On a submarine, the navigation controls are part of a life-critical control system; they link to the hardware, steer the sub, and control elevation. If they don't work right, fatalities can occur. (eg. The sub loses control, hits a reef, or drifts too low, and is crushed under water pressure) Like you noted, control systems are almost never PC based; they're often implemented in Ada, without an OS, directly on a microcontroller.
He's talking about replacing submarine navigation code in Ada with code written in Perl. Which is why I called him an idiot; because that's just plain wrong.