© 2013, IGI Global. Computer sciences have deeply changed the way by which we make science or produce knowledge. With the era of computers and the development of computer science, quantum chemists were among the first scientists to explore the potentialities of the new tool, and even to collaborate in its development. In this way, they also became participants in what many dubbed as the Second Instrumental Revolution in chemistry. Deeply involved into this research field, QSAR methods are powerful tools to create knowledge on toxicology and drug design, among others. There are several epistemological questions to be analyzed in order to understand the truth and scientific value of their research results (from in silico to wet laboratories and vice versa).