An instructional design process based on expert knowledge for teaching students how mechanisms are explained

Abstract

In biology and physiology courses, students face many difficulties when learning to explain mechanisms, a topic that is demanding due to the immense complexity and abstract nature of molecular and cellular mechanisms. To overcome these difficulties, we asked the following question: how does an instructor transform their understanding of biological mechanisms and other difficult-to-learn topics so that students can comprehend them? To address this question, we first reviewed a model of the components used by biologists to explain molecular and cellular mechanisms: the MACH model, with the components of methods (M), analogies (A), context (C), and how (H). Next, instructional materials were developed and the teaching activities were piloted with a physical MACH model. Students who used the MACH model to guide their explanations of mechanisms exhibited both improvements and some new difficulties. Third, a series of design-based research cycles was applied to bring the activities with an improved physical MACH model into biology and biochemistry courses. Finally, a useful rubric was developed to address prevalent student difficulties. Here, we present, for physiology and biology instructors, the knowledge and resources for explaining molecular and cellular mechanisms in undergraduate courses with an instructional design process aimed at realizing pedagogical content knowledge for teaching. Our four-stage process could be adapted to advance instruction with a range of models in the life sciences.

the challenge of linking subject matter knowledge to effective teaching is not new. Three decades ago, Shulman (18) identified a lack of scholarship about how knowledge of a discipline (e.g., biology) translates to how one teaches it, which he termed the “missing paradigm.” According to Shulman (18), effective teachers have subject matter knowledge, curricular knowledge, knowledge of teaching methods, and a less-studied form of knowledge for teaching that involves knowledge of the students who study a given subject. To address the gap in scholarship, Shulman forwarded the idea that teachers possess pedagogical content knowledge (PCK). He stated that (18):

[PCK] goes beyond knowledge of subject matter per se to the dimension of subject matter knowledge for teaching [sic]. [PCK includes] the most useful forms of representing those ideas, the most powerful analogies, illustrations, examples, explanations, and demonstrations–in a word, the ways of representing and formulating the subject that make it comprehensible to others.

A teacher with PCK understands the representations of subject matter knowledge effective for teaching and the difficult aspects of learning a given subject (18, 27). Built on the prerequisite knowledge of the discipline, PCK is developed through teaching experience (27) by testing representations, by examining evidence of its impact on student learning, and by deliberately refining and redesigning the representations. We believe it is worthwhile for instructors of physiology and other life sciences to develop PCK, which encompasses 1) the ways of representing biology to make biological processes comprehensible to students and 2) an understanding of student learning to help students develop life science expertise. Our purpose for the present article is to propose and illustrate a four-stage process (Fig. 1) for instructors to transform their own knowledge and understanding of a difficult-to-learn topic into instruction that their students can comprehend.

Fig. 1.

A four-stage process guided refinements of the MACH model [with components of methods (M), analogies (A), context (C), and how (H)] to help students explain mechanisms in three different classrooms. After the expert model (stage 1) was adapted to a physical tetrahedral version of the MACH model for classroom use (stage 2), instructional resources for target learning objectives were developed with activities designed to give students practice using the model. The activities were explored in a field test (stage 3) with students in a biochemistry class for science majors using the MACH model (cycle 1). The results were promising (stage 4), so the model and activities were refined for a second and third iteration of design-based research with a case study approach and a range of students who volunteered to let us carefully examine their work before and after the activity, first in a 100-level biology course (cycle 2) and then by adapting resources for using the MACH model in a 300-level biochemistry course for health science students (cycle 3). To inform improvements in the MACH model and practical activities, student work was carefully examined after each cycle (stage 2-3-4 iterations). The MACH model and instructional resources are available online in an easy-to-edit format (25, 26) so that other instructors can extend use of these instructional resources to their own context and target learning objectives.

A consensus report on the reform of biology curricula and teaching echoes the need to improve undergraduate biology courses by making difficult subject matter comprehensible to students. According to Vision and Change in Undergraduate Biology Education: a Call to Action report (4) recommendations, “many faculty still express uncertainty over how to better connect teaching with learning, how to make approaches to teaching biology align better with the practice of science, and how to fine-tune undergraduate biology courses to better meet the needs of the diverse student bodies we all serve.” As such, there is a need to provide a general process to guide instructors in helping students learn the most difficult material specific to biology. One difficult topic that would benefit from an illustration of this process is the explanation of biological mechanisms.

