SimEarth definitely has a lot of science in it but I'm not sure if the way the game shows the gamestate is informative enough to easily understand what's happening. The whole thing's a planet simulation, it starts with a giant ball of molten rock that cools down and develops oceans, some time after that you get prokaryotes and eukaryotes that then slowly climb the evolutional ladder, become multi-celled, form vertebrates, go on land, evolve into the classes we know and finally produce a sapient species that then goes from the stoneage up to the nanotech age and finally leaves the planet. All of that can happen without you doing anything or you could influence anything from the geology of a given spot to the axial tilt of the whole planet. Hell, you can even hand your favourite species a monolith to make it rapidly advance through the progression or just drop a nuke on Washington for the heck of it.
But as I said, the presentation is fairly abstract, you get a tile view of the planet's surface that can display heights or vegetation (and extra views like temperature, wind, humidity, pressure, ...), you have symbols for animals and people moving around with no easily visible reason, you see icons for "fire" or whatever pop up but that's all you see. You can't look at a city and see what's happening there, you can't see why your mamals are dropping like flies (at least not diectly, you can look at the environment and possibly figure it out though), you don't see volcanoes scorching the cities around them, etc.