TABLE 2.

Codebook of pedagogical practices and associated educational aims

Pedagogical practice	Definition	Specific practices	Associated educational aim
Provide scientific content	A pedagogical practice in which background scientific information is provided to the student	Verbal explanation of scientific background for the technique being used Reading of primary literature Reference to lecture material	Procedure development
Explicit discussion of a CRE	A pedagogical practice in which the specific characteristics of a CRE (authentic research experience) are explained to the student	Differentiation of CRE classes from traditional labs Focus on the importance of generating authentic data Positioning students as researchers and scientists	Being a scientist and generating data
Facing ambiguity	A pedagogical practice in which students are made to face failure, uncertainty, and ambiguity in their scientific work	Allowing students to struggle with ambiguity and uncertainty Explaining that failure is a central part of science and is to be expected Holding back from providing quick answers	Being a scientist and generating data
Modeling scientific thinking	A pedagogical practice in which the instructor models verbally for the students the processes of thinking as a scientist in relation to the issues or problems they present in their ongoing research	Thinking through problems with students Modeling the design, planning, and methodological components of an experiment Critically thinking through and discussing the questions and issues posed by student work	Procedure development Being a scientist and generating data
Protocols and training	A pedagogical practice in which the instructor presents, trains, and supervises students following a new protocol	Provision and reading of the protocol Protocol practice and training Supervision of the following of a protocol	Procedure development Fostering ownership
Mentorship	A pedagogical practice in which the instructor or a peer mentors an individual student during the research process by providing individual guidance and problem solving	Mentoring of individual students by instructor or teaching assistant Peer mentoring and problem solving Provision of specific individualized guidance in writing	Being a scientist and generating data
Peer collaboration	A pedagogical practice that involves groups of students working together on their research	Team or small-group assignments Shared responsibility across the team Shared discussion and support for success and challenges	Fostering ownership
Encouraging independence in students	A pedagogical practice designed to enhance the ability of students to work independently as researchers	Directing students to think independently Asking students to problem solve themselves Positioning students as the decision makers in their scientific work Holding back from providing answers	Being a scientist and generating data Fostering ownership
Fostering personal responsibility	A pedagogical practice designed to enhance students’ understanding of their personal responsibility as researchers	Assigning specific work to be completed Explaining the responsibility of authentic scientific data Monitoring regular reporting of progress Requiring clear and consistent documentation of research Promoting personal reflection on the research that has been conducted	Fostering ownership
Encouraging enthusiasm	A pedagogical practice designed to recognize success and encourage positive enthusiasm toward research	Facilitating and recognizing the joy of discovery Instructor enthusiasm Course recognition of successes	Being a scientist and generating data
Documentation of scientific practice	A pedagogical practice involving the documentation of the research of the students	Lab notebook documentation Notebook discussion Notebook checking	Procedure development
Student presentation	A pedagogical practice involved in creating situations in which the students present their ongoing research	Lab notebook meeting with other students present Poster session for the presentation of outcomes Conference participation	Being a scientist and generating data Fostering ownership
Scientific output	This code relates to the actual scientific output of an authentic research activity.	Specific products of research (such as an isolated phage, electron microscopy, annotated genome)	Procedure development
Future educational and career opportunities	This code relates to the discussion of short- and long-term future educational and career opportunities.	Discussion of graduate school, internships, and related science careers Facilitating future options for scientific development through instructor network	Fostering ownership
Ethical understanding	This code relates to the discussion of ethical issues during course lab time with students	Discussion of ethics of research Discussion of integrity in research	Fostering ownership
Encouraging perseverance	This code relates to the encouragement a faculty member provided during lab work	Helping students overcome short-term frustrations Providing support during difficult periods	Being a scientist and generating data