I am a derp and therefore need to keep track of the shit House has written about the boat. He's got a sloppy timeline which is coming soon. This entire post is not IC. But if you've got any questions or anything, feel free to ask them here. ♥
House's Theories
The System's failures
This theory is fairly simple. House compares Mother to a hard drive full of information. She seems to have infinite storage. Each passenger's information is stored somewhere on the “hard drive”. And with any hard drive that needs defraging, the information isn't stored together completely. And after “accessing” the file a certain number of times, blips in the data begin showing up.
There are obviously holes in this theory, but it's the best answer he's got right now.
The “system” itself
This theory is also simple. The system, or Mother, does much more than regulate passenger death. It/she is the lock for the doors, the reason the food tastes the way it does. Why the paint is peeling off the walls. If the system “dies”, then it's likely the boat's passengers will too. This is why House doesn't believe Mother is dead. But at the rate the boat's going to hell, then she's not too far from it.