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Mammals like seals often dive and can remain under water for more than 70 minutes.

How do seals know when is it the time to come up?

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I imagine that their breathing is controlled in the same way as ours. During a dive, oxygen will be used up and carbon dioxide will be produced, dissolving in the blood as bicarbonate and tending to decrease the pH of the blood.

Peripheral chemoreceptors in the circulatory system detect all of these changes and signal the need to breathe. This would tell the seal that it is time to head for the surface.

Diving mammals have various adaptations for prolonged diving, most importantly large reservoirs of blood containing haemoglobin which is oxygenated before a dive, as well as high concentrations of myoglobin in muscle which can also act as an oxygen reservoir.

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    $\begingroup$ Check this article in the today's issue of science. Was going through the TOC just before I looked at this question. It is about how myoglobin is more efficient in deep divers. Reinforcing the fact in the last statement of Alan's answer. $\endgroup$
    – WYSIWYG
    Jun 14, 2013 at 12:00

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