G. W. Leibniz (1646–1716) did not contribute directly to scientific discoveries in the life sciences, but he provided several relevant analyses on methods of investigation applicable to complex, and in particular organic, phenomena. Leibniz's theory of organic bodies and his methodological model had deep and broad implications for the development of physiology at the turn of the seventeenth and eighteenth centuries. This paper focuses on a methodological issue which divided natural philosophers and physiologists during the early Enlightenment—about which Leibniz supported original viewpoints which have kept a certain relevance, mutatis mutandis, in later contexts. The issue in question concerns the relation between the surface organization of phenomena and the deeper organization of underlying micro-structures and micro-processes. In a search for the sufficient reason for phenomena, hypothetical models are called upon to provide determining reasons for surface effects. These reasons represent processes involving micro-mechanisms combined so as to account for the emerging organization.

In aid of understanding mechanistic explanation and its limits in the 17th century, I examine the views of Pierre Sylvain Régis on generation. Régis departs from Descartes' theories on one key point. Living things, though they do not differ in nature from nonliving things, and are, as Descartes said, machines, are directly created by God, who forms the seeds of all living things at creation. Preformationism gives Régis not only a means of accounting for seeds and for specific differences among living things, but also a basis for attributing purposes to them, and thus for defining health and disease in soulless creatures.

The concept of bodily health is problematic for mechanists like Descartes, as it seems that they need to appeal to something extrinsic to a machine, i.e., its purpose, to determine whether the machine is working well or badly, and so healthy or unhealthy. I take issue with this claim. By drawing on the history of medicine, I suggest that in the seventeenth century there was space for a non-teleological account of health. I further argue that mechanists can and did appeal to structural integrity, as a non-teleological notion of form, to ground the norms required for ascriptions of health.

Malebranche is both an occasionalist and an advocate of the preformationist theory of generation. One might expect this given that he is a mechanist: passive matter cannot be the source of its own motion and so requires God to move it (occasionalism); and such matter, moving according to a few simple laws of motion, could never fashion something as complex as a living being, and so organisms must be fashioned by God at Creation (preformationism). This expectation finds a challenge in Kant's depiction of the relation between causation and generation. According to Kant, preformation is the generation theory one would expect the advocate of the pre-established harmony to endorse, while the occasionalist would endorse a theory whereby God directly forms the organism upon every insemination. I make sense of Malebranche's position in light of Kant's suggestion by examining the relation Malebranche sees between science and metaphysics, the roles that he believes empirical investigations and final causes have in scientific practice and explanation, and the role of the supernatural in Malebranche's philosophy.

In his accounts of plant and animal generation Pierre Gassendi offers a mechanist story of how organisms create offspring to whom they pass on their traits. Development of the new organism is directed by a material “soul” or animula bearing ontogenetic information. Where reproduction is sexual, two sets of material semina and corresponding animulae meet and jointly determine the division, differentiation, and development of matter in the new organism. The determination of inherited traits requires a means of combining or choosing among each parent's contributions, and towards this end, Gassendi outlines the nature of competition and dominance among animulae. Unlike his fellow mechanists, Gassendi can extend his mechanism to his heredity account, because his proposed vehicle for ontogenetic transmission is material. That proposal in turn relies on his atomist hypothesis. The relative uniformity of atoms allows animulae to operate equivalently across different modes of generation, spontaneous or otherwise. Further, his molecular model of atomic structures allows a material means of storing ontogenetic information received from the souls of parent organisms. These accounts—flawed and sketchy—unsurprisingly fail to specify how hereditary information might be borne physically, and in any case do not meet Gassendi's own empiricist standards. Yet this generation theory with pretensions to a materialist mechanism establishes Gassendi's firm commitment to a unity of the sciences through an atomist ontology that underlies all physical phenomena, including the organic.