Our goal in the paper is to offer both an eulogy and a critique of the machine metaphor as a theoretical resource for understanding organic systems. We begin by presenting an abbreviated history of the machine metaphor, pointing out how it was instrumental in the development of modern biology, as it provided a conceptual basis for an analytical program in the sciences of life. Then we deal with what exactly makes the machine metaphor such a successful resource, pointing to what organisms and machines in fact share in common – based on the relational approaches advanced by Varela and Rosen, we suggest that both are ʻconstrained systemsʼ. In the third part, we present an alternative way of conceptualizing living systems, bringing now the disanalogies with machines to the foreground. Reviewing the independent work of different authors, we show that there is distinct organicist theoretical camp, where the organism is generally understood as an autonomous system. Finally, we observe that many authors from that camp are now reclaiming Kant’s treatment of organisms in the Critique of Judgment, in particular the concept of «natural purpose» – but those authors do that with a markedly anti-Kantian goal: to naturalize teleology. Our conclusion is that the view of organism as an autonomous system gives us the key to a naturalistic understanding that can finally overcome the mechanical view of nature so characteristic of modern thought. The machine metaphor, despite all its undeniable contributions to the advancement of biological research, shows itself ultimately insufficient for a complex view of the phenomena of life – and discarding it doesn’t need to mean any concession to vitalism: on the contrary, it may be exactly what we need to invigorate a robustly materialist project.

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