Stephanie M. answered 07/29/15
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"Although the precise details of its chemical structure and performance are only just emerging, the X chromosome has long been renowned among geneticists, who named it X not because of its shape, as is commonly presumed — the non-sex chromosomes also vaguely resemble an 'X' at times during cell division — but because they were baffled by the way it held itself apart from the other chromosomal pairs. 'They called it X for unknown,' said Mark T. Ross of the X Chromosome Group at the Wellcome Trust Sanger Institute in Cambridge. (When its much tinier male counterpart was finally detected, researchers simply continued down the alphabet for a name.)"
http://www.nytimes.com/2007/05/01/science/01angi.html?_r=0