Quantifying a natural system is possible when the controlling mechanisms and their interactions are well known. This is not always the case, especially for large-scale systems with limited access to direct observation, such as the underground or in deep time. Therefore, observation and characterization are not necessarily sufficient to determine the controlling mechanisms that are needed for predictive models. A procedure developed to verify, validate or refute a hypothesis on controlling mechanisms is, thus, needed: experiments where a particular set of factors is manipulated might provide insights on cause-and-effect dependence by recording different output for different/controlled system configurations. This is done (i) in the field, where, for instance, the natural medium is stimulated by the injection of special tracers or the production of artificial and engineered flow configurations, and (ii) in laboratory environments, where chemical, biological and physical conditions can be finely controlled. Experiments on modern animal systems can also act as a proxy for understanding ancient ecosystems and the interactions between the biosphere and the geological environment.

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