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. 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.

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