(Note: Throughout this post, I will be using the term evolution to refer to the evolution of animals and man through natural selection, and the phrase "theory of evolution" to refer to modern biology's conception of evolution, including gene theory.)
It would be difficult to overstate the influence that the theory of evolution has had on my thinking and philosophical outlook. It forms, in many ways, the core of my philosophical anthropology, my epistemology, and my ethics. It is a brilliant example of how a solid scientific theory can have tremendous philosophical implications (a fact that no doubt frustrates many ivory tower philosophers who see themselves as above the messy, empirical world).
That being said, I think it is also easy to misapply the theory of evolution, so I think it is important to clarify its proper use in philosophy and general thinking. There is a crucial error that many thinkers commit that bears some similarity to the famous "is-ought" gap in the field of ethics. The fallacy can be stated, in its simplest and most consistent terms, as follows:
The good is that which we have adapted for through natural selection.
Now, on its face, this claim is easy to refute. Few would argue that we would be better off without modern conveniences in general. Modern dentistry is a brilliant example of something we clearly haven't adapted to through a process of natural selection but is very, very good; until its invention, death by tooth decay was surprisingly common.
Few people make the claim so boldly and consistently; the error is often committed in a more subtle fashion and in specific contexts rather than in general. Here is an example you might actually see:
Eating grains and drinking cow's milk is bad for you because we didn't evolve to eat and drink those things.
Now, it might actually be true that eating grains and drinking cow's milk is bad for you (I'm not a nutritionist), but the truth value of that claim is not contingent on whether or not we evolved for it. As stated above, many things are very good for us even though we didn't evolve for them at all.
Evolution can still provide crucial insights into diet, however. The key is to not crudely assume that the diet of our tribal ancestors is the most optimal diet for human beings today. Rather, we should use our knowledge of evolution and genetics as one source of knowledge (out of many) to gain insight into the optimal diet. Empirical evidence is another crucial and important source of knowledge on such matters.
In other words, evolution should inform our conclusions, but it should not define them.
Another crucial thing to keep in mind, which is often forgotten by those quick to use evolution to defend certain philosophical perspectives or lifestyle choices, is that evolution didn't just stop 50,000 years ago when we were all hunter-gatherers in the savanna of Africa. The relatively strong correlation between skin color and the amount of sunlight in a given region is a perfect example of how natural selection continued to play a role as human beings migrated to different parts of the world.
While we are no doubt very close to the human beings of 50,000 years ago genetically, it should be noted that we are not identical, and the changes in lifestyle from hunter-gatherer tribes to agricultural and urban environments are going to be the very environmental changes that would affect natural selection. Once people began to live in cities, for example, the genes best capable of spreading in a city environment are, of course, going to be the ones that spread.
One interesting example of how this has affected diet is lactose intolerance. Lactose intolerance is much higher in populations that, traditionally, did not drink animal milk or eat dairy products. It is relatively rare, by comparison, in European populations, where cows were widespread as a source of meat and milk. Someone may actually be predisposed to being able to gain nutritional benefits from cow's milk even though his tribal, hunter-gatherer ancestors never drank cow's milk. This is a perfect example of how someone might be adapted to his environment in ways we might not expect using tribal ancestors as our standard. Evolution didn't stop 50,000 years ago.
Evolution is driven by an invisible hand, very similar to the one that drives free market economics. There is no actual hand, of course, but it is a metaphor for how coherent, functional systems form with no top down authority planning for them to be that way. Anyone skilled in free market economics will tell you that, while we can make reasonable guesses about why the market is the way it is, there are just too many variables to know for sure.
Evolution is the same way. We can infer various things about why we have certain traits (such as opposable thumbs), but we can't know for sure without substantial research. Often, research yields surprising conclusions; many bodily organs have functions that were completely unknown until modern medical research.
This is important to bear in mind when drawing inferences using evolution. I might assume that our feet evolved to operate a certain way (say, to chase down boars in the grass of the savanna) and therefore conclude that running barefoot in grass is the best way to get exercise, but my inference could be wrong. What if it turned out that humans rarely ran, and the majority of their time on their feet was spent standing or walking, and that even the most primitive humans had some kind of crude footwear? Running through the grass barefoot might, in this instance, be something that actually puts my body under stress it was not built for.
To wrap this up, my point is this; evolution is a tremendously useful tool for understanding how we are the way we are, and can provide amazing insights into how to live a better life. But it is not the only tool for doing so, and it's important that we integrate all of the data we have available before drawing hasty conclusions.