The news has a way of trotting around my mind while I wait for the snow to melt. One recent item was that Elsevier, the academic publishing giant, has acquired Mendeley, a startup that runs one of the most popular academic citation management applications.

This news comes on the background of the persistent rumblings that have been going on in the  journal publishing space. There are many ways of approaching this debate, which revolves around the keyword “open access” and by now has matured to the point of touching on business models (who should pay? how much? what’s the role of institutional libraries and repositories?), pitfalls (what about academic vanity presses? how how to make peer review both effective and transparent ?) and a variety of interests (the taxpayer, who funds research that is locked behind paywalls; the corporations who are making large profits based on researchers’ volunteer work; the individual scientists who want to do the right thing without jeopardising their career).

Reference management is only a tiny aspect of the whole mess, but an interesting one. If we’re changing how scientific publications are disseminated the workflows and habits of researchers, who are both readers and authors, and the data we produce about them, become very relevant. Software can be a tool to empower the individual. I use Zotero, which makes my collection searchable, retrieves and manages metadata and PDF files from countless journal sites, and lets me export citations in any format I could wish for, saving me oodles of time and hassle.

Mendeley and Zotero are often mentioned in the same breath as they are similar in capabilities, and the basic offering is free of charge. Now some will disapprove of Mendeley’s decision to sell the company to Elsevier simply on the basis of Elsevier’s role as the principal bad guy in the story of large publishing corporations’ abusive practices towards academic scientific research. There’s a boycott going on after all. Others speculate about consolidation within Elsevier’s services.

But to understand why the unhappiness goes even deeper it is useful to step back and consider what’s at the bottom of it: the ways to make such software viable and the trade-offs they involve:

• Charge for the software license itself. This is the strategy pursued by EndNote (which belongs to Thomson Reuters and has a list price US $ 250-300) as well as RefWorks (ProQuest, US $ 100/year) and the slightly cheaper Papers (a small startup acquired by Springer, $ 80). Such a strategy requires a sales and marketing team and substantial overhead that make your cost go up. The competition for software licensing fees from institutions is crowded, however, and the pot is limited.
• Charge for storage of documents you save within the software. Zotero and Mendeley both do this. This is a straightforward, useful service offer, but I believe somewhat limited in how much revenue can be generated. Online storage is getting cheaper and cheaper, unlike staff to manage the offering. In the case of Zotero, a technically savvy user (or their institution) can get around storage limitations by setting up their own WebDAV service, as described in the product documentation. (This is what I do.)
• Charge for premium features, such as collaboration tools, and thereby target institutions or teams. Mendeley does this. 
• Get supported by institutions and non-profits. This is Zotero’s case: it is free and open-source software that started as a simple Firefox plug-in and is now a project of George Mason University’s Roy Rosenzweig Center for History and New Media, which receives funding from various big-name charitable foundations; it also incorporates volunteer contributions from the user community.
• Or get supported by a large commercial company. What’s in for them? Access to the data you’re collecting: Any reference application that offers synchronisation of metadata is sitting on a large heap of information about what and how researchers — active scientists at the cusp of their careers — are using the scientific literature. If you’re an academic publisher this information is highly valuable.

So clearly Mendeley isn’t the first to be associated with a publishing house, and all of the major reference management tools pursue multiple approaches at once. But the last two of them are pretty much mutually exclusive: An open-source project can’t simply sell their users’ data to the highest bidder. If they tried, they might get forked and see their users run away. Zotero’s privacy policy is admirably clear, Conversely, if you start out with the intent to mine user-generated data you can hardly claim you’re serving the public good, and can’t very well open up your source code — your very competitive advantage. Not even Google, who do support free software projects, do that.

So this is where the rub is: Mendeley didn’t just sell themselves out; they sold their users out. Even if contrary to expectations the assurances that “nothing changes” turn out to be the truth, they still turned their users into cogs in Elsevier’s profit-generating machine (36% margin, last time I checked). Like Papers is, most likely, for Springer, or RefWorks for ProQuest, or even the expensive EndNote for Thomson Reuters. There’s a saying that if you aren’t the customer you are the product, but I think this is not quite correct: you can also be the means of production.

And this, too, is why I did pay attention to who is behind the reference management software I was choosing. It may be naive and sometimes premature, but I’m more inclined to trust a project that has a strong non-profit institution behind it. If it’s a big corporation, I want to know up-front and make a choice about sharing my data with them. If it’s a start-up, the question is how much can I trust in their integrity and ability to develop a sustainable plan without selling me out, as well as themselves?