The question of what is "real," defined here as the physical universe, acquires special subtlety from the perspective of brain and cognitive science. The question goes beyond semantic quibbling about the difference between physical stimuli and our perception of them. (Consider the old question, "If a tree falls in the forest, was a sound made if no one is present to hear it?" The answer is "no," because a sound is a sensation that must be perceived by an observer, and no observer was present to hear it.) The startling truth is that we live in a neurologically generated, virtual cosmos that we are programmed to accept as the real thing. The challenge of science is to overcome the constraints of our kludgy, neurological wetware, and understand a physical world that we know only second-hand. In fact, we must make an intuitive leap to accept the fact that there is a problem at all. Common sense and the brain that produces it evolved in the service of our hunter-gatherer ancestors, not scientists.
Sensory science provides the most obvious discrepancies between the physical world and our neurological model of it. Consider these physical to perceptual transformations: photons stimulate the sensations of light and color; chemicals produce tastes and odors; and pressure changes become sounds. Yet, there is no "light" or "color" in the wave or photon structure of electromagnetic radiation, no "sweet" in the molecular structure of sugar, no "sound" in pressure changes, etc. The brain produced these sensory attributes. Sensation is the arbitrary experience that is correlated with a physical stimulus, but is not the physical stimulus itself. Our brain manages these psychophysical transformations in such a convincing manner that we seldom consider that we are sensing a neurological simulation, not physical reality. When do we question the physical meaning of "blue," "pain," or "B-flat?" Consider also the apparent seamlessness of the reality illusion. Using a visual metaphor, our sensory environment is like that of a person trapped in a tiny house, through which the universe must be viewed through peep-holes, one per each sensory channel, such as vision, taste, hearing, etc. From this limited, peep hole vista, we synthesize a seamless, noisy, bright, flavorful, smelly, three dimensional panorama that is an hypothesis of reality. The peep-hole predicament is invisible to us. (Some animals have peep-holes we lack, such as those associated with electric or magnetic field perception.)
Sensory examples are instructive because the nature of the psychophysical linkage is relatively clear. It's easy to imagine sensory limits of bandwidth (the size of our "peephole"), absolute sensitivity, or even modes of sensitivity (our "peep-holes"). Neurological limits on thinking may be as common as those on sensing, but they are more illusive — it's hard to think about what you can't think about. A good example from physics is our difficulty in understanding the space-time continuum — our intellect fails us when we move beyond the dimensions of height, width, and depth. Other evidence of our neurological reality-generator is revealed by its malfunction in illusions, hallucinations, and dreams, or in brain damage, where the illusion of reality does not simply degrade, but often splinters and fragments.
Why am I interested in this question? As a neuroscientist, I want to understand how the brain evolved, developed, and functions. As a biologist, I believe that all organisms are a theory of their environment, and it's necessary to understand that environment. As an amateur astronomer and cosmologist, I want to know the universe in which I live. To me, physics, biology, neuroscience and psychology are different approaches to a similar set of perceptual problems. It's no coincidence that Herman Helmholtz, a great physicist of the past century, appreciated that you can never separate the observer from the observed, and became a founder of experimental psychology. The distinction between psychology and physics is one of emphasis. The time has come for experimental psychologists to return the favor and remind physicists that they should be wary of confusing the physical world with their neurologically generated model of it. The frontiers of physics may be an exciting playground for the adventurous cognitive scientist. Ultimately, physics is a study of the behavior of physicists, scientists trying as best they can to understand the physical world. The intellectual prostheses of mathematics, computers, and instrumentation loosen but do not free our species of the constraints of its neurological heritage. We do not build random devices to detect stimuli that we cannot conceive, but build outward from a base of knowledge. A neglected triumph of science is how far we have come with so flawed an instrument as the human brain and its sensoria.