An interesting readable review in PLoS Genetics taking on population genetics, Frail Hypotheses in Evolutionary Biology:
In conclusion, I return to Michael Lynch's challenging questions about blind spots and bad wheels in evolutionary biology which motivated this review...Concerning blind spots I have pointed out some limitations of current population genetics. There is too much emphasis on elegant mathematics, and not enough concern for the real values of the critical parameters -in particular, in models of mutation spread and fixation, or in models of optimal mutation rates. Recombination, a crucial genetic mechanism, is misrepresented in the models. Features that looked anecdotal, such as recombination between sister chromatids and germ-line mutations are perhaps central to the mechanisms of evolution in higher organisms. My proposals on mutation strategies...—see also Amos...—lead to rather precise insights on compensatory mutations or polymorphism propagation, yet they are largely ignored by population geneticists.
The beauty of population genetics is that it leads to relatively simple algebras which one can use to guide one's intuitions. Phenomena such as selection or drift are more than words, they're specific values. That being said, plenty of readers of this weblog have expressed caution, and skepticism, at the over-utilization of monogenic diallelic models as "quick & dirty" prototypes for evolution more generally. More concretely small changes in parameter values can lead to radically different inferences within the real context of natural history. Excessive reliance on elegant population genetic theory can lead one astray just as excessive reliance on economic theory can. The real world introduces so many complications that discarding too many of them to make a model tractable may render the framework of trivial importance, or even lead one down false paths. I don't find author's specific objections of distinction, but the paper is useful as an entry-point into the debate within the literature. The fact that R. A. Fisher, J. B. S. Haldane, and Sewall Wright, did not predict the full path of empirical discovery over the 20th century indicates very concretely the limitations of theoretical frameworks within biology.