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Let’s get the obligatory Terrence Malick comparisons out of the way: To anyone familiar with Malick’s work, Shane Carruth’s “Upstream Color” will appear to be an admiring homage to Malick’s poetic style. Visually and sonically hypnotic, it’s an intensely sensory blend of internal monologue and unsettling mystery, draped over a thin skeleton of plot approached so obliquely that it seems almost inconsequential.

That’s about as far as the comparisons go. Whereas Malick’s work is deeply and simultaneously rooted in both natural and spiritual worlds, Carruth’s long-awaited sophomore feature (like his highly acclaimed 2004 debut “Primer”) is another exercise in metaphysical science fiction. “Primer” put a cleverly resourceful, no-budget spin on time travel, and this time the multitalented Carruth (credited as director, writer, producer, cinematographer, score composer, co-editor and lead male actor) applies defiantly avant-garde style to a conspiracy yarn involving bio­terrorism and mind control, made possible by inserting fast-growing, parasitic worms into unsuspecting humans.

Two of those humans are Kris (Amy Seimetz, so memorable in the made-in-Seattle indie gem “The Off Hours”) and Jeff (Carruth), who are mysteriously drawn together by their shared and traumatic experience at the seemingly villainous hands of Thief (Thiago Martins), who cons a hypnotized Kris into emptying her bank accounts. Kris escapes with the help of a character named Sampler (Andrew Sensenig), a sound-effects artist and pig farmer who briefly steers “Upstream Color” into David Cronenberg territory.

Seemingly … apparently … experiments with pigs? Carruth offers few if any easy answers as to what exactly is going on (prompting the zinger, does even he know?), but forget all that. You’ll be better off letting Carruth’s arresting visuals and ambient score flow over you while pondering his extensive quotations from Thoreau’s “Walden.” Perhaps, in the final analysis, “Upstream Color” (a title as ambiguous as the movie) is the kind of puzzle one solves for oneself, in peaceful solitude and silent rumination.

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