As I understand it the first three are just achievements that are optional.
To graduate you must earn enough TT (some un-yet-known value) in the skills of anatomy, geology, AND/OR engineering.
(even these three are somewhat debatable as a soc mate was testing them the other day).
The discipleship bar, which can be found by right clicking then going to system > mentoring, tracks these skill gains on a percentage of completion with 100% being the level of graduation.
JEHU