The concept lens diagram: A new mechanism for presenting biochemistry content in terms of “big ideas”

Authors


  • A University of Queensland Faculty of Science Teaching and Learning Grant

Abstract

A strong, recent movement in tertiary education is the development of conceptual, or “big idea” teaching. The emphasis in course design is now on promoting key understandings, core competencies, and an understanding of connections between different fields. In biochemistry teaching, this radical shift from the content-based tradition is being driven by the “omics” information explosion; we can no longer teach all the information we have available. Biochemistry is a core, enabling discipline for much of modern scientific research, and biochemistry teaching is in urgent need of a method for delivery of conceptual frameworks. In this project, we aimed to define the key concepts in biochemistry. We find that the key concepts we defined map well onto the core science concepts recommended by the Vision and Change project. We developed a new method to present biochemistry through the lenses of these concepts. This new method challenged the way we thought about biochemistry as teachers. It also stimulated the majority of the students to think more deeply about biochemistry and to make links between biochemistry and material in other courses. This method is applicable to the full spectrum of content usually taught in biochemistry. Biochemistry and Molecular Biology Education Vol. 39, No. 4, pp. 267–279, 2011

As the amount of knowledge we possess in the field of biochemistry grows, the problem of how to teach it all in just a few courses also compounds [1]. Even for us as teaching academics and experienced scientists, the breadth and depth of material in modern textbooks is overwhelming [2]. Pity the poor student who is starting from scratch and attempting to build an integrated picture of a field during one short semester.

When designing a course that deals with heavy or difficult content there are some common strategies that we as teachers use. There is a temptation to teach from a textbook and focus on isolated pieces of important content. This approach tends to be sequential and inflexible, because it follows the structure of the modularized textbook [3]. This text-structured approach will probably increase the satisfaction reported by the student who wants to be “spoon fed” or have all the information laid out in a single pathway so it can be memorized. It is unlikely, however, to foster lateral thinking or transfer of concepts from one course (or course module) to another.

Another approach is to cover the whole field and “teach everything,” in an attempt to build a big picture by default. This supplies a lot of information to a class, but large-scale information transfer often occurs at the expense of a deeper conceptual understanding [4]. The “teach everything” approach has been described as “drinking from a fire hose” by some STEM students [5]. It can generate “weed out” courses with high attrition rates.

In developing a new generalist undergraduate biochemistry course at the University of Queensland, Australia, we encountered the problem of taking a difficult, content-heavy, subject and reducing it to something intelligible and useful for a large number of mixed-ability students. Like many other educators [6, 7], we wondered about the essential, enduring, conceptual core of our subject.

A strong conceptual framework for a subject can provide a powerful device for long-term understanding and incorporation of new material [8], and the explicit use of concept mapping has been conclusively shown to increase knowledge retention [9]. This is true for several disciplines (including science) using varied teaching methodologies [9]. The use of concept mapping in the design and delivery of biological sciences is becoming a reality. There is a current push to define the essential conceptual underpinnings of biology, and five core concepts have recently been generally agreed upon [10]. These are as follows:

  • Evolution

  • Pathways and transformations of energy and matter

  • Information flow, exchange, and storage

  • Structure and function

  • Systems

Although these core concepts apply to the biological sciences in general, the “fit” of these ideas for most biology subdisciplines has not yet been extensively tested. An initial unpacking of some of these ideas with reference to core competencies for a discipline has begun in the field of physiology education [11].

The goal of our approach was to help students develop a set of key understandings in biochemistry that would enrich their understanding of other courses in their programs of study and be useful to them in the long term, regardless of their career ambitions. We decided to define a few overarching “priority learnings” [12] in biochemistry. We use the term “key concepts” to describe these overarching ideas and use the definition of “big idea” from Duschl et al. [13] to define what they represent.

“Each [big idea] is well tested, validated, and absolutely central to the discipline. Each integrates many different findings and has exceptionally broad explanatory scope. Each is the source of coherence for many key concepts, principles and even other theories in the discipline.”

We also think of a “key concept” as “a concept, theme, or issue that gives meaning and connection to discrete facts and skills” [8]. For this project, the most important operational aspect of these definitions is that a “key concept” provides and promotes connections between different areas of biochemistry.

The key conceptual underpinnings of biochemistry are not readily apparent from the many modern textbooks we perused during our initial phases of this project. The literature on biochemistry courses gives guidance on a core curriculum for the subject [14], indicates what other courses can or should be taken alongside biochemistry [15, 16], provides comprehensive coverage of the skills taught during biochemistry degree programs [17], and suggests minimal requirements for a qualification in biochemistry [18]. There is also a current effort to define the “big ideas” in biochemistry by the American Society for Biochemistry and Molecular Biology [19], but the results have not yet been published.

This article describes the concepts we defined as “important” in biochemistry and the novel mechanism we used to link them consistently and explicitly to the course content. We discuss how these concepts compare to thecore concepts defined for general biology as part of the Vision and Change project [10]. We also describe the student responses to our conceptual teaching approach and some unexpected effects that it had on our own way of teaching and understanding biochemistry.

