The circling gulls caught Bill Keener's attention as the Boston Whaler swung to starboard, drifting with the swiftly ebbing tide on the bay toward the birds and the Golden Gate Bridge.

Keener and the two marine biologists aboard had found what they were looking for: a harbor porpoise diving for its prey 50 yards away, the dark triangle of its dorsal fin lifting out of the water for an instant before disappearing once again. Gulls dived for bits of flesh as another porpoise seized a fish just beneath the water, heedless of a lost scrap or two from its meal.

A few moments later, closer to the bridge, another porpoise rose within a yard or so of the boat and rolled on the surface to reveal its light-brown mottled flank, which gleamed in the sun. It was a rare warm, bright day last week - perfect conditions for the ongoing porpoise census.

These shy, elusive harbor porpoises were rarely seen inside the bay for 65 years. Yet in the past two years, they have been returning in increasing numbers, and biologists want to know how many there are in the bay and why they've returned.

Keener's team, which calls itself Golden Gate Cetacean Research, has secured a first-of-its-kind, five-year permit from the National Marine Fisheries Service to approach the protected animals by boat to count them, study their foraging habits, courting behavior and survival rates. Their ultimate goal is to learn what ecological changes in the bay might explain their increasing numbers.

Keeping count

When the tide is right, the team cruises the bay in the research boat, armed with long-range cameras. The researchers can recognize many individuals by their coloring or the scars they bear from tangles with fishing lines, collisions with ships or perhaps attacks from larger predators like the bottlenose dolphins that cruise the open ocean.

Keener, former executive director of the Marine Mammal Center, is an environmental lawyer; his colleagues are biologists who research the world's marine mammals, cetaceans from whales to dolphins, and pinnipeds from seals to walruses.

On Wednesday, their small boat, rolling in 12-foot swells, was steered by Jon Stern, who teaches at San Francisco State University and is a minke whale expert who has studied the ecology of harbor porpoises up and down the Pacific. Another biologist was Isidore Szczepaniak, a naturalist with the Oceanic Society, who also teaches at San Francisco State. Earlier that day, he had watched the porpoises from atop a rocky bluff at Cavallo Point and counted 15 within a few minutes.

This day, Keener and the scientists scouted an area of the bay off Cavallo Point where the porpoises gather most often to seek all kinds of small schooling fish.

They are also regularly found outside Raccoon Strait between Tiburon and Angel Island, as well as off Fort Point on the San Francisco side. Some have been sighted as far inside the bay as Carquinez Strait.

A real comeback

Shell mounds remaining from prehistoric Native American populations around the bay show that harbor porpoises were abundant here for centuries and an important source of food, Keener said.

But at the onset of World War II, submarine nets stretched across the Golden Gate to bar enemy submarines, and military sea traffic crowded the water. That probably turned away the harbor porpoises that had regularly passed in and out of the bay, Keener explained.

There is less pollution in the bay now, thanks to the onshore treatment of sewage and restrictions on what can be discharged. Porpoises are even reproducing here. But researchers believe there are other factors that might help explain the animals' return.

In all, Keener's team has photographed and described details on more than 150 porpoises in the past two years. Every working day they also photograph them from a regular vantage point on the bridge, and the scientists believe there are more that remain uncounted.

On the group's recent cruise, the team sighted three pairs of young calves and mothers, surfacing and diving together as the mothers taught the young ones how to forage for the smelt, anchovies, herring and other schools of small fish that make up a porpoise's diet. Virtually unique among cetacean species, Keener said, the harbor porpoises apparently lactate and feed their young even while pregnant with another infant.

In the next five years, he said, "our team will begin unraveling the mystery of the porpoises' return. Longer term, we hope to learn how they interact with all the other inhabitants of the bay - both on and under the water."

Harbor porpoises

Scientific name: Phocoena phocoena.

Size: Harbor porpoises are usually less than 5 feet long and weigh up to 130 pounds; bottlenose dolphins, by contrast, can grow to 12 feet and 1,000 pounds.

Characteristics: The porpoises have a small, triangular dorsal fin; the bottlenose dolphin's fin is larger and more sharply curved.

Feeding: Porpoises use acoustic senses to find prey such as anchovies, smelt, herring and other small fish.

Location: The porpoises, which are returning to the bay in increasing numbers, can be spotted in the water near the Golden Gate Bridge, either from the bridge's sidewalk or from the shore around, for example, Fort Point.

Source: Chronicle research