Because it's not 3% of the total fish population, it's 90% of the populations of each species for 29% of species. Perhaps the wording of the sentence was not clear enough.
Keep in mind that those species whose populations have decreased by 90%:
(a) will probably have a hard time recovering their populations, and are likely to die out entirely, especially if humans continue to deplete their remaining population
(b) are most likely exactly those species that make up the bulk of commercial fish stocks (because those species would be the natural candidates for the most intensive fishing), and that therefore 90% of their populations is probably quite a bit more than 3% of total commercial fish population, by perhaps as much as an order of magnitude or more
The article was not in fact abusing math to make a small number seem big; I hope that Slashdot members will not misunderstand math to make the numbers seem smaller than they are either.
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Because it's not 3% of the total fish population, it's 90% of the populations of each species for 29% of species. Perhaps the wording of the sentence was not clear enough. Keep in mind that those species whose populations have decreased by 90%: (a) will probably have a hard time recovering their populations, and are likely to die out entirely, especially if humans continue to deplete their remaining population (b) are most likely exactly those species that make up the bulk of commercial fish stocks (because those species would be the natural candidates for the most intensive fishing), and that therefore 90% of their populations is probably quite a bit more than 3% of total commercial fish population, by perhaps as much as an order of magnitude or more The article was not in fact abusing math to make a small number seem big; I hope that Slashdot members will not misunderstand math to make the numbers seem smaller than they are either.