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One hint is found in Port Neptune, on an audio diary from Chief Sullivan under a dock behind a turret. The entry reports that the bathyspheres are locked down with genetic locks that allow only Ryan to use them -- but due to a flaw in the locks, any relative of Ryan can use them.

In Fort Frolic, in back of the pole dancing stage of Eve's Garden, the hallucinatory scene, the flashback and the tape under the bed of the doomed Jasmine Jolene strongly imply that Ryan was the father of the embryo that Fontaine bought off Jolene using Dr. Tenenbaum as his agent.

In Hephaestus, after boiling away the water with magma, as you move through the corridor to the core platform, and as Ryan talks to you, you have a flashback of Jack's family that focuses on his father.