In the examples you used (no legs and no arms) the benefits are very small. But resistance to malaria is a huuuuuuge advantage (malaria being the world's biggest killer). If there is a chance some people may develop a resistance to the ill effects and therefore would be MUCH more likely to have children and pass on this gene. Therefore the human race will have evolved a resistance to malaria. This is just one way that evolution can take place.
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