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Originally Posted by BusterPorn
it probably has something to do with air movement and the vibrations an object moving through air causes.
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from wiki
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Flies have a very highly-evolved evasion reaction which helps to ensure their survival. It is possible to confuse a fly's evasion system by swatting it with two objects simultaneously from different directions. The holes in a fly swatter minimise the air current which warns the fly of being hit, whilst reducing air resistance and increasing speed of the swat. This evasion reaction can also be used against the fly. Clapping your hands several inches above the fly will cause it to try to escape, usually into your just closing hands.
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I guess a computer mouse wouldnt set off a flies evasion reation