The important role of conceptual thinking in learning language and for deep comprehension of a knowledge domain is now widely recognized. Still, traditional pedagogy and learning assessments focus on memorization of facts and procedures, presented through structured items such as true/false and multiple-choice questions. In contrast, teaching and learning of language and content in the digital age is facilitated by pedagogy for conceptual thinking that focus learners’ attention on meaning. Conceptual thinking enhance ways of thinking that explore patterns of equivalence-of-meaning among ideas, relations, and underlying issues; and understanding of multiple representations of meaning that are encoded, in addition to natural language, also in other sign systems. Evolution of pedagogy for conceptual thinking follow insights from several recent developments, including the emerging digital cyber-infrastructure of networked information that facilitate searching for patterns of content and structure of concepts - labelled patterns in human experience. This led to the emergence of concept science, a novel generic methodology for parsing and analysing concepts, applicable to the various knowledge domains and professions, with tools for recognizing, representing, organizing, exploring, communicating, and manipulating knowledge encoded in controlled vocabularies of sublanguages. Research in neuroscience and brain imaging provide experimental support to the semiotic construct ‘representational competence’, demonstrating that exposure of learners to multi-semiotic inductive questions enhance cognitive control of inter-hemispheric attentional processing in the lateral brain, and increase higher-order thinking.