For the past few months I’ve been experimenting with markdown and multimarkdown as authoring formats for academic work. This is especially the case when you need to produce a document in multiple formats, or if the format required by the publisher changes.
In general you have two choices, using a new flavour of markdown called multimarkdown (specifically created for academic work); or markdown via the pandoc commandline processor, which is more powerful than MMD (IMO) but not as well integrated into editing tool (MMD has it’s own editor too).
However, the problem I see is that both systems do not handle the requirements of academic work very well, specifically citations and cross referencing. At this point I’m leaning towards pandoc because I can build my own tools and plugins to help with generating stuff like indexes etc. But still LaTeX has these features already so adding additional stuff to another language seems to be a backward step.
I do think that markdown is useful for new electronic reader type publications, and that markdown may indeed start to gain share. I also think that markdown is a great idea that should gain traction, just because it can be used to generate multiple formats. But, this said it isn’t ready for complex academic documents, it just doesn’t have the machinery to make academic writing a pleasure. Indeed, I would suspect that it would take less time to change end formats – from pdf to word, say – than it would to update the citations in an academic markdown paper. Without some additional tooling, markdown isn’t useable for academic publications, for the jobbing research who may need to change citation formats, bibliographic systems, produce indexes, auto number figures and the like. And the solutions that seem currently to be available have a tendency to destroy the base formating once they have parsed and re written the file.