Back in the Oregon forest, McCafferty pulled out a second mouse for the owl, whose beak was stained with blood from eating the first. Now that she’d had a snack, he hoped she would bring this one to her nest, finally revealing that there were, indeed, babies. Again, he placed a mouse on a log. Again, the owl swooped in and grabbed it. But again, she did not fly to the treetops, instead settling on a nearby stump, killing the mouse and caching it in the tree for later. She did the same with two more mice. Then she stared at the biologist, a stoic competitor in a blinking contest that began 11 years earlier, when McCafferty caught and tagged her with two ID bands on her ankles at a spot about 25 miles away. “I’ve got history with her,” he said.

The bird seemed both acutely aware of the people looking at her and intensely engaged with McCafferty in particular. She occasionally shifted on her perch like a posing teenager, revealing a personality typical of spotted owls, according to biologist Lowell Diller. Diller became engrossed with the birds in 1989, when he moved from an academic job in Maryland to work as a consultant for a northern California timber company, now called Green Diamond Resource Co. With spotted owls about to be listed under the Endangered Species Act, the company had an imminent problem: Its land was teeming with the birds.

Diller’s first task was to survey the property for spotted owls. He quickly fell for the animals, which are sharply intelligent, charmingly interactive and mesmerizing to behold. “It’s hard for a biologist who cares about animals to study spotted owls and not fall in love with them,” he says. “They’re amazing birds. They’re icons of mature forests. They’re so charismatic.”

His findings, which came out just as the listing decision was being made, were surprising. As with all things owl at the time, they were also contentious: spotted owls were doing fine in Green Diamond’s managed redwood forests. Conservationists reeled at the results, fearing they would give loggers free reign to decimate ancient forests. On the flip side, many local residents worried that the quest to save owls was going to rob people of jobs. As the situation became increasingly politicized, Diller’s personal life suffered. Once a revered professor, he was blindsided by the sudden prejudice he faced. He was accused of being a “biostitute”—selling out to his employer, willing to say anything for money. One salesperson at a local camera store refused to help him when he explained why he needed to take photos of the treetops. “She said, ‘Oh, you’re that kind of biologist,’ and she turned and walked away,” Diller recalls. “She left me standing there and wouldn’t sell me camera equipment because I worked for a timber company.”

Those ruffled feathers had mostly settled by the time Diller got a call, 17 years later in 2006, from Jack Dumbacher, a molecular geneticist at the California Academy of Sciences in San Francisco. Dumbacher had been talking with Fish and Wildlife officials about trying some barred-owl removal experiments to find out whether the birds were pushing spotted owls out or simply filling in the spaces left behind by the spotted owl declines. In an early test, they removed a few barred owls from Oregon’s Klamath National Forest. But public opposition quickly stopped the effort, and the wildlife officials introduced Dumbacher to Diller instead. On Green Diamond’s private redwood forests, they would be able to circumvent some of the legal and political pressures that were likely to hold up their work on federal lands. Working for a museum, Dumbacher could also get permits to kill as many as 20 individuals of a species for his collections. Diller joined Dumbacher in the field over two cool, foggy nights in May 2006, during which Dumbacher shot three pairs of barred owls. Diller couldn’t watch. “It seemed so wrong,” he says. “I had to turn away.”

It was harder to ignore what happened next. In every place where Dumbacher had removed barred owls, spotted owls appeared, often after long absences. One banded individual that hadn’t been seen in three years greeted Diller at its original roosting site just 13 days after Dumbacher’s visit. It was powerful, if anecdotal, evidence that Diller thought was worth testing with a controlled experiment. Soon, he was pulling the trigger himself, eventually killing more than 80 barred owls over the next few years in three treatment areas on Green Diamond land near the Pacific coast, in California’s Humboldt and Del Norte counties.

The results were dramatic. Compared to similar plots of land where spotted owl populations continued to decline, in the treatment areas, the birds rebounded. Although it was a small pilot study in a region where barred owl numbers are relatively low, the findings offered support for the new experiment to try removals both on a larger scale and in other, more typical, parts of the owls’ range throughout Washington and Oregon.