Students Have Difficulty With Molecular Mechanisms

Molecular and cellular mechanisms are notoriously difficult to explain in the classroom. This is due in part because mechanisms are characterized by a complexity of interactions between intangible molecular components that are often represented by abstract models of systems and language with heavy jargon (20). Alberts (2) has gone so far as to compare protein machines to the irrational complexity of the cartoons of Rube Goldberg. Based on a faculty survey about what makes physiology hard for students to learn, Michael (12) reported that the highest rated factor was related to the need for students to be able to do causal (mechanistic) reasoning to understand physiology. Quinn et al. (16) confirmed the importance of mechanistic reasoning as follows:

Cause and effect: Mechanism and explanation. Events have causes, sometimes simple, sometimes multifaceted. A major activity of science is investigating and explaining causal relationships and the mechanisms by which they are mediated. Such mechanisms can then be tested across given contexts and used to predict and explain events in new contexts.

To further reinforce the importance of mechanisms, according to Michael et al. (13), one of nine “core principles” in physiology is “levels of organization,” because biological organisms function with processes that can often be explained by mechanisms occurring at lower levels. For physiology and biology instructors, the challenge is to make molecular systems comprehensible to students who are beginning to learn about such systems.

In the classroom, when instructors explain molecular and cellular mechanisms, they might ensure that students get practice interpreting and generating their own explanations. One reason this might be challenging for students is that explanations about molecular systems are often entangled with everyday language (20) and the way a scientist explains to a student may differ from the way he or she explains to another scientist (21). Because of this, a teacher may deliver an explanation about molecular and cellular mechanisms that lacks some elements a biologist would use to explain such systems. Additionally, students tend to overestimate their ability to explain hidden and hierarchical processes (17), so many students may have an illusion of understanding molecular and cellular mechanisms. Furthermore, education research reports show that students, across many age groups, often create explanations of molecular and cellular processes that differ from the explanations accepted by scientists (1, 6, 8, 10, 11, 21). As such, there is a need for life science educators to address molecular and cellular mechanisms during instruction in a way that is sensitive to the documented difficulties so that students develop expertise to understand, interpret, evaluate, and generate explanations as biologist do.

A Process for Developing Pedagogical Content Knowledge for Teaching

Given the known difficulties associated with teaching biological mechanisms and the need to address how an instructor develops and applies PCK, the present report asked the following question: how might an instructor transform their knowledge and understanding of molecular and cellular mechanisms into instruction that their students can comprehend? An answer to this question was guided by a four-stage instructional design process (Fig. 1). First, we represented biological knowledge of mechanisms by modeling the components used by scientists to explain molecular and cellular mechanisms. Second, we modified the resulting model to make the components understandable to students. Third, we taught students to use the model, and, in so doing, we tested the efficacy of the model and gained understanding of student learning. Fourth, to address challenges that emerged during stage 3, we modified the teaching materials. In fact, we implemented several iterations of a design-based research cycle (5) by repeating the above stages. The findings informed the development of a rubric to shed light on student performance levels and areas of difficulty. In the present report, we review two previous studies, which addressed stages 1–3, and present teaching resources designed to address the challenge of teaching students to explain molecular and cellular mechanisms. As such, this report has been written for life science educators who are concerned about students' difficulties with biological mechanisms (12, 13) and who strive to teach undergraduate students to achieve according to recommendations of the Vision and Change report (4).

Stage 1 Characterization: Develop a Model of Explanations Given by Life Scientists

At stage 1 of developing knowledge for teaching, we focus on understanding and characterizing the knowledge used by biologists to explain mechanisms. In a previous study (24), the components present in biologists' explanations of molecular and cellular mechanisms were identified and defined based on a literature review and interviews of seven biologists who conduct research on molecular and cellular mechanisms in different biology subdisciplines. Four components, which were always present, are carefully defined in Table 1: references to research methods (M) that inform the mechanism; analogies (A), such as models and actors, to illustrate and tell a story; a social or biological context (C) to show the importance of the mechanism; and how (H) the mechanism works (24). The four components informed the creation of the MACH model of components included by biologists when they explain molecular and cellular mechanisms (24).

Table 1.

