In this paper we will offer a few examples to illustrate the orientation of contemporary research in data analysis and we will investigate the corresponding role of mathematics. We argue that the modus operandi of data analysis is implicitly based on the belief that if we have collected enough and sufficiently diverse data, we will be able to answer most relevant questions concerning the phenomenon itself. This is a methodological paradigm strongly related, but not limited to, biology, and we label it the microarray paradigm. In this new framework, mathematics provides powerful techniques and general ideas which generate new computational tools. But it is missing any explicit isomorphism between a mathematical structure and the phenomenon under consideration. This methodology used in data analysis suggests the possibility of forecasting and analyzing without a structured and general understanding. This is the perspective we propose to call agnostic science, and we argue that, rather than diminishing or flattening the role of mathematics in science, the lack of isomorphisms with phenomena liberates mathematics, paradoxically making more likely the practical use of some of its most sophisticated ideas.