In this paper we examine two policy questions about the COVID 19 pandemic in the Philippines. These are science informed policy questions that will have to take into consideration a large degree of uncertainties in outcomes. The first question is on when to lift the Enhanced Community Quarantine (ECQ) as informed by epidemiological modelling. The second deals on how the Philippines can respond to a future pandemic crisis. We review the Philippine government's responses and introduce the complicating scientific, social, and political contexts for both questions and address proposals for strengthening the science advisory structures. We propose a permanent science advisory body for emergencies with the widest source of expertise as needed.