This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development and evolution. In (...) developmental biology the MCO underlies a logically incoherent model of ontogeny, the genetic program, which serves to legitimate three problematic theses about development: genetic animism, neo-preformationism, and developmental computability. In evolutionary biology the MCO is responsible for grounding unwarranted theoretical appeals to the concept of design as well as to the interpretation of natural selection as an engineer, which promote a distorted understanding of the process and products of evolutionary change. Overall, it is argued that, despite its heuristic value, the MCO today is impeding rather than enabling further progress in our comprehension of living systems. (shrink)