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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 some measure of his genetic material, gained when he touched the Flesh.
The 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 and presumably due to the more complex nature of a Time Lord body it took the Flesh longer to generate the Doctor Ganger than it did a human Ganger. (DW: The Rebel Flesh)