On a hot July day in a Louisiana marsh in 1999, Daphne Soares was riding in the back of a pickup truck next to a thrashing six-foot-long alligator. Though the reptile was tied up and its mouth cinched shut, Soares couldn’t take her eyes off its jaws—but not for the obvious reason.

The University of Maryland neuroscientist had noticed hundreds of dark bumps all over the animal’s upper and lower jaw. "They were each about the size of a little blackhead, and raised like a pimple," she says. But this was no case of alligator acne. She knew that other alligators sported these bumps, yet she’d never seen them on any other creature. "I began wondering what those little spots were for," Soares says.

Those musings had little to do with her reason for visiting the 76,000-acre Rockefeller Wildlife Refuge, which stretches along the Louisiana coast in the Cameron and Vermilion parishes. The 28-year-old graduate student was there to compare the brains of birds and large reptiles for her PhD dissertation on the mechanisms of avian hearing. But "a great thing about science is that you can follow your curiosity," she says.

Back in her lab she found that the bumps were characteristic not only of the American alligator (Alligator mississipiensis) but of the 22 other species in the 220-million-year-old crocodilian family, which includes alligators, caimans, crocodiles and gharials. For years, crocodilian biologists have used the number, placement and patterns of these bumps as a means of distinguishing between different species. But no one had been able to explain their function. So Soares placed some alligator skin under the microscope and began her own investigation.

Her first reaction was disappointment. "I was hoping to see a pore or a hair or an eyeball looking back at me," Soares jokes. "But all I saw was a bump."

Dissecting an alligator’s head, she found that the bumps were connected to nerves, which led into the skull through holes in the bones of the jaws. These holes, known as foramina, are found in all animals and serve as conduits for blood vessels and different facial nerves, such as those that transmit optical and olfactory signals.

To identify which kind of nerve was connected to the bumps, she injected a dye into the nerve itself. As the dye was absorbed slowly by the nerve cells, it left a telltale trail that enabled Soares to determine that each bump was connected to the large trigeminal nerve, which stimulates the skin and muscles of the face. Whatever their purpose, these bumps appeared to be important.

It occurred to Soares that the fossil record might be helpful. So Soares approached James M. Clark, a paleontologist at George Washington University and an expert on crocodilians. She learned that not all ancient skulls had these foramina: those with similar holes in the jaw were species known to have lived where land meets water, as alligators and crocodiles do today; crocodilians without bumps lived entirely on dry land.

"But I still didn’t know what these things did!" says Soares. Clearly the bumps were some kind of sensors that passed along information about the animal’s environment directly to the brain. And they appeared to be useful primarily to animals that spent their lives between land and water.

In 2001, Soares won a three-month Grass Foundation Fellowship to the Marine Biological Laboratory in Woods Hole, Massachusetts, a major center for neuroscience research. Until Soares arrived with 20 baby alligators in June, however, no one had used its sophisticated equipment on a crocodilian. At the lab, she taught herself to open the skull of a sedated but living animal and to insert an electrode into the area of the brain that receives electrical signals from the trigeminal nerve.

She hooked up the electrode to a bank of equipment capable of amplifying and recording brain activity in response to nerve stimulation. When nerve cells fired, loudspeakers sounded a series of rhythmic pops.

It took a month of experimenting before Soares could even begin to investigate what kinds of stimulation would make the nerve fire. She tested whether the bumps might be sensitive to light, or to electrical fields, like the skins of some eels and fish. She blew tiny particles of ground-up fish over the bumps to see if they were sensitive to taste or odor. But the loudspeakers stayed silent.

Then, one day, Soares reached into the tank and the speakers went brrraap.

After conducting further experiments, Soares concluded that the ripples in the water had caused the bumps to vibrate, which in turn caused the nerve to fire and send a message to the brain. This made sense for an animal that spends much of its life lying quietly in the shallows waiting for its prey to swim by or come to the water’s edge for a drink. And it also offered an explanation for why crocodilians that lived on dry land did not have bumps.

Still, Soares wasn’t ready to break out the champagne. "If someone pokes you in the eye, your optic nerve fires, but that doesn’t mean your eye is a poke-detector," she says. Was detecting ripples the bumps’ primary purpose? What if they served some other function that Soares didn’t know about? What if alligators found their prey, as do most animals, by sight and hearing?

Soares covered several alligators’ ears with fine plastic and placed them in a tank of water. In complete darkness, using an infrared camera to record the animals’ reactions, she let a single drop of water fall onto the surface. Though deprived of sight and hearing, all of the animals swam directly toward the spot where the drop hit the water.

Soares next covered several alligators’ snouts with the same plastic wrap, so that the bumps no longer came into contact with water or air, thus ensuring they had no way of detecting surface waves. She again dropped water into the tank. The alligators did not respond. Now she was ready to celebrate.

In a paper she published last year in the journal Nature, Soares wrote that the alligators’ bumps are "pressure receptors" that evolved millions of years ago and solved the problem of how a creature with armorlike skin could have tactile sensitivity. This sensory system is "a specialization of crocodilians that other animals don’t have," says Clark. It’s a "major breakthrough in crocodilian sensory physiology," says Valentine Lance of the Center for the Reproduction of Endangered Species in San Diego.

Soares still has questions she wants to answer. Alligators have bumps on their jaws and mouths, she points out, while other crocodilians have them all over their bodies. How come? "It’s a wonderful mystery. Their world is so different from ours."