Numerous studies have been carried out in computer-mediated and computer-supported learning environments. They have reported the effectiveness of scaffolding strategies for engaging students in the learning process. These studies in variety of subjects such as economics, mathematics have focused mostly on developing illstructured problem solving, decision making, and critical thinking skills and rarely on argumentation skills. On the other hand, concept attainment is discussed and studied intensively from various theoretical perspectives for more than 50 years. Theory-based concept learning claims that people understand and explain new situations based on their prior experience which has resemblance to a theory in itself. It is compatible with constructivist approaches. For a basic 8th Grade Genetic Simulation, a scaffolding model is developed according to the theory-based concept view and scientific discovery learning. Toulmin argumentation model as scaffolding strategy is functionalized by Socratic questioning technique to engage learner in analysis and reflection in a simulated concept learning environment. In this paper, the model for scaffolded simulation and the development process are explained. The issues arising from a successful application study of simulation model are presented.