In “The Tree of Life”, Terrence Malick refers to two ways of life: the way of nature and the way of grace. This is no doubt in the tradition of Aquinas (as “taught by nuns”). This grace is a gift from God, which perfects nature, and is embedded in nature. Nature is not totally autonomous and isolated nor totally corrupted, but God is immanent, incarnate, and exercising providence through nature. For example, Proverbs 8:22-31 speaks of lady Wisdom’s role in creation, by which His wisdom is incorporated into nature. Note, incidentally, that this wisdom is a “tree of life” (Proverbs 3:18).
I believe a roughly equivalent presentation of these two ways, perhaps more comfortable for Protestants, is that of living according to the Spirit versus living according to the flesh (Romans 8:1-17). Revelation by the Spirit supplements empirical sensory experience. When we are open to and responsive to such revelation from the Spirit, we can see God and His love in the book of nature. It is a knowledge acquired through empirical experience, but transcending such experience, by grace, or by the Spirit.
In “The Tree of Life”, there is a remarkable scene in the sequence on creation where the dinosaur spares the life of it’s prey. It reveals nature and its evolution as involving something more than rivalry for survival, “red in tooth and claw”. It reveals an element of grace. Some biologists surmise that sociality and a kind of altruism developed solely because they have survival value for a species. But Malick seems to be saying here that there is something more – that there is something mysterious that comes from outside of nature, the mystery of grace (or the gentle breathing of the Spirit). And part of our own personal journey in life is to acquire the eyes to see, and to become responsive. The mother in the story, and the brother, had the vision to see it clearly, and they walked according to it. The father came to this awareness much later, and regretted the wasted years when he was blind to it. He had lived most of his life in vanity, “under the sun”, as described in Ecclesiastes.
The story is about seeing that there is something more to life and to the world than our superficial “under-the-sun” experience, to see that there is grace in the world; and even to see it, and to learn of it, in the tragedies of loss – perhaps especially in such tragedy. When they asked God, “where were You?”, God replies with the same question, as He had done with Job: “Where were you when I laid the foundations…?” (Job 38:4). This challenge stimulates a train of thought that opens the eyes and opens the heart. The laments in scripture are similarly confessions of those who sank into the lowest depths of grief and despair, but who then rose up to the highest expressions of faith and hope in God (e.g. Psalm 22, 102). That is the same dramatic arc that we see in “The Tree of Life”.