The color of blue eyes is due to the Tyndall scattering of light by a translucent layer of turbid media in the iris containing numerous small particles of about 0.6 micrometers in diameter. These particles are finely suspended within the fibrovascular structure of the stroma or front layer of the iris. Some brown irises have the same layer, except with more melanin in it. Moderate amounts of melanin make hazel, dark blue and green eyes.
In eyes that contain both particles and melanin, melanin absorbs light. In the absence of melanin, the layer is translucent (i.e. the light passing through is randomly and diffusely scattered by the particles) and a noticeable portion of the light that enters this translucent layer re-emerges via a radial scattered path. That is, there is backscatter, the redirection of the light waves back out to the open air.
Scattering takes place to a greater extent at shorter wavelengths. The longer wavelengths tend to pass straight through the translucent layer with unaltered paths of yellow light, and then encounter the next layer further back in the iris, which is a light absorber called the epithelium or uvea that is colored brownish-black. The brightness or intensity of scattered blue light that is scattered by the particles is due to this layer along with the turbid medium of particles within the stroma.
Thus, the longer wavelengths are not reflected (by scattering) back to the open air as much as the shorter wavelengths. Because the shorter wavelengths are the blue wavelengths, this gives rise to a blue hue in the light that comes out of the eye. The blue iris is an example of a structural color because it relies only on the interference of light through the turbid medium to generate the color.
Blue eyes and brown eyes, therefore, are anatomically different from each other in a genetically non-variable way because of the difference between turbid media and melanin. Both kinds of eye color can remain functionally separate despite being "mixed" together.