“The pressing question is whether similar results can be obtained in other conditions,” says Wiens, the USGS biologist, who is in charge of removals in the Coast Range region, “because it has become clear that, without management intervention of some kind, spotted owls will be lost in most if not all portions of their range.”

Killing animals in the name of conservation has become common practice, both in the U.S. and abroad, often in cases where invasive species have wreaked havoc on ecosystems. In recent years, government agencies have killed, issued permits to kill, or considered killing: ravens to save desert tortoises, hawks to save Hawaiian crows, mute swans to protect New York’s ducks, geese and other water fowl, and sea lions to protect salmon, which are also getting assistance from the systematic killing of cormorants, Caspian terns, and northern pike.

Some culling efforts have helped, like the removal of parasitic cowbirds in the Midwest to protect willow flycatchers, Kirtland’s warblers and other birds. Others have been disastrous, like the removal of feral cats in Tasmania, which only caused more cats to creep in. Many have been controversial. And while it’s not so hard to convince people to accept the killing of dangerous or unappealing invasives, like Burmese pythons in the Everglades (which has taken on festival-like status), killing animals that are cute, fluffy, or charismatic is a harder sell, even if the animals are raising all sorts of hell.

When the U.S. Fish and Wildlife Service started to consider an experiment to kill barred owls on federal lands, it was clear they would need to manage emotions as much as they needed to manage the animals. “We knew any kind of removal of something as charismatic and fuzzy and brown-eyed as a barred owl, no matter how good the data, was going to be uncomfortable for people,” says Bown, the Portland-based FWS biologist.

To preempt the fallout, the FWS went on a public-engagement offensive in 2009, organizing workshops in Portland and Eugene with a diverse list of guests that included representatives from conservation groups, tribes, timber companies, and animal welfare organizations, as well as scientists and a bioethicist named William Lynn. Participants discussed a variety of non-lethal alternatives—sterilizing barred owls, luring them away with food, capturing them to keep in captivity. And they discussed the potential downsides of those alternatives, including stress for the animals and costly or unrealistically labor-intensive work for the researchers. Bown had already conducted a nationwide search for facilities that would take captive barred owls and found homes for fewer than 10 individuals.

Lynn, who is based at the Marsh Institute at Clark University in Worcester, Massachusetts, led the ethics conversations, aiming to help the people involved use logic instead of emotions to make decisions. Ethics reviews force a hard look at moral values—like an aversion to killing animals or an affinity for native species. In the style of a Quaker meeting, Lynn listened to everyone and then articulated what he heard them coming to agree on.

Rigorous ethical analyses are common in biomedical studies, but this was the first time one was applied to a federal wildlife management decision in the U.S., Lynn says. And that marked a profound shift toward recognizing the potentially devastating impact of environmental decision-making—and the tough position that ordinary scientists face when given the task of choosing between life and death. “These are absolutely tragic decisions—one way or another, there’s tragedy involved,” says Michael Paul Nelson, an environmental ethicist at Oregon State University in Corvallis who was not involved in the meetings but has watched the issue develop. “It’s not clear that people who have to make these tough decisions are trained or capable of doing it, and that’s putting them in a weird position.”

The Oregon meetings lasted for days, and Lynn noticed several pivotal moments, when participants on different sides of the issue realized they actually shared a deep caring for animals and that nobody was thrilled with the choices. In the end, consensus emerged that the removal experiment was worth trying as a stopgap measure, to prevent spotted owls from disappearing in the wild. Even the ethicist was moved by the experience, and came to realize that doing nothing would likely mean that spotted owls would go extinct. “I went in profoundly skeptical,” Lynn says. “This changed me.”

The official plan designates four study areas. During the summer and fall, research teams at each site conduct surveys to get a barred owl head count. Come winter, they then try to remove as many of those birds as they can. The killing must be done as humanely as possible, via a quick and clean shot and only when birds are in close range. Nestlings and parents with dependent young must be spared. “People were unwilling,” Lynn says, “to go in and massacre a family.”

