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There are several "clone lines", each at least slightly different from the others. Also, even when individuals start as identical, events during life can cause differences (scars, for example, which are especially likely among warriors like the Sontarans). The nurse Strax, in "A Good Man Goes to War" spoke of another cause of differences -- deliberate modifications during life. In the case of Strax, he suggested hormonal treatment that would allow him to produce milk for baby Melody.