This article empirically validates an existing content analysis scheme and addresses a main concern of researchers about text-based, online transcripts in the form of code-recoding by mapping our scheme to the practical inquiry, cognitive presence model's five phases directly to realise higher-order thinking or critical thinking aspects for our software engineering students at London Metropolitan University. Two case studies are presented from final year undergraduate students. We also evaluated a semi-structured CMC environment called SQUAD, developed in-house for scaffolding small group collaborative learning. We argue that the empirical study conducted with software engineering students in Hong Kong and London gives an indication that critical thinking or higher-order thinking certainly exists within online collaborative learning teams where knowledge emerges and is shared. We claim that responses in the integration and resolution categories are more pertinent to critical thinking or higher-order thinking in the context of online, small group, collaborative learning environments when using the cognitive presence model as a framework for measurement purpose.