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Indonesian military carry a casket containing the body of a AirAsia Flight 8501 passenger at a Military base in Surabaya, Indonesia, on Dec. 31, 2014.SIGIT PAMUNGKAS/Reuters

Heavy rain, strong winds and high waves hampered recovery efforts Wednesday – keeping divers out of the water at the crash site where AirAsia Flight 8501 slammed into the shallow Java Sea, killing all 162 passengers and crew on board.

(AirAsia Flight 8501: What we know so far about the plane's disappearance)

More bodies and floating wreckage was pulled from the surface and large objects – believed to be the shattered remains of the Airbus A320 – were located by sonar.

Among the bodies recovered was a flight attendant in her red AirAsia uniform, said Henry Bambang Soelistyo, chief of Indonesia's Search and Rescue Agency.

Current and winds were dispersing floating wreckage and some had "drifted more than 50 kilometres from yesterday's location," said Vice Air Marshal Sunarbowo Sandi, search and rescue co-ordinator in Pangkalan Bun on Borneo island, the closest town to the site. "We are expecting those bodies will end up on beaches."

Recovery of bodies remains the first priority, followed by the so-called black boxes – actually bright orange and each equipped with a 30-day "pinger" to aid location.

Finding them should be relatively straightforward in the shallow waters at the crash site, only 15 km from where the plane vanished from radar shortly after dawn on Sunday as it flew into a line of towering thunderstorms.

Relatively new, the six-year-old Airbus was equipped with sophisticated digital flight data and cockpit voice recorders, capable of detailing hundreds of parameters. They will allow investigators to reconstruct, with second-by-second precision, the exact chronology of the pilots' actions as they flew into a massive tropical storm. The voice recorder will reveal what the pilots said to each other. The flight data recorder will show how the controls were handled and whether there were any mechanical or electrical failures during the doomed flight's last minutes.

Determining the sequence of events that led to the crash will take months but recovery of the flight recorders should simplify the task.

The accident investigation will be led by Indonesia's National Transportation Safety Committee, because the aircraft was registered in that country and crashed in international waters.

Investigators will want to know which pilot was flying as the A320 approached the huge storm system.

The captain, Iriyanto, an Indonesian who uses only one name, was a former Indonesian air-force fighter pilot with more than 20,537 flying hours, of which 6,100 were on Indonesia AirAsia Airbus A320s. The less experienced co-pilot was Rémi Emmanuel Plesel, a French citizen who gained his pilot's licence at age 42 and had 2,275 hours on the Airbus A320.

Usually, one pilot flies a flight segment while the other operates the radios and communicates with air-traffic control. It's not yet known who was the "pilot flying" the flight. However, in case of difficulties or unforeseen problems, the captain can, and usually does, take control.

About 50 minutes after takeoff, the twin-engined Airbus A320 was already at its planned cruising altitude and nearly halfway to Singapore when the "pilot not flying" asked air-traffic control for permission to climb from 32,000 to 38,000 feet. The request was denied because of other aircraft already occupying the higher flight altitudes. A few minutes later – at 6:17 a.m. local time – controllers offered Flight 8501 permission to climb to 34,000 feet, but there was no reply.

Suggestions that air-traffic control should have immediately accommodated the AirAsia pilots' request for an altitude change misinterpret aviation protocols. An aircraft captain can always – in an emergency – change course or altitude and, if pilots declare an immediate need for safety reasons to air-traffic control, they will be given priority.

However, routine requests for deviations are accommodated only if they won't create a potential collision conflict with other flights in the area.

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