A re-visitation of Joule’s experiment motivates a critical analysis of thermodynamic notions: heat, total energy, first principle, organization of a scientific theory, its relationships with logic and mathematics. A rational re-construction of thermodynamics is suggested according to the model of a problem-based organization, that Sadi Carnot applied to his formulation. The new formulation accomplishes the long time theoretical process started by Joule’s experiment within physicists community's collective mind, i.e. the process of exiting out Baconian science for suggesting a first theory (...) out Newton’s paradigm, and eventually for introducing a pluralism of incompatible physical theories. (shrink)