The problem is that transitive builds up a relationship between a functor and it's variables by trying to unify them with already known facts. But no new fact is generated.

     transitive(Functor) :-
       Rel1 =.. [Functor,A,B],
       Rel2 =.. [Functor,B,C],
       Rel3 =.. [Functor,A,C],
       call(Rel1),call(Rel2),call(Rel3).
 
     descendant(a,b).  #fact1
     descendant(b,c).  #fact2
     transitive(descendant) ;; says 'no'
     descendant(a,c).
     transitive(descendant) ;; says 'yes'

This functor only tells us if the database has a transitive relationship recorded.

If one wants the truth to be derived from the first two facts one would have to say

     transitive(F,A,B,C) :-
       R1 =.. [F,A,B],
       R2 =.. [F,B,C],
       call(R1),call(R2).

which derives transitivity from the first two facts, the last relationship (R3) is what we want to conclude, not what we want to find in the database.

Neither call though, will derive from fact1 and fact2 that "descendant(a,c)." is true. To arrive there you would have to "assert" these (new) facts explicitly in the transitive(...) definition.

But Prolog is not my comfort zone, there might be (and probably is) a way out of that dilemma.