I'm not quite sure if I can answer that correctly, but MakgSnake will probably correct me if I'm wrong... Here's what I believe to be the situation:
Big Boss was a very powerful man, in the military, I think. Scientists decided to make clones of him in order to form the "Perfect soldier". They knew that, by using the genes on someone as powerful as Big Boss, they could make almost invincible soldiers. They made Solid Snake and Liquid Snake. At fist, Solid is rumored to be the "good one" and Liquid only the "left overs". But, when you listen carefully at the end of Metal Gear Solid, you hear that Liquid was in fact supposed to be the superior one and Solid the left overs...
The project was called "Les enfants terribles", witch is french for "The terrible children", but it was terminated for reasons I don't quite know...
... That's about all I can remember for now.
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