Start of revision for PLOS Biology

This is the start of the revision in response to the reviews at PLOS Biology. It only tackles what I've had time to get to today, but I thought we might as well go ahead and get this much in if it's heading in the right direction.

The one major thing has been a substantial shortening of Practice 7 to allow us to remove the second level headings as requested by the editors. Attempting to comply with this request made it quite clear that this section was overly long and detailed compared to the other sections and I consulted with Greg before making major cuts.

An updated copy of the letter is available upon request.