( ( The problem ) ( ( is ( that ( we ( see ( ( ( ( with ( our eyes ) ) , ) not ) ( with ( our brains ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT The) (NN problem)) (VP (VBZ is) (SBAR (IN that) (S (NP (PRP we)) (VP (VBP see) (PP (PP (IN with) (NP (PRP$ our) (NNS eyes))) (, ,) (RB not) (PP (IN with) (NP (PRP$ our) (NNS brains)))))))) (. .)))
The problem is that we see with our eyes, not with our brains.
(ROOT (S (NP (NNS Brain) (CC and) (NNS eyes)) (VP (VBP are) (S (NP (DT the) (NNS organs)) (VP (VB work) (PRT (RP together)) (S (VP (TO to) (VP (VB allow) (S (NP (PRP us)) (VP (TO to) (VP (VB see)))))))))) (. .)))