PROBLEM OVERVIEW AND CONTEXT

The University of Queensland, Australia (UQ), is currently undergoing a science curriculum review. A new, generalist undergraduate biochemistry and molecular biology course was created and coded “BIOC2000: Biochemistry and Molecular Biology.” The course has an annual enrolment of ∼450 students, most of whom have completed 1 previous year of tertiary study. BIOC2000 students come from more than 20 different programs of study and are a mixed-ability cohort. About 25% of them intend to pursue science or biotechnology as a career; the remainder wants to do medicine, nutrition, engineering, law, food science, or education (this list is not exhaustive). Approximately 15% of the cohort has not completed the prerequisite courses (UQ does not enforce prerequisites). This course is usually the first time the students have encountered material that is explicitly described as “biochemistry.”

In the first year that we taught this class (2009) we attempted to cover too much content as gauged by students' grades and comments on course evaluations. Upon reflection, and while attempting to reduce the amount of content we were teaching, we decided BIOC2000 was lacking a unifying conceptual framework and that we did not have a clear idea of the key concepts in biochemistry. In an attempt to simplify and contextualize the content, we decided to develop this framework and present it explicitly to the BIOC2000 students on a consistent basis during the 2010 iteration of the course.

DEFINING THE “KEY CONCEPTS IN BIOCHEMISTRY” WITH THE HELP OF COLLEAGUES

The first step in this process was to determine what working biochemists considered the key concepts in biochemistry.

Survey Rationale and Methodology

We chose 120 science academics at two large, research-intensive, Australian universities (University of Queensland and University of Sydney) as the reference group to complete a survey we designed. These academics were chosen based on the inclusion of biochemistry in their departmental name or declared research and teaching strengths. In many cases, the study authors knew the members of the reference group personally and were aware of their teaching and/or research programs in biochemistry. This knowledge was used as part of the selection criteria. All academics possessed a PhD in biochemistry or a relevant biology or chemistry discipline.

We invited potential respondents by email to access a Survey Monkey link (http://www.surveymonkey.com/s/LRFDK9K). The survey at this link delivered a question set entitled “The Fundamentals of Biochemistry.” The questions are shown in Table I. Respondents could choose to include a contact email address in their response, but this was not accessed during processing of the results. No other identifying information was collected. The deidentified data were processed independently by the first and second authors (SLR and CAS). The authors of this study did not complete the survey.

Table I. Questions and demographic responses from “The Fundamentals of Biochemistry” survey
Question textAnswer optionsAnswers given
1) Did you study biochemistry at University?A) Not at all 5 (13.9%)
B) 1–2 years13 (36.1%)
C) 3–4 years11 (30.6%)
D) 5 or more years 7 (19.4%)
2) Was biochemistry your major at University?Open answer62% defined themselves as having done a major, PhD or postdoctoral study in biochemistry.
3) Do you use biochemical concepts or techniques in your work?A) All the time24 (66.7%)
B) Quite often 8 (22.2%)
C) Sometimes 2 (5.6%)
D) Infrequently 2 (5.6%)
E) No 0 (0%)
4) Please list three to five concepts that you think are central to biochemistry.Open answerSee Table II
5) Which of the concepts you listed in Q4 above is the MOST important in biochemistry?Open answerSee Table III

Survey Results and Analysis

The demographic data obtained from the survey results are shown in Table I. In toto 36 academics completed the survey. More than 85% of the respondents had formally studied biochemistry for at least 1 year at university (degree-granting college) level, and 62% of respondents defined themselves as having done a major, PhD or postdoctoral study in biochemistry. More than 88% of respondents said they used biochemical concepts or techniques “quite often” or “all the time” in their work.

The respondents provided a total of 142 responses to the question “please list three to five concepts that you think are central to biochemistry.” We considered all of these responses as part of our data set, except if the respondents indicated that they were not qualified to answer the question (two did this).

In reviewing the responses we noted that many of the responses could be classed as content rather than concepts.

We define concepts as

  • (i)words or phrases that define a topic or fact that could be taught as a stand-alone, decontextualized item and
  • (ii)words or phrases that do not link, explicitly give meaning to, or contextualize discrete facts and skills.

We applied both of these criteria to responses to gauge if they were content. For example, the term “sugar chemistry” exemplified content because it is not a contextualized statement that gives a sense of how or why things happen in biology; sugar chemistry could be taught as a set of chemical reactions without an understanding of how these reactions fit into the biochemistry of a cell or organism. Similarly, we consider submissions of single words like “proteins,” “metabolism,” and “central dogma” to be “content” because they are decontextualized, devoid of abstraction, and limited in their wider meaning.

We define concepts as

  • (i)words, phrases, or sentences that give a sense of how or why things happen in biology and
  • (ii)words, phrases, or sentences that give meaning and connection to discrete facts and skills and
  • (iii)words, phrases, or sentences that require understanding of more than one content area in an abstract manner.

Criterion (iii) draws upon the Webster's dictionary definition for “abstract” as being something “considered apart from any application to a particular object; separated from matter” [20].

For example, a concept related to sugars would be “sugars are a source of energy in biological systems,” because teaching this would require an integrated discussion of sugar chemistry, general metabolism, and an abstract link to the role of thermodynamics in living systems. This statement is also abstract because it refers to the general principle of conversion between forms of energy. This conversion will not be readily apparent to students until they grasp fundamental ideas about the role of electrons in biomolecules. A concept related to proteins might be “the function of a protein is driven by its arrangements of weak and strong bonds.” Again, this statement gives us “how” and “why” information that requires integration of more than one idea or content area for it to be understood.

