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The Flesh was 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 was programable matter that was often used in dangerous industrial work, to create clone bodies operated by human drivers. Through the Flesh, thousands of lives were saved due to the clone body being killed in the place of the Human.
The Flesh even learnt to self-replicate, meaning there was never a risk of work forces running out of it.
When the Doctor met the Flesh in the 22nd century, he claimed to have met them previously.
In the 22nd century, a solar storm caused a group of Gangers to be separated from their human controllers. Rather than reverting to Flesh, as was expected, the Gangers operated independantly of the humans, though they still had the memories of the Humans that they were based on. After failed peace attempts with the Humans, the Gangers rebelled because they wanted the right to exist.
Later the Flesh created a Ganger of the Doctor on its own, without human manipulation or assistance, having used the sample it took from the Doctor's handprint and the psychic contact it made with him.
Sentience
While humans acknowledged the fact the Flesh was alive, they considered it to be little more than moss. Cleaves explained that the Flesh only knew how to mimic life, but did not actually know how to be life.
The Doctor, on the other hand, was not so sure. When he scanned the Flesh with his sonic screwdriver, he was suprised to note that it responded with an attempted scan of its own. When he touched the substance he noted that he felt a consiousness in the flesh that curiously investigated him when he made contact. He told the others that the Flesh might have a consiousness of its own but not one that humans could understand; each time they made clones it learned more and more about humans.