"blow up the sample" ... interesting perspective. When a sample of something is found at a crime scene it can be analyzed. During the first reading for DNA, the sample can be weak and require further zooming or cycling. Additional cycling can lead to a DNA reading, although it must be identified as LNC DNA.
As LNC DNA, it can only be used for comparison to a known sample or as an exclusionary tool, not an identifying tool. The DNA sample on the knife could not exclude Meredith Kercher according to the academics and was a match according to the state.
Low count number DNA is widely accepted in Europe, where it was first developed. It was used as an argument during the Casey Anthony trial - because it wasn't done.
Should all research into DNA analysis be parallized and stop in it's tracks because at a certain point there is too much skepticism? That hasn't yet been established, and tests so far (zoomed and recycling to detect lower levels of DNA) have been accepted internationally,
The fact of the matter is that it has not been reported at what magnification the testing was done to return the result of NO DNA (to my knowledge). Either the sample was only rye starch and was magnified at the highest possible level, or it was magnified to some lower level that the prosecution found insupportable. Without that actual information we are all arguing conjecture.
As much as I can understand it, the machine returned the answer "NO DNA" and the prosecution wanted them to run a DNA test anyway and see if the print out looked like Meredith's profile. In other words, despite the fact that the machine stated there was no DNA, they saw a reason to try running the test anyway to see what happened. Maybe there really was DNA at such miniscule levels that the machine could not see it, but a result could be found. (Which seems kind of counter-intuitive to me.)
I don't understand the technology, so I can't argue if it was the right decision. I could see the forensic people saying "This is stupid, they are asking if you can see bigfoot in a four pixel picture. I can't believe people are buying this." Contrariwise "They had a 100 pixel picture, and they didn't bother to see if it even vaguely looked like her? Who cares if the machine said it was just 100 pixels of light leak on the lens."