at the risk of being impish, though, it's a bit sad that any opportunity to blame whale problems on a military cause gets a lot of press, but I was shocked and saddened by Steve's research that a lot of whale strandings are driven by starvation in otherwise healthy whales, presumably due to overfishing or pollution-related die-offs.
I should ask my dad about the actual discussions the navy has about these issues, since in his retirement he gets invited to consult for the Navy on sonar-related issues. I know they bring in MBARI researchers and whatnot, so it's not as if the Navy refuses to have meaningful dialogue with marine biologists...although they do refuse to have meaningful dialogue with activists, since the activists and Navy treat each other as enemies of convenience... my dad used to give money to Greenpeace for whale conservation, but stopped when he witnessed firsthand that they actually spent a lot of that money on anti-nuclear protests that had nothing to do with whale conservation (and the guy going door-to-door responded to this with "I don't know what you've heard, but I was on the Greenpeace boat and we were the victims" which was not really a good strategy, since my dad could say "well, it sure didn't look that way from the submarine...")
I can imagine that the Navy hasn't done a good job of protecting whales, but I could also imagine that the Navy is bending over backwards about it, but that conservation groups know that if they sue the Navy, they can raise more money, so they may have incentive to blow the problems out of proportion. It would be really interesting to get the inside story on these issues, but presumably what the Navy does and doesn't do with their sonar is classified...