After asking about how the Machines would breed humans, one of the answers raises a related issue in the Matrix universe.
People in the Matrix are going to have sex and have children. It's not clear (at least from what I remember) if those in the Matrix are in the first generation of their world, but at some point the people in the Matrix will have children (or they'll notice something is wrong and wonder why babies are no longer born).
After childbirth (within the Matrix) there's a new human in the Matrix. Is this a simulated human? Will another bred baby eventually be hooked up to the Matrix and live out the life of the non-real baby that was just born?
Where does the new baby come from in terms of the illusion of the Matrix and is it always matched with a real human who is in the Machines' power plant/human farm?
Answer
I don't really see a problem here. The machines have the real bodies of the humans and can easily (remember all the knowledge they have about the human body) reproduce the in-Matrix intercourse with in vitro fertilization. Although this procedure is never directly shown, it is hinted when Morpheus explains how the breeding facility operates: You see a newborn (or at least very young baby) in a cocoon that is being filled with the nurturing goo all people are lying in.
The Matrix is definitely not populated by first-generation prisoners. When Neo asks why his eyes (or was it his muscles?) hurt, Morpheus says: "Because you have never used them before." (paraphrased) If Neo was a first-generation prisoner he would have used them as child.
If you're still not convinced: Remember how old Zion (i.e. the latest (re-)population) appears to be. I find it very hard to believe that this could have been built by just one (23-person weak) generation!
Somewhere (maybe on this site) I read an approximation of the age of the current Matrix (unfortunately I do not remember where). It was closer to Groundhog-Day dimensions than one generation!
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