The "Problem" of Qualia
The following diagram shows an idealized process by which different colors of light enter the eye and are converted into "qualia" -- the brain's internal representation of the information. Obviously the brain doesn't represent color as 10 bits of information. But the principle remains the same, even if the actual engineering is more complex.
We now observe that the brain is able to distinguish between qualia. "This set of bits is the same as that set of bits." (This red color is the same as that red color). "That set of bits is different from the other set of bits." (That blue color is not the same as a green color). "This collection of sets of bits is the same as that set of collection of bits." And so on. It doesn't matter whether the comparison circuitry is built out of NAND gates as in a computer, or out of neurons as in the brain. It's just a sophisticated network to test for equality between internal representations. The complexity is in the engineering, not in the basic principle.
Next, we notice that the brain is able to associate qualia, for example, it can associate the qualia for the color "red" with the qualia for the sound of the word "red." This is just another use of the mechanism that says "these two things are equal."
One key point is that it doesn't matter what the representation of the qualia happens to be. It doesn't make any difference if the qualia for the sound "red" and the qualia for the color red are the same or not. How the qualia are stored is just an engineering detail. An important one, and a fascinating one, but it is secondary to the association between the two things. The "dotted line" in the above diagram is the key component. While I have no idea how that dotted line is represented in the brain, I know any number of ways to do it in computer software and all computer programs have physical representations.
Another key point is that these associations, these "dotted lines," the "circuit" that says "these two things are equal" are dynamic. The brain is forming associations all the time. Associations can also be lost.
With this as background, we can now look at one of the supposed problems of qualia through the eyes of "Mary," the world's foremost expert on color vision1. As the thought experiment goes, Mary has lived in isolation her entire life and has never been allowed to see color. Her television and computer screen are black and white, her furniture is black and white, and (bear with me), either via dress or some other means, she has never seen the color of her skin, the color of her eyes, the color of her hair. Through intense study, she learns everything there is to know about color and color vision. Finally, she is permitted to go out into the real world and actually see the red of a rose, the blue of the sky, and the green grass. Quoting , "She seems to find out things she did not know before. How can that be, if, as seems possible, at least in principle, she has all the physical information there is to have about color and color vision — if she knows all the pertinent physical facts?"
The answer, of course, is that this is a form of the black-or-white fallacy2. After all, Mary could just as easily have known everything there is to know about money but not have a penny to her name. The answer to the supposed dilemma is that, like not having any coins, she didn't have the physical wiring in her brain between her brain's encoding of the wavelength for red and the other items associated with color. The moment she saw red for the first time, her brain encoded a new datum that it hadn't previously experienced and started making associations with the stored qualia for her knowledge, as well as associations with her other new sense data. New physical changes took place in her brain.
Another argument against physicalism is that of the appeal to the possibility of zombies, that is, a creature that is atomically identical to an individual, but lacking phenomenological consciousness. Such a creature, being imaginable, is metaphysically possible. This begs the question as to whether an identical creature would actually lack phenomenological consciousness. Build one and then we'll talk.
 Stanford Encyclopedia of Philosophy: Qualia: Are Qualia Irreducible, Non-Physical Entities.
 False dilemma