I have been studying ocean currents and associated energy flows in the eastern Pacific and western Atlantic oceans. I also looked at El Nino cycles.
I also noted when the large glacial periods started 3 million years ago and noticed that these began when what is now Panama formed between North and South America by continental drift effectively separating the Gulf of Mexico from the Pacific Ocean. The ocean currents from the Atlantic and Pacific no longer mixed from then on. However, this article in Scientific American mentions some evidence that the isthmus of Panama actually formed enough to block ocean currents 10 million years ago.
I am not sure on the macroscopic thermodynamics on how this contributed to the start of the Ice Ages but this is the situation. Could be coincidental.