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So we know that surface air temperatures are warmer during El Niño events (which implies that there is more heat in the atmosphere, although maybe it's possible that it also means there's less heat in the oceans?).

I'm wondering... though.. Could this simply mean that the land surface emits more longwave radiation out into space during periods of El Niño.

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During El Niño heat is transferred from ocean to atmosphere. If atmosphere gets warmer, yes, it generates more radiation and more heat escapes into space. The same about land surface - if it's warmer, it radiates more heat.

Of course that's all with assumption that there are no other factors influencing it - like e.g. greenhouse gases.

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