It seems to me that a big problem with discussions between Massimo and EY is that EY is a hardcore reductionist (The sciences are, at base, just physics) and Massimo is not. It seems like they're talking past each other, and it's hard to tell which are valid points in the light of that confusion.
To me their expressed views on the matter seemed very similar.
Pigliucci:
http://rationallyspeaking.blogspot.de/2013/01/lesswrong-on-morality-and-logic.html