My interest lies with a collection of scholarship labelled the ‘Standard Model’, which I propose constitutes an emerging explanatory framework for theoretical and empirical work on religious cognition. I map the features of the Standard Model and assess the strength of its claims to offer a program for understanding religious cognition. My conclusion dilutes the Standard Model in that I suggest it overstates the mind’s susceptibility to religious content and sidesteps other culturally prolific activities that also engage emotion, memory, belonging and belief. While I acknowledge some convergence pressures upon cultural activities, I argue that these pressures lead towards more generic tendencies such as the ability to hold belief sets, rather than the predisposition to hold religious beliefs. While I do agree that the evidence suggests that religious content will be attractive to human minds, it is neither inevitable, nor possible, without the structure of cultural reinforcement. On this view, religion is not a unique domain, but operates within the more general domain of social agency. I also note that the mind is adept at learning; we can change our minds, discard ideas we acquired in the past, and choose to become or remain an atheist. On the basis of this case study, I argue that an explanatory framework in cognitive science demonstrates progress (towards becoming a research program) when it reveals hitherto unforeseen connections between analytical levels. Boundary-breaking, inter-level connections represent markers of progress. The Standard Model is an overconfident but nevertheless progressive explanatory research framework guiding work on religious cognition because it has revealed previously unforeseen connections between theories and observations derived at different analytical levels. A progressive framework exposes previously unconnected propositions or theories and stimulates new empirical work around them. The Standard Model case illustrates how progress can come about through unforseen connections as well as through predictions. Progressive frameworks make both new and more links. I suggest that a progressive framework encourages the tensions that arise when inter-level connections become messy. Tension leads to sharper empirical questions where progress is served by a framework that stimulates empirical work in trying to find resolutions. In reaching this conclusion, I also recommend a suite of seven analytical criteria for assessing an explanatory framework in cognitive science, building on Thagard (2005a). The Standard Model case suggests that progress in an inter-disciplinary area can be achieved without a unifying or reducing model, and may even be best seen through a complex set of relations that facilitate the development of novel predictions and the specification of inter-level connections. I argue that the lessons in the case of the Standard Model of Religious Cognition underscore the importance of a working framework—a principles-driven, neo-Lakosian ‘soft’ core—in facilitating unforeseen connections between theories and observations arising from different analytical strata.