Board Thread:Questions and Answers/@comment-68.2.144.3-20130418101731/@comment-1210805-20130418112032

Dr Clark was only explicitly referred to as a male in the English version and perhaps some other translations but not in the original Japanese. I'm fairly sure that in the original Japanese they used a gender neutral pronoun, which are often translated to male pronouns when changed to English.

I'm fairly sure that somewhere in MGS4 (or perhaps the novelisation) they touched on the discrepancy and had Naomi say that she'd never actually met Dr. Clark and knew very little about her. Clark was apparently quite mysterious and Naomi just assumed it was a man.

So while it may not be the most sensible explanation, it has at least been acknowledged.