From the Propaedeumata through the Libri mysteriorum, and the Monas and the Praeface in between, however, the expression of Dee's intellectual life assumed considerable variation. His development over the course of his career was significant in terms of both intellectual content and motivation. Despite the abyss that separates the Propaedeumata and the Libri mysteriorum, there is a thread that ties the various manifestations of his natural philosophy together, a thread not of philosophical principles but of intellectual intent. This common intent was the desire to know nature, not superficially but through the 'preeminent virtues', the hidden springs and ultimate reasons behind the processes and very existence of the cosmos. In addition, he had a firm conviction that mathematical principles and procedures offered important aid in understanding nature. Dee considered that the understanding he sought was something not
His earliest philosophical studies were predominantly Aristotelian, although he showed little inclination toward being a professional Aristotelian. Rather, his equally early interest in mathematics and a variety of mathematical arts and sciences motivated him to seek avenues to integrate mathematical studies with natural philosophy leading him progressively to soften traditional Aristotelian divisions among the sciences and to appropriate quite eclectically increasingly non-Aristotelian materials into his natural philosophy. The central formative influence that may well have suggested the potentialities of integrating mathematics and natural philosophy
Bacon's influence on Dee's natural philosophy is most direct in the Propaedeumata. Here the main problem Dee addressed was 'occult' causality as it pertained to astrology. He developed what he considered were the foundations of astrology through a mathematical physics of radiated influences as the fundamental causal mechanism throughout the cosmos within an Aristotelian idea of demonstrative science. The central inspiration for this formulation came from the distinct interpretation of Aristotelian physics Dee found in al-Kindi, Grosseteste, and particularly Roger Bacon. In this interpretation of Aristotelian physics a crucial but 'occult' Neoplatonic element of emanationism provided the foundation for extending the model of geometric optics to the analysis of a broad range of causal relationships. This served both to provide an intelligible and non-spiritual, non-demonic treatment of the action of 'occult' qualities and influences and to facilitate the extension of mathematical treatment to domains of physics beyond those Aristotle had considered appropriate for mathematical study. This 'Baconian' approach toward understanding the behaviour of the physical world through a physical causality and mathematical models also carries through to analogous material in the Mathematical! Praeface in his treatment of astrology, perspective, grading, and statics.