It is considered in some quarters that hypothesis‐driven methods are the only valuable, reliable or significant means of scientific advance. Data‐driven or ‘inductive’ advances in scientific knowledge are then seen as marginal, irrelevant, insecure or wrong‐headed, while the development of technology—which is not of itself ‘hypothesis‐led’ (beyond the recognition that such tools might be of value)—must be seen as equally irrelevant to the hypothetico‐deductive scientific agenda. We argue here that data‐ and technology‐driven programmes are not alternatives to hypothesis‐led studies in (...) scientific knowledge discovery but are complementary and iterative partners with them. Many fields are data‐rich but hypothesis‐poor. Here, computational methods of data analysis, which may be automated, provide the means of generating novel hypotheses, especially in the post‐genomic era. BioEssays 26:99–105, 2004. © 2003 Wiley Periodicals, Inc. (shrink)

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a ‘landscape’ representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems ‘hard’, but as such these are to be seen as combinatorial optimisation problems that are best attacked (...) by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the ‘best’ experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes. (shrink)

Scientists routinely solve the problem of supplementing one’s store of variables with new theoretical posits that can explain the previously inexplicable. The banality of success at this task obscures a remarkable fact. Generating hypotheses that contain novel variables and accurately project over a limited amount of additional data is so difficult—the space of possibilities so vast—that succeeding through guesswork is overwhelmingly unlikely despite a very large number of attempts. And yet scientists do generate hypotheses of this sort in very few (...) tries. I argue that this poses a dilemma: either the long history of scientific success is a miracle, or there exists at least one method or algorithm for generating novel hypotheses with at least limited projectibility on the basis of what’s available to the scientist at a time, namely a set of observations, the history of past conjectures, and some prior theoretical commitments. In other words, either ordinary scientific success is miraculous or there exists a logic of discovery at the heart of actual scientific method. (shrink)