Facially, it seems to contradict what the eyes say! (4)
I believe the answer is:
nose
'eyes say' is the definition.
The definition and answer can be both related to thinking as well as being singular nouns.
Perhaps they are linked in a way I don't understand?
'facially it seems to contradict what' is the wordplay.
I cannot quite see how this works, but
'it' could be 'e' ('e' can mean 'electronic' which is similar to 'IT') and 'e' is present in the answer.
The remaining letters 'nos' is a valid word which might be clued in a way I don't see.
This explanation may well be incorrect...
'the' is the link.
Can you help me to learn more?
(Other definitions for nose that I've seen before include "Olfactory organ" , "Cyrano's large feature" , "Organ of face" , "Schnozzle" , "Front of an aircraft" .)