Reading a book should be a conversation between you and the author. Presumably, he knows more about the subject than you do; if not, you probably should not be bothering with his book. But understanding is a two-way operation; the learner has to question himself and question the teacher. He even has to be willing to argue with the teacher, once he understands what the teacher is saying. Marking a book is literally an expression of your differences or your agreements with the author. It is the highest respect you can pay him.