With my recent paper on Measuring Fitness I realize that my previous responses to evolutionary drift, though not incorrect, may have not stated the solution particularly clearly. When fitness is defined and measured as described in the aforementioned article, evolutionary drift is irrelevant. The method of measuring the fitness of an organism or species makes no reference to any mutations whatsoever. Therefore evolutionary drift is no problem for the theory of fitness described here.
If we are trying to identify whether a certain mutation makes an organism more fit, we can of course test it against an organism without that mutation. However if we are unable to test it (say we are studying a historical period or it is just unfeasible), then I believe my previous posts are accurate. I mainly argue that you can’t tell what exactly makes an organism more fit- it’s an underdetermination thesis of sorts – based upon our limited evolutionary perspective.
I think I just failed to say how irrelevant drift was to fitness before this.