One morning in March of last year, I set out from Gulfport, Mississippi, on a three-week mission aboard the U.S. Navy research vessel Atlantis. The 274-foot ship, painted a crisp white and blue, stood tall in the bright sunlight. On its decks were winches, cranes, seafloor-mapping sonar, a machine shop, and five laboratories. Stowed in an alcove astern was Alvin, the federal government’s only manned research submarine. “Research vessel Atlantis outbound,” A. D. Colburn, the ship’s captain, reported into the ship radio.

The water was calm and the bridge crew quiet as they steered us into open water. For the…