Current trends in scientific collaboration focus on developing effective Web-based communication tools, such as instant messaging (i.,e IM) or video-conferencing. One objective is to provide informal communication opportunities for collaborating scientists. This paper focuses on developing an assistive technology for predicting where breakdown situations have likely occurred in chat communications. The immediate goal of the assistive technology is to help users cope with discrepancies between their expectations and the tools they are using during scientific collaboration. The ideas in this paper also have far reaching implications, introducing a method that can be used by any human-interactive application to help the application understand when the user does not know what to do.