So [1] claims "A variant of fully homomorphic encryption scheme for Turing machines, where one can evaluate a Turing machine M on an encrypted input x in time that is dependent on the running time of M on input x as opposed to the worst-case runtime of M".

I admit understanding this paper is a bit beyond me. But, does their construction evaluate Turing machine conditionals by evaluating both branches? If it did, how could the running time be "dependent on the running time of M on input x as opposed to the worst-case runtime of M"? It seems to me that having to evaluate every branch irrespective of the input would result in the running-time always being M's worst case, not varying runtime depending on the input.

[1] https://eprint.iacr.org/2013/229.pdf

I think this is a different approach to FHE that concedes to timing based side channels to get this speedup.