Wiens, who is 47, uses a 12-gauge shotgun that was designed by Diller’s brother. It is equipped with a flashlight, red laser spotter and four-foot long silencing extension. Standing a lanky 6 feet 6 inches tall with a hopeful, kid-like face, Wiens had never held a gun before he went through extensive training for the experiment. The job still makes him uncomfortable. Still, it didn’t feel right to lead the study if he couldn’t do the dirty work himself. “I never envisioned myself doing this sort of thing,” he says. “I also believe that, to run an experiment like this, I have to know what it’s like. I still do it a limited amount because it’s pretty disturbing to me.”

It will take at least four years of data to know if the experiment is making a dent, Wiens says. In the meantime, he tries to focus on the good that stands to come from it. He plans to send some of his barred owl kills to universities, museums, and other facilities, including the Cal Academy, where Dumbacher and colleagues are investigating the effects of rodenticides on the birds and using genetic analyses to reveal new details about both owl species and the interbreeding that sometimes happens between them. (It’s another odd twist that adds yet more questions about what we should do when natural selection escapes our control.) The experiment might also benefit other animals that have been decimated by barred owl invasion, such as frogs, salamanders, and other owl species. Disrupted food webs are often overlooked with so much focus on birds.

Controversy over the plan has been surprisingly quiet, perhaps because the Fish and Wildlife Service has been so transparent about its motivations. Beneath the basic question of whether it’s okay to kill in the name of conservation, though, is a deeper conundrum that digs into the heart of the Endangered Species Act. The law was designed to preserve the diversity of life on earth—but it also mandates that listed species must be protected, no matter what. To do right by the ESA, in other words, scientists must sometimes cause harm—a paradox that may be cropping up with increasing frequency as conflicts between animals and people escalate.

By chopping nature into discrete species, the ESA also forces black-and-white thinking onto the fuzzy reality of the natural world. And that approach fails to accommodate changes that can occur with migration, natural selection, the merging of genomes through interbreeding, and other messy ecological processes—all of which are happening to owls on a national stage. If given a chance, Dumbacher says, the owls could force fresh conversations about what deserves protection and at what costs, offering an unprecedented opportunity to alter society’s deep-level thinking about how to make wildlife management decisions. What if a heart-tugging story about owls could get ordinary citizens to finally care about the gritty details of how evolution and conservation work?

Still, yet to be determined is how to define success, and how to know when to stop. As large scale as it is, the federal removal experiment is still relatively narrow in scope. It is not intended to wipe out barred owls from the West completely or to kill barred owls forever. Instead, the goal is to test whether barred owl removal in some areas will enable spotted owl populations to rebound. It may just be the first step in determining whether both species can co-exist, at least until biologists can find a more sustainable way to manage the situation. The project is capped by a 10-year timeline. Stopping early is always an option. Wiens suspects five years will be enough to know if it’s working.

Not everyone is on board, including Eric Forsman, the biologist who initially raised concerns about spotted owls in the 1970s and has argued vocally that the killing, even for a finite period, is likely futile. Another concern is that shooting barred owls will take yet more attention away from the habitat loss that slammed spotted owls in the first place, says Shawn Cottrell, northwest director of Defenders of Wildlife in Seattle and former executive director of the Seattle Audubon Society. His organization supports the federal experiment, he says, but he doesn’t want to see barred owls become a scapegoat for everything else that’s going wrong in the environment. “If we think we can solve the problem just by dealing with barred owls,” he says, “it’s not going to work.”

The uncertain finish line raises another lingering concern: if the experiment doesn’t work, will thousands of animals have died in vain? “There is an absolute absurdity to it, maybe a whole set of absurdities, like nested layers of absurdity,” says Nelson, the Oregon bioethicist. “Do we really believe we can fine-tune the world so much that we can predict how all these things will interact? Haven’t we learned that lesson?”