The Neanderthals, once considered dull-witted brutes, are now known
to have had brains fully as large as our own.
(A) to have had brains - Correct
(B) as having brains that are - tense issue 'are'; Here, the usage of having implies that the Neanderthals are HAVING brains NOW.
(C) to have brains that were - the Neanderthals ARE NOW KNOWN (in the present) TO HAVE brains (also in the present).
Since the Neanderthals no longer exist, this meaning is nonsensical.
(D) that their brains were - incorrect structure The Neanderthals are now known that...
(E) that they had brains that were - same as D
Mary knows that the house is blue.
Here, the that-clause in blue serves as the DIRECT OBJECT of knows.
WHAT does Mary know?
She knows THAT THE HOUSE IS BLUE.
Rule:
A passive verb -- is + VERBed, are + VERBed, etc. -- cannot take a direct object.
Answer A
In English, we have two infinitive tenses: the present infinitive (to + VERB) and the perfect infinitive (to have + VERBed).
The present infinitive expresses CONTEMPORANEOUS action (an action happening AT THE SAME TIME as the main action):
John IS proud TO BE president.
Here, John IS proud (in the present) TO BE president (also in the present).
The perfect infinitive expresses PRIOR action (an action that happened BEFORE the main action):
John IS proud TO HAVE BEEN president.
Here, John IS proud (in the present) TO HAVE BEEN president (in the past).
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The perfect infinitive can be used to refer to something in the past.
Dinosaurs are known to walk the Earth.
Present infinitive. Implies that dinosaurs still walk the Earth.
Dinosaurs are known to have walked the Earth.
Perfect infinitive. Used here to indicate that Dinosaurs no longer walk the Earth.
Note that we can't simply change the are to were to communicate that dinosaurs no longer walk the Earth, as doing so could be interpreted as implying that the knowing is not current, that is, we no longer know that dinosaurs walk the Earth. Alternatively, the sentence could be talking about the state of knowing at some time in the past (for example, to point out when that fact was first known).
Option D should use it as the subject to delay the that clause instead of providing a completely different subject.
It is known that dinosaurs walked the Earth.
This sentence is fine.
Dinosaurs are known that they walked the Earth.
This one is not.