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The Doctor was a Ganger cloned from the Time Lord of the same name. When a bolt of solar energy struck the vat the Flesh was contained in, it was able to form a copy of the Doctor from a measure of his genetic material, gained when he touched the Flesh.
This Ganger was created by the Flesh without instruction from the human workforce; seemingly by the consiousness that the Doctor was able to sense in the substance. Without human instruction, it took the Flesh longer to generate the Doctor Ganger than it did a human Ganger. (DW: The Rebel Flesh)
When the humans and the Doctor fled from the other Gangers into the church, this Ganger confronted them and told them to trust him. (DW: The Rebel Flesh)
The Ganger Doctor can Regernarte as he does in DW: The Almost People