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A respiratory bypass system was a part of Gallifreyan physiology which allowed Time Lords to go without breathing for longer periods of time than most humans could. (AUDIO: Return of the Krotons) It also allowed them to filter out unpleasant smells. (PROSE: Cat's Cradle: Witch Mark)
The Doctor used it to survive more than once. The Second Doctor credited his survival on the surface of Mnemosyne to his respiratory bypass system. (PROSE: The Wheel of Ice) The Doctor's fourth self used his respiratory bypass system to survive being strangled by an Osirian service robot. (TV: Pyramids of Mars) He later used it to avoid inhaling helium. (TV: The Robots of Death) The fifth incarnation used it to survive brief exposure to the vacuum of space (TV: Four to Doomsday) as well as being hanged (PROSE: A Town Called Eternity) and retrieving the milk from a queen bat in an airless cavern. (TV: The Caves of Androzani)
His sixth persona avoided hypoxia when he shut down atmospheric controls to the mines on the planet Onyakis to defeat the Krotons there (AUDIO: Return of the Krotons), using this advantage again to avoid breathing in nerve gas. (TV: The Two Doctors) In his seventh body, the Doctor used his respiratory bypass system to avoid being overcome by ether. (PROSE: Timewyrm: Genesys) His eleventh incarnation survived the vacuum of low earth orbit long enough to find and put on an impact suit—backwards. (TV: The Doctor, the Widow and the Wardrobe)
When the Doctor's second heart was extracted by Sabbath in his eighth incarnation, one of the abilities the Doctor lost was the respiratory bypass system, leaving him vulnerable to being strangled until Sabbath allowed the heart to die and the Doctor to grow a new one (PROSE: The Adventuress of Henrietta Street, PROSE: Hope, PROSE: Camera Obscura).
At least one human may have developed such a system: Timothy Dean, who gained one when he was infected with the Seventh Doctor's DNA. (PROSE: Human Nature)