Machine Spirit

In the grim darkness of the 41st millenium, everyone thinks machines have souls.

This isn't really that absurd a belief, considering how we tend to personify things like computers and cars - ascribing them personalities, habits and so on. The idea of Machine Spirits is what develops when you let this rampage unchecked by common sense among a technocratic & theocratic ruling class. However, what's important to know is that prior to humanity's downfall and the Dark Age of Technology, artificial intelligence was widespread in what was a typically utopian future. Given that the Adeptus Mechanicus have a hard-on for hoarding ancient technology, it's not unreasonable to assume that particularly old and/or complex machines do in fact think for themselves. This turns into nightmare fuel when you realise that Mars is honeycombed with factories, warehouses and other facilities in varying states of disuse - facilities that were the battlegrounds between the loyal and heretical halves of the Mechanicus during the Horus Heresy. Hideous self-aware weapons of death may still stalk the lower levels, insane from 10,000 years of solitude. For the rest of the Imperium, Machine Spirits are a reason to maintiain machines and treat them with respect - from rituals of cleaning to appease a simple Lasgun to the complex rites performed to reawaken the demanding and tempramental machine spirits of Titans.

There is also one other problem that one tends to forget--there actually are things called Machine Spirits. After the rebellion of the Men of Iron during the Age of Strife, Artificial Intelligence was declared "Abominable Intelligence" by decree of the Emperor of Mankind. To get around this, human brains were recycled and placed into the more complex machines (such as Robots, Titans, and shipboard AIs) which would then process the more complex information and control systems under the direction of a human. Being recycled from dead humans, they're understandably pretty cantankerous.

It is also implied sometimes (depending on the source) that Machine Spirits may be more real than first thought. There are examples of weapons that have no power source still being able to fire themselves. There was also at least one instance of a bunch of gears that were not connected to anything but each other (i.e. no motor) actually moving on their own after being talked to by a Tech-priest (maybe micro-motors? The Mechanicus is actually advanced). Considering the Dark Age of Technology's feats, it is possible that dark age humans had successfully found a way to bend the warp into machines to give the machines their own "soul". This may also have helped cause the Iron War. After all, what does Chaos do with unprotected, unaware souls? Heh, yeah. Anyway, most "leftover" Machine Spirits tend to be a bit crazy, though, and using human brains merged with tech is safer because at least you know how the brain works.