The all-time best in-joke regarding names, stems from a somewhat easy-to-miss line in Modern Who episode Human Nature. When John Smith, a human version of the Doctor filled with false memories, addresses the subject of his origins he says "My father Sidney...and my mother Verity". This is in tribute to series creator, Sydney Newman, and first producer, Verity Lambert, who are very much the parents of Doctor Who indeed. It is briefly revisited when, on his farewell tour in End of Time, the Tenth Doctor goes to see Joan Redfern's granddaughter, named Verity Newman.
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