| Some odd mutations in fruit flies cause legs to grow from their eyes. Disconcerting enough for anyone; but also a thought provoking phenomenon. Surely the eye genes have not all suddenly changed to leg genes at once?
This is where hox (homeobox) genes come in. They produce proteins that regulate the construction of whole sets of other genes. Like master switches, their influence extends over whole legions - they are cellular commanders, if you like. They exert control by binding to the area upstream of other genes - the promoter regions.
One possible explanation, therefore, for the odd leg/eye mutants is a switch of commands. A hox gene that controlled the legion of genes necessary for leg construction has defected. When given orders to start making eyes, in the cells in the appropriate part of the head, it subversively switches on leg genes instead. This seems to make much more sense; changes to one gene causes changes in expression of sets of other genes rather than many genes mutating simultaneously.
However, these are mutant fruit flies in the traditional sense. It's not only unlikely that this would benefit an organism, such radical changes to body plan sound positively dangerous. On the other hand, by simply shuffling and altering these master switches whole sections and parts of a creature can be manipulated at a time. This is a simplified account - but it illustrates the ability of evolutionary forces to work at many levels, with sometimes surprising results. | 
