This is a bit of evolutionary baggage left over from our fish and amphibian ancestors. A hiccup is a specific pattern - a spasm in the diaphragm followed by a closure of the glottis, producing the "hic" sound. It is caused by a misfiring nerve somewhere along the line between the chest and the brain stem.
The reason why we have this odd pattern - taking in air but shutting off the airway - dates back to when we were amphibians. Tadpoles, which have lungs and gills, use this breathing pattern when pushing water through their gills. The glottis closes to keep the water from going into their lungs. Though we lost the gills hundreds of millions of years ago, the nerve circuit for this pattern remains. Hence the hiccup.
Neil Shubin discusses in more detail here: http://magazine.uchicago.edu/0812/featu … ater.shtml
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