One of the more concise and salient points in the Ryan Braun argle-bargle (or foofaraw) comes from Jeff Fletcher, who takes us into a hypothetical world in which we know that Braun is completely clean. False positives aren't that rare, so it is possible. What would happen if a completely clean player failed a test?
Braun’s only defense is to challenge the accuracy of the test, whether he is totally innocent or whether he’s guilty and looking for an out. Doesn’t matter. His only defense is to challenge the accuracy of the test.
You'll read a lot about technicalities and red tape, but this is one of the most important points to keep in mind. There's a reason for the appeals process.
Braun's lawyers might have jumped on the improperly handled sample because they knew it offered the best chance for a successful appeal. That doesn't mean that his positive test was or was not a false positive -- that wasn't challenged. But if it was a false positive, and if Braun knew it, he would have had no choice but to do exactly what he did.
The important thing, though, is to make up your mind right when you read the breaking news, and find supporting evidence as it comes in.