Show me the data!

For those that know me as a biologist it might perhaps surprise you to know that my most cited publication so far is on Open Access and Altmetrics (published in April 2013, 25 cites and counting…) — nothing to do with biology per se!

So I took great interest in this new publication:

Wang, X., Liu, C., Mao, W., and Fang, Z. 2015. The open access advantage considering citation, article usage and social media attention. Scientometrics, pp. 1-10. DOI: 10.1007/s11192-015-1547-0

The authors have gathered some really fascinating data measuring day-by-day altmetrics of papers at the journal Nature Communications, which at the time was hybrid: some articles behind a paywall, some articles were paid-for open access at a cost of $5200 to the authors/funders. (The cost of open access here is an absolute rip-off. I do not endorse or recommend outrageously priced paid-for open access outlets like Nature Communications. PLOS ONE costs just $1350 remember! PeerJ is just $99 per author!)

The paper is by no means perfect – I’m not saying it is – but the ideas behind it are good. Many on twitter have commented that it’s ironic that this paper on open access advantage is itself only made available behind a paywall at the publisher.

The good news is, Dr Xianwen Wang has responded to this and has made an ‘eprint’ copy (stripped of all publisher branding) freely available at arXiv as of 2015-03-19 (post-publication).  The written English throughout the manuscript is not brilliant but I feel this reflects poorly on the journal rather than the authors – it’s remarkable that Scientometrics can charge a subscription fee to subscribers if they offer no copy-editing on accepted manuscripts!  Finally, technical detail on precisely how the data was obtained is rather lacking. So that’s the critique out of the way…

My tweets about this paper have been very popular e.g.

But I wanted to dig deeper into the data. So I emailed the corresponding author; Xianwen for a copy of the data behind figure 2 and he happily and quickly sent it to me. I was fairly shocked (in a good way) that he sent the data. Most of the times I’ve sent email requests for data in the past have been ultimately unsuccessful. This is well documented in the field of phylogenetics *sad face*. The ’email the author’ system simply cannot be relied upon, and is one of many reasons why I feel all non-sensitive data supporting research should be made publicly available, alongside the article, on the day of publication.

I did my own re-analysis of the raw data Xianwen sent over, and discovered there were lots of odd jumps in data, which couldn’t really be explained by peaks in social media activity e.g. for A cobalt complex redox shuttle for dye-sensitized solar cells with high open-circuit potentials (visualized below). ~520 days after it was first published, in one single day it apparently accumulated 21,577 page views! There was also a smaller spike of 2000 page views earlier.

Article View Spikes

Xianwen had filtered these suspicious jumps out of his figures but neglected to mention that in the methods section, so upon informing him of this discrepancy he’s told me he’s going to contact the editor to sort it out. A great little example of how data sharing results in improved science? The unfiltered data looks a little bit like the plot below:

Anyway, back to the spikes/jumps in activity – they certainly aren’t an error introduced by the authors of the paper – they can also be seen via Altmetric (a service provider of altmetrics). The question is: what is causing these one-day spikes in activity?

I have alerted the team at Altmetric, and they have/will alert Nature Publishing Group to investigate further

Most of the spikes are likely to be accidental in cause but it would be good to know more. A downloading script gone awry? But there is still a possibility that within this dataset there is putative evidence for deliberate gaming of altmetrics, specifically: article views. I look forward to hearing more from Altmetric and Nature Publishing Group about this… the ball is very much in their court right now.

Moreover, now that these peculiar spikes have been detected; what, if anything, should be done about it?

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?


  • you weren’t much loved in your short existence
  • you weren’t much use to readers or text-miners because we often couldn’t find where you were – hiding amongst shadows.
  • you were significantly more expensive than your ‘full’ open access cousins


In March, 2015 ‘hybrid OA’ died after a short-life of neglect. Elsevier put the final nail in the coffin, but it wasn’t just they who were responsible, other publishers were plainly guilty of hybrid OA neglect too.

Publishers gave birth to the cash-cow that was hybrid OA not long ago. The profits were immense: $5000 for a single article in some greedy cases. Yet after each ‘hybrid OA’ article was born, and the profit raked in, the hybrid OA articles were completely neglected post-publication. Much like their shuttered, not-allowed-to-play-outside-the-paywall brothers & sister articles. They were forgotten about, even though their authors had stumped-up significant funds upfront to ensure their freedom forever.

Hybrid OA - a cash-cow

Hybrid OA was a wonderfully profitable system for the publisher/carers. It enabled bountiful double-dipping – additional revenue for providing exactly the same content. Laughably, the publisher/carers claimed  that it was “not happening at all“, but anyone with a brain knew better.

But too much neglect of the hybrids over the years led to many high-profile instances of triple-dipping: subscription revenue, APC fees, AND $31.50 (+ tax) per article reader charges (for content that had already been paid to be made free for readers, forever).

A variety of rightly concerned funders started a trend banning authors from sending their articles to hybrid OA profiteer-merchants, for their own good. Only full OA venues could be trusted to actually do the job and the keep the articles outside paywalls.

In short, legacy publishers themselves killed hybrid OA through their own carelessness. Authors, librarians, research funders and readers simply didn’t trust publishers to do hybrid OA properly, and had amassed plenty of evidence of their ineptitude. They tried to sweep the problem of a flawed and difficult system under the carpet as just ‘bumps in the road‘ to open access but actually hybrid OA was just a wrong turn all along.

Hybrid OA Is The Wrong Way

Hybrid OA Is The Wrong Way