"To have a good command of English" is correct modern British usage, "to command English" is not.
SOED has "command of language", meaning "skill in speech, articulacy" (SOED noun sense 3). Oxforddictionaries.com has "he had a brilliant command of English" (noun sense 2) as an example of "the ability to use or control something".
That's using "command" as a noun, broadly meaning "mastery". You wouldn't "mastery English" (you'd "have mastery of English"), so instead of "command English" it's "have command of English".
Why it doesn't work using the verb "to command": I can command the strings of a musical instrument (although it sounds a bit archaic) because I have control over them - I can make them sound in response to my will. I can give them commands and they will act in response to those commands. I can't make the English language act in response to my will - if I tell the English language to do something, it won't - so I can't "command English".
(To "master English" is fine, by the way, although if someone can master English it just means they're capable of mastering it, not that they necessarily have mastered it).
The Davidson example (raised by user "what" in their answer), "if he commands a language", is correct (though unusual) usage but is not the same as the OP's example "a scientist who can command English".