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Concerning genetics: it has been touched briefly, but the purpose of
the One may have to do with his DNA.
I would posit that the Source wants his DNA because he is an actual evolutionary adaptation, a reaction to generations bred for insertion in the
matrix. This mutation IS the integral anomaly: it is unpredictable when it will occur, and difficult to spot, except by his abilities in the matrix. It is integral because evolution within that environment is bound to produce such an individual. Even if you kill him, it is inevitable that another will occur because of the inbreeding discussed above, and the artificial environment that demands such an adaptation. The eye has been developed over 6 different times over different ecological eras, each time independently - just because it's such a useful adaptation. Being able to control the matrix is also a most useful adaptation.
Now, some would say that DNA is not a part of the Matrix, because within that environment nothing is chemical, it's all digital. However, I argue that the complexity of the Matrix does go down to that level, because if people wanted to, they could test reality down to that level. That is, there are chemists and biologists within the Matrix, and if DNA wasn't part of the Matrix code, then these people would notice that their experiments don't hold together under the microscope. Therefore, we'd see a lot more sober scientists in the rave scene, standing awkwardly on the sidelines, fixing the scotch tape on the rims of their glasses. Just kidding. But seriously, the Architect wouldn't leave a hole like that for biologists to question reality and possibly awake because cells don't really exist.
On the other hand, that could be why we've got particle physicists with their weird ideas. Current theories about the fundamental - or smallest units of - reality says that there are no particles. Theories vary from holographic energy waves to string theory, and those that say that matter is tiny folds and foamy variations in space-time itself. If you can't see the smallest constituents of matter, maybe that's because the smallest unit of matter is the quark, below that it's pure code.
Regardless of how deep the rabbit hole goes, even if people are shells with no insides until they're punctured, the One's real brain may be the integral anomaly, and eliminating that individual and resetting the Matrix may be the only way to prolong the existence of the Matrix. That's why Zion has to be destroyed at the same time as the Matrix is reloaded: the One has to be killed in real life and all his mischief within the Matrix erased. You have to let the One get through to the Source before he's had a child, though, because that would certainly be one of the people he'd pick to live in the next version of the Matrix, carrying the naughty gene.
And that might just be the problem the Architect is seeing now: Trinity is pregnant, and the One will return in 9 months, even if you kill Neo.
Just some thoughts.
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But someone once said something like "One day man will look through his best microscope and look into the eye of God."
