Which philosopher was Jonathan named after?
Assuming that all the chickens are related to Touko's friends, it becomes quite obvious who Jonathan is meant to represent.

Kakeru reminds Touko of Michelangelo's "David" and is often referred to by that name. In the Biblical story of David, his best friend is a man named Jonathan.

Jonathan is not a philosopher, but in the same way, Kakeru is not friends with Touko's other friends. It separates him from the others and Touko does pay more attention to that chicken.