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I’m not sure I can buy into the central premise of this article. It alludes several times to almond pollination being a major factor in killing off bees, but several of the causes listed (mites, African bee species, etc) are never directly linked to the almond pollinization process.

It also seems to rely on the comparison between the number of bees dying each year and the average death rates for other animals, and at one point even for humans (“In any other industry, the death of a third of your workforce would cause an international outcry – but this staggering loss is now considered the normal cost of doing business.”). Given that the average lifespan of any honey bee appears to be well under a year, and also the fact that bees are not human workers, this comparison seems forced at best. If 30% of beekeepers were being killed every year while transporting their bees, yes, I’d be very concerned.

Until traversing California's Central Valley, I'd have questioned premise of the article. The concepts of "farm" I've held all my life don't apply. Even the industrial farming of the midwest is discontinuous. Industrial hydroponics outdoors at agricultural scale. That's why the premise is plausible: these sound like systemic problems in a hydroponic system. YMMV
I guess to clarify: the farming itself seems like a fascinating bit of industrial insanity. But the bees-dying—a-lot bit doesn’t make sense, given that any given bee is already likely to die in the year that it is born, given its average lifespan.
When the bees used to pollinate almond farms are dying at 5 times the rate of bees pollinating, say, apples — there's cause for concern.