All of the responses are presented in Table II in somewhat abbreviated form. Many areas such as “metabolism,” “the central dogma,” and “molecular interactions” were mentioned repeatedly. These are reported in Table II as a single idea with a number indicating how many times it was mentioned.

Table II. Ideas, terms, and concepts identified as “central to biochemistry” by survey respondents
#Response
18Molecular recognition and interactions (including receptor–ligand binding), signal transduction, the role of affinities in interactions.
14Metabolism (breakdown and synthesis pathways for complex biomolecules).
14Central dogma; DNA replication/transcription/translation/protein processing. Protein production is related to regulated gene expression.
11Enzyme catalysis, including the regulation, structure, and function of enzymes.
11Cellular systems are in dynamic (not thermodynamic) equilibrium. A thermodynamically favorable reaction will not necessarily proceed spontaneously. Entropy. Reaction kinetics, energetics, and rate equations for (bio)chemical reactions.
11Food, stored substrates, and light are converted to energy currency. This currency is used of to drive biochemical and cellular processes and build order.
10Structure and its relationship to function. Proteins carry out the essential functions of the cell. Molecular machines and how they work to accomplish their function.
9Biochemistry provides tools for analytical and quantitative measurements, assays, and analyses. Structural biology is important.
8Chemical structure of biomolecules (chemical structures and 3D structure).
8Biochemistry is chemistry in a biological setting. The same fundamental principles apply (e.g.: rules of organic chemistry and chemical concepts such as redox, kinetics, thermodynamics, and equilibrium).
6Compartmentalization and partitioning of cell spaces and components including the role of water as a solute.
6Membrane biology (how the properties and asymmetry of membranes define and organize biochemical processes).
5The idea of regulated pathways and networks and their breakdown during disease.
4Information storage, transmission, and conversion into structure.
4Shapes and interactions of molecules based on charges, hydrophilicity, hydrophobicity, and so forth. Biomolecular tertiary structure is dominated by weak intermolecular interactions, whereas backbones are built from strong bonds. Structures are dynamic.
2Regulation and modification of protein function (allosterism, phosphorylation, signal transduction, etc.).
2Cellular structures at the molecular level (nuclear envelope, ER, Golgi, actin fibers, prokaryote structures).
2The correct pH and salt concentration is required to maintain the proper function of the cell (homeostasis).
1Evolution and selection pressure.
1The idea of what happens at the molecular level versus the bulk properties of the system.

The respondents provided 39 concepts and ideas that they defined as “most important to biochemistry.” A summary of these is shown in Table III. Again, many of them could be considered as content rather than concepts.

Table III. Ideas, terms, and concepts identified as “most important in biochemistry” by respondents
Concept and # of instances
  1. Ideas, terms, and concepts have been grouped for this analysis. Statements, words, or ideas followed by a number in parentheses (x) appeared “x” times in the response set.

Protein structure and function (8)
Molecular recognition (7)
The central dogma (6)
Enzyme-mediated catalysis (4)
Information flow (2)
Energy flow (2)
Basic chemical concepts (2)
Biosynthetic pathways (2)
Homeostasis and flux (2)
Lab approaches in biochemistry (1)
Structure of biomolecules (proteins, nucleic acids, lipids, sugars) (1)
Water is essential for the chemistry of life (1)
How living organisms transform energy and build biological order (1)

To get an idea of the most important words in the responses (rather than the commonly used ideas), we collated all of the words from the answers to Questions 4 and 5 and mapped them according to frequency of use (Fig. 1). The most commonly used word was “protein” (30 instances), followed by “structure” (22 uses), then “function” (17 uses). All of the words or terms shown in Fig. 1 were used at least three times in answers.

Figure 1.

Frequently used words in the “core concepts in biochemistry” responses. The larger the word, the more frequently it was used. To obtain this diagram, an edited text file containing the pooled responses from Q4 and Q5 (Table I) was processed using wordle.net. Before the responses were inserted into Wordle (http://www.wordle.net/), common words like “at,” “the,” and so forth were removed. The text was edited to remove negatives (e.g.: terms like “not bulk properties”) and words that were unrelated to science (e.g.: “I think that” or “I frequently use”). Some pairs of words were hyphenated to indicate that they regularly occurred together (e.g.: amino-acid). Some words have been changed to normalize plurals, tenses, and spellings. Only words used three or more times in the responses have been included in this image.

We were satisfied that our survey participants had provided input that accurately reflected the mainstream topics in biochemistry—their responses contained words and phrases that were similar to the content areas we had obtained by looking at textbook tables of contents, and they also fit well with the core curriculum for biochemistry outlined by Voet et al. [14]. It remained, however, for us to extract a conceptual perspective from the results.

EXTRACTING A CONCEPTUAL FRAMEWORK FROM THE SURVEY RESPONSES

Implications of Commonly Used Words

We initially examined the implications of the commonly used words in the responses (Fig. 1). Although “protein,” “structure,” and “function” were used most frequently, there were many other words provided in the answers that connoted things about how the respondents perceived aspects of biochemistry. Words such as “encodes,” “signal,” “relationship,” “energy,” “synthesize,” “interaction,” and “currency” (to name a few) suggest that biochemistry is “about” molecular structure and function, communication, and processes feeding and linking to one another. The ideas came through strongly that (i) molecules, cells, and organisms make (or build) and break connections, and (ii) they have to service these connections in terms of communication and energy currency.

