The twin drilling platforms rising from the waters above BP's blown well look like the brooding guard towers of a lost ruin, which in a sense they are: the relics of a disaster zone now turned into an open-air science quest to claim a slice of $500m (£316.5m) in research funds.

Ten days after BP's well was plugged with cement, teams of scientists are scrambling to set sail in the Gulf to collect baseline data on the oil before it biodegrades and changes, as well as get noticed by the distributors of the fund pledged by BP for research into the ecological consequences of the spill.

Below deck on the Arctic Sunrise, five miles off the BP well, Rainer Amon, an ocean scientist at Texas A&M University at Galveston is looking over data on hydrocarbon and oxygen levels generated by sensors lowered to depths of about 1,000 metres.

It's his second trip to the waters around the well since the BP spill. In June, Amon was part of a Texas A&M team that made a crescent-shaped tour around the well, finding high concentrations of methane gas as well as oil.

Instead of today's deserted seas, his photos from June show dozens of oil response boats, and thick clouds of black smoke billowing from the surface of the water.

On his return voyage he is encountering a void. "If that oil and gas had been consumed by bacteria you would expect to see more oxygen depletion than what we have seen," he said.

"Was it just a fluke that we found it, or is there an oil carpet on the ground?"

So where is the oil? It's been two months since any new crude from BP's well entered the Gulf. Independent estimates suggest 4.4m barrels of oil spewed out into the Gulf of Mexico, but there is no scientific agreement on its fate. "You could say it's a mystery," said Amon.

Did the oil sink to the bottom? A University of Georgia research expedition earlier this month discovered a thick coating of oil on the sea floor, 16 nautical miles from the BP well-head.

Is it floating in the depths? One team of researchers reported finding a deep sea plume of oil and natural gas the size of Manhattan, that was slow to degrade. A second study of the plume found the oil and gas were quickly being gobbled up by microbes.

Federal government agencies, meanwhile, have been seen to play down the long-term effects of the oil.

"We still have not got to the bottom of where the majority of the oil went," said Adam Walters, a Greenpeace scientist. "The work is sound but the conclusions are really clutching at straws."

The uncertainty about the fate of the oil has deepened the sense of urgency among scientists to gather evidence from the deep water and the ocean floor, and to begin weighing the effects of the spill on marine life.

That in turn has scientists clamouring for the release of the BP research funds, the bulk of which have yet to be awarded.

Amon, who faced a long wait for grant money to come through, got out to sea again by jumping on board a Greenpeace ship. The campaign group has been offering the Arctic Sunrise to research scientists. That was a definite attraction for Amon, who was otherwise facing a seven-month wait for a research grant – by which time the processes governing the oil that entered the Gulf would be well advanced.

Another A&M researcher on board, Cliff Nunnally, is hoping to gather samples from the sea floor.

In addition to the headstart on research, there is a cost incentive. Research vessels, depending on their equipment, can cost upwards of $30,000 a day, the biggest single expense on a scientific mission. Then again, as Amon notes, on a fully staffed research voyage, he would not be personally overseeing the winch lowering his massive steel-framed device into the depths.

Other traditions are being challenged in these early days of the quest for oil, fuelling suspicions among some scientists that the White House and BP are trying to dictate the agenda for the next generation of Gulf research.

At first, BP intended to follow standard academic protocols and hand control of the fund, which will be awarded over 10 years, to a consortium of independent scientists to review research proposals.

But the White House later instructed BP to involve Gulf governors, who have been pushing to direct money towards in-state researchers over the more prominent and widely recognised ocean science institutions. There are also concerns that politicians, rather than scientists and other technical experts, could define the parameters of further study.

But even with those reservations, there is a sense in the scientific community that the catastrophe of the BP oil spill is opening up an entirely new frontier for research in one of the most highly industrialised, yet biologically rich, marine environments on the planet.

A decade ago, Nunnally, then working on his master's degree, was part of an ambitious product to conduct a census of marine life, on the ocean floor and in the depths, from Texas to the Florida coast.

The project was commissioned by the Minerals Management Service, which was the government agency overseeing offshore oil drilling until it was reorganised following the Deepwater Horizon disaster.

The project took four years, but in all that time Nunnally said it never occurred to the scientists they would soon be out there again.

"For all the ship time and all the conversations that we had with our colleagues that is the one conversation we did not have: what will we do in 10 years' time if there is an oil spill and we have to come out and do it all over again?"