Even to this day, the highest academic degree in sciences is a PhD (Philosophiae Doctor, or teacher of philosophy).
Thomas Jefferson lists the "sciences" that interest him as, "botany, chemistry, zoology, anatomy, surgery, medicine, natural philosophy [this probably means physics], agriculture, mathematics, astronomy, geography, politics, commerce, history, ethics, law, arts, fine arts."
Medicine has from the earliest days of learning institutions in Medieval Europe been treated as separate from philosophy and was award a different diploma so as not to confuse it with "real" medical sciences such as zoology, botany, anatomy, etc.
This distinction is maintained to this very day in the degrees awarded—MD for medicine (requires no dissertation), and PhD for medical sciences (anatomy, physiology, pathology, etc.)