Extraction of Concepts

We classified the responses as content or concept, using the operational definitions given above. The classified results using the exact wording of the responses are shown in Table IV. Of the responses, 108 fell into the content category (we discarded these from our analysis of concepts) and 70 fell into the concept category. Some of these concepts are more fully or clearly articulated than others, but each of them contains a link between two or more areas of content, and each has an abstract component.

Table IV. Concept responses and their classification
  1. The exact wording provided in responses has been used in this table. Statements or words followed by a number in parentheses (x) were used “x” times in the response set.

Information Transfer and Storage10 responses
•DNA carries the genetic code
•Genetic information flow; the central dogma!
•Storage and retrieval of information
•Protein–protein/enzyme interactions in relation to the transmission of cell signals
•Flow of information
•Conversion of information into structure
•The idea that not all processes are 100% efficient or faithful—e.g. occasionally the wrong base will be incorporated during DNA synthesis
•Molecular recognition and specificity—how functional organic groups and metal ions provide specificity in biological processes
•Information storage and transmission—DNA makes RNA makes protein and its variants
•Protein modification and link to function
Thermodynamics and Energy12 responses
•Energy production/use is fundamental to chemistry of life systems
•Cellular systems are in dynamic equilibrium not at thermodynamic equilibrium
•The role of charge, pH, and pI in determining electron/proton flow
•Conversion of food/substrates to energy currency in the cell; uses of that currency to drive biochemical and cellular processes
•Storage and retrieval of energy
•Protein–protein/enzyme interactions in relation to the transmission of cell signals
•Understand energy metabolism (how is ATP made and which pathways are most important)
•Energetics and catalysis—how living organisms transform energy and build biological order. This is the big concept—without an understanding of how thermodynamics applies to biology then we cannot understand life—the rest is detail
•Conformational dynamics—the idea that structures are not static
•Thermodynamics versus kinetics—a thermodynamically favorable reaction will not necessarily proceed spontaneously
•Use of energy
•Energetics and catalysis—how living organisms transform energy and build biological order
Structure/Function of Biomolecules16 responses
•Structure and its relationship to function (5)
•Proteins carry out the essential functions of the cell
•Hydrophilicity and hydrophobicity; water and lipids and their role in compartmentalization
•Partitioning of cellular reactions in different compartments and organelles
•Dependence of protein function (3D protein structures, active sites, motifs, etc.) on amino acid sequence
•Shapes and interactions of molecules based on charges, hydrophilicity/hydrophobicity, and so forth
•Conformational dynamics—the idea that structures are not static
•Biomolecular structure is dominated by weak intermolecular interactions
•Molecular recognition and specificity—how functional organic groups and metal ions provide specificity in biological processes
•Protein modification and link to function
•Structure–activity relationship
•Molecular machines and how they work to accomplish their function
Regulation and Organization in Living Systems21 responses
•All is in a state of flux!
•Homeostasis (2)
•The correct pH and salt concentration is required to maintain the proper function of the cell
•Water is essential for the chemistry of life
•Biochemical systems exist in a dynamic state
•Biochemical processes are highly regulated
•Synthesis pathways—monomeric units that build complex biomolecules
•Water plays a major role in biochemical systems
•The idea of what happens at the molecular level versus the bulk properties of the system
•Membrane biology—how the asymmetry of membranes defines and organizes biochemical processes
•Biochemistry is chemistry in a biological setting. The same fundamental principles apply
•Biological catalysts; enzymes and RNAzymes and their role in metabolic and regulatory pathways
•Energy pathways used by the body (glycolysis, Kreb's, ETC)
•The idea of pathways and networks
•Evolution and selection pressure
•Biochemical principles of genetics
•Semipermeable membranes
•Compartmentalization (2)
•Principles of organization of biomolecules in a cell including signaling and metabolic pathways
Experimental Approaches (or Disciplinary Practice)11 responses
•Central dogma—DNA->RNA->Protein 1) because it is so central 2) it can be used as a platform to enter into all other aspects of biochem listed above
•Enzymes are to a biochemist as maps are to a geographer, or stars are to an astronomer, or molecules are to a chemist, and so forth:-)
•Be able to establish enzyme assays
•Analysis of structure of proteins
•Analysis of function of proteins (role in cell/interaction with other proteins/biomolecules)
•Analysis of chemical reactions that occur in living cells
•Understand proteins and enzymes and how to treat them in the lab
•Understanding quantitative aspects of biochemical processes
•Study of biological processes
•Use of recombinant DNA technology (in its broadest sense) as an experimental tool
•Tool for analytical measurements

We found the concepts dealt with five major areas of importance:

  • 1)Thermodynamics and Energy (12 statements)
  • 2)Information Transfer and Storage (10 statements)
  • 3)Structure and Function of Biomolecules (16 statements)
  • 4)Regulation and Organization in Living Systems (21 statements)
  • 5)Experimental Approaches (or Disciplinary Practice) (11 statements)

These have significant similarity to the five core concepts defined by the Vision and Change project [10] and listed in the introduction. Some of them are slightly modified to reflect the discipline of biochemistry (e.g.: the inclusion of biomolecules in the title for the Structure and Function area).

There are two exceptions to the alignment with the Vision and Change core concepts.

