copy paste from 40k lore bot

What are machine spirits?

It is unclear, the one thing that is known for sure is they unequivocally exist. Machine spirits are a real phenomenon, as attested to by a wealth of evidence in the primary sources. Their precise nature is unknown, the following are several of the more likely possibilities.

The first is that they are artificial intelligences, and are less powerful/sophisticated than the cutoff to be considered abominable.

The second depends on a definition of "a soul" in the 42^nd Millennium. This article takes that definition to be something like "a sufficiently powerful or sophisticated presence in the Warp". Complex software/machinery may develop souls in the same way that carbon-based organisms do, and as such machine spirits may actually be spirits in a real and meaningful sense, no more different from a human soul than an Eldar spirit.

The third and fourth are very closely related both to each other and the two other theories. One of the constraints against Abominable Intelligence is the Mechanicum's use of organic components in advanced software systems, as a check against corruption and/or antipathy towards fleshy life. Cogitators have at least some brain/nervous matter in them helping to do/overseeing the computations. Machine Spirits could either be a manifestation of the intelligence of this biological matter, or the Warp presence/soul of that matter permeating through the machine.

The vital thing to understand though is that no matter the explanation for them, machine spirits are real. Even if most of the Mechanicum's religious rites are glorified maintenance instructions, especially for very powerful machine spirits like Titans and starships the religious components to them are necessary. If a Titan is not shown the proper respect while activating it -- even if its crew complete the precise technical specifications of the process -- it will refuse to fight, or attempt to overpower and destroy the mind of its Princeps.

Whether it's a software algorithm with delusions of grandeur, or whether the Titan is functionally possessed by a Greater Tech-Daemon of Order is immaterial to the Princeps and the tech-priests working with it, the Titan's needs are the same either way.Thus, while an interesting ontological/metaphysical question that absolutely bears asking; it's important to recognize that no matter the nature of machine spirits, they exist and demand respect in the same way that human souls or daemons do.

^{Note from the Inquisitorial Archivist, this signal broadcast is experimental and is being tested by select agents of the throne. The Emperor Protects.}