The so-called “Scientific Revolution” is the result of a complex interaction between the world of ideas and that of concrete human activity with the aim of discovering the mysteries of nature. Not only books but also notebooks mediate this dialectical relationship: in this way, the complex features of a theoretical system can coexist with the detailed observations of everyday natural phenomena (like water drops, or burning candles), in order to test the foundations of a whole philosophy of nature in the (...) micro-world. Bacon himself suggested leaving general observations aside in order to reach closer to phenomena: Isaac Beeckman, in the isolation of his Journal, notes in chronological order his own laboratory and reading experiences, together with his meditations, producing an intellectual account of great cultural and scientific interest, discovered by Cornelis De Waard in 1905, in the Provincial Library of Zeeland [Middelburg]. Beeckman also owned some of Francis Bacon’s major works: from some of the notebook annotations presented in this article it is possible to see that Bacon’s explanations of simple natural phenomena did not always agree with the emerging physico-mathematical turn. Bacon is blamed for the use of old-fashioned categories, like sympathies and occult qualities, which need to be replaced by a fully corpuscular, mathematical and geometrical mechanical philosophy. (shrink)