It is that science is an inherently limited view. The limitation is the requirement for a completely mechanistic description of the universe to exist. The major conflict between theology and science is where the boundary lies. Roger Penrose believes the mechanisms are not quite known. Both are scientific positions.
Theology generally believes that consciousness derives from something transcendent.
The problem for theology is that it is difficult to say where science's boundary lies, as science may make progress and identify apparent mechanisms in areas that theology didn't anticipate. For example, theology's non-mechanistic view of consciousness might become obsolete in light of new scientific discovery. Theology has occasionally been wrong on these types of points before. My own view of the universe is that the issue is not drawing the line between areas of application, but the level of description. I think that the relationship of science to reality is like the relationship of newtonian mechanics to quantum mechanics.