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According to a study published recently in The Journal of Experimental Biology, when they ascend to the surface is determined by how many times they flap their wings.
Kozue Shiomi and colleagues from the University of Tokyo, Japan, and the Scripps Institution of Oceanography, USA, analysed the dive profiles of emperor penguins and found that the birds used on average 237 wing beats before embarking on their return.
The scientsts suggest that the penguins' decision to return to the surface was constrained not by how much time they are underwater, but how much power their muscles can produce after every pre-dive breath.
Penguins time dives by wing beat by Kathryn Knight, Inside JEB, The Journal of Experimental Biology
How penguins "time" a deep dive, 8 December 2011, BBC News
Journal of Experimental Biology citation
Shiomi, K., Sato, K. and Ponganis, P.J. (2012). Point of no return in diving emperor penguins: is decision to return time limited by the number of strokes? J. Exp. Biol. 215, 135-140.