Operational definitions of the MACH components

	Component	When Explaining Molecular and Cellular Mechanisms, Biologists…
Methods	M	Include the research methods, such as informative data, procedures, or instruments that inform how the mechanism works.
Analogies	A	Contain a wide variety of analogies including scientific models, visual representations, metaphors, and stories that treat molecules as if they have an intention or purpose.
Context	C	Contextualize around an important biological or social setting, such as a type of organism or how the mechanism relates to a disease.
How	H	Include how the mechanism works by addressing the spatial and temporal organization of entities and their respective activities and interactions.

When biologists explained their mechanisms, they naturally integrated each of the MACH components. For the purposes of this report, we define “integration” as the act of combining the components to make a coherent, whole explanation with systematic or logical connections among the included components. By coherent, we mean the explanation of the mechanism is written or spoken with logical incorporation of diverse elements and with relationships expressed to make clear that the components work closely and well together. The previously interviewed scientists each produced an integrated explanation by combining all of the components as a whole to make the explanation understandable. An explanation considered nonintegrated might lack the essential parts or it might lack systematic or logical connections, making it unintelligible. Overall, previous research results including the MACH model provided a useful starting point to understand the components for explaining molecular and cellular mechanisms. Thus, based on our previous study (24), stage 1 is characterized by an active review of the literature and interviews with practicing scientists to understand the key elements included in explanations of biological mechanisms.

Stage 2 Representation: Transition the Produced Model for Classroom Use

In stage 2, the MACH model was transformed to make the representation comprehensible for students. To help instructors teach the components, the MACH model, which was originally in the form of a Venn diagram (24), was converted to a physical tetrahedron model with each component positioned at a vertex. This was done to represent the connections between each pair of the four components. Key terms for each component were printed on the physical model. For instance, the M vertex includes “Tools, data, and procedures,” the A vertex includes “Analogies, models, and narrative forms,” the C vertex includes “Biological and social,” and the H vertex includes “variable states of entities, activities, and organization.” Later, the tetrahedron was modified to include colors and symbols (squares, triangles, stars, and circles) for students to more easily annotate parts of an explanation. This tetrahedral MACH model is available in a format that can be used and modified by other instructors (25). In general, the purpose of stage 2 is to represent the explanatory components in a way that can be easily understood by students in the classroom.

Stage 3 Field Test: Teach With the Representation in Several Design-Based Research Iterations

Once the mechanistic explanations were modeled and represented in a teachable form, stage 3 involved field testing the MACH model in the classroom. In addition to understanding the effectiveness of MACH as a teaching tool, stage 3 helped us gain information about student learning of biological explanations. By examining student work and interviewing students, we were able to identify aspects of the learning that were easy or difficult with MACH.

With a physical model suitable for use in the classroom, we attempted to address the previously documented challenges by implementing a lesson using the physical model in three courses (Table 2) with undergraduate life science students of diverse degree objectives and educational levels (Table 3). The learning objectives, which remained the same across the courses, established that students would be able to do the following: identify the MACH components when learning about a molecular or cellular mechanism (learning objective 1), apply the MACH components to explain a molecular or cellular mechanism (learning objective 2), and create an explanation of a mechanism of their own choice using the MACH model (learning objective 3). The lessons and their presentations were adapted to accommodate the biological context relevant for each course and the preferences of the different instructors. In this way, content factors, teaching factors, educational context factors, and student factors that influence the successful transition of an explanation into the classroom were accounted for and revisited as each setting changed and new insights were gained (21).

Table 2.

The MACH model was used in three courses from two science departments

Course	Instructor	Semester	Lesson Time	Example Context
400 Level Biochemistry for Life Science Majors	T. R. Anderson	Fall 2013	2 × 50 min	Vesicle trafficking
100 Level Biology: Development, Structure, and Function of Organisms	N. J. Pelaez	Spring 2014	1 × 50 min	Vesicle trafficking
300 Level Biochemistry for Health Science Majors	T. R. Anderson	Fall 2014	1 × 50 min	Membrane transport

Table 3.

