As if the whole reading "Moreau" to a 7 year old wasn't creepy enough, to find it was his secret notebook takes it to a whole other place. I suppose it's now turned into Chekov's Book and we just have to wait until it goes off.
And while i think "Tony" was something of a stunt - even with his secret message - kudos to the writers for figuring out how to have a male clone in a completely different way from what I'd thought they'd do. I like that the transgender part just adds a variable to the "what parameters were they messing with in the petri dish" to come up with as wide a range of personalities, abilities and issues out of the same basic genes.