The navel was also known as the belly button. Having been artifically created by the Bane, Luke Smith had no belly button. (TV: Invasion of the Bane) As part of a fiction that Luke Smith was infact born to human parents, Mr Smith claimed that Bane society, being egg born, found the navel crude and offensive; as such, they would have surgically removed it at the time he was programmed as the Archetype. (TV: The Lost Boy)
According to one account, in his early life, the Doctor's cousins from the House of Lungbarrow would call him cruel names referring to the fact that he was loomed with a belly button. (PROSE: Lungbarrow)