This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual practice of biological inquiry.

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This paper is concerned with reasonings that purport to explain why certain organisms have certain traits by showing that their actual design is better than contrasting designs. Biologists call such reasonings 'functional explanations'. To avoid confusion with other uses of that phrase, I call them 'design explanations'. This paper discusses the structure of design explanations and how they contribute to scientific understanding. Design explanations are contrastive and often compare real organisms to hypothetical organisms that cannot possibly exist. They are not causal but appeal to functional dependencies between an organism's different traits. These explanations point out that because an organism has certain traits (e.g., it lives on land), it cannot be alive if the trait to be explained (e.g., having lungs) were replaced by a specified alternative (e.g., having gills). They can be understood from a mechanistic point of view as revealing the constraints on what mechanisms can be alive.

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