This chapter reports on findings from classroom communication in secondary chemistry teaching and learning. The data was analyzed qualitatively regarding the use of metaphors and analogies in relation to atoms and ion formation, with an intention to shed light on students’ scientific understanding as well as on their enculturation into the disciplinary discourse. Theoretically we draw on social semiotics, which allows analyses of language use in its widest sense, comprised of verbal language, images, action, gestures, and more. In our data, we identified common disciplinary metaphors in science, as well as metaphors connected to everyday life. Through the analyses based on systemic functional linguistics (SFL), we also identified anthropomorphic metaphors, with particles, atoms, and ions being humanized with intentions and feelings. Linguistic choices signaling metaphoric language were mainly noted in relation to quite obvious metaphors whereas no such signals or explanations were noted in connection to anthropomorphic metaphors. The study has implications for the design of classroom practices, including the use of discussions to enhance a more reflective use and understanding of the gains and losses around metaphors.