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The overarching goal of this project is to help students improve their biological thinking and reasoning skills - to approach biology questions and issues like a biologist, which we call principled thinking?. One reason why it is so challenging for faculty to help students use core biological concepts and principles? is because this thinking is so automatic for us.


This is the Hidden Curriculum, which is:

So familiar to biologists that they are hardly aware that they use it

Assumed by biologists to be also understood by students

Not understood by students

PRINCIPLED THINKING: All of the topics in this set of Diagnostic Question Clusters (DQC's) deal with two overarching principles - conservation of energy? and conservation of matter?. We want students to use "principled reasoning" to think about processes? involved in ecosystem carbon cycling. By using principled reasoning, students are less likely to form misconceptions, they will more easily dispel misconceptions, they will be better able to connect the same process across scales, and they will be better able to reason about processes when they are presented in novel contexts.

Four Categories: Throughout this site the Hidden Curriculum includes 4 categories: See for example

1) PRINCIPLES: Conservation of Matter: matter - carbon in this case - cannot be created or destroyed (and therefore must be kept track of). Conservation of energy: energy cannot be created or destroyed (and therefore must be kept track of). In most biological / ecological systems sunlight is the ultimate source of energy (the biosphere is open with respect to light energy).

2) PROCESSES: All of the topics within the DCQs can be reduced to three basic processes: generation?, transformation?, and oxidation? of organic carbon. By helping students to categorize specific topics (e.g. photosynthesis, decomposition) under a more general process, they will be better able to see similarities between topics and make knowledge transfers.

3) SCALE & TIME: biologists automatically shift among organizational scales (processes across atomic/molecular-organismal-ecosystem scales) and time scales (e.g. instantaneous-seasonal-annual) when they think about a biological phenomenon. This type of thinking is very challenging for students.

4) FORMS & REPRESENTATIONS: Within typical biology curricula are standard forms and representations? that help biologists reason about ecosystem carbon cycling. Biologists share this symbolic language, but students may well not "get" what seems obvious to us. For instance, glucose molecules are shown as 3 dimensional balls and sticks, 2 dimensional organic compounds, or C6H1206. Unless we are explicit that these represent the same thing, students can become confused.


The Hidden Curriculum we focus on in this project is transformation of carbon (matter) and energy in 4 levels of organization: cells, organisms, ecosystems, and human energy production/consumption. Our research shows that students have a great deal of trouble thinking through questions involving carbon and energy, especially if cellular, organismal, and ecosystem level processes are all involved. Our principled reasoning framework will help you link fundamental biological processes that change carbon and energy, regardless of the biological scale at which we work.


The PRINCIPLED REASONING FRAMEWORK provides the underpinning for the whole DQC project and should be referred to often. (You will likely realize something new each time you look at it).
  • The framework is based on the principles of conservation of matter and energy. Derived from these principles are 3 fundamental Processes: organic carbon generation (photosynthesis), organic carbon transformations (biosynthesis), and organic carbon oxidation (cellular respiration). If students can truly understand these 3 processes (what happens to carbon and energy and why), they will be able to answer all the DQCs and therefore understand basic transformations of matter and energy at all scales in biology.
  • One representation of this FRAMEWORK is a table with scales in 4 rows (atomic/molecular to ecosystems). The "Process" columns depict the 3 Processes at the 4 different scales (e.g. oxidation at the technology scale has a different focus from oxidation at the organismal scale). Students who understand the "big ideas" of these 3 fundamental processes working at different scales (i.e. can consciously move between the rows and columns of the table) should be able to reason based on key biological principles.
  • We also include "Forms and Representations" (mentioned above) as columns to emphasize this aspect of the Hidden Curriculum.
The framework will help you identify core ideas you need to emphasize across the course as a whole - so students appreciate, for instance, that ecosystem C flow involves cellular respiration at the atomic-molecular, cell, organismal, and ecosystem levels.


The Diagnostic Questions are Clustered (hence the DQC designation) around ecological topics (e.g. food webs) or biological processes (e.g. photosynthesis). The DQC's organized around topics start with a multiple process or "umbrella" question followed by several single process questions.  This organization helps to gauge student understanding of smaller scale processes that limit their ability to understand the "umbrella" question. The DQC's organized around processes focus on one of three fundamental processes: photosynthesis, biosynthesis, or cellular respiration. We have identified a total of 12 DQC's to include in this project. The 6 topic DQCs cover topics commonly found in introductory ecology classes, and the 6 process DQC's cover biological processes commonly taught in introductory biology classes.

DQC organization is shown below in a topic table and in a process table.

DQC Organization in Three Topics

Carbon Cycling

 Energy Flow in Ecosystems  Climate Change







DQC's Organized by Biological Processes




Cellular respiration  





These four steps are designed to expose students' faulty thinking, help students improve their thinking, and allow faculty to assess progress in students' thinking.

1. Select the DQC you want to use: this depends on what you want your students to know and be able to do (student outcomes).

2. Administer the DQC and make a diagnosis: each set of DQCs has an interpretation key to help you decide how to actually give students the question sets and then interpret their responses. In other words, what do they seem to understand pretty well and what do they need help with? Knowing this, you can focus on the latter.

3. Use student-active approaches to help students improve their ability to use principled reasoning skills. How can you help students improve their skills and thinking? There are many different types of student-active teaching? and learning approaches (e.g. cooperative groupwork, making concept maps) that involve students in the learning process. In the teaching activities section of this site, tables link specific outcomes with active approaches you can try. These student-active approaches are examples to modify and add to.

4. Evaluate progress: Are students' skills and thinking improving (i.e. formative evaluation)? Did students' skills and thinking (the specific outcomes) improve? Did the active approaches work (summative evaluation)? The purpose of formative evaluation is for the instructor and students to monitor students' progress during a curricular unit. You can use any number of active learning strategies, discussions, minute papers?, and / or questions from the DQC's to keep track of students' progress toward reasoning like a biologist.  We have provided several suggestions on the teaching activities page.  The purpose of summative evaluation is to check on final progress toward biological reasoning at the end of a curricular unit. For each of the ecological topics and the biological processes there are two DQCs that address the same outcomes. Therefore you can use one set questions as a pre-test to diagnose potential problem areas and the second set to evaluate progress if you wish.