Have Scientists Made Any Changes To Darwin's Theory Of Evolution?

Darwin's theory of evolution is still widely accepted as being the definitive answer to the question of how animals (including humans) have developed.
However, a slight change has been made to one of his central themes, that of natural selection.  Darwin thought that natural selection happened to the individual.  So, for example, in a littler of pups, the weakest one could and probably would die, whilst the biggest and cleverest one would survive.
However, biologists now know that the characteristics of organisms are actually determined by genes.  So instead of natural selection weeding out less fit individuals, it is actually a force which tends to eliminate genes which produce less desirable characteristics.  
Since natural selection takes place over many hundreds of generations, this is why we still have genetic 'faults' which can appear in some animals/humans today.  But in say, four or five thousand years time, natural selection may have eliminated the genes which cause these faults.