Open Science, Closed Source and Microsoft

Glyn Moody and I share many of the same views but here is an area where we differ. His position is straightforward and logically defensible – mine is less clear but – in my own mind – tenable. Currently I am funded by Microsoft – is this compatible with being an activist for Open Knowledge? I reproduce Glyn’s post in full (see also one by Bill Hooker which shares some, but not all views.)

Open Science, Closed Source

One of the things that disappoints me is the lack of understanding of what’s at stake with open source among some of the other open communities. For example, some in the world of open science seem to think it’s OK to work with Microsoft, provided it furthers their own specific agenda [PMR emphasis]. Here’s a case in point:

John Wilbanks, VP of Science for Creative Commons, gave O’Reilly Media an exclusive sneak preview of a joint announcement that they will be making with Microsoft later today at the O’Reilly Emerging Technology Conference.
According to John, who talked to us shortly after getting off a plane from Brazil, Microsoft will be releasing, under an open source license, Word plugins that will allow scientists to mark up their papers with scientific entities directly.
“The scientific culture is not one, traditionally, where you have hyperlinks,” Wilbanks told us. “You have citations. And you don’t want to do cross-references of hyperlinks between papers, you want to do links directly to the gene sequences in the database.”
Wilbanks says that Science Commons has been working for several years to build up a library of these scientific entities. “What Microsoft has done is to build plugins that work essentially the same way you’d use spell check, they can check for the words in their paper that have hyperlinks in our open knowledge base, and then mark them up.”

That might sound fine – after all, the plugins are open source, right? But no. Here’s the problem:

Wilbanks said that Word is, in his experience, the dominant publishing system used in the life sciences, although tools like LaTex are popular in disciplines such as chemistry or physics. And even then, he says it’s probably the place that most people prepare drafts. “almost everything I see when I have to peer review is in a .doc format.”

In other words, he doesn’t see any problem with perpetuating Microsoft’s stranglehold on word processing. But it has consistently abused that monopoly by using its proprietary data formats to lock out commercial rivals or free alternatives, and push through pseudo-standards like OOXML that aren’t truly open, and which have essentially destroyed ISO as a legitimate forum for open standards.
Working with Microsoft on open source plugins might seem innocent enough, but it’s really just entrenching Microsoft’s power yet further in the scientific community, weakening openness in general – which means, ultimately, undermining all the other excellent work of the Science Commons.
It would have been far better to work with OpenOffice.org to produce similar plugins, making the free office suite even more attractive, and thus giving scientists yet another reason to go truly open, with all the attendant benefits, rather than making do with a hobbled, faux-openness, as here.

PMR: First the facts. My group are funded by Microsoft to work on Chem4Word – an Add-in for chemistry in Word2007 – and also as part of the OREChem communal project organizing semantic chemistry under ORE. I personally get no financial reward other than meetings in Seattle. The Add-in will be Open Source.

To state my position on the various potential concerns…

• Microsoft is “evil”. I can understand this view – especially during the Hallowee’n document era. There are many “evil” companies – they can be found in publishing (?PRISM), pharmaceuticals (where I used to work) Constant Gardener) , petrotechnical, scientific software, etc. Large companies often/always? adopt questionable practices. [I differentiate complete commercial sectors – such as tobacco, defence and betting where I would have moral issues] . The difficulty here is that there is no clear line between an evil company and an acceptable one
• Monopolies are unacceptable. I have some sympathy with this view. It’s not quite the same as above, as the categorisation is simpler. By this measure all monopolies should be opposed, regardless of whether they are evil or not – this includes Google – for example.
• Capitalism is evil and should be opposed. This is logically defensible but I don’t hold this view myself.
• Microsoft has abused the standards process. I’m prepared to believe this, just as I am prepared to believe that publishers hired Dezenhall to rubbish Open Access.

So why am I working with funding from Microsoft? The project(s) are aimed at developing semantic documents – just as John Wilbanks is doing. Microsoft Research believes in semantic documents for research and it is encouraging to find a supporter when the chemistry sector is still in the dark ages. At the end of this we shall have made significant progress towards linked, semantic science.

Is this perpetuating the monopoly? The monopoly exists and nowhere more than in in/organic chemistry where nearly all chemists use Word. We have taken the view that we will work with what scientists actually use, not what we would like them to use. The only current alternative is to avoid working in this field – chemists will not use Open Office.

For the record we also work with Open Office – primarily through Peter Sefton. That at least is encouraging alternatives. But – whether you like it or – Open Office has too many rough edges to make it easy for those who are not early adopters.

However monopolies do not last forever. I’ve lived hrough “Nobody was sacked for buying IBM”, “… DEC”. Substitute  “… Google,  Microsoft, etc.” I’m also optimistic that the hegemony of the commercial publishers will also crash.  Has the pressure of anti-trust, etc. has caused re-orientation in Microsoft? Are projects such as ours helping to promote change? Or simply adding legitimacy?

What I can say is that the individual people I work with in Microsoft Research are genuinely looking to engage with the scholarly community and to help promote Openness. What I have little insight into is the soul of the large corporate itself. I’ve worked for Glaxo, and am sponsored by Unilever and Microsoft (as well as having been funded by IBM). One can never be easy with large companies, but at the moment I can draw the lines.