Perhaps spooked by everything that has unfolded over the past few minutes—the turbulence, the strange electrical phenomena, his colleague's failure to route around the potentially dangerous storm—Bonin reacts irrationally. He pulls back on the side stick to put the airplane into a steep climb, despite having recently discussed the fact that the plane could not safely ascend due to the unusually high external temperature.
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While Bonin's behavior is irrational, it is not inexplicable. Intense psychological stress tends to shut down the part of the brain responsible for innovative, creative thought. Instead, we tend to revert to the familiar and the well-rehearsed. Though pilots are required to practice hand-flying their aircraft during all phases of flight as part of recurrent training, in their daily routine they do most of their hand-flying at low altitude—while taking off, landing, and maneuvering. It's not surprising, then, that amid the frightening disorientation of the thunderstorm, Bonin reverted to flying the plane as if it had been close to the ground, even though this response was totally ill-suited to the situation.
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The men are utterly failing to engage in an important process known as crew resource management, or CRM. They are failing, essentially, to cooperate. It is not clear to either one of them who is responsible for what, and who is doing what. This is a natural result of having two co-pilots flying the plane. "When you have a captain and a first officer in the cockpit, it's clear who's in charge," Nutter explains. "The captain has command authority. He's legally responsible for the safety of the flight. When you put two first officers up front, it changes things. You don't have the sort of traditional discipline imposed on the flight deck when you have a captain."
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HT Surse Pierpoint