Final answer:
Descartes used the analogy of a tree's roots to illustrate that metaphysics is the foundational part of knowledge necessary for the flourishing of all other sciences.
Step-by-step explanation:
René Descartes emphasized the importance of theory using the analogy of a tree's roots. In this analogy, Descartes compared the entire body of knowledge to a tree. He explained that metaphysics forms the roots of the tree, physics represents the trunk, while the branches are the specific sciences like mechanics and medicine. This analogy was meant to show that a strong foundation in metaphysics is essential for any other sciences to grow and flourish, just as the roots are essential for a tree's growth and stability.