I couldn't believe this would be a MGS game at first, but this is just too fucked up and fishy not to be. Also: http://en.wikipedia.org/wiki/Phantom_eye_syndrome
"Visual hallucinations. About 30% of patients report visual hallucinations of the removed eye. Most of these hallucinations consist of basic perceptions (shapes, colors). In contrast, visual hallucinations caused by severe visual loss (Charles Bonnet syndrome) are less frequent (prevalence 10%) and often consist of detailed images."
Enucleation of an eye and, similarly, retinal damage, lead to a cascade of events in the cortical areas receiving visual input. Cortical GABAergic (GABA: Gamma-aminobutyric acid) inhibition decreases, and cortical glutamatergic excitation increases, followed by increased visual excitibility or even spontaneous activity in the visual cortex. It is believed that spontaneous activity in the denervated visual cortex is the neural correlate of visual hallucinations.
People suffering from CBS may experience a wide variety of hallucinations. Images of complex colored patterns and images of people are most common, followed by animals, plants or trees and inanimate objects. The hallucinations also often fit into the person's surroundings.
I know Big Boss had his right eye damaged by a heated muzzle/bullet, but was it ever removed completely? Like, did he ever get the dead eyeball removed?