With The Tree of Life, some would assert - as if it is self-evident - that "the film" sets up a nature/grace dichotomy. (Usually the next step is to grant that it's a simplistic binary, etc.) But I am not convinced that it is "the film" which does this. The binary itself is associated with the character of the mother, Mrs. O'Brien. It is her voice-overs which introduce and maintain the concept, and I think it is a hasty rush to judgment which presumes that "the film" aligns her with grace and Pitt with nature. "The film" - if we attend to what's up on screen, and on the soundtrack - instead associates the the nature/grace distinction as a binary with Jessica Chastain's character.
One of the opening segments depicts what we might presume to be Mrs. O'Brien's childhood - we see a ginger girl on farmland. Why does this sequence exist at all, especially when it bears no explicit story relation - in dialogue or voice-over - to the rest? I suspect that its role is to ground Mrs. O'Brien herself in a specific milieu, to grant her character a bit (but a crucial bit!) of historical specificity precisely to circumvent the criticism that she's a long-suffering wife, i.e., more or less a sexist failing on Malick's part. But I think the glimpse we get of her upbringing, if indeed it is that, instead works to ground this character. She's a farmgirl, brought up with a Christian sense of love and grace. She remarks, when she introduces the nature/grace distinction in VO, that it is what "they" told "us." She was gettin' religion on the farm.
These very values - the ever-renewing sense of grace and acceptance, which also provide her with her almost saintly ability to be that long-suffering, quiet, ideal housewife. But the film does present us with cracks in the facade, and as Jack tells his mother, "You let him walk all over you." Pitt's Mr. O'Brien doesn't have a similar scene of his own childhood because of his dominating presence: we can draw out something about his background and his beginnings by looking at how he verbalizes, how he gestures and acts.
... We can maybe think of Malick as something like a "symphonic modernist." When I say this, though, I specifically want to avoid the vagueness that comes with airily gesturing toward Malick and his films as being "poetry," "poetic," "musical," etc. Maybe "symphonic" is not the best word. (But can we borrow from letters? To call Malick "literary" might just invite people to automatically assume that I mean "novelistic" ...) I use it to gesture, perhaps clumsily, to the way he organizes his material so as to construct meaning. In Tree of Life, there are "movements" (Mrs. O'Brien; adult Jack; birth of the universe; etc.). The connective significance of these movements is not narrative, though the film sort of tells a story. (But more primarily it organizes a web of experiences: this is something narrative does, but not all things that do this must be narrative.)