The new study suggests the reverse: that both mining and metallurgy might spur the rise of complex society.
Preferential access to exotic goods such as cinnabar and gold would have supported the rise of early leaders, Cooke said.
Yale University archaeologist Richard Burger said Cooke's research supports his hypothesis that trade in cinnabar contributed to the rise of the Chavín culture.
Since the Chavín herded llamas, Burger said, they would have been able to haul vermilion throughout the Andes.
"This [new research] was an independent body of evidence that never occurred to me, and it independently confirms the hypothesis," Burger said.
The Chavín, and later the Inca, covered themselves in vermilion for ceremonial purposes, Burger said. The pigment was also used to decorate gold objects such as burial masks.
By 1450, long after the Chavín had collapsed and as the Incas were expanding their reach, levels of mercury pollution in the lakes had spiked more than tenfold and the type of pollution recorded there shifted from cinnabar dust to mercury vapor, Cooke's study shows.
This suggests the mercury was being heated, though it's unclear why.
Cooke said there is no evidence that the Inca were using mercury as part of the silver or gold extraction process. Rather, he said, they may have been experimenting with how to produce vermilion paint more efficiently.
"They are actually driving the mercury out of the [cinnabar] ore and into a gas phase, and that is recorded as a shift in the kind of pollution that's registered both in the sediments and how far that pollution is traveling," Cooke said. He and his team found traces of vapor in lakes several hundred miles from the main Huancavelica mine, while cinnabar dust settled only within a few miles of the mine.
Burger said the increase in pollution from that period makes sense, because the Inca Empire encompassed an area more than three times as large as the Chavín territory and because vermilion pigments played a large societal role in Inca rituals and burials. As a result, mining would have grown substantially during Inca times.
But Burger believes the shift from dust to vapor likely correlates with the transition to colonial mining practices, which included smelting, even though the radiocarbon dates suggest that transition happened about a century before Spanish arrival. "Radiocarbon dates are really not sufficiently precise to distinguish between the late Inca and the early colonial," Burger said.
Jerome Nriagu, an environmental chemist at the University of Michigan who has compiled historical documents on the colonial use of mercury in Peru, said Cooke's study suggests mercury could have been used in silver production in pre-colonial times, especially during Inca rule. If so, the mercury pollution from smelting would have been lethal to the miners, he said. Cinnabar dust is lower in toxicity.
The three-millennia-long mercury mining tradition at Huancavelica—including a 450-year colonial history that earned the mine its nickname Mina de la Muerte (Mine of Death)—has likely left behind a poisonous legacy in this central Peruvian highland region, Cooke believes.
"We haven't done any direct measurements of mercury in fish or blood-mercury levels in the residents or anything, but I would suspect it is probably one of the more polluted regions in the world," Cooke said.
Today the known mercury pollution from centuries past "should be of some concern," the University of Michigan's Nriagu said.
According to Nriagu, mercury emissions averaged about 600 tons per year during Peru's colonial period, when mercury was used in silver amalgamation. That amount is "approximately equivalent to current emissions from China," Cooke notes in his new study.
Further research will be needed to determine the environmental effects of ancient Peru's obsession with this toxic substance.
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