There is metaphysics in science, but not everyone acknowledges this. A recent paper by Fredrik Andersen and Jonas R. Becker Arenhart, published in Metaphilosophy, argues that Physics is no exception and that all successful scientific research presupposes metaphysics.
A philosophical controversy is whether we should adopt a “metaphysics first” approach, where metaphysics is seen as our most fundamental assumptions, or whether the role of philosophers is to wait for scientists to tell us what the world is like before deciding on the ontology. In this paper, Andersen and Arenhart argue for the first view against the naturalistic metaphysics proposed by Ladyman and Ross in their book Every Thing Must Go.
Causality, Complexity and Evidence in Health Sciences 