Here is a response from Riddel et al. to the Krkosek et al. paper claiming Pink salmon in the Broughton Archipelago were, “on a trajectory toward rapid local extinction.” due to sea lice from farms.
http://www.sciencemag.org/content/322/5909/1790.2.full.pdf
It points out my previous concerns with other papers of its type - I call it "Fill In the Blanks Science" where data is massaged to get the result you're looking for.
"Their conclusions follow directly from their data selection process."
"they attributed all differences in wild pink salmon mortality between exposed and unexposed populations to sea lice infection, ignoring other potential sources of between-year variation in survival."
"Krkošek et al.’s prediction of rapid extinction only holds if the exposure period is defined to begin in 2000, the year of highest abundance, and returns after 2002 and 2003 are misrepresented."
"Krkošek et al. overstated the risks to wild pink salmon from sea lice and salmon farming. Furthermore, their predictions are inconsistent with recent observations of pink salmon returns to the Broughton Archipelago. Their alarming statements of extinction of pink salmon in the BA are only possible with highly selective use of the available data and extrapolation of their results to all pink salmon in the BA."
So, they start with the assumption that farms caused the declines, gather evidence which supports this view, while ignoring all that does not, then create a model based on the assumptions to project a possible future scenario.
If you have to ignore data to make it work for you - it is junk science, especially when observation also runs counter to your theory.
Here is a good video of Richard Feynman explaining the scientific method, well worth 10 minutes of your time.
http://www.youtube.com/watch?v=EYPapE-3FRw&feature=youtu.be
"It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong."