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WHERE HAS ALL THE CARBON GONE?: A THOUGHT PAPER ON
FRAMEWORKS FOR ASSESSING BIOLOGY UNDERSTANDING
Joyce Parker, Charles Anderson, John Merrill, Merle Heidemann, Tammy
Long, John Merrill, Brett Merritt, Gail Richmond, Duncan Sibley, Mark
Urban-Lurain, and Christopher Wilson
Michigan State University
NSF grant DUE-0243126
PROJECT FOCUS
In an interview exploring students’ understanding of metabolism, we asked an
introductory biology student, Susan about the inputs and outputs of
photosynthesis. She replied, “In photosynthesis, [coming in are] CO2, starch or
glucose. Coming out is oxygen, water, and energy.” She stuck to this response
despite prodding from the interviewer. The fact that she was describing a
process where carbon disappeared did not occur to her.
There are two ways to look at Susan’s response. She does not know/remember
the equation for photosynthesis. Alternatively, she does not worry about
accounting for the matter in the process she describes. The first is a problem
that affects only her understanding of metabolism. However, the second
explanation indicates a problem that may affect her understanding of much of
biology. Therefore, we see the second interpretation of Susan’s thinking to be
more important. If Susan’s thinking is characteristic of that of a significant
number of students, this interpretation points to what may be powerful
interventions.
This discussion of the interpretation of Susan’s thinking illustrates the goals of
our Diagnostic Question Cluster Project:
 Identify content that is problematic for students.
 Identify problematic patterns in students’ thinking.
 Frame content in ways that help students develop more robust
understanding.
Like many assessment developers, our ultimate goal is improvement of
instruction. In order to achieve this, we need to articulate what content is
problematic for students, so that we know where to focus our efforts as we move
through the curriculum. However, this approach alone may yield a lengthy list of
problematic content areas, each of which needs to be addressed independently.
Therefore, our second goal is to identify problematic patterns in students’ thinking
that extend across content. Such patterns would provide targets for instructional
interventions that might improve students’ understanding of more than individual
concepts. Our ultimate goal is to use knowledge of these problematic patterns in
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students’ thinking to frame the content in ways that lead to systematic
approaches to biology content and ultimately better understanding.
DEVELOPMENT PROCESS
Figure 1 shows the development process that we use to produce both content
frameworks with learning outcomes and valid assessment tasks. The important
elements are show in red. Patterns in students’ thinking are the focus of our
work. Problematic patterns in students’ thinking are what we want to
reveal/diagnose with our question clusters. In addition, once aware of
problematic patterns, we can seek to organize the content in ways that help
students develop more systematic approaches to complex biological processes.
We begin by asking students open-ended questions where they must apply what
we initially defined as the big ideas or most important ideas in a general area of
biology. We turn common wrong answers into foils for multiple choice questions.
We test the utility of these multiple choice questions by interviewing students
about the reasoning behind their answer choices and by getting written
explanations from students about their answer choices. We also do statistical
analyses to determine if question results track indicators of general
understanding such as grade point average and if students perform consistently
on items designed to assess particular objectives. We adjust the questions
according to these results. We also adjust the target content framework so that
our objectives focus on the most far-reaching and powerful ideas.
Figure 1. Development Process
Define the target
FRAMEWORK we
want students to
be able to use.
Give students
open-ended
application
questions.
Identify
PATTERNS’
IN
STUDENTS’
THINKING.
CLUSTERS of (multiple choice) DIAGNOSTIC QUESTIONS
Where foils represent common problematic patterns in students’
thinking
Student
interviews
Students’
written
explanations of
answer choices
Statistical
analyses
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RESULTS
We are currently working in three topic areas in biology: cellular respiration,
photosynthesis, and genetics – specifically meiosis and fertilization. We present
here the content framework and objectives (what we call practices) for cellular
respiration plus three questions from our diagnostic question cluster.
Figure 2 shows our content framework. In this framework, we have organized
the content into three scales or levels: sub-cellular, cellular, and organismal,
because we picture biological processes as happening in nested systems.
Cellular respiration is a process that happens in cells. The subcellular level can
be described as sets of reactions that occur at specific locations within the cell.
At the organismal level, the related inputs into heterotrophs are food and oxygen
while carbon dioxide is a key output.
The other organizational dimension includes two practices that we see as
essential to understanding: tracing matter and tracing energy. By tracing matter,
we mean knowing the inputs and outputs of reactions or groups of reactions or
following the fate of atoms or molecules. One of our instructors likes to frame this
for his students as “What’s happening to stuff?”, to avoid any potential conflict
with a more limited view of the scope of “matter”. For example, during aerobic
cellular respiration, the carbon atoms that were originally in the sugar end up in
carbon dioxide. By tracing energy, we mean following the energy
transformations or accounting for the sources of energy that allow living things to
perform endergonic reactions. For example, during cellular respiration part of the
chemical energy that was originally in the C-C and C-H bonds of the sugar ends
up in the phosphate bond of ATP. The third organizing principle is knowing the
location of events. Taken as a whole, the content framework shown in Figure 2
allows us to organize in an abbreviated way most of what is typically taught about
cellular respiration in an introductory biology course.
There are four practices that describe what we want students to be able to do
with the content in the framework. These practices are roughly equivalent to
learning objectives. Two of the practices, tracing matter and tracing energy,
have already been described. The third practice is related to these –
segregating matter changes from energy changes. We mean not equating or
confounding matter and energy changes. For example, during cellular
respiration, the chemical potential energy resides in the bonds of a sugar.
However by the end of the process, the chemical potential energy has been
transferred to ATP. The matter (carbon atoms) has separated from the energy.
Students sometimes miss this and mistakenly think that the atoms rather than the
energy have moved from the sugar to the ATP. Another way that students
sometimes fail to segregate matter and energy is to invoke processes where
matter is converted to energy. For example, when a person looses weight, these
students think that the fat is converted to energy and is therefore lost.
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Figure 2. Content Framework for Cellular Respiration
Tracing Matter
Tracing Energy
Context/Structure
ORGANISMAL LEVEL
Using Food for Energy Food provides molecules that serve as
fuel and building material for all
organisms. Some of the matter in food
leaves aerobic organisms in the form
of carbon dioxide and water.
Food is transported through the body.
Occurs in all cells in all living
Then individual cells transform the
organisms.
chemical energy in the food into usable
energy in energy management molecules.
CELLULAR LEVEL
Cellular Respiration
C6H12O6 + 6H2O + 6O2  6CO2 + 12H2O Some chemical energy in the C-C and C-H Occurs in the cell cytoplasm,
bonds in glucose
chemical energy in mitochondrial matrix, and
ATP
mitochondrial membrane.
SUB-CELLULAR LEVEL
Glycolysis
(1)6-carbon glucose 
(2)3-carbon pyruvate + (2)H2O
Some chemical energy in the C-C and C- Occurs in the cytoplasm in all living
H bonds in glucose  chemical energy cells.
in (2)ATP & (2)NADH
Pyruvate oxidation
(Acetyl CoA
production)
(2)3-carbon pyruvate 
(2)2-carbon acetyl CoA + (2)CO2
Some chemical energy in the C-C and C-H Occurs in the mitochondrial matrix in
bonds in pyruvate  chemical energy in eukaryotes, in the cytoplasm in
(2)NADH
prokaryotes.
Kreb’s Cycle
(2)2-carbon acetyl CoA  (2)2CO2
Some chemical energy in the C-C and C- Occurs in the mitochondrial matrix in
H bonds in acetyl CoA  chemical
eukaryotes, in the cytoplasm in
energy in (2)ATP, (2)3NADH & (2)FADH2 prokaryotes.
Electron Transport
Chain & Oxidative
Phosphorylation
Electrons from NADH & FADH2 +O2
-H2O
(No carbon skeleton)
Some chemical energy in (10)NADH &
Occurs in the inner mitochondrial
(2)FADH2  chemical energy in (~34)ATP membrane in eukaryotes, in the
plasma membrane in prokaryotes.
