Without a doubt there are significant concerns about LOCAL impacts of net pen operations. Those concerns can and should be addressed. However that doesn't mean the pens should be eliminated.
As WN1A is pointing out much of the "Science " being reported to support the negative impacts from the net pens are being cherried picked to provife a slanted view. If one digs into many of those sources you will find that the funding sources come from the commmerical fishig industry, which has a huge concern about the impacts from farmed fish on their profits.
Just one example from the toxic issue referred to by WN1A; in this case PCBs. There was much made about the farmed fish having higher levels than wild fish - of course those making those claims didn't mention that they were comparing most wild chums to the farmed fish or that the famed Copper River Chinook had higher PCB levels than the farmed fish - wonder why?
As with most of this type of issues I encourage folks to take the time to local at the full range of information before making snap judgements.
FNP -
Regarding the polution by other commerical sources of protien. Who are cleaning up after the free ranging cattle - those grass feed animals that are so much better for you than those grain fed feed lot animals? While the feed lots may control the fecas of the animals what are the environmental impacts from the agiculture associated with the grain produced to feed the animals.
The real issue is where is the protein we human's want going to come from? Without a doubt it would be much better for the ecosystem if we all got our protein from sources much lower on the food chain. Instead of eating salmon (either farmed or wild) we limited our fish diet to such sources as fish meal from bait fish would be much better. However I suspect that most of will continue to want to enjoy a nice piece of salmon or a juicy steak from the grill.
Tight lines
Curt