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Our journey begins as we drive south from Arica on Route 5, part of the Pan American Highway that bisects the Chilean desert. It's a road of ghosts, littered with the skeletons of wrecked vehicles and roadside shrines to crash victims adorned with crosses and plastic flowers. No villages here, no rancheros, no fences: only a few scruffy rest stops called posadas, collections of flat-roofed shacks huddled against each other. The mountains—which look as if they've been skinned, showing vein and sinew—break the eerie flatness.

More than 10,000 years ago, when the Atacama's climate was more moderate, humans started to populate the region. Archaeologists have long known about the desert's coastal civilizations, such as the Chinchorro, and have recently found evidence of human settlements in some of the Atacama's driest caves and valleys. Life could not exist at these inland sites today: An immense and permanent high-pressure cell over the Pacific Ocean fends off weather systems from the west, and to the east Andean peaks drain moisture from clouds formed in the Amazon Basin. On the coast the cold-water Peru Current streams in from Antarctica and chills the desert air, creating a temperature inversion that further inhibits rain clouds.

The arid climate helped spur the desert's first period of industrial development. In the 1830s prospectors found surface deposits of caliche, a raw nitrate formed over millions of years. Without vegetation to absorb it or rainfall to flush it away, the "white gold" encrusted much of the desert's surface. Nitrates were urgently needed in Europe to manufacture explosives and fertilizers. British and other European mining companies arrived with know-how, and by 1895 the nitrate trade to Europe was thriving, supplying Chile with more than half its income.

Soon thousands of workers were migrating to the Atacama's hundred-plus oficinas salitreras (nitrate collection and processing depots), built in the starkest, most inhospitable parts of the desert. The nitrate-era laborers were a mixture of immigrants, unskilled rural workers, and unemployed men from overcrowded Chilean cities. "One great-grandfather came from Liverpool. My other great-grandparents were Swiss Germans," says Patricio Fischer. "Atacama immigrants were mostly young, making a break with their homelands."

In the last half of the 19th century, stiff-upper-lipped and ambitious English mining engineers set up their enterprises in the desert and imposed a culture of time clocks, tennis courts, and Sunday suits on their managers. Ordinary laborers were treated less well: Bosses exercised nearly complete control of workers, who were often paid with tokens good only at the company store. The nitrate industry soon became fertile ground for new, radical concepts of class struggle and labor unions. When the industry bottomed out in the 1930s, thousands of laid-off workers headed south to the cities with anger in their hearts and communist ideology in their heads. It was back to the desert that many Chilean communists would, years later, be sent to die.

In 1970 the nation became the world's first to freely elect a Marxist leader, Salvador Allende. He tried to help the poor by redistributing farmland among rural workers and nationalizing key industries. But his efforts triggered nationwide strikes led by the business community and well-to-do Chileans. Amid severe food shortages, Gen. Augusto Pinochet, a right-wing authoritarian, ousted Allende in a military coup on September 11, 1973. Pinochet's army took revenge on Allende supporters, casting a wide net to jail, exile, or execute tens of thousands.

Many of those who were exiled ended up in remote, throwaway locations such as Pisagua, one of the Atacama Desert's former nitrate-exporting ports. By the mid-1970s Pisagua was a concentration camp that ran out of jail space; the overflow of men were housed in a ruined fish-processing plant, and women were kept in the anterooms of a quaint old British theater.

The theater is still there today. I stop by shortly after we arrive in town and ask historian Catherine Saldaña Suárez, a bright, erudite woman, about the building's history. She says the rooms have been redecorated, the handwritten notes on the walls erased. "The mentality of Chileños is to fix things up. We don't want to remember how bad it was." But her eyes, shining darkly, betray her: "I think a lot," she says, "and there are some things I cannot forget."

Pinochet left power in 1990. One of his prisons here is now a hotel, its cinder blocks painted red and blue. At the town pier I meet Oscar Romero Gallo, a portly fisherman with a wreath of black hair framing wire-rimmed glasses. He has just published a book on the history of Pisagua and says that when people arrived here after the coup they simply disappeared. "I have a feeling that many were killed and put into the sea," Romero says carefully. "How many? I don't know, and I will never know."

At Pisagua's cemetery by the sea, where the thunder of breakers might stifle a scream, a symbolic open pit and bronze marker commemorates 19 people found there, murdered by Pinochet's troops.

The road from Pisagua returns to the haunting loneliness of the pampas and their deep arroyos. Some water in the gorges still reaches the ocean during the peak snowmelt season. We follow one anemic stream to the coast, where the pastel plywood shacks of Caleta Camarones, a fishing village, simmer in the sun like a set from a spaghetti Western.

Eighteen families have lived in Caleta Camarones since the 1970s. To grow plants they use saline river water—brackish from flowing over the desert's surface minerals. The grounds are littered with old nets, broken-down skiffs, and the hulks of cars that have succumbed to the rutted roads and sandstorms. The community's small fishing boats are anchored off a rugged beach, a five-minute walk from the village. Manuel Ardiles, a ruddy-faced fisherman with large, callused hands, isn't very optimistic about the future here. "I'd like to sell my boat because you really can't make money fishing anymore," he confides. "We want to start an aquaculture business here to grow abalone."

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