This article considers the optimal structure of institutions that respond to existential threats such as climate change and pandemics. While science must play a central role in guiding policy responses, there are many values at stake that ought to be reflected in institutional design. There is a distinction between risk assessment, a science-driven analysis in these contexts, and risk management, in which trade-offs are considered in responding to the threats. Moreover, the nature of these threats depends on complex, uncertain and fluid scientific knowledge that requires institutions to be sensitive to communication challenges. Finally, institutions should consider collective action problems and defer or delegate to jurisdictions and institutions whose scope of mandate is appropriate. We assess the Canadian response to the COVID-19 pandemic from an institutional perspective and conclude that, amongst other things, it was insufficiently multidisciplinary, which risked marginalizing the non-public health costs of policy responses to the pandemic.