The scientist's understanding begins from the outside and attempts to figure things out from the inside, from the bottom up. They start with a subjective, empirical reality and try to deduce an objective model.
The wisdom of the Torah begins from within and unfolds outward, from top to bottom. In this approach, you meditate on the objective model of the Creator Himself and apply it to uncover the truth behind this world.
The good scientist will realize that he can benefit greatly from combining both approaches.