Several States Investigating the Catholic Church

There appears to be confusion in people’s heads about ontology (the way things are as we find them) and ontogeny (how things got to be the way they are). This makes it hard to talk about origins, because what things are now, become how they have always been. This is not so much a well reasoned argument, as a rigidity of thinking.

With their strong sense of ontology, this is a prominent in conversations with Thomists. See: A Catholic Approach to the Genealogical Adam.

Has this problem come up before in any other context? What is the best way to overcome it?