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Renowned Brazilian environmentalist Chico Mendes poses outside the headquarters of his rubber-tappers union in 1988. Dec. 21, 2013, marks the 25th anniversary of his killing.Reuters

Three days' journey by boat away from his home in the rain forest, Herculano de Oliveira sits in a cramped office and works painstakingly to protect his trees.

A local environmental institute has taught him – the son of illiterate parents, with just a few years of education himself – to translate his intimate knowledge of the forest into GPS points and maps. Mr. De Oliveira, a slight, diffident and determined 24-year-old, has plotted all the damaged points in his patch of forest – a designated conservation area – and brought them to the nearest town. Here he works with a geo-processing expert, hunched over a map to match those points with satellite images that show a decline in forest cover and rough roads made by illegal loggers and those who seek to clear the forest to raise cattle and soybeans.

Mr. de Oliveira compiles a file, and takes it down the street of this sleepy frontier town, to report to the Chico Mendes Institute for the Conservation of Biodiversity – a conservation authority named after the forest's most famous defender.

Mr. Mendes was another rubber tapper's son, who in the 1980s rallied tens of thousands of his people to confront illegal ranchers at the height of rain forest destruction. The international community feted him but his own government ignored the turmoil on his land; as his fight intensified, so did threats on his life, and in early December, 1988, he warned that he would not live to see Christmas. He was killed by a shotgun blast to the chest by a rancher as he walked out of his small house, 25 years ago today. It took 15 more years for Mr. Mendes' vision to be realized. In 2003, the newly-elected government of Luis Inacio da Silva set aside 485,000 square km of acres of forest as national parks, conservation areas and "extractive reserves." Mr. De Oliveira lives in one of these, the kind of reserve that Mr. Mendes championed – where traditional communities of rubber tappers, nut-gatherers and indigenous people are permitted to live in and use the forest sustainably. The institute named for Mr. Mendes was charged with defending it all.

Logging, agricultural and mining are banned in these areas, and consequently the pace of deforestation has slowed from the ferocious rate of the 1980 and 90s. But the Amazon basin – home to 10 per cent of the world's plant, animal and insect species – remains the site of some of the fastest forest degradation in the world, as Mr. De Oliveira's painstakingly plotted maps make clear.

From August, 2012, to March, 2013, 49 of 660 protected areas in the Amazon experienced new logging or farming activity – that's seven per cent of the total – and 208 square km of forest were destroyed, according to Imazon, a non-profit research institute that tracks deforestation and forest degradation. That is a 41-per-cent increase over the same period between 2011 and 2012, a hike largely driven by work on infrastructure megaprojects such as the Belo Monte dam, here in Altamira. Six of the 10 areas in Brazil experiencing the most intense deforestation are in this state, Para, which is also the mining capital of the country, and where politicians have a notoriously cozy relationship with the resource business.

Maurício Torres, a former professor of human geography with São Paulo University who now lives in Para and studies its deforestation, called the Chico Mendes Institute a mockery of what the late activist stood for, a fig leaf of enforcement. (Just four agents are charged with protecting 6.5 million acres of forest around Altamira, he noted.)

"To put one person, without any logistical help or infrastructure, to monitor 700,000 acres of land is to pretend to protect these areas," he said. "The minister of environment has no political will [for conservation]. She is there merely to ensure that the environmental issues don't get in the way of the government interests [for extraction and infrastructure megaprojects such as the giant Belo Monte dam]. Loggers, he said, are the largest donors to political campaigns in Para. And indeed when institute agents busted up a large illegal logging ring earlier this year, the deputy mayor of the region was allegedly found to be at its head.

Roberto Vizentin, the head of the institute, said in a telephone interview from Brasilia that government has given them the budget to double the size of their enforcement staff next year and denied that the federal government is not sincere about protecting the forest. "It's not only propaganda: We have deforestation under control," he said. "We came from having 27,000 square km of deforestation every year to having about 5,000." A couple of months ago, Maitê Guedes, one of the four institute agents in Altamira, was out in a boat on the Xingu River checking on her forest when she got a radio call – a rubber tapper in an extractive reserve was reporting illegal activity. She had the boat pilot rush back to town, where she collected a detachment of four military police officers. They headed back down the river, where they came across a canoe full of armed men, caught in the act of using GPS equipment to demarcate a tranche of river-front protected forest.

The police confiscated the men's weapons, and escorted their boat back to Altamira to arrest them; Ms. Guedes was relieved that it went off peacefully, for that's not always the case. It was up to her to compile the evidence of what those men were doing in the forest – and often, these days, it's not as simple as just cutting down its valuable trees. They were, she suspects, mapping the land in order to register it for a grileiro, a land thief, who would then present the phony claim as a sort of deforestation offset credit for land he plans to deforest elsewhere, a practice accepted in the new forest code adopted in 2012.

That was a good day, that arrest. But over the following days, there would be plenty more calls about illegal logging – and Ms. Guedes can't get to all of them.

A lawyer-turned-conservationist, Ms. Guedes has wide-set eyes behind rectangular black glasses and a rueful grin that reveals braces: she was five when Mr. Mendes was murdered.

"The human conflict from that era hasn't been resolved at all – these reserves all see illegal logging on their land, and that means there is also conflict," she said. Last year a logger who had a change of heart and reported illegal activity in Mr. De Oliveira's reserve was murdered, allegedly by his former colleagues.

"They tell us, 'If you don't sell me this wood, I'm going to buy it from your widow,'" explained Mr. De Oliveira.

He will soon leave the town, armed with his new mapping skills, and head back to the forest: the environmental group supporting him, the Institute for Social and Environmental Studies, has put in a satellite Internet connection an hour by boat from his home, so he will be able to track the trees and report illegal activity from there.

"People who say we don't belong there don't understand that the forest is still standing because we are there," he said. "We know a bit about the world now and we know there is environmental stress in many places – that there is not enough rain in some, that the weather is changing. We live in a bit of the world that still has the forest and we can protect it."

Mr. Vizentin, the institute head, knew Chico Mendes at the height of his activism and thinks from time to time about what he would say about the work now done in his name. "I think, first, he would say that the fight was worth it." Mr. Mendes dreamed of extractive reserves, and of environmental policy that emphasized conservation, he said. "But if Chico were still alive, I expect he would be even more mobilized … to create more protected areas, new conservation units. Because the agriculture areas [in the Amazon] are still growing."

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