A 6-hour commentary hosted by integral philosopher and mystic Ken Wilber, along with religious scholar Cornel West, accompanies the release of 'The Ultimate Matrix Collection' - reviewed on WIE. An extract relates how:
“Light and energy represent spirit in this trilogy,” Wilber points out at the end of the first film. Piercing through the Wachowskis' layers of arcane symbolism, he adds: “The machines themselves appear to be beings of light—they're not just evil or bad as you might think at first.” He explains that the Wachowski brothers have established a recurring pattern of “body, mind, and spirit” throughout the trilogy: everything in blue hues (screen tint, background colors, clothing) represents Zion, the last human refuge, which equals the level of “body”; everything tinted green represents the Matrix or “the world of the mind”; and everything that appears as golden light—i.e., the external machine world through Neo's psychic eyes—corresponds to spirit. Wilber then summarizes the trilogy's plot in one sentence: “There's an inherent instability in all three of these worlds—the world of the machines, the world of Zion, and the world of the Matrix—until they're integrated.” And that integration occurs when the fully evolved Neo merges, Christlike, with the central computer of the machine world at the end of the third movie, an event that Wilber concludes is the culmination of Neo's own enlightenment and the spiritual salvation of all three mutually interdependent realms.
Another independent voice on this subject is Ramsey Dukes who wrote about this originally in a book released in 1988 called: 'Words Made Flesh: Virtual Reality, Humanity and the Cosmos'
Still the question revolves around not only simulation and intelligence, but also consciousness and wisdom. Can technologically enhanced transcendence catalyse emergent cosmic consciousness. In such a scenerio, molecular and matter engineering with be voided by the encapsulation of light and energy... I wonder...