Soft Image is running a detailed story about the making of Metal Gear Solid 4. They explain the game's development cycle, from the art direction to the animation of characters to the building of models and textures.
"In terms of bones used for constructing the bodies of characters, about 21 joint bones were used that contained animation data and were activated through these data. But many auxiliary bones were also used to supplement movements such as the twisting of knees, elbows, legs and arms. These were not activated by animation data. Rather, they were linked to the values of the basic joints that were activated by animation. ... They also used a tool to automatically generate the rig for controlling eyeball movement and the muscles around the eyes. Because the area around the eyes is also controlled using both shapes and bones, when the eyeball locator is moved, the muscles move smoothly just like they do for the mouth. Further, even if the shape is edited to redefine the eye edges, it does not spoil the blinking or brow furrow expressions at all."