'Orphan Black' recap: The most confusing thing that happened this week (Season 2, Episode 7)

At first, the main question going into this week is: Who's really running the show at the Dyad Institute? Rachel Duncan or Dr. Aldous Leekie? At times, it seems like Leekie is scared of Rachel (like when he assures Cosima he'll keep running the treatments, but won't tell Rachel). Other times, Leekie seems so evil that Rachel better watch out.