Anders_H comments on Open Thread April 8 - April 14 2014 - Less Wrong Discussion
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Smoking is not "accused" of being strongly correlated with negative outcomes. It is strongly correlated with negative outcomes, as a simple empirical fact. This is a statement about the joint distribution of the observed variables "smoking" and "negative outcomes", and it has nothing to do with causal inference. I cannot even imagine a scenario where the statement "Smoking is strongly correlated with lung cancer" is false, short of a vast conspiracy among scientists and doctors
A slightly more interesting question is whether the correlation between smoking and cancer is due to causation. It is theoretically possible that an unmeasured confounder is responsible for the observed correlation. In fact, R.A. Fisher believed such a confounder was probably at work . One of the first uses of sensitivity analysis was to show how unrealistic Fisher's claim was. A sensitivity analysis is essentially a thought experiment that lets you play around with how "strong" a confounder has to be, in order to account for the observed correlation if the causal null hypothesis were true. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755131/.
In this case, I think any reasonable investigator who looks at the data and does some basic reasoning about possible confounders, will come away with a very strong posterior in favor of smoking causing lung cancer. However, the relationship between smoking and certain other negative outcomes is in some cases much more questionable, and it would not surprise me if publication bias accounts for many of the negative outcomes smoking has been connected to