In the summer of 1965, a female Dalmatian was stolen from a farm in Pennsylvania. Her story changed America.

For 100 years or more, scientists and activists had traded blows over the ethics and practice of research on dogs and cats. Through all that back-and-forth, lab rodents were always left just across the moral frontier of live-animal experimentation—close enough to humans to remain a meaningful source of knowledge but not so close that we couldn't slaughter them in droves. Yet it's not obvious—to those who might consider the question—that the welfare of a rat or mouse is any less important than that of a dog. Recent research suggests that the health of mice improves when they're given cage toys, running wheels, and crawl tubes to play with. Rats can learn to respond to a name and recognize individual people. We might quarrel over the inner lives of honeybees or river trout, but is the suffering of our fellow mammals really in question?

Meanwhile, rats and mice are subject to some of the most extreme and invasive experiments in biomedicine. By the early 1980s, we were spiking mouse DNA with cancer-causing genes; a few years later, we started to "knock out" specific lines of genetic code. (Scientists mapped out the entire mouse genome in 2002 and the rat genome in 2004.) We regularly subject rodents to pain, starvation, solitary confinement, and grotesque disfigurement. Whatever misery they endure is multiplied across the hundreds of millions of rats and mice used in labs every year.

The animal-welfare groups have failed in their most ambitious efforts to protect laboratory rodents. "We did and do strongly support the inclusion of rats and mice," says Cathy Liss, current president of the Animal Welfare Institute. "But the question is how can we properly address that? At this juncture, it's premature to go forward and rally support." With rodents off the table, though, it's not clear what's left for the activists to do.

Me and My Monkey

My research monkey had a pink face, dark eyes, sandy fur, and a 2-inch titanium rod screwed into the top of his skull. His name was Clayton.

It's customary to name research macaques in alphabetical order according to when they arrived at the lab. Clayton showed up after Axel and Bongo and ahead of Duper, Einstein, and Freud—but whatever institutional seniority he had meant little in the monkey room. Clayton, a juvenile, was skittish and shy, submissive as a rule, and generally afraid to leave his cage. When I'd finally manage to coax him out, he would leap straight into the "monkey chair," preferring enclosure in a small, plastic box to the thought of ambling across the laboratory floor.

Though he hardly needed it, Clayton was leashed even for these short trips from cage to chair. I'd hook a chain to his collar and slide it through a loop at the end of a 3-foot pole so he couldn't get close enough to bite or scratch. Macaques can harbor the deadly herpes B virus, and it's generally forbidden to approach one that's unrestrained and un-anaesthetized. Though Clayton and I spent hours together every day, I never so much as touched his fur during an experimental session. If he came to recognize me—and I believe he did—it was despite the surgical mask, goggles, hair net, and other safety accoutrements of any visit to the monkey room.

The monkey chair wasn't much bigger than the animals themselves, and Clayton's head poked out through sliding panels at the top. I'd roll him in front of a computer monitor and fasten his protruding metal post to an external frame. With his skull fixed in place, only his eyes could move to follow the targets that zipped across the screen. (By tracking the direction of Clayton's gaze, I'd hoped to learn something about how smooth pursuit eye movements are controlled in the brain.) His eyes would follow me, though, as I loaded up the software and filled his juice dispenser; sometimes I'd place a jelly bean or a raisin delicately on the edge of his mouth, which he'd gobble up before flashing his gums in the deferential gesture of silent bared teeth. I talked to Clayton, too, trying to keep him entertained. But every once in a while he'd show his impatience with a gesture that was disturbingly human: I remember the day he crossed his legs on the shelf of the chair and started strumming his fingernails against the wall.

The one time I held Clayton in my arms, he was asleep and swaddled in a blanket. He'd just undergone a minor surgery, probably to repair a broken eye coil. (Most of the monkeys in the lab had a thin wire implanted under one eyelid that could be used to track their eye movements.) As a junior graduate student, I wasn't allowed to do more than observe the procedure, but when it was done, one of the postdocs lifted Clayton off the table and beckoned me over. I was to carry him back to the monkey room and deposit him gently into a cage before the anesthesia wore off.

For the first time, I felt the shape of his body—the outline of his little shoulders and spindly legs. For weeks we'd interacted across bars and through thick plastic; now I had him cradled him against my chest, his eyes closed and his head tucked into the crook of my arm. He was about the size and weight of a newborn baby; with the blanket wrapped around him, only his pink face was showing, and his eyelids fluttered as I carried him down the hall.

I rocked Clayton back and forth as we made our way to the monkey room. The rest of the animals were stored in interlocking cages, stacked two high on either side; a television in the corner was showing The Lion King on an endless loop. Axel, Bongo, and the other macaques watched as I squatted next to an open enclosure, with the bundle now nestled in my lap. I pulled one end of the blanket and began slowly to unwrap it. First once around and then again—the monkey was stirring now, his head rolling from side to side—and then the blanket was open, laid across my thighs, and there was Clayton's naked body in full view. His chest wasn't soft and pink like a baby's but tan and rugged. He had a tattoo across his abdomen of letters and numbers like the ones painted on houses in the aftermath of Katrina. And further down, nestled amid the light fur of his thighs, lay his penis—hardly the smooth, unformed genitalia of a baby but something like that of a fully grown man, shrunken down to the size of a crayon and adorned with a pair of swollen, red testicles.