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Board Thread:Assassin's Creed general discussion/@comment-26314858-20150714112803/@comment-2112031-20171112170125
I think it's safe to say that the Father of Understanding is more of a title and an idea rather than an actual entity. It symbolises the Templars' goals and ideals. Lucius referring to Caesar by that title could simply indicate that he thought of him as the embodiment of what the Order strove for with regard to creating the ideal society.
Of course, the religious members of the Order could just as easily consider the Father of Understanding to be whichever deity they believed in.