Fanny Birden may be a bit of a nut, but she introduces a symbol that haunts Charlie through the whole book. Break out your Bibles, Shmoopers: the tree of knowledge is making an appearance. "It was evil when Adam and Eve ate from the tree of knowledge" (107), Fanny tells a terrified Charlie after telling him to go back to the way he was. Thing is, she doesn't really tell him why it's evil or what the story even means. Charlie has to puzzle this out for himself throughout the whole book, and he never really gets his answer.
Quick refresher on your Bible trivia: Adam and Eve chowed down on an apple from the tree of knowledge after God told them it was off-limits. Voila, they were banished from Paradise and forced into the cold, hard world. Of course, that gets us to Charlie's number-one fear—it's hard to be alone in the world, and Charlie's intelligence has secluded him from everyone else. A big bite from that metaphorical apple landed him in a world of hurt.
But did Charlie really choose to chomp on that apple? Symbolically speaking, it was shoved into his mouth by Nemur and Strauss, thereby putting a whole new spin on the Adam and Eve story…. So does Charlie get a pass here? Maybe, maybe not. We know he wanted more than anything to have the surgery, but he was mentally unable to make that decision, and as a result he has a deep conflict about whether he's really made a deal with the devil.
When Charlie picks up Paradise Lost after he's mostly regressed, he can only remember "it was about Adam and Eve and the Tree of Knowledge" (17.289) but he can't figure out what's going on. All his conflicted emotions about gaining illicit knowledge are gonezo, replaced by a vague sense that the Tree has significance in his life. We might say that while Charlie has lost his intelligence, at least he also got rid of something heavy weighing on his conscience—it's a small consolation, but at least he's got something.