Demographic information of students from the three courses

	100-Level Biology	300-Level Biochemistry	400-Level Biochemistry
Class status
Freshman	18	0	0
Sophomore	23	2	0
Junior	11	37	2
Senior	4	33	51
Degree program
Biology	38	3	50
Chemistry	2	2	0
Engineering (Chemical, Electrical Computer, and Other)	5	8	0
Health Sciences (Preprofessional, Kinesiology, Nutrition, and Other)	0	50	0
Prepharmacy	0	4	0
Undecided	4	1	0
Other	7	4	3
Total students	56	72	53

Cycle 1 explore: pilot in an upper-division biochemistry course for science majors.

In the first attempt of an instructional activity using the MACH model, life science students in an 400-level biochemistry course (Table 2) viewed molecular animation of vesicle trafficking (9), created an explanation of vesicle trafficking, read a written explanation about the mechanism (29), and rated their understanding of the mechanism. Students then received a lecture on the MACH model and how to use the tetrahedral model to explain. Next, they analyzed an article about vesicle trafficking to identify the MACH components included by the author (which addressed learning objective 1). Finally, students generated their own explanation of vesicle trafficking with the MACH model (learning objective 2). For homework, students were asked to explain a mechanism of their choice (learning objective 3). The rationale for these activities was to expose students to a clear example of a mechanism, help them to understand the components authors include in an explanation, and teach students about the MACH model so that they might use this model to interpret and generate explanations. The first instructional activity, which occurred over two 50-min course lessons, was intended as a pilot, and was videotaped. The pilot provided motivation to extend the MACH model for use across a range of courses and with a more rigorous study.

Cycle 2 refine: design-based research with a case study of MACH used in an introductory biology course.

In a second course of mostly lower-division biology students (100-level biology course in Tables 2 and 3), a similar activity was successfully implemented. This instruction took place during one 50-min lesson. As with the first iteration of the activity, the students performed the same tasks, viewing an animation, writing an explanation, reading, and rating their understanding. They then learned about the MACH components and the tetrahedral model and applied these to analyze an explanation and generate an explanation of vesicle trafficking and of their own mechanism of choice (learning objectives 1–3). Similar to the first instructional activity, the lesson was videotaped. However, unlike the first, results from a case study were compiled and reported to understand the impact of the lesson on student explanations (23).

THE ISSUE OF METHODS.

Explanations from four interviewed students were collected throughout the semester, including before and after the instructional activity. These written artifacts were subjected to detailed analysis by coding for MACH model components. In contrast to the scientists in our precious report (23), our case study students struggled to incorporate the M complonent initially. The following excerpt exemplifies a mechanism explained by a student before the activity:

When blue light strikes a photoreceptor (i.e., Phot1) in the guard cells, high phosphorylation of the H⁺-ATPase occurs as H⁺ is pumped out of the cell. This results in the inside of the cell becoming more negative. Then, K⁺ ions begin entering via passive transport. Through secondary active transport, Cl⁻ ions enter as do some H⁺ ions and some KCl is formed. As a result of the increased solute concentration inside the cell/negative membrane potential, water enters the cell. Overall, this process is responsible for the opening of the stomata in response to blue light. An influx of water is necessary for the essential increase in turgor pressure.

100-level biology course, exam 2

The explanation addresses how the Phot1 receptor changes the states of H⁺-ATPase to change the solute concentration inside the cell (the H component). The C component of the mechanism is within a guard cell, and a visual representation (Fig. 2) serves as the A component, but the student did not refer to any research M component that inform how scientists know about the mechanism for opening stomata. Our exploratory case study of students suggested that M components were an important component to target in the teaching intervention. Overall, the preactivity student explanations integrated some of the essential components into a coherent explanation, since the three components were well connected and easily understood. However, due to the lack of the M component, our case study students' explanations were incomplete compared with biologists' explanations.

Fig. 2.

A diagram made by a student to explain the Phot1 mechanism (100-level biology course, exam 2, before the activity).

THE ISSUE OF INTEGRATION.

After doing activities using the MACH model, most of our students began successfully incorporating all four components into their written explanations. However, the findings revealed a new difficulty: students struggled to integrate the components into a coherent explanation as biologists do (23). For example, the following explanation of the photoreceptor response to light, written after the activity, failed to integrate the components, even though all four components were present:

M - The photoreceptor in the retina was discovered by a German physiologist, Franz Christian Boll. The researchers found the mechanism for our eye to receive the light signal. This mechanism is measured by voltage-sensing microelectrode and the intensity of the light.

A - [Figure 3].

