I'm thinking that, as abstract as it sounds, the birds or pidgeons are a clue. Infact, I think they are the big "clue" at the end of episode 1, which Heller said wouldn't make sense in context. I say this after episode 2 because we got another shot of pidgeons/birds for no real reason that I could find...Lisbon and Jane are sitting on the bench, and Jane looks at the birds the lady is feeding. It's just strange...