As you may have heard, the FAA is investigating whether two pilots for "go!" airlines (a regional airline serving the Hawaiian Islands) fell asleep on a short flight this past February from Honolulu to Hilo.
Yes, I read that both the pilots were sleeping on the job! According to the NTSB preliminary investigation report, the two pilots probably fell asleep for the short period when the controller was trying to contact them.
Of course, when such a scenario arises, it may give rise to suspicions similar to those seen in the Helios case - pilots incapacitated due to hypoxia (lack of oxygen) in flight (see here). That was why the NTSB report stated that there were no problems with the pressurization system or carbon monoxide in the plane.
An experienced flight attendant may realize something was not right but in this flight, (she was the only crew in the cabin) she may be very busy attending to the 40 passengers on the Bombardier CRJ-200 plane. Some airlines have a policy whereby the flight attendants are required to contact the cockpit now and then to make sure everything is okay with the pilots. On more sophisticated planes like the Boeing 777, the in-flight computers would sound an aural warning (to wake up the pilots) if no activity is sensed inside the cockpit for the last 15 minutes!
As for the ATC, the normal protocol is that they would try all means to contact the plane. Normally the plane would be tracked on radar as a blip as they are equipped with transponders. As such, they would not alert the search and rescue emergency services yet. Finally, after about 32 minutes into the flight, contact was established with the plane and it landed safely without further incident.
Meanwhile the airline has grounded both the pilots as investigation continues. If the investigation showed that the pilots did fall asleep while the plane was on autopilot, the normal FAA penalties would range from a warning letter to license suspension or revocation.
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