C - The importance of the experiment was to find the molecular mechanism of retina and find the treatment for a photoreceptor-mutated gene, such as retinitis pigmentia, color blindness. It was to understand how humans see things.

H - When light, or a photon, reaches it, rhodopsin sends signals to a G-protein that activates the G-protein. The activation leads to activation of cGMP phosphodiesterase by GTP. The cGMP diesterase activation uses cGMP in the cell to produce 5′-GMP and closes Na⁺ ion channels and hyperpolarizes the cell.

100-level biology course, exam 4

Fig. 3.

Diagrams and a graph created by a student to explain phototransduction in the retina (100-level biology course, exam 4, after the activity).

Figure 3 indicates the corresponding A component drawn by the student as a diagram. The student wrote appropriately for each of the components but did not integrate the components as an expert would. The postactivity explanation included all of the MACH components like a research scientist would, but this explanation was dissimilar to the explanations made by biologists because the student explanation is not structured as a coherent whole; the explanation is separated into distinct parts, making it hardly coherent to a reader.

From the four case studies, including this example, we learned that the interviewed students used the model to help them identify gaps in their explanations, communicate concisely, and monitor their understanding (23). However, in their explanations, some struggled to incorporate the M component and to integrate the components fully. Such responses suggested a need to modify the activity to emphasize integration of the MACH components.

Cycle 3 extend: bring MACH to a biochemistry course for health science majors.

The third design-based research cycle, conducted in a 300-level biochemistry course (Tables 2 and 3), provided an opportunity to apply the knowledge from the previous cycles to help students in health science majors integrate the components as a biologist would when explaining mechanisms. The activity was revised as detailed below and implemented in an upper-division biochemistry course during a single 50-min lecture. The topic of membrane transport was situated in the context of cystic fibrosis, which aligned with the intentions of the course instructor and made the model relevant for students who were mostly in the health sciences (Table 3). For the instructional activity, students read a one-page excerpt either from an article by Skwarecki (19) or an article by Trivedi (22); to address learning objective 1, they analyzed and marked the excerpt as follows: science research methods (■); models, figures, graphs, or analogies including anthropomorphic stories (▲); biological and/or social contexts (⋆); how the phenomenon works through physical causes (●); and places where the above components blend and interweave (✓). Students then discussed their findings with a partner and shared their ideas with the class. Next, they were given a brief lecture about the MACH components and the tetrahedral model, which helped to clarify ideas from the class discussion. The tetrahedral model had been modified to contain the symbols to facilitate matching it to the components students had identified in a written explanation of a mechanism. Finally, a lecture on the membrane transport mechanism of the cystic fibrosis transmembrane conductance regulator was presented to exemplify an explanation that included all of the MACH model components. No animation was presented. As before, practice with the MACH model was incorporated into homework assignments and assessments throughout the semester. For example, students were asked to explain how aquaporins work using MACH (learning objective 2), and they used the MACH model to explain a molecular membrane transport mechanism of their choice (learning objective 3). The order of events was done so that students read and discussed the author's integration of the components before learning about the abstract aspects of the MACH model. In this way, examples of integration were introduced to students before learning about each component in depth.

The excerpt below contains an example of a student explanation after the instructional activity in the third design-based research cycle. The student explains how electron transport is coupled to ATP synthesis using the MACH model in an integrated matter:

. . . ATP is considered the “energy currency” because it converts readily to ADP, while releasing energy simultaneously to create muscular contractions within the body, as well as various intracellular interactions. The electron transport chain (see figure attached) [Fig. 4] is a series of proteins within the mitochondria. The complex, comprised of 4 proteins, passes electrons through their interior, which powers a hydrogen ion pump. The pump creates a H⁺ gradient across the inner membrane of the mitochondria. The gradient then powers the final protein, ATP Synthase, which as its name implies phosphorylates ADP to form ATP. The electron transport chain is the root cause of the hydrogen ion gradient; the chain uses reduction potential to drive the hydrogen pump and power ATP Synthase. A series of studies dealing with muscular contractions in the spine, inhibited the transport chain by forcing a powerful reductive agent to attach to the complex before one chain could pump hydrogen ions out of the matrix. By testing the number of contractions per minute, they could see a substantial decrease due to lack of ‘available ATP.’

300-level biochemistry course, exam 3

Fig. 4.

