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I agree that we should try to learn how to lessen the environmental impact of farmed salmon before trying to genetically modify salmon specifically for farming. I think it is important to work out the kinks in the system before taking it to another level, like the cheaper AquaAdvantage would if it were introduced to the market.
I agree that we should shift our attention from farmed fish to conserving and supporting wild salmon, if only because it is a far more sustainable solution. I also think that you make a good point about salmon being important to other predators. The captain of the boat that I fished on this summer talked about how he used to see boats in a neighboring fishery pull in nets loaded with jacks, immature Chinooks, and how that must have hurt the killer whales that feed on Chinooks.
I agree that the limited gene pool that domestic salmon have is worrying. However, I do not believe that interbreeding is a major concern for wild salmon, or at least those in the Yukon, because I do not believe that the domesticated salmon could get up to the spawning grounds.
Fish and Fisheries in a Changing World