  • (i)We have not included an “evolution” category. We only received one response that specifically addressed evolution, and we classed this under Area 4. We also received one response that described errors in DNA replication; this was classified under Area 2.
  • (ii)We have included a category related to experiments and disciplinary practice. We received 11 concept statements about experiments, experimental approaches, and ways of thinking that define biochemistry practice. These do not fit into the core conceptual framework defined by the Vision and Change project. They do, however, come under the “need to understand the process of science” discussed in the Vision and Change Call to Action [10]. We have retained these statements as concepts because they fit our operational criteria; experimental approaches give meaning and context to discrete areas of content, and they require understanding of more than one aspect of biochemistry. They are special to biochemistry, and we assume that an analysis of other disciplines would find a similar pattern of generalist and specialist key concepts.

DESIGNING A COURSE AROUND KEY CONCEPTS PROVES TO BE CHALLENGING

Rationale and Methodology for Course Design

Once we had defined these group headings we considered using them as the titles of five sequential teaching modules in our revised course. In theory, this would have allowed us to present content in each of the modules as groups of conceptually related topics, which would help students make links between the content areas. We also designed the conceptual map shown in Fig. 2 as an initial teaching tool for the course, with the intention of presenting the modules as described.

Figure 2.

Biochemical concept map and proposed teaching module framework for an introductory biochemistry course. Large-font terms in bold indicate key concepts we defined from the survey responses. Smaller phrases or words in nonbold indicate content we wanted to teach as part of the course BIOC2000. These were placed into key concept areas that seemed most logical as a module in which they could be taught. Words placed on top of the dividing lines indicate that this item spans more than one concept classification—this was the beginning of our realization that there was a problem with our approach. We could not confine content to just one conceptual area (as described in the text). This initial diagram became obsolete as we realized we could not justify placement of our content as shown here. This teaching approach was replaced with the conceptual lens diagrams.

Problems with Course Design Validate our Definition of Concept

We found that there was a problem with this approach. We could not confidently assign items of content to only one heading for teaching purposes. For example, teaching of the central dogma fits well in the “Information Transfer and Storage” category (since the central dogma is based on the premise of information flow). One could, however, easily teach central dogma under other headings as well. As the structures of bases define the process of complementarity during DNA replication, transcription, and translation, it is valid to teach the central dogma under the “Structure and Function of Biomolecules” heading. Similarly, the crucial role of DNA, mRNA, and proteins in organismal function means we could also teach these subjects in a “Regulation and Organization in Living Systems” module. If one considers that the processes of base matching, DNA replication, transcription, and translation are driven by overall negative Gibbs free energy changes, we could also discuss “central dogma” under the “Thermodynamics and Energy” heading.

This “problem” is actually a validation of our methodology—an important piece of content can be taught under the headings defined by each concept. Thus, in the example just used, each concept has enough breadth to make sense of and give wider meaning to the processes of DNA replication, transcription, and translation. We have now created a conceptual framework that precludes a simple arrangement of content under single conceptual headings and demands a new teaching method.

CONCEPTUAL LENSES PROVIDE A NEW WAY OF ORGANIZING CONTENT USING CONCEPTS

We looked for a novel and thought-provoking way to present important biochemical content from a conceptual standpoint and decided to employ conceptual lenses. Erickson [21] described a conceptual lens as a device used to “supersede the specific topic and moment” which develops a metacognitive approach to a subject by forcing thought on a larger and more integrated scale. This is similar to the “big ideas” technique discussed by Wiggins and McTighe [12] and diagramed by Howitt et al. [22] and Wright and Hamilton [23].

We used our biochemical big ideas of Thermodynamics and Energy, Information Transfer and Storage, Structure and Function of Biomolecules, and Experimental Approaches (or Disciplinary Practice) as conceptual lenses to describe several content areas. For simplicity of presentation, they were represented by the shortened terms “Thermodynamics,” “Information,” “Structure/Function,” and “Experiments.” An example diagram for “Macromolecules” is shown in Fig. 3. In each case, a term describing the subject, topic, or content area was placed on the left of the lens diagram. Then, four lenses were placed on the right of the diagram. In each of them, the topic was discussed using the perspective of the lens.

Figure 3.

An example concept lens diagram for the content area of “Macromolecules.” Each lens diagram was set up in the manner shown. The topic was placed on the left, and the topic was discussed from a conceptual perspective under each lens. The lens contents were not designed to cover all of the course content.

We did not use “Regulation and Organization in Living Systems” as a conceptual lens, because we found it became redundant as we were preparing statements for the other conceptual lenses. For example, our “Thermodynamics” lens for “Free Energy” has the following text:

“Biological macromolecules have a high Gibbs free energy. They take energy to build. They can be broken down to yield electrons. A reaction that has a positive ΔG (change in Gibbs free energy) will not occur spontaneously. To make such a reaction occur, energy must be fed into the reaction in some way. The concurrent breakdown of high-energy molecules (e.g.: ATP or NADPH+ hydrolysis) can be used to drive a positive ΔG reaction into an overall negative ΔG state. An example of this is the DNA ligase mechanism. Reactions that use this type of coupling mechanism can occur spontaneously in biological systems.”

