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"But this is important."
"Something you have to say is more important than the Ministry of Magic, Potter?"
"Look," said Harry, throwing caution to the winds, "Professor—it's about the Sorcerer's Stone—"
Whatever Professor McGonagall had expected, it wasn't that. The books she was carrying tumbled out of her arms, but she didn't pick them up.
"How do you know—?" she spluttered.
(Harry Potter and the Sorcerer's Stone)

It seems that the highlighted part has the perfect tense meaning –– for “the perfect is a kind of past tense (SGEL,p78, 86)” and Harry’s knowing is preceding the speech time. He’ve known the fact and now he speaks out what he’s known. And ‘how do you know’ seems to contain all this. Can this be right, and the present also have the perfect tense meaning?

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    You say "How did you learn?" but "How do you know?" That's because you only learn something once, but once you learn it, you keep knowing it (unless you forget it). – Peter Shor Aug 8 '13 at 1:39
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Stative verbs like know, love, be, express a state rather than an activity. States persist over time: once you know something or love something or are something you continue to know, love, be that without further effort. Consequently, these verbs are not usually used with perfect constructions unless you are addressing the duration of the state:

 I have known that for a long time.
 I have known that since last week.
I have known that.

Prof. McGonagall is not asking How long Harry has known about the Stone, but How it comes about that he knows it now.

You know about the Stone! How do you know about it?


marks a usage as unacceptable

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No, the Simple Present doesn't have a Present perfect meaning, which means you cannot always replace a sentence using the Simple Present with a sentence using the Present Perfect.

Generally speaking, the Present Perfect is used for a past state that is still relevant to the present; the Simple Present is used for a present state, and it doesn't say anything about the past state. If I say "Mario has arrived home." I mean that Mario arrived home earlier, he was at home, and he is still at home. If I say "Mario is at home." I mean that Mario is at home now, but I don't say anything about the past; it could be Mario was already at home 3 hours ago, or Mario just arrived home 1 minute ago, but I am not saying anything about the past.

As for using "how have you known" instead of "how do you know," Google NGram doesn't have any sentences using the first phrase. The Corpus of Contemporary American English has 3794 sentences matching how do [pp*] know (where [pp*] stays for any personal pronoun), but 0 sentences matching how have [pp*] known.

I can imagine somebody asking "How did you know?" (the Simple Past) but that would mean "How did you understand it?" or "What made you understand it?"

Know is then a particular verb (as many others), since it is not used with progressive tenses.

* I am knowing her.

* I was knowing her.

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