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The discovery of an eagles’ nest in Toronto is part of a larger story: the return of nature in modern cities.

The nest was spotted earlier this winter. Conservation authorities are not saying where for fear of attracting gawkers who might frighten the birds away. A male and a female were seen cartwheeling through the air together – part of their courtship behaviour – then adding sticks to a big nest in a tree. The Toronto and Region Conservation Authority says they are the first breeding pair of bald eagles in the city’s recorded history.

That is great news for the species. Just a few decades ago, bald eagles were under threat of extinction. Hunting in the 19th and early 20th centuries slashed their numbers. From 1917 to 1952, bounty hunters in Alaska alone killed more than 100,000. An even greater threat came after the Second World War, when the widespread use of the agricultural pesticide DDT caused the shells of their eggs to grow thin, leading many to break.

It is even greater news for the urban environment. In fact, it suggests we may have to start thinking about cities and their effect on the natural world in a whole new way.

Most people see cities as enemies of nature, blisters on the surface of the planet. For a long time, they were.

Early Toronto fouled its land, water and air. Tanneries, sawmills, slaughterhouses and distilleries turned the lovely Don River into the “Dirty Don.” Engineers filled in the teeming swamp at the river’s mouth, destroying one of the biggest wetlands on the Great Lakes. With houses and buildings heated by coal, the atmosphere filled with smoke, leaving buildings (and lungs) coated with soot.

It was the same in most other cities. In 1858 London suffered the Great Stink, when the smell from the polluted Thames, described in one account as “a bubbling vat of stinking filth,” reached the offended nostrils of members of Parliament at Westminster. As late as 1952, the British capital was struck by the Great Smog. A temperature inversion trapped the exhaust of countless coal fires, filling the street with a soupy fog that killed thousands.

But in recent decades, urban nature has been making a comeback. Many polluting industries closed down. Services, not manufacturing, are the engine of the modern urban economy. Today’s homes run mainly on natural gas and electricity instead of coal and oil. Thanks to emissions standards, automobile exhaust doesn’t clog the air the way it did.

The air and the water in places like Toronto are cleaner than they have been in generations. The smog alerts that used to be a regular occurrence in the city are a thing of the past, though air quality suddenly plunged during last year’s wildfires. Ontario’s last coal-fired power plant closed in 2014.

The water at Toronto beaches is clean enough for swimming most of the summer. Anglers pull bass, trout, walleye and pike from local waters. The Don and the Humber rivers have salmon runs again. The city is restoring the mouth of the Don, giving it a new, naturalized route into Toronto Harbour.

Coyotes can be seen trotting through High Park and the Leslie Street Spit. Vast flocks of waterfowl shelter in the protected waters of the Spit, where more than 300 species of bird and 50 varieties of butterfly can be found.

So the image of cities as a plague on the planet is out of date. At least in rich countries, and increasingly in those that are growing rich, cities are becoming cleaner and greener all the time.

Those who live in them consume less energy than those who inhabit sprawling suburbs and exurbs where the houses are bigger and more expensive to heat and you need a car to get around. They are more likely to take transit or walk. Their environmental footprint is smaller. Densely built, high-rise districts like downtown Toronto are especially good for planetary health.

Those two majestic eagles are keeping watch from their big nest of sticks and limbs. If all goes well, they will be joined by hungry eaglets this spring.

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