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While the naming of the chromosomes was somewhat arbitrary, you have to credit the scientists who made the discovery that men have a different shaped 23rd Chromosome than women. He observed that all the Chromosomes in women (and the females of all other sexual species) all had the same shape, and they all resembled the letter X. He also observed that in males one of the chromosomes had a different shape. Strictly speaking he could have used any one of the letters of the Alphabet, but the shape most reminded him of the letter Y, so he named it the Y chromosome.
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