This is actually a fairly serious question in philosphy: how do we know what "blue" is? How can i be certain that the way this wavelength of light appears to me as the exact same shade of grey that you see?

Picture if you will: a person whose eyes function differently than ours. S/he is shown a specific color on a card. If we saw through his/her eyes, we would call it "red", but looking at the card through our own eyes we would see it as green. S/he goes through life seeing "green" things as "red" ones, but nobody ever knows because s/he learned that that specific color was "green".

If my green is not your green, is it still green?

As for the problem with the Matrix, allow me this hypothesis:

The Matrix interfaces directly with the brain. Whatever it tells the brain is what is accepted as "true". When one is freed from the Matrix, the brain has only that information to rely on. The Matrix probably managed to download the pertinent information from the brains of those first trapped within. Those who managed to break free saw the world through eys tainted by exposure the Matrix. Those born free would still have been taught that "this is what tuna fish tastes like by those who were grown in the batteries. Thusly, the (mis?)information propagates itself and the Matrix shows a "realistic" view of the world.

Ye gods, i hope this made sense...

The AI(s) were smart enough to analyze the way that the cones inside the humane eye interpret color through the optic nerve, and thus knew that the human brain would take care of this by itself. Color actually, ironically enough, depicts absence of certain pigments (as opposed to presence).

When light strikes a piece of green cloth, pigments in the cloth absorb the light. Any wavelengths of light that aren't absorbed, are reflected back off the object. When we see color, we are seeing these reflected wavelengths. Black means all wavelengths absorbed, white means none.

The human brain associates different colors with wavelengths of light. There's no way to tell (yet) if two people associate the same color in there mind with the same wavelenght of light. As a child, if they pointed at something green in their mind, and their parents said it was red, the word red would be associated with the color green in that persons mind. Therefor, two people looking at the cloth could call it green and really be seeing different colors. Although the colors may change in the mind's eye, the wavelengths associated with words do not.

All the AI(s) had to worry about was knowing which pigments reflected which wavelenghts of light. To them, it was simply a chemical formula of sorts. I imagine that would be fairly trivial when you're an artificial intelligence who has managed to spawn an entire race of machines.

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