The rise of cell and molecular biology marked a renewed philosophical interest in mechanisms. Unlike the ‘old’ mechanistic philosophy, closely linked to the clockwork view of the universe, the new mechanistic philosophy had to come to terms with the fact that biological mechanisms are complex and ‘noisier’ systems composed of thousands of non-fixed, non-rigid parts whose behaviour is nevertheless constrained by the properties of the parts and spatiotemporal organizational features as to sustain biological phenomena and, ultimately, life itself. The project aims to develop a metaphysical account of mechanisms compatible with the methodological assumptions and practices underlying experimental design in biological research and the scientifically accepted interpretation of experimental results. Such an account will provide an answer to three key questions: “What are biological phenomena and how are these phenomena individuated?”; “What is the nature of the relationship between mechanisms and phenomena?”; and “What is the nature of biological mechanisms?”