There are a lot of bioinformaticians in my office and I also hear that Word is common in that world. One told me that he uses pandoc to convert Word documents from/to something more pleasant, and doesn't even tell his co-authors that he's not using Word.

In bioinformatics this works for me too, up until I get comments and tracked changes back from co-authors - getting Word comments/changes back into a md file isn't worth the headache, after that step I have to use Word too.

I've made some good experiences with Authorea, a paid online collaborative scientific writing tool, I think that one runs on top of Pandoc+git too, but it doesn't have full Word import support yet AFAIK

Edit: 0 mentions for Authorea in this entire discussion, I guess these guys need to do a bit more advertising :)

I've never used pandoc, but I was told that tracked changes were do doable. I see that pandoc converts them from/to special markup which includes the author, etc. It sounds like receiving Word documents with tracked changes is not a problem, but you would need a special tool to turn a diff into a document marked up with your changes when you want to send it back as a Word doc (similar to latexdiff).