This is a collective case study seeking to develop detailed descriptions of how programming an agent-based simulation influences a group of 8th grade students' model-based inquiry (MBI) by examining students' agent-based programmable modeling (ABPM) processes and the learning outcomes. The context of the present study was a biology unit on natural selection implemented in a charter school of a major California city during spring semester of 2009. Eight 8th grade students, two boys and six girls, participated in this study. All of them were low socioeconomic status (SES). English was a second language for all of them, but they had been identified as fluent English speakers at least a year before the study. None of them had learned either natural selection or programming before the study. The study spanned over 7 weeks and was comprised of two study phases. In phase one the subject students learned natural selection in science classroom and how to do programming in NetLogo, an ABPM tool, in a computer lab; in phase two, the subject students were asked to program a simulation of adaptation based on the natural selection model in NetLogo. Both qualitative and quantitative data were collected in this study. The data resources included (1) pre and post test questionnaire, (2) student in-class worksheet, (3) programming planning sheet, (4) code-conception matching sheet, (5) student NetLogo projects, (6) videotaped programming processes, (7) final interview, and (8) investigator's field notes. Both qualitative and quantitative approaches were applied to analyze the gathered data. The findings suggested that students made progress on understanding adaptation phenomena and natural selection at the end of ABPM-supported MBI learning but the progress was limited. These students still held some misconceptions in their conceptual models, such as the idea that animals need to "learn" to adapt into the environment. Besides, their models of natural selection appeared to be incomplete and many relationships among the model ideas had not been well established by the end of the study. Most of them did not treat the natural selection model as a whole but only focused on some ideas within the model. Very few of them could scientifically apply the natural selection model to interpret other evolutionary phenomena. The findings about participating students' programming processes revealed these processes were composed of consecutive programming cycles. The cycle typically included posing a task, constructing and running program codes, and examining the resulting simulation. Students held multiple ideas and applied various programming strategies in these cycles. Students were involved in MBI at each step of a cycle. Three types of ideas, six programming strategies and ten MBI actions were identified out of the processes. The relationships among these ideas, strategies and actions were also identified and described. Findings suggested that ABPM activities could support MBI by (1) exposing students' personal models and understandings, (2) provoking and supporting a series of model-based inquiry activities, such as elaborating target phenomena, abstracting patterns, and revising conceptual models, and (3) provoking and supporting tangible and productive conversations among students, as well as between the instructor and students. Findings also revealed three programming behaviors that appeared to impede productive MBI, including (1) solely phenomenon-orientated programming, (2) transplanting program codes, and (3) blindly running procedures. Based on the findings, I propose a general modeling process in ABPM activities, summarize the ways in which MBI can be supported in ABPM activities and constrained by multiple factors, and suggest the implications of this study in the future ABPM-assisted science instructional design and research. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]