PLOS is a non-profit, and employs full-time professional editors.
People forget the weird workflow in any journal that does biomedical work (including most of the PLOS family): manuscripts are submitted as Word files, then converted to XML and reformatted by a semi-automated process. There's manual labor involved to format the references and cross-references, mark up tables and figures, and proofread the HTML, PDF, and XML versions. The XML is then submitted to PubMed Central for archival storage.
There's a lot of manual labor involved in the profess. You can't just hand-wave away and say "peer review is provided for free" and assume the rest of the process is free.
For all that matters , a badly formatted "times 12" word document is just as fine as a "polished" research article. This is science we are talking about, it's not an infomercial. Besides, all journals have strict and long guidelines that all presumbissions follow. I just don't buy the manual labor argument.
Proper formatting makes it possible to automatically extract bibliographic reference data, text-mine the contents for whatever interesting purposes you might think of, display it in apps and new formats, and store it for decades in a stable format.
I've read enough journal articles that I've come to appreciate proper formatting, rather than "Time New Roman 12" Word documents or "Generic LaTeX Template #17"
Then they should tell authors: "give us your material conformant to our schema and we'll cut the price in half" That way the author can decide. I bet that most would stil submit Word documents.
Then just make the Word document open access. Someone at Google or Facebook can come up with some machine learning tools to automatically convert these into the proper format and add cross references.
Markdown does not support cross-referencing of figures, tables, and sections, and doesn't have numbered "environments" like LaTeX (e.g. theorem, definition, example). It would need to be extended.
There's a slow-moving Scholarly Markdown project, but I don't know what its status is. http://scholarlymarkdown.com/
I agree with the sentiment, though. If there were some markup language that supported what academics do with LaTeX and Word, and converted cleanly to JATS XML and to nice-looking PDFs, it would be enormously useful.
People forget the weird workflow in any journal that does biomedical work (including most of the PLOS family): manuscripts are submitted as Word files, then converted to XML and reformatted by a semi-automated process. There's manual labor involved to format the references and cross-references, mark up tables and figures, and proofread the HTML, PDF, and XML versions. The XML is then submitted to PubMed Central for archival storage.
There's a lot of manual labor involved in the profess. You can't just hand-wave away and say "peer review is provided for free" and assume the rest of the process is free.