In this paper, we propose computational scientific inquiry (CSI) as an innovative model for learning important scientific knowledge and new practices for "doing" science. This approach involves the use of a "game-like" virtual world for students to experience virtual biological fieldwork in conjunction with using an agent-based computer model to enable computational inquiry activities. After an overview of literature into learning about scientific inquiry and the use of virtual worlds and game-like systems for learning science, we provide a description of the technology systems we developed and the methods of the study. The results are reported of a two-week intervention involving the use of a CSI approach in two eighth-grade classes that found significant learning gains by students. The paper concludes with a discussion of the findings and a consideration of CSI more generally for learning important and difficult scientific knowledge and practices.