Sheldon hires Alex, a female grad student, to comb through his childhood journals for ideas with the most scientific merit. This episode's log line said that Amy would feel threatened by Alex, but more significantly, after seeing Leonard and Alex talk in the cafeteria, Penny felt threatened.
The gentle pressure on Penny to face her feelings for Leonard continued for a third straight episode. Amy's prodding helped Penny discover she was bothered by how easily Leonard and Alex talked.
From Leonard's perspective, the conversation was innocent, though he probably wouldn't have had the confidence for it in earlier seasons. Since Season 3, we've known he loves Penny. How Penny feels in return is still in question. If she doesn't find the words, she may very well lose Leonard.