Debates over controversial articles often highlight important issues regarding academic freedom, transparency, and how to handle disagreements in publishing. I argue that a response outlining criticism is generally a more productive course of action than calling for retraction. However, there are a number of constraints that impede meaningful debates, and a problematic divergence between our common ideals of open research and free debate and the actual practices that we see in academic publishing, where our current practices often undermine transparency, replication, and scientific debate. I argue that research can benefit from more explicit recognition of politics and preferences in how we evaluate research as well greater opportunities for post-publication debate. The successful initiatives to promote data replicability over the past decade provide useful lessons for what improved post-publication transparency may look like.