This article is about the role of metaphor in scientific knowledge formation and reasoning. These issues are studied by means of an example of the theory of evolution through natural selection. The premise is that the theory of evolution contains a set of problems regarding metaphor. A second premise is that these problems have to be handled in one way or another when trying to learn, explain, or discuss the theory. How metaphor plays a role in Darwin's writings is analyzed through examples taken from "On the Origin of Species". Which metaphors are used by Darwin and which problems do they solve and raise, respectively? It is shown how Darwin uses a variety of metaphors, and that he grapples with this issue. The findings are discussed in terms of the implications for teaching evolutionary theory. Some inherent difficulties in learning the theory of evolution, and more generally abstract complex scientific knowledge, are discussed.