Bioscientific advances raise numerous new ethical dilemmas. Neuroscience research opens possibilities of tracing and even modifying human brain processes, such as decision-making, revenge, or pain control. Social media and science popularization challenge the boundaries between truth, fiction, and deliberate misinformation, calling for critical thinking (CT). Biology teachers often feel ill-equipped to organize student debates that address sensitive issues, opinions, and emotions in classrooms. Recent brain research confirms that opinions cannot be understood as solely objective and logical and are strongly influenced by the form of empathy. Emotional empathy engages strongly with salient aspects but blinds to others’ reactions while cognitive empathy allows perspective and independent CT. In order to address the complex socioscientific issues (SSIs) that recent neuroscience raises, cognitive empathy is a significant skill rarely developed in schools. We will focus on the processes of opinion building and argue that learners first need a good understanding of methods and techniques to discuss potential uses and other people’s possible emotional reactions. Subsequently, in order to develop cognitive empathy, students are asked to describe opposed emotional reactions as dilemmas by considering alternative viewpoints and values. Using a design-based-research paradigm, we propose a new learning design method for independent critical opinion building based on the development of cognitive empathy. We discuss an example design to illustrate the generativity of the method. The collected data suggest that students developed decentering competency and scientific methods literacy. Generalizability of the design principles to enhance other CT designs is discussed.