The fourth practice is moving between levels. Students need to know when the
answer to a problem posed at one level is actually due to processes occurring at
another level. For example, weight loss in animals and plants (an organismal
issue) is explained by the cellular process of respiration.
We have chosen these four practices as the focus for the content framework
because of their fundamental place in many disciplines. Also we have found that
many students who can recite the mantras of conservation of matter and energy
do not actually use these ideas when approaching complex processes. Susan,
the student who was comfortable with sugar and carbon dioxide turning into
water and oxygen, showed no disposition to check her recollection of the
equation for photosynthesis by tracing matter. Other students say that during
cellular respiration, the glucose reacts to become ATP or the glucose is
converted to energy. They fail to segregate the matter and energy changes. We
also found many students who attribute weight gain or loss to other processes
that occur at the organismal level such as sweating, waste production, or
digestion. These students do not move appropriately between the levels. Thus
we believe that the content frameworks and practices describe a general
approach that will help a large number of students when used consistently
throughout courses.
Figure 3 shows three questions from our cluster on cellular respiration. Each foil
represents a common incorrect response to open-ended questions and can be
seen as an indication of a problem with one of the four practices described
above.
Figure 3. Three questions from our cluster on cellular respiration.
An agar plate was left uncovered for two weeks. Three different kinds of mold grew on
it. Assuming that the plate did not dry out, which of the following is a reasonable
prediction of the weight of the plate and mold?
A) The mass has increased, because the mold has grown.
B) The mass remains the same as the mold converts agar into biomass.
C) The mass remains the same as the growing mold converts agar into energy.
D) The mass decreases as the mold converts agar into biomass and gases.
Jared, the Subway man, lost a lot of weight eating a low calorie diet. Where did all the
fat / mass go?
A) The mass was released as CO2 and H2O.
B) The mass was converted to energy and used up.
C) The mass was converted to ATP molecules.
D) The mass was broken down to amino acids and eliminated from the body.
E) The mass was converted to urine and feces and eliminated from the body.
You eat a grape high in glucose content. How could a glucose molecule from the
grape provide energy to move your little finger?
A) The glucose is digested into simpler molecules having more energy.
B) The glucose reacts to become ATP.
C) The glucose is converted into energy.
D) The energy of the glucose is transferred to other molecules.
E) The energy of the glucose is transferred to CO2 and water.
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IMPLICATIONS
We call the systematic approach to biological processes described by the four
practices principled-reasoning from scientific models. We chose “principled”
to denote a systematic and widely applicable approach that uses fundamental
principles such as the conservation of matter and energy. We added “from
scientific models” to distinguish between those who are systematic in their
approach but use flawed models and those students who use accurate models.
The most common problematic ways of thinking involve misconceptions or
procedural display. We define misconceptions as deeply-rooted, incorrect
ideas that arise from personal experience. Procedural display we use to
describe problem solving based on superficial relationships and/or recall. For
example, when asked about energy associated with metabolism, many students
will look for an answer choice containing “ATP” regardless of the specific context
of the question. Thus misconceptions are usually associated with particular
ideas or situations, while procedural display is a more general problematic
approach.
We have found that the content frameworks and this particular definition of
principled reasoning are broadly applicable. We use them in geology to organize
content and define objectives for the water, rock, and carbon cycles, as well as
plate tectonics. In the geology context we use tracing matter and energy as the
main practices and macro (global or larger than human scale), meso (human
scale), and micro (molecular) levels. By adding the idea of tracing information
and a fourth level, ecosystems, we are finding that the same basic approach
works for most of biology. For example, broadly speaking the carbon and
nitrogen cycles can be described by tracing matter through the nested levels.
The central dogma is about tracing matter (understanding how the cell uses DNA
to build RNA and subsequently proteins) and information (understanding how a
sequence of four flavors of bases taken in triplets contains the information that
dictates a particular sequence of amino acids in the resulting protein).
Finally, we see our emphasis on broad patterns in students’ thinking as
complementary to an inventory approach focused on identifying particular
content that is difficult for students. We are seeking a discipline-wide approach
while the inventory approach works at the concept level. The two approaches
deal with different grain sizes, but will both inform changes in instruction.