Download An introduction to system models and using them in your

Guiding Principles for the Use of System Models in Science Instruction TM Long, E Bray Speth, J Momsen, S Wyse October 2011 Biology is the study of systems
In biology, systems are assemblages of components that
interact in biologically meaningful ways. Biological systems
are characterized as having emergent properties that arise
as a result of interactions among system components. An
important distinction of systems biology is in its focus on the
interactions among system components, rather than the
components themselves.
Scale is important
Image source: http://www.bluechillies.com/
What system(s) are represented in the aquarium image above? How you answered that question
depends upon the scale at which you were thinking. Biological systems and their component parts occur
at multiple scales of both space and time. Examples of system scales represented in the aquarium might
include:
• ecosystem (the fish, water, rocks, plants, nutrients, and organic material)
• population (all of the fish living in the aquarium)
• organism (the tissues and organ systems of an individual fish)
• cells (kidney cells in a fish)
• organelles (a mitochondrion inside the kidney cells)
• molecular (ammonia produced by the fish’s kidney as waste)
• elemental (nitrogen, a component of ammonia that is required by other
organisms in the aquarium, including plants and bacteria)
Systems perform functions
A scientist would never say that she is studying “aquaria”. Instead, she would frame her response to
include the particular question or process within the aquarium system in which she was interested. For
example, she might study “species diversity”, “foraging behavior”, or “nitrogen cycling” as functions of
aquarium systems.
Consider each of the examples below. What system components are important? At what scale(s) would
each study be conducted?
Aquarium System Process/Attribute
System Components?
Scale?
Feeding behavior of goldfish
Oxygen concentration in aquarium water
Bacterial abundance
Phenotypes (traits) of new generations of fish
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Guiding Principles for the Use of System Models in Science Instruction TM Long, E Bray Speth, J Momsen, S Wyse October 2011 System models for teaching and learning biology
Scientists regularly use models as a way to communicate and think about complex
biological systems. Models reduce complexity by necessarily omitting or
abbreviating some of the information we know exists in “reality”. For example, we
know that the structure of DNA arises as a result of myriad biochemical
interactions that occur among thousands to millions of component parts. However,
the model to the left still serves as a useful way of communicating critical features
of DNA structure despite its omission of volumes of information.
Our team has developed an approach that uses system models as a way to teach and learn biology in
a variety of college-level courses. System models are simple box-and-arrow diagrams that are adapted
from Structure-Behavior-Function Theory (SBF; Goel 1996). Below, we describe system models with
respect to the elements of SBF. Briefly, SBF states that all models have:
1. Structures: the parts (elements or components) of a system. Structures are generally nouns. In
system models, structures are represented in boxes.
Fish
Nitrate
Plants
Ammonia
2. Behaviors: processes or mechanisms operating within the system. Behaviors tend to be verbs and
explain relationships among model structures. In system models, behaviors are represented on
directional arrows that link pairs of structures.
produce
eat
release
provide nutrients for
3. Function: the role or output of the system. A model’s function is what it is intended to represent when
all the structures and linking behaviors are considered together. For example, a model that has the
function of explaining “nitrification” in an aquarium system might be represented as:
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1. All structures are nouns and are
represented in boxes.
2. Behaviors are active (verbs, short phrases)
and are represented on arrows.
3. Each box is connected with at least one
arrow.
4. Each arrow has a direction.
5. Each “box-arrow-box” group reads as a
complete, coherent statement.
6. The overall model “tells a story” meaning
that all of the structures and behaviors
together illustrate a function of the system.
While system models have potential to facilitate learning and probe student thinking about complex
ideas, it is important to note that in this approach, there may be multiple “right” answers and no single
“perfect” model. For example, how might you apply the rules to improve the model above?
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Guiding Principles for the Use of System Models in Science Instruction TM Long, E Bray Speth, J Momsen, S Wyse October 2011 Putting it all together!
There are many possibilities for how SBF models can be integrated into instruction and assessment from
elementary – college levels. Below, we detail the steps and provide examples of how we typically use
models and modeling in a college-level introductory biology classroom. We encourage you to
experiment, adapt, and improvise – and hope you’ll share your experience with us!
1. Assign a “reading”.
Readings might include chapters from textbooks, excerpts from articles in newspapers, scientific
journals, or other popular media. Contexts for a modeling assignment may also come from variety of
other “non-readable” sources such as podcasts or video-clips, or from personal experiences (e.g.,
classroom assignments, experiments, or everyday occurrences, such as building a PB&J sandwich!)
