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When a clock gene is switched on, it directs the cell to produce proteins, which eventually trigger a signal that switches the gene off.
BBC: Body clock 'set before birth'
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This is because of molecular switches that turn parts of the genome on and off depending on what the cell in question is up to.
ECONOMIST: Human genomics
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That you need a profusion of such switches to get the right pattern of genes turned on and off in a given cell at a given time is obvious.
ECONOMIST: Human genomics