These statements address regulation and organization of metabolism from the fundamental perspective of energy pathways. There is no need to have a separate lens about regulation and organization in this case, as we would be repeating ourselves. This does not mean, however, that the “Regulation and Organization in Living Systems” is truly redundant, as we did not make lens diagrams for metabolism topics in this project. We may incorporate it as a lens in future iterations of the method if we are unable to explain phenomena without it.

Although the term “Experiments” is not truly abstract (it is more an “activity” than a “concept”), we felt it was important to keep this lens, as students regularly have trouble linking experimental exercises to the lecture content. In addition, much of the experimental practice in biochemistry involves heavy conceptual understanding and abstract thinking. We used this section to describe some aspects of why experiments work (e.g.: why do you need ATP in a PCR?), and how some of the great experiments and methods in biochemistry related to the lecture content. Examples of these are discussion of the Levinthal paradox, the Ramachandran plot, and the Anfinsen paradigm under the “protein folding” topic. We have not completed an exhaustive inclusion of the great experiments in biochemistry in these lens diagrams—there is definitely scope for more work in this area of the approach.

We were initially concerned that the lenses would limit the topic areas we could present, but found that the lens titles were functional for every topic we considered. We prepared 11 concept lens diagrams using the following topics: (i) macromolecules, (ii) DNA replication, (iii) free energy, (iv) protein folding, (v) lipids, (vi) carbohydrates, (vii) ligand binding affinity, (viii) enzymes and their substrates, (ix) enzyme kinetics, (x) enzyme kinetics (inhibition), and (xi) enzyme kinetics (regulation). Each of these diagrams is shown in the Supporting Information (S1).

These topics reflected the chronology of the subject matter in the course, with one lens for every major topic area covered in the first 22 hours of course lectures. A 12-hour lecture block on metabolism was presented after the lectures covered by the lenses. Concept lenses were not produced for these lectures; the course is team taught, and the third team member chose not to use lenses.

Each lens diagram took between 15 minutes and 2 hours to prepare, depending on how much reading we had to complete to check the validity of our statements. As we prepared the lens diagrams, we often found ourselves exploring new perceptions of the material, especially in the less obviously linked content-lens areas. One example of this is the discussion of lipids under the “information” lens.

“Lipids in membranes are structural, but their variable properties also help order the membrane into domains that allow for informational and functional differentiation. The various head group modifications of phospholipids and sphingolipids provide functional and informational variability. The polar head groups of these molecules are charged near pH 7.0, which helps stabilise the membrane bilayer configuration. The sugar modifications on the surfaces of membrane lipids define our blood groups.”

Some of these ideas were not part of content that was explicitly taught in the BIOC2000 lectures. They were often not assessable. In this case, however, these ideas are key to understanding how the biochemistry of lipids maintains both (a) cell and organismal function and (b) information transfer, by segregating regions of the cell and providing a platform for attachment of other molecules such as sugars. This places the “biochemical” description of lipids in a life context for the nonchemist. In addition, these ideas often provided horizontal and vertical links to material in other courses.

As teachers, we found these lens diagrams difficult to make. They challenged our understanding of content and forced us to examine material from perspectives that we found difficult or even unknown. Considering the thermodynamics of sugar interactions, or the information content of Gibbs free energy was confusing and sometimes confronting. We found ourselves questioning what we knew and understood.

“Having to do them [the lens diagrams] made me think about aspects of the topic I would not have naturally considered...especially for the thermodynamics and information lenses. This may have made my coverage of the topic more holistic and better integrated with other aspects of this course and others.”

Elizabeth Gillam, lens developer and course lecturer.

PRESENTATION OF THE LENS DIAGRAMS TO STUDENTS

Method of Presenting the Lens Diagrams to Students

We presented the lens diagrams to the students at the beginnings or ends of lectures and did not spend significant time on them in the lecture session. Instead, we suggested that students read through them when they revised the lecture material and ask themselves if what they had understood from the lectures made sense in relation to the lens diagrams. We also asked students to focus on the ideas stated on the concept lens slides, rather than trying to memorize the content of them. We did not assess (or intend to assess) the lens diagrams. This was made clear to the students. The lens diagrams were included with the online course materials for each lecture (comprised of posted lecture slides and visual/voice recordings).

The lectures were taught “as usual” without using different methods of presentation than those normally used in the course. Each week this included (i) 3 hours of mostly transmission-style lectures with included active learning stop-pair-share exercises and (ii) 3 hours of experimental laboratory. Approximately 1 hour of lectures per week was a “lab lecture” in which we discussed the theory and practice of laboratory courses. No lens diagrams were produced for the lab lecture topics, although the labs were sometimes addressed in the “Experimental Approaches” lens text.

Results of Presenting the Lens Diagrams to Students

Considering that we did not directly assess the concept lenses or their contents, we were unsure of how much the students would use them. At the end of the course, before the final examinations had been completed, we surveyed the BIOC2000 cohort using an email invitation and question set delivered via Survey Monkey (http://www.surveymonkey.com/s/BIOC2000_Concepts_Student_Survey.) The questions and student responses are shown in Fig. 4.

Figure 4.

Student perceptions of the lens diagram approach. One hundred sixty students responded to the (voluntary) online course survey. They were asked if they agreed with, disagreed with, or had a neutral opinion of the statements shown on the Y axis. Agree is shown in mid-gray, neutral in pale gray, and disagree in black.