Example: Consider the following paragraph:
“Nitrogen is the fourth most abundant element in living things, being a major constituent of proteins
and nucleic acids. Vertebrate organisms, including fish, produce and eliminate ammonia (NH3) as a
result of the breakdown of organic sources of nitrogen. Ammonia is toxic to aquatic life at high
concentrations, and in the environment there are bacteria that transform ammonia into less toxic
nitrogen compounds, such as nitrites (NO2-) and nitrates (NO3-). This process is called nitrification.
Two different types of bacteria carry out the nitrification process: Nitrosomonas carry out the first step
of the process, producing nitrite from ammonia. Nitrobacter then converts the resulting nitrite to
nitrate. Nitrate is directly absorbed and used by plants for their growth.”
2. Determine model function.
Students cannot build a system model unless they know the intended purpose or function of the model
(aka, the “F” of SBF). Depending on your specific goals as the instructor, you may choose to (a) provide
students the intended model function, or (b) have students deduce a function from the assigned reading.
Example:
(a) The paragraph above explains how the process of nitrification occurs in an aquarium.
<OR>
(b) Q: What do you think is the intended purpose of the information provided in the above paragraph?
A: To explain how nitrification occurs in an aquarium.
3. Identify relevant system components and construct the model.
In addition to knowing the model’s intended function, students must also think about what components
(“structures” in SBF) will be necessary to build an appropriate model. Again, depending on your goals as
instructor, you may either (a) provide these to your students, or (b) have students derive them from the
reading.
Example:
(a) Construct a system model that illustrates the process of nitrification in the aquarium system
described. Be sure to include the following structures in your final model: fish, ammonia, plants,
Nitrosomonas, Nitrobacter, nitrate, and nitrite. You may use structures more than once and/or
incorporate additional structures if you find it helps you build an accurate model.
<OR>
(b) List the structures you think are important for constructing a system model illustrating the function
you described above. Construct your model by linking structures with appropriate behaviors.
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Guiding Principles for the Use of System Models in Science Instruction TM Long, E Bray Speth, J Momsen, S Wyse October 2011 4. Go Meta! Reflection, feedback and revision.
We feel strongly that a critical component for success of a model-based pedagogy is incorporating
opportunities for students to develop metacognition about their learning with models. Following a
modeling task, we provide opportunities and resources for students to reflect on their models and to think
about revisions that would improve their model’s efficacy. Below, we provide examples for how we might
do this (a) in the context of an in-class assignment where students work with groups and are provided
guiding questions, and (b) when the model serves as an individual assessment on a quiz or exam.
Examples:
(a) Feedback derived from in-class group discussion:
1. In your groups, arrange all your models in a way that everyone can view them. Discuss the
variation you see among the models of different group members. Use these questions to guide your
discussion:
• Did all members use the same model structures? What variation, if any, did you see?
• Did all members use the same model behaviors? How does the language used in model
behaviors vary across different models?
• In this assignment, your model was to have the function of “illustrating the process of nitrification in
an aquarium system.” Does each model accomplish the assigned function? If so, does each
model accomplish it equally well?
• How does model shape vary among different models? Are they linear, or are there loops? How
does model shape influence your interpretation of the system function?
2. Pool all the ideas of your group collectively to construct an “ideal” version of the model. What
characteristics do you see in the “ideal” model that represent improvements over the one you
constructed on your own? List the characteristics that make a model effective.
(b) Feedback provided in form of exam rubric.
Exam item: Construct a box and arrow model that shows the origin of genetic variation at the
CFTR gene and resulting phenotypic variation in expression of cystic fibrosis. Use language in
the structures and behaviors of your model that are specific to this case.
Include the following structures in your model:
gene, allele, DNA, chromosome, protein, phenotype, nucleotide sequence
• 10 pts – Correct model with no biological inaccuracies. Mutation is shown as origin of variation,
resulting in new alleles. Alleles are distinguished from one another by unique nucleotide
sequences. The expression of genetic information (from allele to protein) is represented by
alternative paths resulting in different phenotypes.
• 8-­‐9 pts – Model is essentially correct, but may be lacking some degree of specificity to the
problem or critical connections that characterize a “10”. Alternative paths from allele to protein to
phenotype must be present to illustrate the origin of genetic variation and expression of
phenotypic variation.
• 6-­‐7 pts – Model contains 1 or more errors or omissions of required structures, or is not specific to
case. No representation of alternative paths to illustrate “variation” (e.g., model may converge onto
common protein or phenotype).
• 5 or lower – Significant errors or omissions. Links (behaviors) may lack directionality or words to
describe the nature of the relationship. Organization of genetic information is incorrect for a
significant portion of model.
Recommended Resource:
Hmelo-Silver C, Jordan R, Lui L, Gray S, Demeter M, Rugaber S, Varrtam S, Goel A. 2008. Focusing on
function: Thinking below the surface of complex natural systems. Science Scope 31: 27-35.
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