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Science is one of the most respected journals, but its editors and reviewers are not infallible. Plenty of articles in Science have gone on to not hold up or to have been based on false assumptions. Counting the fish in the sea is a notoriously hard problem, building models of those numbers even harder. I haven't read the actual paper but my guess is that the authors acknowledge the limitations of the models and data and are putting forth what could be described as a "best guess". The popular press likes to play up the sexxy headline "Ocean running out of fish", but the truth of the authors statements is undoubtedly more complex.
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