The majority of students (88%) reported that they understood the purpose of explicitly incorporating concepts rather than just content into lectures, and 65% of students agreed that they thought more deeply about the lecture content because of the concept lens approach. Most students (60.6%) also indicated that the conceptual approach helped them see links between BIOC2000 and their other courses.

In their open comments, some students demonstrated a sophisticated understanding of the role of the concept lenses.

Student 1: “Biochemistry along with a lot of other courses of similar nature is largely made up of abstract concepts. Some people are much better at grasping abstract concepts and applying them to problems and situations, but some people have a hard time. Teaching using concepts instead of completely via rote learning is much better as more students are more likely to understand and process concepts and create mental maps a lot easier than other methods.”

Student 2: “I think that the conceptual lens approach, instead of being a very different approach, strongly reinforces appropriate learning strategies that students should be engaging in normally, as long as ALL of the course material is present in them [..] the lens diagrams [..] provide a useful summary for learning the important concepts of the course.”

Student 3: “All courses should use lens diagrams as I struggle to summarize lots of information myself.”

Student 4: “It was a great way to see important things on a topic on one page. Because in science it can get very confusing when every little thing is introduced (sometimes in a weird order) in different lectures and it is hard to link it all to see it as a whole. The lens was great because I could see why I was taught certain things and how they all link together to tell me something on the general topic. And in doing so, things were easier to understand =D.”

These comments indicate that the students had grasped how the lens diagrams could be useful to them.

Not all students, however, thought conceptual learning was helpful. Despite being told the lenses were aids for reflection on understanding (not lecture summaries or lists of core points to be memorized), students expected to be able to study for exams from the lenses. Some struggled to use them as an aid to integrating material and thinking about the course from an abstract perspective. They wanted point-form content summaries instead.

Student 5: “I really disliked the lens diagrams for a number of reasons. I found they often did not reflect lecture content accurately, and they were not clear enough to be studied from like the lecturers advised. [sic—we did not advise this]. Personally, I would much prefer a simple—and concise—list of main points at the end of the lecture.”

Some students think conceptual learning is “too easy,” or irrelevant, and that it does not help with final exams.

Student 6: “I would say [..] that one of the biggest problems with the conceptual teaching approach [..] is the problem that, often, concept-based teaching can be *too* easy. This stems from the fact that often the general details regarding exam questions may be very easy to understand, and thus any application or context that examiners create for these concepts is ridiculously easy to comprehend.”

We are not quite sure how to further interpret the comment from Student 6 to provide useful modification of the method, but it is true that the exams were not set to test the lenses. This was purposeful for the first iteration of the lens diagrams—we felt it was fairer on the students to trial the method for effectiveness and comprehensibility before we assessed students directly on the lenses.

Some students learn better by doing than reflecting, and they did not find the process of considering the diagrams to be useful. This reflects the disparity in learning styles in our cohort.

Student 7: “Concepts are important, but it's the content that's really important, and once we start going through content and applying it it's much easier to understand the concept. That's why the concept approach is $#@% [expletive modified]. Move on to the content already.”

Students wanted consistency from one lecturer to another, with a neatly packaged course product. Because only the first two of the three lecturers in the course used the concept lenses, some students complained in the open comments about inconsistency of approach, and 61% of students indicated that they found the concept lens framework easier to understand from some lecturers than others.

DISCUSSION

In attempting this project we wanted to address the problem of content overload in a generalist undergraduate biochemistry course by defining the core ideas in biochemistry or “those fundamental conceptions which are ageless and persist, however much they may be altered, extended, or transformed by the discovery of new facts” [24]. Finding concepts that are not altered by the discovery of new facts is particularly appropriate for biochemistry teaching, since we are in an age of exponential information expansion, especially in the areas of (i) protein sequence and structure data and (ii) data obtained from systems biology studies that include metabolomics, glycomics, lipidomics, and proteomics. All of these new data feed into the biochemistry pool of knowledge, but we cannot possibly teach everything we know in one undergraduate course.

Our initial aim was to find unifying themes or key concepts that would allow us to link areas of content under one umbrella as shown in Fig. 2. We found, however, that the concepts we defined could regularly be applied to all of the content areas we were teaching. This forced us to rethink our proposed “conceptual” course structure, and consequently we adopted conceptual lenses to help us examine the content from various different viewpoints.

The majority of students responded positively to this new approach, indicating that it made them think more deeply about the content and develop links between biochemistry and other courses they were taking. A minority complained that the lens diagrams were not concrete enough, and that they just wanted lists of points to memorize or more hands-on activities to help them learn.

Interestingly, as teachers, we also struggled with having to think about the material we were teaching from multiple viewpoints. We had difficulty thinking about the material abstractly and conceptually, rather than just as content. Initially, we did not know if we were putting the right ideas in the right lenses. We even had some difficulty defining what a concept was when we started the project. This is not surprising. Biochemistry is traditionally taught from a content perspective; this is how most current faculty learnt it from their teachers (the authors included). This tradition is also reflected in the “concrete,” content type of answers provided by our survey respondents, when we had asked them about concepts.

This blurring between “concept” and “content” has been commented on before. Garvin-Doxas et al. [25] said “it is difficult to separate the notion of topics (which is how most postsecondary material is currently organized) from what we mean by concepts” and go on to suggest that the term “big ideas” is a better descriptor than “concept.” In a larger, follow-up study to this one, we have replaced the term “concept” with “big ideas” in the survey questions. It will be interesting to compare the effect that this explicit rewording has on the nature of the answers collected.