A diagram of the electron transport chain and ATP synthase to explain ATP synthesis (300-level biochemistry course, exam 2, after the activity).

This response explains as an expert would by integrating the four components into a single coherent explanation. The student addresses how the research M component informs our understanding of the mechanism by referring to an experiment taught in class where contractions were measured in the presence of a reductive agent (dinitrophenol). The explanation includes the A component by naming ATP as “energy currency,” by using everyday terms such as “power,” and by drawing a scientific diagram (Fig. 4). The response has a C component for the mechanism within the muscles of the spine. Finally, the H component explains a potential cause that drives ATP synthase to convert ADP to ATP by describing the electrons, hydrogen ions, and proteins (interacting entities) and how their location and spatial organization relates to changes in their states. This response is a typical example to show most students were able to address the components in an integrated manner after they were introduced to the modified physical model and activity.

Overall, field tests of the MACH tetrahedron representation and teaching activities provided many insights and unforeseen obstacles when students learned to explain biological mechanisms. By working with a range of students at different educational levels and with a variety of degree objectives to understand their performance, we identified ways to modify the implementation and model to help make the integrated components of explanations comprehensible. Our knowledge for teaching with MACH improved when we attended to the difficulties that students faced according to their written explanations of mechanisms.

Stage 4 Redesign: Iterative Improvement and Repurposing the MACH Teaching Resources

Student performance results and the successes and drawbacks of the MACH model in the classroom were analyzed to inform modifications of the teaching resources in the stage 4 redesign step after each cycle. After the third cycle, we were encouraged by colleagues to disseminate our resources to other instructors who might implement an instructional activity with the MACH model to help students explain mechanisms in their own classrooms. Therefore, an instructional activity and the tetrahedral MACH model are available in pdf, MSWord, or ppt formats for easy modification to suit other courses, students, teaching preferences, and the content of other disciplines (25, 26).

A rubric to evaluate student explanations of mechanisms.

In addition to providing the teaching materials, we identified a need to evaluate the quality of students' explanations in a way that was practical for instructors and could provide feedback to students about the goals and their progress toward achieving the learning objectives. A rubric was designed based on careful examination of student responses while focusing on three purposes (Table 4): to be theoretically consistent with the explanations made by biologists when they explain molecular and cellular mechanisms, to be useful and practical for teaching instructors, and to be able to distinguish high-quality student explanations from low-quality explanations. The resulting performance-based rubric (Table 5) was slightly modified according to the expected learning outcomes for each assignment to assess the integration and quality of the MACH components in explanations of molecular and cellular mechanisms. As with the other produced materials, the rubric was designed to be practical for instructors who teach physiology or biology in a range of molecular and cellular contexts, so the language is not specific to a single biological mechanism. Even without scoring, the rubric informs students of the expectations so they may reflect on their own learning. The suggested scoring scale of 1–5 for each component can be modified according to the goal for a particular assignment or applied with a degree of flexibility with intermediate scores (2 and 4) to rate explanations that fall between criteria. An expert explanation would contain all components to their fullest detail and would fully integrate all parts into a coherent whole. Therefore, biologist explanations would receive M: 5, A: 5, C: 5, H: 5, and integration: 5, so the perfect score is 25. Instructors may gather information on performance and provide concise feedback to students when guiding them with the rubric.

Table 4.

Considerations for developing a rubric to guide explanations with the MACH model

Purpose	Evaluative Questions	Addressed in Development
Theoretically consistent	Does the rubric capture the components of an expert explanation?	Alignment of rubric to the integration and quality of MACH components as seen in explanations by biologists.
Usefulness for instruction	Does the rubric provide useful information for teaching and learning?	Consultation with students and instructors to clarify and modify the rubric's language and content.
Discriminating high from low performance	Does the rubric discriminate the quality of the explanations?	Separation of high- and low-quality explanations by ranking explanations and comparing with rubric scores.

Table 5.

