Prior specification in Bayesian statistics: Three cautionary tales

One of the most important differences between Bayesian and traditional techniques is that the former combines information available beforehand—captured in the prior distribution and reflecting the subjective state of belief before an experiment is carried out—and what the data teach us, as expressed in the likelihood function. Bayesian inference is based on the combination of prior and current information which is reflected in the posterior distribution. The fast growing implementation of Bayesian analysis techniques can be attributed to the development of fast computers and the availability of easy to use software. It has long been established that the specification of prior distributions should receive a lot of attention. Unfortunately, flat distributions are often (inappropriately) used in an automatic fashion in a wide range of types of models. We reiterate that the specification of the prior distribution should be done with great care and support this through three examples. Even in the absence of strong prior information, prior specification should be done at the appropriate scale of biological interest. This often requires incorporation of (weak) prior information based on common biological sense. Very weak and uninformative priors at one scale of the model may result in relatively strong priors at other levels affecting the posterior distribution. We present three different examples intuïvely illustrating this phenomenon indicating that this bias can be substantial (especially in small samples) and is widely present. We argue that complete ignorance or absence of prior information may not exist. Because the central theme of the Bayesian paradigm is to combine prior information with current data, authors should be encouraged to publish their raw data such that every scientist is able to perform an analysis incorporating his/her own (subjective) prior distributions.