"Boeing said the autopilot system is designed so that if it senses faulty data from the captain's altimeter on the left side, the autopilot, including the autothrottle system that controls engine thrust, is supposed to switch to the altimeter on the right side used by the co-pilot. Boeing would not comment about what may have gone wrong on the Turkish jet, saying that is part of the investigation."
Seattle Post Intelligencer writes the above cited. Sheds a completely new light on the A/T system logic. The link to the complete article:
Faulty altimeter led to 737 crash in Amsterdam