Morendil comments on Causal Diagrams and Causal Models - Less Wrong
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That's a clear outline of the theory. I just want to note that the theory itself makes some assumptions about possible patterns of causation, even before you begin to select which causal graphs are plausible candidates for testing. Pearl himself stresses that without putting causal information in, you can't get causal information out from purely observational data.
For example, if overweight causes lack of exercise and lack of exercise causes overweight, you don't have an acyclic graph. Acyclicity of causation is one of the background assumptions here. Acyclicity of causation is reasonable when talking about point events in a universe without time-like loops. However, "weight" and "exercise level" are temporally extended processes, which makes acyclicity a strong assumption.
This is a hugely important point in practical, everyday reasoning about causality. Feedback loops abound.