title: The challenges and scope of theoretical biology.
abstract: Scientific theories seek to provide simple explanations for significant empirical regularities based on fundamental physical and mechanistic constraints. Biological theories have rarely reached a level of generality and predictive power comparable to physical theories. This discrepancy is explained through a combination of frozen accidents, environmental heterogeneity, and widespread non-linearities observed in adaptive processes. At the same time, model building has proven to be very successful when it comes to explaining and predicting the behavior of particular biological systems. In this respect biology resembles alternative model-rich frameworks, such as economics and engineering. In this paper we explore the prospects for general theories in biology, and suggest that these take inspiration not only from physics, but also from the information sciences. Future theoretical biology is likely to represent a hybrid of parsimonious reasoning and algorithmic or rule-based explanation. An open question is whether these new frameworks will remain transparent to human reason. In this context, we discuss the role of machine learning in the early stages of scientific discovery. We argue that evolutionary history is not only a source of uncertainty, but also provides the basis, through conserved traits, for very general explanations for biological regularities, and the prospect of unified theories of life.
authors.affiliation: Santa Fe Institute, Santa Fe, NM, USA. krakauer@santafe.edu
authors.forename: David C
authors.initials: DC
authors.lastname: Krakauer
authors.forename: James P
authors.initials: JP
authors.lastname: Collins
authors.forename: Douglas
authors.initials: D
authors.lastname: Erwin
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Flack
authors.forename: Walter
authors.initials: W
authors.lastname: Fontana
authors.forename: Manfred D
authors.initials: MD
authors.lastname: Laubichler
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.forename: Geoffrey B
authors.initials: GB
authors.lastname: West
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001695:Biology; D006801:Humans; D007802:Language; D008954:Models, Biological