OPELIKA, Ala. — All dressed up in a shiny new red shirt, little Opelika could not stand still in the anteroom of the City Council chambers. And who could blame her? In a few minutes she would meet the mayor of this Alabama city for which she is named. Her meltingly calm mother, Lily, ignored her fidgeting.

They were being honored this day for their community service, and midway through the presentation, as little ones will do, Opelika stole the show from the starchy lawmakers: She barked.

Opelika and Lily, yellow Labrador retrievers, are part of the Canine Performance Sciences Program at Auburn University, which breeds and trains dogs to use their powerful sense of smell to keep people safe. After a year of preparation, Opelika will probably be placed with a government agency or a private security firm to sniff out bombs, narcotics or other threats.

For about half of that year, she will live in a state prison, where inmates who have earned the right to work with the program’s dogs lavish time and attention on them to hone their detection skills and reinforce basic socialization.

It’s a lot for a 6-week-old puppy like Opelika to take on; most dogs spend their early months learning little more than how not to gnaw on the living room furniture. But program organizers say the regimen produces highly disciplined dogs whose abilities rival or surpass cutting-edge technology.

The dogs, mostly Labradors — a breed chosen for its sociability and physical resilience — emerge from the prisons “more mature mentally,” said Jeanne Brock, a chief instructor at Auburn. “They have more stamina and endurance.” And along the way, moments of startling humanity come to light: One older inmate, Brock recalled, cried when he met his puppy. “I haven’t touched a dog in 40 years,” he told her.

Moving Targets

A couple of miles from the verdant quadrangles of Auburn’s main campus sits the Canine Performance Sciences building. Its otherwise humdrum conference room is crowned with the skin of a 13.5-foot python caught in the Florida Everglades, where Auburn dogs stalked invasive snakes.

For many years, dogs here were trained to find improvised explosive devices — homemade bombs — that had been planted in a parked car or stashed in a village bazaar. That focus changed somewhat about eight years ago, when Auburn’s scientists and trainers were approached with a new challenge: how to detect an IED that is on the move, carried by a would-be bomber.

“The first application we were pointed toward was mass transit,” said Paul Waggoner, a program co-director. The idea was to preserve crowd flow while identifying suspicious individuals. If you make people walk through checkpoints like the kind in airports, Waggoner explained, then “mass transit becomes nonmass transit.”

What was the most effective way, Waggoner and his colleagues wondered, for dogs to patrol crowded areas? They found their answer in the work of Gary Settles, a mechanical engineering professor at Penn State whose research had shown that humans produce thermal plumes that emanate from our bodies and entrain gaseous particles. Most of these particles, like traces of perspiration or perfume, are benign, but the plume can also betray contact with hazardous materials, like those used in bombs. Instead of screening each person, then, the dogs could inspect the “human aerodynamic wakes” that trail behind people in motion and alert a handler to the presence of explosives.

If that sounds fairly straightforward, “it’s a bigger challenge than you think,” Waggoner said. “Dogs naturally want to interrogate things and people, and not open space.”

Among the first animals trained under the new protocol were dogs deployed by Amtrak in 2007, and the rail service has used more than 70. Dogs schooled in vapor wake detection have also guarded the New York City subway system, presidential inaugurations and sporting events at Busch Stadium in St. Louis.

Buoyed by the dogs’ advances in tracking air currents, Waggoner and Craig Angle, a co-director of the Canine Performance Sciences Program, began experimenting with even more elusive targets, including pathogens. In a video shown to a visitor, a dog named Baxter sniffs at the cabinets in a vacant house used as a research site, alerting when he finds a swab of a nasty cattle virus. Researchers are interested in, among other things, whether dogs can be used to find viruses that affect livestock, in the hope that ranchers would no longer need to destroy entire herds to eliminate a few infected animals.

No one knows precisely what makes a dog’s sense of smell so sensitive, but Waggoner and others say olfaction may be “the most ‘preserved’ sense — it’s probably the most ancient one.” Dogs’ eyes and ears remain closed for about 14 days after birth, Waggoner said, but “pups come out smelling; that’s how they interact and get around the world.”

By most estimates, dogs have 40 times as many olfactory receptors as humans do — 220 million versus 5 million. Studies using rats, another animal with superior smelling abilities, have indicated that even when 95 to 98 percent of the receptors are degraded, a sharp sense of smell remains intact.

Yet what might be most striking is not that dogs can detect odors at parts per trillion (“like a splash of Kool-Aid in a swimming pool,” Angle said) but that they can discriminate among so many scents. Arson investigators have witnessed this for years, as dogs sift through smoldering ruins to find accelerants. “Think of it like picking out someone’s voice in a crowded conversation,” Waggoner said. “Dogs can detect a very small sample amidst a lot of odor noise.”

A Dog’s Brain

Since their program’s inception, Auburn’s trainers have known that the dogs must be continually rewarded, primarily through toys and verbal encouragement, when they have given an alert they have found a target odor. Until recently, however, the scientists could only speculate on the brain activity behind the dogs’ extreme drive.

That picture is becoming clearer now, through a neuroscience project financed by the Defense Advanced Research Projects Agency. In the study, Gopikrishna Deshpande, Waggoner and their colleagues are using functional magnetic resonance imaging recordings to better understand what happens in a dog’s brain when the animal is presented with odors and with photographs and videos of human faces. (Auburn is one of only a handful of sites studying fully awake, unrestrained animals with MRI, largely because it takes months of painstaking training to get the dogs to lie with the stillness the machines require.)