Performance rubric for guiding molecular and cellular explanations with the MACH model

	Inadequate (1 pt)	Needs Improvement (3 pts)	Exemplary (5 pts)
M component	Fails to address how science research methods and measurements support ideas about the mechanism and/or contains major flaws.	Addresses only some minor aspects of how science research methods and measurements support ideas about the mechanism and/or contains minor flaws.	Demonstrates a clear and complete explanation of how science research methods and measurements support ideas about the mechanism and contains no flaw.
A component	Tells or illustrates a completely inappropriate analogy or fails to include an analogy about the mechanism.	Tells or illustrates a somewhat inappropriate or incomplete analogy about the mechanism.	Tells or illustrates a clear and coherent analogical story about the mechanism.
C componenet	Fails to mention any context to show why the mechanism is important or contains major flaws in relating the mechanism to a biological or social context.	Addresses only some minor aspects of a context that show why the mechanism is important and/or contains minor flaws.	Demonstrates a clear and complete context to show why the mechanism is important and contains no flaw.
H component	Response does not address how the mechanism works and/or contains major flaws.	Addresses only some of the entities, their activities and interactions, and organization involved in how the mechanism works and/or contains minor flaws.	Demonstrates a clear and complete explanation about how the mechanism works by addressing the spatial and temporal organization of entities, their activities and interactions, and contains no flaw.
Integration	Response does not integrate the above components into a coherent explanation about the mechanism.	Integrates only some of the above components into a coherent explanation or displays flawed logic in explaining the mechanism.	Integrates all of the above components into a coherent explanation about the mechanism.

Note that the rubric can be used by students as a guide to reflect on their own work even without scoring. For scoring, point values can be adjusted according to the expected learning outcomes. Two points may be given to categorize explanations that fall between inadequate and needs improvement of the respective criteria or four points between needs improvement and adequate. Needs improvement may be applied to explanations containing a flaw such as an incorrect fact, vague information, or insufficient information.

To exemplify the application of the rubric (Table 5), it was applied to the presented explanations. For the preactivity explanations about the Phot1 mechanism (100-level biology course, exam 2; Fig. 2) the score would be M: 1, A: 5, C: 4, H: 5, and integration: 3. The produced score indicates that the explanation did not show how the research M component informed ideas about the mechanism (M score of 1) and coherent integration was included for some but not all of the components, resulting in a 3. The C component of the mechanism could be improved to connect to a more detailed context, so this was given a 4. The other components were reasonably clear and thus received scores of 5 (total score = 18 for the Phot1 mechanism). The explanation about ATP synthase and the electron transport chain (300-level biochemistry course, exam 2; Fig. 4) achieves M: 5, A: 5, C: 5, H: 3, and integration: 5 (total score = 23 for ATP synthase and the electron transport mechanism). While integration and most components were exemplary, the instructor wanted more detail on the specific proteins involved in the electron transport chain, so the response received a score of 3 for the H component. These examples serve to demonstrate the potential of the rubric as a useful tool for evaluating student explanations and providing feedback about areas students need to work on to improve. Such feedback will be instrumental in making the MACH model comprehensible and useful to students. The resources can be modified to be sensitive to the observed difficulties associated with learning the MACH model for a particular group of students.

Discussion

Summary and future directions.

To summarize, in the present study, students were helped to learn how molecular and cellular mechanisms are explained by giving them practice using educational resources developed in a four-stage instructional design process. Stage 1 involved dedicating careful attention to characterize the specific components biologists use to explain molecular and cellular mechanisms by conducting a literature review, gathering evidence from interviews with expert life scientists, and generating the MACH model (24). Stage 2 involved transitioning this model to the classroom with an activity using a physical model for representing the components to students. As part of an exploratory cycle, we taught life science students in biochemistry to use the model to analyze, interpret, and construct explanations with representative examples of molecular and cellular mechanisms. The instructional resources, which are available for anyone to modify and use (25, 26), were improved through a series of three iterative cycles focused on transforming our understanding of biological mechanisms into a format our students would comprehend. Informed by our experiences during the pilot, a refinement cycle of design-based research was conducted by field testing the model while teaching organismal biology students about vesicle trafficking. Because student work and interviews revealed issues surrounding integration and difficulty relating research methods to their explanations (23), the instructional resources were modified (26) and the physical model was revised (25) with color and symbol codes to help students identify and integrate the MACH components. Finally, in an extension cycle, the modified resources were adapted for teaching membrane transport to health science students in a biochemistry class. Findings from the third iteration were used to inform development of a rubric (Table 5) to aid instructors and students in recognizing key differences between high and low quality work.

