It’s not that the chemical itself is making a distinction, it’s that it’s only bioactive in certain plants. It’s the same thing that lets us take antibiotics which kill bacteria but don’t harm us: the molecule is only harmful under certain conditions. We can take advantage of slight differences in the way different organisms perform important chemical processes that are vital to their survival to target one specific organism over another.
So, the herbicide interrupts a critical reaction in the weed which kills it, but has no affect on the plants we want to save.
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