Deshpande said early data revealed that dogs presented with a learned odor show increased activity in two brain areas: the hippocampus, where memories are stored, and the caudate nucleus, which is associated with rewarding feelings. “Say you eat something good, or buy something that makes you feel good,” he said. “That part of the brain will show blood flow.”

They are also focusing on the default mode network. The more integrated the network is with the rest of the brain, the higher the likelihood of “referential thinking,” a foundation necessary for sophisticated emotional states, like empathy.

Though the research is in its early stages, Waggoner said it could have implications for identifying which dogs will succeed in detection roles and which will thrive as assistance animals.

Getting to ‘Left of Boom’

On a day cold by Alabama standards, a black Lab named Gus ignored the biting wind and sprinted through a pavilion in a grassy clearing at a training site to scrutinize half a dozen wooden boxes, each with a hole in the top. One of the boxes hid a powder that mimics explosive chemicals, and when Gus alerted on it, he was given a toy.

Gus and his sister Gala had returned to Auburn days earlier, after six months with their prison handlers. While Gus had immediately stood out, Gala was tentative, “a little more squirrelly,” said Terry Fischer, a chief instructor. As she hunted targets in the brush and gamy husks of felled trees, she looked to her trainer Bart Rogers for help. “Coyote or whatever else she’s smelling out here, it just shut her down,” he said.

In the next few weeks, Fischer and Rogers would work with the dogs on increasingly challenging tasks, adding to the number of boxes and then moving on to vehicles and complex settings like warehouses and power plants.

If one of the Auburn research projects proves viable, dogs like Gala will no longer be able to seek aid from their handlers. Borrowing driverless-car technology, the scientists are exploring ways to set dogs off on their own. The goal, Waggoner said, is to examine wide areas where bomb-making components are stored “before they’re live.”

“It’s about getting to what people call ‘left of boom,’” he added.

‘We Will Find It’

Among people who work with dogs, it is widely understood that the first year of an animal’s life is vital for imprinting. That is when it learns how to socialize, and grows accustomed to the sights and sounds of its environment. For the Auburn dogs, this is when they must grasp the kind of trusting but strict relationship they will have with their eventual handlers.

Originally, Auburn relied on local families to foster the puppies, said James Floyd, former director of the Canine Performance Sciences Program. Despite the precise guidelines the volunteer hosts were given to maintain the dogs’ fitness and not spoil them, Floyd said, “you’d visit to check on them and there they’d be, up on the couch, watching TV, being fed potato chips.”

About 80 percent would fail to meet the rigorous detector-dog standards: “They had been raised as pets,” said Brock, the Auburn instructor. “The main problem was lack of structure.” (Dogs that drop out are offered for adoption or retained for noninvasive research.) Knowing that service animals had been successfully trained in prisons, the program leaders decided in 2004 to place dogs at Bay Correctional Facility, in Florida. The failure rate fell quickly with the shift to a more stringent environment, and now Auburn has partnerships with five prisons in Florida and Georgia.

One of them is Coffee Correctional Facility in Nicholls, Georgia, which houses men serving sentences of up to 25 years, for “multiple DUIs to murder, and just about everything in between,” said Grady Perry, a former warden.

Perry and his “hall team” led a visitor past the library and the barbershop to the dog-training room, where, on a Friday morning, 10 inmates in white shirts, white pants and slip-on shoes stood in a line, steely and silent.

James Reeves, the co-manager of the prison’s dog program, retrieved a black Lab named Keisha from the dog dormitory. She bounded in, and though she looked alarmed by her audience, she quickly found the target odor. In response, the inmates whooped and hollered and clapped, and one of them tossed her a red ball.

Next up was her littermate Kevin (litters are named by letter), who sent his reward skittering across the floor toward the warden’s feet. As Perry bent to pick it up, one of the inmates approached. “I’ll get it, Warden,” said the man, the words “God’s Child” tattooed across his Adam’s apple in gothic letters. “It’s all slimy.”

Some of the Coffee trainers are old pros — one was working with his 10th dog — while others are new to the program. They live in a dedicated dorm, where the dogs’ crates nestle against the inmates’ bunks.

Perry says he is tremendously proud of the Auburn partnership, crediting it with improving inmates’ morale and behavior. “The incident rate in that unit is almost nonexistent,” he said. “That dog program just kind of calms everyone.”

Not every inmate is eligible. To apply, inmates must have a high school diploma or its equivalent and be free of disciplinary reports for a year — a considerable challenge, Perry said.

“These aren’t heinous individuals,” he said. “They’re men who’ve made mistakes, serious ones, and they deserve to be forgiven. And the sooner they can forgive themselves, the sooner we can.”

Working with the dogs, he said, speeds that process. “A lot of these guys have never been given a lot of responsibility, and this is their chance not only to be a responsible adult but a responsible citizen,” he said.

That sense of duty is explained in a mantra displayed on a wall:

You Can Design It

You Can Make It

You Can Hide It

K9

We Will Find It

Striding past it, Perry and Brock, the Auburn instructor, paused at the end of a row of bunks, an empty crate brushing their knees.

Until a few days before, the crate had housed a dog named Joel, who had graduated and gone back to Auburn. “I know you’re wondering,” Brock said to his trainer. “Joel is doing great.”

The inmate gestured at the metal grate, onto which he had taped a photograph of a Lab. It was not Joel but a look-alike from a magazine. Possessions are few here, some flimsy, all of them essential. As was this one, a reminder of a dog trained to protect, who may have already done some of his most wondrous work.