Recent reports indicate that farmed salmon contains higher levels of pollutants than wild salmon. The cause of these increased levels is likely the salmon's feed, which is an oil-rich food containing ground up fish. This seems like a good example of how relatively low levels of pollutants in the environment can become concentrated in animals that are higher up in the food chain (though, in this case, the process is aided by humans).
Another related example of this phenomenon occurs during algal blooms, wherein toxins produced by algae are concentrated in algae-consuming animals (e.g. mussels, anchovies, krill). Thus, during algal blooms, animals that eat those algae-consuming animals (e.g. humans, sea lions, whales) may receive potentially lethal doses of the toxins (see this UCSC press release for an example of this in Monterey Bay).
It's unclear what levels of the pollutants found in the farmed salmon are safe for humans. The LA Times (article free with registration) reports, "None of the high levels exceed standards set in 1984 by the Food and Drug Administration for commercially sold fish. But they are higher than the guidelines set by the Environmental Protection Agency in 1999 for recreationally caught fish, which are 40 times more restrictive."
I'm quite impressed by the variety of locations the study sampled fish from (multiple locations in both the US and Europe it seems), as well as the number of fish they used (apparently 700, at least some of them bought from markets), and the number of "contaminants" they sampled for (around 50). It'll be nice when I can get my hands on the actual paper.
Toxins aren't the only reason to examine farmed salmon, though, as the industry doesn't seem to have a great environmental record either. A good article from Mother Jones (a very left-wing source) brings up some concerns regarding the environmental impact of modern salmon farming, including (among others) their use of antibiotics/antiparasitics, introduction of non-native salmon species, and production of huge amounts of waste.
I've chosen to avoid farmed salmon for a while now (largely due to the environmental reasons listed above), though even with the toxins and environmental problems I suspect eating farmed salmon is probably healthier than eating a bacon cheeseburger.
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