We designed a serious game, MolWorlds, to facilitate conceptual change about molecular emergence by using game mechanics (resource management, immersed 3rd person character, sequential level progression, and 3-star scoring system) to encourage cycles of productive negativity. We tested the value-added effect of game design by comparing and correlating pre- and post-test misconceptions, interaction statistics, and engagement in the game with an interactive simulation that used the same graphics and simulation system but lacked gaming elements. We tested first-, second-, and third-year biology students' misconceptions at the beginning and end of the semester (n = 526), a subset of whom played either the game (n = 20) or control (n = 20) for 30 minutes prior to the post-test. A 3x3 mixed model ANOVA revealed that, while educational level (first-, second-, or third-year biology) did not influence misconceptions from pre-test to post-test, the intervention type (no intervention, simulation, or game) did (p <0.001). Pairwise comparisons showed that participants exposed to the interactive simulation (p = 0.007), as well as those exposed to the game (p<0.001), lost significantly more misconceptions in comparison to those who did not receive any intervention, while adjusting for educational level. A trending difference was found between the simulation group and the gaming group (p = 0.084), with the gaming group resolving more misconceptions. Quantitative analysis of click-stream data revealed the greater exploratory freedom of the control simulation, with greater accessibility to individuals who do not play games on a regular basis. However, qualitative analysis of gameplay data showed that MolWorlds-players experienced significantly more instances of productive negativity than control-users (p<0.001) and that a trending relationship exists between the quality of productively negative events and lower post-test misconceptions (p = 0.066).