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WITWATERSRAND BASIN, South Africa — A mile down in an unused mine tunnel, scientists guided by helmet lamps trudged through darkness and the muck of a flooded, uneven floor. Leaning a ladder against the hard rock wall, Tullis C. Onstott, a geosciences professor at Princeton, climbed to open an old valve about a dozen feet up. Out flowed water chock-full of microbes, organisms flourishing from heat generated from the interior.