The changing world of scholarly communication and the emerging new wave of ‘Open Science’ or ‘Open Research’ has brought to light a number of controversial and hotly debated topics. Evidence-based rational debate is regularly drowned out by misinformed or exaggerated rhetoric, which does not benefit the evolving system of scholarly communication. This article aims to provide a baseline evidence framework for ten of the most contested topics, in order to help frame and move forward discussions, practices, and policies. We address issues around preprints and scooping, the practice of copyright transfer, the function of peer review, predatory publishers, and the legitimacy of ‘global’ databases. These arguments and data will be a powerful tool against misinformation across wider academic research, policy and practice, and will inform changes within the rapidly evolving scholarly publishing system.