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.

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