The last quarter-century bore witness to a sea change in academic involvement with commerce. Widespread university-based efforts to identify, manage, and market intellectual property (IP) has accompanied broad shifts in the relationship between academic and proprietary approaches to the dissemination and use of science and engineering research. Such transformations are indicators of institutional changes at work in the environment faced by universities. This paper draws upon a fifteen-year panel (1981-1995) of university-level data for 87 research-intensive US campuses in order to document trends and transitions in relationships among multiple indicators of academic and commercial engagement. The institutional environment for public and private science is volatile, shifting in fits and starts from a situation conducive to organizational learning through high volume patenting to a more challenging arrangement that links indiscriminate pursuit of IP with declines in both the volume and impact of academic science. The pattern and timing of these transitions may support an enduring system of stratification that offers increasing returns to first-movers while limiting the opportunities available to universities that are later entrants to the commercial realm. Unpacking the systematic effects of university research commercialization requires focused attention on the sources and trajectories of profound institutional change.