Consider Jessica Chastain’s opening monologue on the “Way of Grace” and the “Way of Nature”. I believe the message of The Tree of Life lies in these distinct concepts.
Ms. Chastain, as Mrs. O’Brien, is the film’s manifestation of the former ideology: kind, unconditionally loving, and readily willing to take insult and abuse.
Brad Pitt, as Mr. O’Brien, epitomizes the latter ideology: harsh, self-centered, and mainly concerned with his own comfort and satisfaction. The strong clash of the couple’s personalities sparks intense frustration and confusion in their son Jack. The boy’s torrential waterfall of emotions forces him to let go of his childhood innocence very early on.
Jack’s bitterness with discovering the imperfection of human life seems to stick with him into adulthood; at least, Sean Penn’s performance
as the adult Jack suggests such sentiment.
However, with intense contemplation of his mother’s words regarding the “Way of Grace” (leading into the dream sequence on the beach), Jack finds the solace he had been searching for. He realizes that life is full of imperfections, but he can make the best of them
by living life with a sense of love for all he meets. He may not have control over the entire world, but he can control his part of it. through kindness.
Regarding the early part of the film, I believe Mr. Malick was attempting to create a point of comparison between the development of Earth
and the development of the O’Brien family. It’s arguable that this wasn’t an entirely successful attempt, though its good intentions are evident.