Where and Why: Apoptosis

This article addresses two main questions:
Why are cells that die by programmed cell death generated?

Obviously, the answer would be different depending on different cell types but for the most part some cells are generated in excess and only those that become properly functional survive (as happens in parts of the nervous system). This is kind of like survival of the fittest because only the competent cells will survive. In some cases, the mechanism that generates cells that are needed also generates unneeded ones as well (as happens in the immune system). And some cells that die may be needed, but only temporarily.

 Cells die because they are harmful or because it takes less energy to destroy them than to keep them alive and healthy. As of now, programmed cell death has been known to occur only in animals, although it remains possible that bacteria, fungi and plants may also use similar processes to eliminate unwanted cells.

Why do these cells die instead of surviving?

One of the main reasons for cell death is to get rid of dangerous cells, the one's whose existence can harm the organism. Cells literally "kill themselves for the greater good". They could be mutants that can lead to cancer--apoptosis is therefore very important in the formation (or nonformation) of cancer. Also, positive and negative selection occur among the cells of the immune system. Cells that recognize "self" (ones that would attack the organism's own cells) are instructed to die during this process. Also, cells that are infected by a virus, can sometimes recognize the infection and kill themselves as to not allow the virus to be spread further.