust publishers of ‘hybrid OA’ to keep those paid-for articles outside the paywall, in perpetuity?

A lot of credit for unveiling this latest incident should be given to Marlène Delhaye, whom to my knowledge was the first person to uncover this latest round of problems at Elsevier.

Duration of Imprisonment

If one assumes that these 27 falsely paywalled articles were all from the transfer of the journal Clinical Microbiology and Infection from Wiley to Elsevier, which happened on January 1st, 2015, then we can perhaps assume that these articles were wrongly paywalled for a duration of 2 months and 9 days.

How many readers did these articles lose in that duration because the prospective readers could not get cost-free access to the full text from Elsevier’s websites? Most publisher websites track failed access attempts. For example JSTOR memorably admitted it turned away 150 million people attempting to read paywalled articles in one year.

I have been promised reimbursement for my purchases of articles that should never have been on sale in the first place, but what of the authors & funders of these articles? What compensation do they get? Their articles weren’t freely available to read for over 2 months – I’d be hopping mad if I was an author of one of those works. I think an appropriate calculation of financial compensation would be the price the article was on sale for, multiplied by the number of days it was wrongly behind a paywall.

Thus for this latest incident involving 27 articles, wrongly paywalled for 67 days, at a sale price of $31.50, I estimate the total bill for compensation owed to all the authors is: $56,983.50.  Considering the Elsevier STM publishing division had an adjusted operating profit in 2013 of £826 million, I think they can spare that loose change amount.

Apparently it was not ‘illegal’

Various people, Alicia Wise included, have been telling me that selling access to hybrid OA in this instance was NOT illegal. After a lot of discussion, I think I believe them.

Despite the article being clearly intended to be freely available to readers upon publication by the authors, all parties agree they paid Wiley to make the article freely available, not behind a paywall.

Despite the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 license clearly marked on the article at the Wiley site.


Well, author-publisher contract trickery is the answer, I believe.

Conventional open access publishers simply confirm, via an informed consent process, that the author knows and wants their work to be published typically under the Creative Commons Attribution License (CC-BY). If it gets through the editorial & review process, it is published online solely under the terms of the CC-BY license, and this is clearly marked on the paper. Copyright is fully retained by the authors over their work at all times. It’s a clear one-step process. The publisher AND readers are both bound by the terms of the chosen CC-license.

But Elsevier, Wiley and other merchants of ‘hybrid OA’ do things differently. Typically, they grant themselves carte blanche rights for commercial usage in an author-publisher contract and then afterwards, they publish online the article under a Creative Commons (or other) license. In this case only the readers are bound by the terms of the ‘end-user’ licence – the publisher can to some extent do what they want with impunity.

Needless to say, I think this incident has unveiled a significant flaw / legal loophole in the way that legacy publishers offer ‘hybrid OA’. Authors under these ‘hybrid OA’ systems appear to lose the right to sue their own publisher for wrongful commercial usage of their work.

At the very least I think publishers should print the terms and conditions of the author-publisher contract within each publication itself, so that readers like myself are informed of their ‘special rights’, over-and-above those indicated by the Creative Commons license chosen.

No apologies, no formal statements …so far

I’ve seen a few blog comments here and there from Alicia Wise which has been helpful. It is noted that she has even “thanked” me for raising this issue. I have also been promised a refund for my article purchases.

But thanks is not what I wanted. I didn’t intend to do Elsevier’s system-checking work for them. I want a public apology for this incident, that includes the word ‘sorry’:

  1. To myself and others who were wrongly charged for access to ‘open access’ articles
  2. To the authors & research funders of those 27 articles that were paid-for to be made available to readers for free, ‘open access’.
  3. To all the prospective readers, who didn’t get to read those 27 articles for over 2 months because they were behind a paywall.


I accept that these articles were ‘mistakenly’ paywalled, but even when innocent mistakes are made, it is still polite to formally apologise for making them.

For my part, I’m happy to apologise for alleging that these article sales were ‘illegal‘ – it was a logical, justified statement to make at the time, but with hindsight it might not be factually correct. Sorry Elsevier, what you did was not quite ‘illegal’ it was just wrong.

Now I’ve said my public apology for my innocent mistake, perhaps Elsevier could publicly make their apology too?