The second wave was far more severe and may have happened over as little as 100,000 years.
The relative speed of the extinction seems to rule out gradual processes, like plate tectonics, as the cause. Instead, clues point to a sudden, catastrophic event, such as an extraterrestrial impact.
A giant asteroid that slammed into Mexico's Yucatán Peninsula caused the last mass extinction on Earth, spelling the end of the dinosaurs some 65 million years ago.
The entire global ecosystem collapsed as dust from the impact blocked out the sun and blanketed the planet with thick ash, most scientists believe. (Get the opposing side of the debate: "Yucatán Asteroid Didn't Kill Dinosaurs, Study Says.")
But no spike in iridiuma metal that is rare on Earth but common in meteoritesor other telltale minerals have been found in the geological evidence from the time of the Permian extinction.
Most important, no physical evidence of an impact, such as a gigantic crater, during that period has been found anywhere on Earth.
"Most of what we know [about the Permian extinction] is consistent with [a meteor] impact, but we don't actually have any evidence that that's what happened," Erwin said.
Instead, Erwin believes the answer can be found in the Siberian flood basalts.
The largest flood basalt region in the United States covers most of southeastern Washington State, stretching from the Pacific Ocean and into Oregon.
The eruptions of the Siberian flood basalts, which lasted up to a million years, spilled lava across an area larger than the continental U.S.
Most notably, the eruptions happen to coincide with the Permian extinction.
The problem is that no human has ever seen this type of eruption, which is much larger than any regular volcanic eruption. Scientists don't know what the climactic effects of such an event might be.
"Correlation is not causality," Erwin said. "We would like to know how this volcanic eruption actually killed stuff."
Erwin suggests a series of possible effects, including acid rain, which may have been produced by the sulfur released by volcanoes.
Geological evidence also shows that the volcanic event destroyed a lot of coal in the area where the eruptions took place.
The heating of the coal would have released carbon dioxide and methane into the atmosphere, producing a serious bout of global warming.
"I think it's all of those things put together that explained how the Earth's [life] was wiped out," Erwin said.
Peter Ward is a biologist at the University of Washington in Seattle and author of an upcoming book, The Greenhouse Extinctions.
He says the geologic record indicates that carbon dioxide concentrations skyrocketed immediately before the start of the extinctions and then stayed high for a few million years.
"A byproduct of these major volcanic events would have been enormous volumes of carbon dioxide and methane entering the atmosphere, which would have caused a short but rapid interval of global warming," Ward said.
But other scientists are not so sure.
"Most of the explanations up until now have sort of been arm-waving without any real evidence," said Michael Rampino, an earth scientist at New York University in New York City. "We have no smoking gun for the Permian extinction."
One thing is certain: Earth was a pretty bleak place to live at the time.
"The recovery from the mass extinction didn't even get started for four million years, and then it took another 10 to 20 million years for life to get diverse again," Erwin said.
"That's in remarkable contrast to most other mass extinctions, where the recovery is going within a few hundred thousand years."
Erwin says "recovery" may even be the wrong word to describe the process.
"Ecosystems of the Permian didn't recover, they're gone," he said. "Life had to construct new ecological relationships. This was a turning point in the history of life on Earth."
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