The philosopher of physics David Wallace (currently at Oxford, moving next year to Southern California) has written up an analysis confirming, with much more precision and technical skill than I could have, my worries about the fabrication of the M&E category Bruya uses, and raising other interesting points.  He concludes:

A large fraction of the “data-driven” part of Bruya’s paper is open to severe criticism on methodological grounds, quite apart from one’s assessment of the more qualitative issues. The severity of the criticisms are such that it’s very hard to see the paper passing peer review in any journal of the quantitative sciences. Indeed, the first and most severe criticism in this note – the silence, in the main part of the paper, about the reclassification of the PGR “Science” category as M&E – would in other contexts be troublingly close to academic malpractice.

I don’t use that term lightly and I don’t intend any accusation of malice to Professor Bruya. But as a discipline Philosophy needs to be extremely concerned if it allows publication of material that uses the methods of other academic disciplines but which fails to pass the basic methodological standards of those disciplines.