11 March 2009

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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Anonymous said...

Wilbanks again eh?...



Bill Hooker said...

My reply got too long for a comment so it's here: http://www.sennoma.net/main/archives/2009/03/on_science_and_selfishness.php

Glyn Moody said...

@Bill Thanks for that. No surprises for me there, but probably no surprise for you that I won't change my position - if only because I think useful idiots are, er, useful.

Maybe the funding angle you mention is the solution to breaking the vicious circle.

raphtee said...

The problem in Science is far worse. During my days in academia as a physicist (both as a graduate student and then as a postdoc) the problem is with the publication of the knowledge. Most basic research is published in journals that are not readily available. In Physics, many of the journals are owned by companies like Elsevier, and subscriptions to these magazines are not cheap. So essentially knowledge that was gathered/discovered using in many cases public funds (e.g. government grants) is then published in private journals so that only those with sufficient funds can access. http://librarians.aps.org/combo_2009.pdf gives an idea of the costs involved. So what matters that the paper was written in word. Even if it was written in TeX using vi, almost no one would be able to get access to it.

Anonymous said...

Is there not already a FOSS alternate in Zotero? It's Firefox extension that replaces 3x5 citation cards and allows for sharing of bibliographic citations. So, it's all about hyperlinks. And, it integrates with both MS Word and Open Office.

The scientific community would be better served by building an open bibliographic database than by locking themselves into a particular vendor. The choice is there, right now. Zotero will import Endnote, another bibliographic format, so people with a existing databases have a place to start.

Glyn Moody said...

@raphtee: you're right, but they're really part of the same problem: that companies want to keep information proprietary so as to retain control and extract the maximum revenue.

Glyn Moody said...

@Karl: I don't know Zotero well enough to comment on whether it can do the same thing, although I do know that more and more people are turning to it.

And as you say, an open bibliographic database is clearly the right thing to do.

David Gerard said...

I recommend "After the Software Wars" by Keith Curtis: http://lwn.net/Articles/308309/ Describes Bill Gates as "the richest alchemist who ever lived."

Glyn Moody said...

Nice - thanks.

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