The human body is the most complex system on the planet. Damn those doctors for thinking they have any idea how any of it works.
A blanket statement of "how things work" is pretty telling. You break down the systems to the simple elements, understand those elements, and reconstruct the puzzle from the ground up. You don't look at the thing in totality until you figure out the basic workings of climatology, geology, paleobotany, paleontology, local cosmology, etc.
People much, much smarter than us look at the evidence the Earth has trapped in various ways and reconstruct what happened from that. Same way any mystery is solved. Look at the evidence, work backwards.
If ice cores show an elevated amount of CO2 in the atmosphere, reduced pollen, elevated hydrogen sulfide, and pumice; and then you find the same thing in soil layers by chemical extraction methods there's pretty much only ONE thing on Earth that can produce a climatological effect that can leave behind that evidence. A volcano.
How do we know? Because we can look at ice cores of major eruptions like the one that occurred last year in Iceland and see the evidence it leaves behind.
The Earth is not a static system, but the processes working on the Earth have been the same since it coalesced from dust. If the same thief leaves the same clues, it's pretty simple to figure out what the thief is doing and who he is given enough time.
We've got billions of years of evidence.
Scientists are not idiots.