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Rolf,
I specifically asked Professor Dan Krane, who heads a DNA forensics company, which was more important, to be present at the testing or to have access to the electronic data files. He said that to perform a case review, the electronic data files were very important, and the observation of the tests themselves were not that important. The prosecution never turned those critical EDFs over to the defense, and even the independent experts had to work hard to obtain them. The defense could have used the files to look for evidence of contamination or secondary transfer.
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
Either the knife had bleach on it, or it had DNA on it, not both. A 2-3% dilution of bleach is recommended by Promega for cleaning pipets in PCR work. They also note that if one does not thoroughly rinse away the bleach, it will affect subsequent experiments. There is also a 1998 article in Biotechniques which shows that a 10% dilution of bleach damages DNA within one minute. If the prosection's claim is that the knife was bleached (and I am not certain that it is), then it is in conflict with their claim that the knife had Meredith's DNA when it was taken into custody.
The exact value for the frequency of contamination is a very difficult number to pin down, for a variety of reasons. However, two facts make it more likely that it has occurred with respect to the knife than with a typical object. One is that the sample is in the low template range of analysis but no special handling precautions (a separate building with positive flow air hoods, etc.) were taken. The mere existence of so many special handling precautions in true Low Copy Number (LCN) analysis suggest that contamination is more likely when working in this very low concentration range. Two is that there was no blood on the knife. Two experts have publicly stated that the chances of cleaning a bloody knife to the point at which blood is no longer detected but DNA is detected, are small.