More meta
More shenanigans
More mirroring
When the Doctor is telling Rory to go on and do some rewiring, he's doing double-duty. Triple-duty. He's calling attention to sciencey stuffs that make for the perfect metaphor. And what a wonderful show that can take an iconic action (cables and levers) and do something new with it!
THE DOCTOR: Reroute the blue into the red and the green into the blue, leave the red loose.
Leave the Red loose = leave Amy dangling.
Reroute the Blue into the Red = Amy becoming the Doctor.
The Green into the Blue = The Doctor becoming Rory?!!! Sorry, reverse that polarity.
THE DOCTOR: It's not rocket science, it's Quantum Physics!
There's a branch of Quantum Physics called Quantum Chromodynamics, or QCD. QCD describes the charge of the strong interaction in quarks and gluons using the metaphor of color. This particular charge isn't so much positive or negate (a binary system) but rather can occupy one of three states, red, green or blue. You can imagine the Strong Interaction as something like Gravity, or Magnetic Attraction.
In a composite particle (called a Hadron) of quarks, the a quark can change color by emitting a gluon; the gluon is absorbed by another quark, which in turn changes color, preserving the overall color charge of the hadron.
In other words, in quantum physics, particles exchange colors.
This is a metaphor for the strong interactions of the characters in Doctor Who.
Amy becomes like the Doctor: builds a sonic, fights monsters and becomes like them, understands time-streams, even uses the same dialogue: Eyes front, Soldier.
Rory becomes like the Doctor: holding up a Looking Glass to examine the situation, wears special glasses so the Doctor can see through his eyes, fights monsters with art, goes into the terrible situation in order to save someone.
RORY: It's not fair. You're turning me into you.