Peter Murray-Rust (welcome back to blogging!) has replied to Glyn Moody's post about semantic plugins being developed by Science Commons in collaboration with the Evil Empire, which I discussed in my last post. Peter MR takes the view, with which I concur, that it's more important to get scientists using semantic markup than to take an ideological stand against Microsoft:

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 .

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.

Another, to my mind even more important, point was raised by Peter Sefton in a comment on Peter MR's entry:

I will have to talk about this at greater length but I think the issue is not working with Microsoft it's working in an interoperable way. The plugins coming out of MS Research now might be made by well meaning people but unless they encode their results in something that can interop with other word processors (the main one is OOo Writer) then the effect is to prolong the monopoly. There is a not so subtle trick going on here - MS are opening up the word processing format with one hand while building addons like the Ontology stuff and the NLM work which depend on Word 2007 to work with the other hand. I have raised this with Jim Downing and I hope you can get a real interop on Chem4Word.

(Peter S, btw, blogs here and works on a little thing called The Integrated Content Enviroment (ICE), which looks to me like a good candidate for an ideal Electronic Lab Notebook...)

There's a difference between the plugins being Open Source and the plugins being useful to the F/OSS community. If collaborators hold Microsoft to real interoperability, the "Evil Empire" concerns largely go away, because the project can simply fork to support any applications other than Word.

(I've emailed John Wilbanks to get his reaction to all this, but be patient because he's insanely busy in general, and right now he's on honeymoon!)