One of the first things that drew my attention of this forum was the repetitive discussion of color perception in this particular subforum(red, blue, etc.) and how it was a subjective part of the brain(mind), and not of nature out there(I don't know why but I was always shocked by this - it could be that I was a naïve realist at that time).
This raises a few awkward questions - just how much of all we perceive is modified by the brain?
Is what the brain does merely a re-construction of nature out there or a co-construction of nature out there?
The answer to that question isn't immediately obvious and delving into it has led me to consider that the answer is of the latter type.
What is out there from the perspective of the most fundamental theory of matter we have - is waves(of probability - also called "physical matter") and frequencies(color, light, etc.). It was another shock for the naïve realist that one of the cornerstones of the new theory posits that there be a connection between knowledge and quantities being observed/measured(the so called HUP) exemplified in the DCQE experiments.
Not so surprising, some great scientists have come to similar conclusions - neuroscientist prof. Karl Pribram and physicist David Bohm in the beginning of the 1990's. What the brain appears to do is a projection, a hologram model of the world. We consider that this projection is the world out there with 1:1 correspondence mainly because other observers agree to our observations with close to 100% accuracy(hardly surprising given that human offspring inherits the same brain structure because of the sharing of common DNA - and when we don't due to malformations, a different reality is observed - schizophrenia, etc.). But in the final analysis, it is clear that the world out there can not be 1:1 as it is experienced, it doesn't fit the experiments nor the theory. The observed and how it is prepared to be observed actually influences and to a large extent determines what will be observed. Put another way, it's not obvious how to remove the observer from what is observed as any observation, however it is defined, always forces quantum states to one of eigenstates of the corresponding operator(i.e. experience of the known classical-like world) and this sudden 'collapse' happens whenever there is information about what the system is doing.
David Bohm went further and said that space and time were constructs of the brain, not of nature out there(nature out there seems to be a higher dimensional structure). You can read more about this here:
http://en.wikipedia.org/wiki/Holonomic_brain_theory
The holographic principle in theories of quantum gravity:
http://en.wikipedia.org/wiki/Holographic_principle
Phantom limb sensation in patients with removed limbs:
http://en.wikipedia.org/wiki/Phantom_limb
Quantum entanglement:
http://en.wikipedia.org/wiki/Quantum_entanglement
The brain as an active participant in what is perceived:
http://en.wikipedia.org/wiki/Psychoactive_drug