What distinguishes a man from a mouse is not so much different proteins, but rather the appearance of common proteins (etc.) at different times and positions in the developing organisms. Thus specific genes are transcribed or repressed, proteins degraded or stabilized, RNA transcripts spliced one way or another, and so on. These are examples of 'regulatory' decisions. A rather simple mechanism - called regulated recruitment - lies at the heart of many of these regulatory decisions.
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Mark Ptashne (2003) studied this question.
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