Students need tools, thinking skills, to help them think actively and in depth about biological phenomena. They need to know what kind of questions to ask and how to find answers to those questions. In this article we present a toolkit with 12 "thinking tools" for asking and answering questions about biological phenomena from different perspectives. We show how teachers can use the toolkit to design lessons in which students are stimulated to think deeply and from multiple perspectives about biological phenomena. (Contains 6 tables.)