I thought the same thing about ecosystems!
Evolution by natural selection is a complex adaptive system - it does not have a leader, but a few simple rules generate changes and patterns. Feedback loops occur through coevolution of different species.
The first thing that comes to my mind is with plate tectonics and specifically convection currents in the mantle. The movement of the molecules of magma being heated and then cooled causes plate movement which has some emergent patterns with earthquakes and volcanoes along plate boundaries.
Virus mutation and reproduction is a great example! Definitely did not think of that originally!
This is true. I teach Earth Science and weather definitely comes to mind. I was thinking about clouds but also hurricanes, and tornadoes and how they travel.
I just watched the suggested video. This has to be the coolest thing I have seen in a while. the fact that we are able to take inspiration from nature and program devices to model such behavior is mind-blowing. I am curious to learn how these devices are actually programmed. 
yes i was thinking about the role of decomposers (fungi, bacteria and invertebrates) and moisture and pH