With a practical instructional design process (Fig. 1), we hope others will help solidify and extend previous attempts to bring expert discipline knowledge to the classroom. For example, models such as those proposed by Modell and colleagues (14, 15) can be used as a stage 2 starting point since Modell and others have already modeled various characteristics of expert physiology knowledge for the classroom. We believe instructors who wish to further refine Modell et al.'s models with comprehensible representations and associated teaching materials for the classroom will benefit from iterative cycles across stages 2–4 and from sharing examples of their instructional materials for others to adapt such work to other situations.

In the future, to further advance learning from the products presented here, the resources and activities related to the MACH model may be tested in controlled experimental or quasiexperimental studies to isolate important variables that impact student performance. Alternatively, instructors may wish to continue with their own iterations of the design cycle to modify the rubric, distribute the MACH model, or tailor the instructional activities to better suit the needs of their own students and courses. Indeed, the MACH model, if adapted appropriately, may help students in high school, community colleges, and other educational institutions. Although the MACH rubric may be used to assess mechanism explanations, it will require systematic steps to establish reliability and validation before any claims may be made when using it for a particular group (3). In addition, while some of the activities provided positive evidence of an effective approach, these trends may not be maintained at other universities, over long periods of time, or with different students. Thus, we recommend the four stages and refinement cycles described here as an invitation for others to test how well products such as the rubric, tetrahedral MACH model, and activity will aid instructors and students beyond our local context.

Stages toward pedagogical content knowledge for teaching.

In this report, we present a practical approach to address the uncertainties of connecting current biology research to teaching and learning in a manner that aligns with the framework of PCK by Shulman (18). A logical sequence of four stages guided the development of useful new instructional resources for students and instructors, while helping us to better understand PCK to optimize classroom instruction for explaining molecular and cellular mechanisms. Using the stages shown in Fig. 1, we developed knowledge for teaching based on both subject matter knowledge and knowledge of difficulties encountered by our students as they learned. For prospective and current biology instructors, the process to develop PCK may help those with expert knowledge to translate their understanding into a form useful for their own classroom by attending to difficulties their own students encounter as they learn. For adoption beyond explanations, the stages toward our developing PCK are abstracted as follows:

• 1. Characterization: understand the target knowledge or skills by modeling expertise.

• 2. Representation: make these characteristics comprehensible to students by creating a visual or physical model or representation for classroom use.

• 3. Field test: teach students with activities using the representation and investigate aspects that are easy or difficult to learn.

• 4. Redesign: use the results to modify the representation and other teaching resources for the purpose of improving student learning.

Iterative cycles of stages 2–4 provide a path to focus upon two tenets of PCK: making representation of subject matter knowledge comprehensible to students while understanding the nuances of student learning (18). However, our approach to develop this process has limitations. We do not claim that these four stages are the only way to develop PCK. In fact, four stages may not be enough to fully understand and implement PCK since repetition of the stages in other situations and additional experience are likely to be contributing factors. Biology instructors who apply the PCK development process may need to adapt, modify, or extend the four stages. Additionally, these four general stages may be combined with other instructional design approaches to enhance the development of materials and instructions. For instance, design-based research (5) and backwards course design (7, 28) can be combined into stages 3 and 4 so that instructors may include other well established models for teaching. By providing a general instructional innovation design process, we hope to help those who are aligning curriculum and instruction with the modern life science research practices while meeting the needs of diverse students as recommended by the Vision and Change report (4). The four-stage process might be applied to science subject matter such as the development of novel disease models, research with stem cells in physiology and drug discovery, or the development of cancer-targeted microRNA drugs, to name just a few of the current research topics that should soon be brought into the classroom.

GRANTS

Some material presented here is based on research supported by National Science Foundation Grants 0837229 and 1346567.

DISCLAIMERS

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

DISCLOSURES

No conflicts of interest, financial or otherwise, are declared by the author(s).

AUTHOR CONTRIBUTIONS

C.M.T., T.R.A., and N.P. conception and design of research; C.M.T., T.R.A., and N.P. performed experiments; C.M.T., T.R.A., and N.P. analyzed data; C.M.T., T.R.A., and N.P. interpreted results of experiments; C.M.T., T.R.A., and N.P. prepared figures; C.M.T. and N.P. drafted manuscript; C.M.T., T.R.A., and N.P. edited and revised manuscript; C.M.T. approved final version of manuscript.