The human body is like a crossword puzzle. Every piece has its place, and each must be working properly by itself and in relation to all the other parts in order for the body to come together and do its job.
The science used to explain life is the same way. Biology, Physics, Chemistry, Genetics, and so on, all the sciences work together in the universe to make a coherent whole. That coherent whole is the machinery of the universe.
So what happens when one piece of science or scientific theory contradicts another? Just like the crossword puzzle, the pieces need to be rethought.
One major example is that science needs to explain the contradiction between evolutionary biology and the second law of thermodynamics. The biology says that everything is evolving into something better and more improved, but the physics says the whole universe is not improving but deteriorating.
If you try to solve the problem by asserting that the fittest evolve against the flow of deterioration, you are denying the very laws you are trying to support through your naturalistic worldview. Naturalism tries to show that the universe is based on definite scientific laws that explain everything. But if your science doesn’t sustain those laws, your worldview is still out of line. To use another game analogy, your worldview is still in checkmate.
How does this conundrum get fixed? By rethinking the pieces.