For some time already, scientists have been investigating the effects of overfishing and accidental “bycatch” on specific species. Now they’re widening their field of view: “Understanding the ecological effects is the newer level of inquiry,” said Lindholm.

He and Gleason and several other researchers will use the video and still images gathered by the ROV to monitor the rate at which the seafloor recovers after being dragged. They hope to gain a better understanding of the post-disturbance population dynamics of the fish and invertebrates here.

That kind of research has been made possible only as ROVs have opened wide new windows on the denizens of the deep. Earlier efforts to understand population dynamics relied on relatively crude efforts like sampling species abundance with trawl nets. But as Lindholm said — using an analogy originally made by marine researcher Elliott Norse — that’s like sampling a rainforest by flying over it in a helicopter and dropping a net through the fog.

“You’ll get the squirrels and the hummingbirds and pieces of trees, but it’s all squished in the net. You won’t understand the interactions,” he said. “An ROV allows us to have our eyes underwater, looking at everything that’s going on.”

It turns out that even a seemingly featureless expanse of sand can be rich in “microhabitat” — hideouts created either by currents or by fish and invertebrates as they hunker down and burrow into the sand. If you’re a flatfish flopped over on your side on the bottom, it doesn’t take much of a divot to hide from predators and currents.

“Imagine you’re a fish that’s that flat” — Lindholm indicated something about the width of a chapati — “and then look at the bottom and think, ‘OK, I can use that. I could use that.’ ”

The video and photos from the ROV cruises will show changes in the topography of the bottom immediately after a trawl net sweeps over it, and then six months and a year afterwards. And, Lindholm said, they’ll show whether trawled areas are subsequently colonized by species that weren’t there before.

Back in the Box, Lindholm handed the Beagle’s controls over to Rosen. “To get calibrated,” joked Rosen, “you kind of have to bump into a few things.”

Rosen settled in and quickly attained a state of meditative oneness with the ROV. On the video monitor, soles hunkered down into the sand as the Beagle motored closer, until they accelerated ahead with surprising bursts of power.

“At some point, you really do transform yourself,” he murmured. Anything that breaks the trance can be extremely jarring. Once, a six-gill shark whipped around straight into the ROV’s camera lens. Hundreds of feet above, Rosen shot out of his seat on the boat.

A couple of hours doing a delicate do-si-do with the ROV can turn into a disembodied, bleary-eyed — and, if a good swell’s running — nausea-inducing ordeal, no matter how hot the playlist on Lindholm’s iPod. And the gruelingness doesn’t end once the boat ties up back in Morro Bay. To analyze the data collected, the researchers overlay each still photo and video frame with 50 random dots, and then count and identify habitat types and species under each dot. In May, Lindholm and the other researchers were still analyzing the data they’d gathered last November.

“It’s easy to fixate on the really cool stuff,” Lindholm said, “but there are hours and hours and hours in the video lab, days and days where you do go cross-eyed.”

Ultimately, this research could help fisheries regulators develop more sophisticated ways of managing fishing in California and elsewhere. Rather than outright bans on trawling, for instance, it may be possible to take a more nuanced approach and allow occasional trawling in areas that can withstand it.

And it’s already clear that people are watching Lindholm, Gleason and Rosen’s work with keen interest. “From my perspective, this kind of a study would prove that trawling is good in soft-bottom habitat,” said Maricich, the Donna Kathleen’s skipper.

The wheelhouse of the Donna Kathleen has a live video feed from the ROV, and he keeps a close eye on it. “Fishermen have always said that grounds that are trawled are better fishing than non-trawled grounds — a lot of the organic nutrients get stirred up and reintroduced to the ecosystem.”

Lindholm, for his part, is careful to not jump to any conclusions. It will be years before the team’s formal findings are ready. “If there’s one thing we’ve learned,” he said, “it’s to not make any judgment based on what we see live when we’re flying over the bottom.”

Late that afternoon, the setting sun left a habañero-red smear across the western horizon. Maricich maneuvered the Donna Kathleen with the current, and Rosen and one of his staffers, Steve Holz, used the crane to wrestle the Beagle back aboard the boat. Once the dripping ROV was secured on deck, Holz peeled off his hard hat with a look of relief.

“Every time you throw something into the ocean,” he laughed, “there’s a good possibility you’ll never get it back.”