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The Flesh is a living substance used by humans to create clone workers or Gangers for dangerous labour.
History
Considered the goverment's worst kept secret the Flesh is programable matter that is often used in dangerous industrial work, to create clone bodies operated by human drivers. Through the Flesh thousands of lives have been saved due to the clone body being killed in the place of the human.
The Flesh had even learnt how to self replicate meaning there was never a risk of workforces running out of it.
Curiously the Doctor claims he knowes the Flesh and while not informing Roary and Amy on the details he claims he let it down in the past and he wants to try and help it this time.
Sentience
While humans akowledge the fact the Flesh is alive they considered it to be little better than moss. Cleaves explains the Flesh only knows how to mimic life instead of actualy being it.
The Doctor on the other hand is not so sure. When he scans the Flesh with the screwdriver he is suprised to note that it respondes to this with an attempted scan of its own. When he touches the substance he notes that he felt a consiousness in the flesh that curiously investigated him when he made contact. He then told the others that the Flesh might have a consiousness of its own but not one that humans can understand; each time they make clones it is learning more and more about humans.
Later the Flesh creates a Ganger of the Doctor on its own withought human manipulation or assitance having used the sample it took from the Doctor's handprint and the psychic contact it made with him.