Regardless of our evolving idea of “concepts,” the importance of the essential understandings in biochemistry remains. Biochemistry is a key science in itself, but it is also a crucial enabling science for a considerable number of other fields of scientific and medical endeavor [26–28]. This is evidenced in the educational backgrounds and current work practices of our respondents; some respondents were using biochemical concepts and techniques frequently or all the time in their work, even though they had not taken any formal biochemistry courses during their university education. Presumably they have arrived at using biochemistry through their own experimental interests or needs.

This work goes some way toward defining the key concepts in biochemistry, and it is gratifying to see that they map closely to the core concepts in biological science already defined by the Vision and Change Project. We were able to use headings very similar to the Vision and Change concepts to categorize the responses we received from our reference group; with slight modifications they became relevant to biochemistry. The exceptions were “evolution,” which was not included with significant frequency as a response in our survey, and experimental approaches and ways of thinking about analyses that are specific to biochemistry. This last area sets biochemistry apart as a discipline, so it is logical that it will present in responses obtained from biochemists. It will be interesting to see if our follow-up study, with a much larger group of international respondents, also gives evolution a low priority in biochemistry. Given the important evolutionary information currently coming out of structural biology programs, it is surprising that evolution was so rarely mentioned. Perhaps as scientists who focus on events at the molecular level, we tend to forget the importance of molecular changes to the whole organism—maybe we should consider it more when we talk to an introductory biochemistry class cohort about the importance of biochemistry.

Apart from proposing the key understandings in biology, the Vision and Change project also calls for student-centered classrooms [6]. These, in practice, reflect the constructivist values of “collaboration, personal autonomy, generativity, reflectivity, active engagement, personal relevance, and pluralism” [29]. Our mechanism for presenting biochemistry topics in light of key concepts has had a successful first iteration, but we used a relatively passive mechanism of presentation for the concept lens diagrams. We need to incorporate more active learning opportunities that allow students to explore the implications of the concept lenses and their contents. There are two major mechanisms we can use to achieve this.

First, explicit assessment of “conceptual understanding” will promote student interest in concepts, rather than content. We included an aspect of this in BIOC2000 in 2010, but it requires extension. The course was assessed using the following components: (i) laboratory participation and written report (35% of final course aggregate), (ii) two biochemical concept inventories (an initial diagnostic one where students gained 2% for participating [23], then a second one later in the semester worth 13% of the final grade), and (iii) a final written examination (50% of final course aggregate). The concept inventories tested conceptual understandings using very short case studies and “T/F” answer sets. They did not draw material directly from the concept lenses or from case studies used in the lecture material. The inventories are still under trial and will be presented in separate publications. The laboratory assessment included marks for attitude, technical aptitude, and attendance in the laboratory. The written report was in the traditional Aims, Methods, Results, Conclusions format and was produced without the aid of the Science Writing Heuristic [30]. The final exam contained questions on the lecture and practical material that required problem solving and synthesis of material from multiple learning activities (rather than just rote learning from one lecture or laboratory session).

Although we attempted to assess conceptual understandings from several perspectives, none of these assessment items explicitly tested the concept lenses themselves, and students were not asked to evaluate, construct, or correct a concept lens diagram during the semester or in the final exam. We are particularly interested in providing students with assessable reflective and generative opportunities, and we propose using a tool we call the “Broken Concept Lens” to this end. We envision that in a Broken Concept Lens diagram, a mixture of correct and incorrect statements would be provided in each lens. Students would be asked to indicate which statements are wrong, explain why they are wrong, and propose a more correct statement. We will trial this as an assessment item in upcoming iterations of BIOC2000.

Even in the absence of assessment, a learning activity in which students build a concept lens diagram for a topic they find important or personally relevant would dramatically enhance student engagement with the technique. This is the second way we envision concept lenses could be used in a student-centered classroom. In particular, this activity could build cross-course synergies; students could explore material from other courses using the biochemistry concept lens diagrams. This is important in our context, because more than 70% of BIOC2000 students are not Biochemistry majors. Our Physiology major students could collaborate to create lens diagrams for the topic of “ion channels,” whereas students in the Nutrition and Dietetics program could generate a diagram for “amino acids.” In this case, they could pinpoint relevant aspects of thermodynamics, structure/function, and information flow that they may (or may not) have considered in their other courses, and thus the technique becomes doubly valuable for enriching learning. The idea of creating explicit cross-course synergy in science education is reflected in the new Senior Secondary Australian Curriculum for Science [31], and this process should continue at the tertiary level.

It is deeply important that we find a less content-heavy and more holistic way of thinking about and teaching biochemistry. This is especially important for the majority of our students who need to take the big ideas of biochemistry into their future lives, but who do not need to be functional biochemists in the laboratory. Explicitly scaffolding the content in terms of concepts for both the teacher and the student is a good and fairly simple way to begin. This work provides some progress in the discussion of how we should do that.

Acknowledgements

The authors thank Susan Hamilton, Susan Howitt, and Eileen Chung for helpful discussions. They thank Nancy Pelaez for constructive reading of the manuscript. They also thank their academic and student survey respondents for generously giving up their time to help with this research. This project has been approved by the University of Queensland Ethics Committee.

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