I would also point to the apparent lack of negative controls and substrate controls as something that increases the odds of contamination. My point in bringing this to everyone's attention is that I am not certain that I am seeing bias here, so much as I am seeing two people with different beliefs about the facts of the case. That would have to be addressed first, IMO. Finally, I have given a brief case for innocence on my blog: http://viewfromwilmington.blogspot.com/2011/01/why-i-believe-that-amanda-knox-and.html