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hyporational comments on Fighting Mosquitos - Less Wrong Discussion
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How large is the population of the problem species compared to the population of the benign species? There probably won't be more mosquitoes of the benign species if we eradicate the problem species, unless we start to farm the nice kinds of mosquitoes or something. Also the problem species might behave more predictably to certain predators than than the benign species, and populate certain niches that have certain predators that are used to have them around.
Given that the whole process is about farming mosquitos, producing a few extra of the nice mosquitoes might be worked into the plan for reasonable extra cost.
Replacing the bad mosquitos with nice one's is also likely to make it harder for bad mosquitos to come back because their niche is filled.