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If you've seen Second Renaissance you'll have noticed that the machines are spoken of in high regard, in fact humans are downplayed to be inferior.
My theory is that after Zero One was bombed the machines lost. Please note here that Zero One and Zion are pretty much the same word. I believe at this point in Second Renaissance the machines were enslaved into a Matrix and in order to make them believe that they were real in the real world they were put into a sub-matrix governed by the machines we see (like the sentinels).
Why would the machines be enslaved? Ethics. If we clone a human, does that give us any right to kill the clone? Is it any different from killing a normally bred human? No. The fact of the matter is that the clone is a sentient living being. To a certain degree the machines are too. AI, it thinks therefore it is. The machines know pain, they know what feelings are, they know oppression, they're social and they have the desire to pro-create. All just like humans.
Think about it.
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