Welch is, in my opinion, guilty of some serious confirmation bias.
For example, that paper he tried to debunk, where he says they never found any cysts so how could it be giardia? What he does not mention is that the filter design they were using to determine if there were cysts present in the stream DID NOT WORK! Seriously. He is all over the internet quoting himself, but his work, in my opinion, does not stand up to a close look. I just finished a blog post debunking one of the Welch giardia papers, including the aforementioned "oversight." I would appreciate any of you here, especially those with a science or medical background, to read through what I wrote and critique it in the comments, because I want it to be logical and correct.
The second paper you cited is my idea of a scientific paper, letting the evidence lead where it will. Thanks for the link. But it deals with gastrointestinal illness in general and not giardiais specifically and I think the two are often confused in the debate.