New scientific markup language
hackpad.com
hackpad.com
I use Pandoc + pandoc-citeproc + mathjax and a Haskell code to make it more useful for writing math on the web. (basically, define theorem enviroments, and allow one to refer to theorems from before) https://github.com/Mgccl/blog/blob/master/mathdoc.hs
It is almost good enough, the only problem is there is no way to number the sections and refer to sections. Note it can be fixed in the output side.
An example: http://www.chaoxuprime.com/posts/2014-03-08-even-cycle-in-a-...
Bear in mind that LaTeX itself is a layer to TeX.
A discussion of new scientific markup that doesn't mention org-mode is, IMO, skipping the background research.
Not that org-mode necessarily solves your problem, but it is the center of mass of a pretty substantial research publication community.
It's something I would love to have, and that I've thought about myself. However, I'd love if someone sees into this hackpad more than a list of wishes by a group of folks.
Is this group of folks notorious for solving and shipping problems of this kind?
1. As for any use of Markdown, it is aimed at short notes and things which are (and should be) more lightweight than full LaTeX (to make them easily editable + make it possible to have them as webpages, etc).
2. Open collaborative pads: I enjoyed a lot collaborative discussions, where anyone can edit. Most of the time results were wonderful (and for this pad, up to 8h ago, it was great). I was both sad and disgusted to see an anus instead of the content (as I see it takes only 2 malicious users among a few dozens to spoil the experience). I reverted them and set some moderation options.
edit: this is called "goatse" btw. Don't google it.