It seems likely to me that this is a data- and domain-dependent question. I forwarded this article to the whole research group I work in -- many of us try to infer causes from data while looking at data concerning the concentration of a small subset of biological molecules at a small number of time points in some cell line of interest. This is a *hard* problem, and the data may well not be sufficient to the task at all, *even though it's not hard to convince yourself you've learned something causal when you turn the crank on your mathematical methods*.