In stark contrast with today's oceans—where cold, highly oxygenated water is drawn to great depths—Marshall and colleagues theorize that during the Permian period, the deep ocean may have become stagnant and oxygen poor. Since nearly all life depends on oxygen, this would have created a lethal chemistry dramatically different from today's.

It's an attractive explanation, but hardly the only one. In the past few months other research groups have reported evidence that volcanic activity altered the climate or that a devastating meteor hit the earth.

Late Permian thermal mode ocean circulation scenario. Here convection is triggered by cooling at the pole. The color map is the sea surface temperature, the overlapped contour is the stream function showing the pattern of horizontal flow. Note the marked difference between the haline and thermal modes in the pattern of circulation in the semienclosed Tethis Sea.

"If it had been easy to settle, it would have been settled long ago," says Knoll, adding that there have been only two extinctions of this magnitude in the last 500 million years. "Because this event was so unusual, you can trot out unusual hypotheses to explain it."

Given the paucity of observations, physical and biogeochemical models may offer the best way to constrain speculation. "It's best to build and study simple models first, and only then combine them together," Marshall notes. "What the Alliance computers help us do is to study the synthesis and connection between the component models in a comprehensive way."