I think the way you're looking at systems is wrong. The systems don't magically harmonize with each other. They became the way they were because of each other. We are one big system.

For example humans aren't a system which conveniently harmonize with plant and animal systems, so that there is food for us. We all exist off each other. The "systems" that do not adapt, die out. Only the "systems" that worked continue to prosper. Humans breathe in oxygen and breath out carbon dioxide. Plants utilise carbon dioxide and emit oxygen. The plants who were not able to exist on carbon dioxide did not survive to be in existence today.

The modern world that you see today is the result of only the species that were able to adapt. The ones that did not adapt, the "systems" that did not work, are a trillion times more plentiful then the ones that did.