GENERAL INSTRUCTIONS
All of the sims reviewed here can be found on http://phet.colorado.edu/ (click "play with sims"). There are two ways to find biology-related simulations: go to the "biology" tab (http://phet.colorado.edu/en/simulations/category/biology), or type in "biology" in the search bar. There are a few bio-related sims that aren't sorted into the bio tab, for some reason, so I would recommend searching as well to see if the site has what you're looking for.
All of the sims reviewed here can be found on http://phet.colorado.edu/ (click "play with sims"). There are two ways to find biology-related simulations: go to the "biology" tab (http://phet.colorado.edu/en/simulations/category/biology), or type in "biology" in the search bar. There are a few bio-related sims that aren't sorted into the bio tab, for some reason, so I would recommend searching as well to see if the site has what you're looking for.
CRITERIA
Level 1: A sim that provides little in the way of user interactivity, and simplifies the biological processes that it simulates. Good as an introduction to a given topic, but cannot sustain more than five minutes of meaningful student work due to a lack of interactivity.
Level 1: A sim that provides little in the way of user interactivity, and simplifies the biological processes that it simulates. Good as an introduction to a given topic, but cannot sustain more than five minutes of meaningful student work due to a lack of interactivity.
Level 2: Simulates a given biological process with more detail and accuracy, but still lacks interactivity. Helps students visualize scientific phenomena, but gives them no way to engage in investigation or experimentation.
Level 3: A complex simulation that can be changed in many ways by the user, allowing for experimentation and user-created scenarios. These sims can be used as the focal points of inquiry-based lessons.
THE SIMULATIONS
Gene Expression Sim
Level 2
Overview: The simulation is centered around a strand of DNA. In a window, the user has a selection of proteins and enzymes involved in transcription and translation: positive and negative transcription factors, RNA polymerase, ribosomes, et cetera. If you drag any of these pieces to their proper place in the simulation, they will start carrying out their function-- for example, RNA polymerase will create RNA, and ribosomes will read any RNA strands and create proteins. The enzymes will continue to carry out their function until the simulation is stopped.
There are three different proteins that can be created using different combinations of transcription factors; these are represented by different geometric shapes. When these are created, students can drag them to a bank in the upper right corner of the screen. The simulation is "over" when all three are created, although transcription processes will continue.
Role in a lesson: While this simulation provides a useful visualization of the transcription process, it has very limited interactivity and could not sustain more than 10 minutes of meaningful student work. It is unlikely that a student starting a transcription unit could understand what processes the model is demonstrating, and understanding the role of the individual parts would require more in-depth activities and exploration than the model can offer.
Therefore, the best place for this model is near the end of an expression-focused lesson or unit. Once students are able to explain the role of molecules like transcription factors and ribosomes without prompting, the model could be used to help them tie these individual parts together into a larger system.
Natural Selection Sim
http://phet.colorado.edu/en/simulation/natural-selection
Level 3
Natural Selection Sim
http://phet.colorado.edu/en/simulation/natural-selection
Level 3
Overview: A complex model with a wide range of options. In the simulation is a rabbit on a plain environment. After adding another rabbit, the population will start expanding whenever the "new generation" timer reaches 0. During each generation, limiting factors will also appear-- either wolves, which eat rabbits that don't blend in with the environment, or food scarcity, which starves out rabbits with shorter teeth. The environment can also be changed between a prairie (brown rabbits blend in) and a tundra (white rabbits blend in).
The real complexity occurs with the mutations. At any point, the user can introduce a mutation to the rabbit population-- long teeth, or brown fur (vs. white). These mutations can be set as either recessive or dominant, affecting their rate of inheritance. Depending on the limiting factors and environment chosen, rabbits with certain mutations will be more likely to survive and bear offspring, increasing the prevalence of beneficial mutations in the population.
A plot of prevalence vs. time ticks across the bottom of the screen, showing how the representation of certain phenotypes changes over time. You can also click on an individual rabbit to see a "family tree" of its ancestors, including their phenotypes and whether or not they are still alive.
Role in a Lesson: This simulation is complex and accurate enough to be the center of a lesson's Explore portion! Students could work in groups or pairs in a computer lab, with the sim installed on each machine. After giving them ~5 minutes to experiment with it freely, the students would have a list of scenarios to test out; for example, what happens if the environment turns snowy when the brown rabbit population is high? What if both favorable mutations are recessive? After testing these scenarios, they would explain what happened and what aspects of natural selection and heredity caused it to happen. These answers could be shared by the groups during an open class discussion later in the lesson.
If time permits, the groups could also be tasked with coming up with their own scenario, theorizing what will happen, testing it, and explaining if, how and why the results differed from their prediction. The ease of creating a unique situation to investigate makes this simulation excellent for open-ended student inquiry.
Neuron Action Potential Sim
Level 2
Overview: The sim shows us a "slice"
of the axon of the neuron. The relevant neuronal ions and membrane
channels are present in the sim-space, and a key on the side of the
screen identifies them. You can adjust the sim's speed and
magnification.
Pressing the "stimulate neuron"
button sends an action potential down the axon to your "slice;"
gated channels open, Na+ flows in, K+ flows out, and the leak
channels reestablish equilibrium. Radio boxes on the side of the sim
give you options for a more in-depth view of the action potential: a
chart that plots membrane potential vs. time, a display of the
charges on the sides of each channel, and the molarity of the inner
and outer-membrane solutions. True to biology, the axon can only be
fired again after its refractory period has ended.
Role in a Lesson: While this sim is
scientifically accurate and very detailed, its interactivity is
limited to pressing the "stimulate neuron" button. There
are no experimental variables that can be changed within the sim, so
investigation is impossible. However, the complexity with which it
displays the action potential would make it inappropriate for an
"engage"-level task; students would need some understanding
of the subject matter to make sense of it.
A Level 2 sim like this one would work
best as a supplement for a more involved Explore exercise. It would
fit best at the beginning of the second day of a two-day lesson, as a
way to assess students' understanding of the previous day's material.
Students could fill out worksheets asking for the "what" of
certain phenomena-- "what happens to the membrane potential
after depolarization ends?"-- as well as the "why"--
"why is this refractory period necessary?"
Membrane Channel Sim
Level 3
Overview: The sim presents a square
space divided by an impermeable membrane. On either side of this
membrane are pumps that can be used to inject "molecules"
of solution into the sim space: green triangles, or blue squares. A
key on the right side of the screen contains four types of channels:
two "leak" channels for green triangles and blue squares,
respectively, and two gated versions of the same channels. A toggle
allows the user to open and close these gated channels.
The sim provides a surprisingly
in-depth recreation of membrane flow. Molecules ricochet randomly in
the sim space, and only pass through a channel if they collide with
it. Collisions become more common and energetically favorable if the
molecule is travelling from an area of high to low concentration. The
sim also shows how membrane flow works in a system with multiple
solutes, permeable to different membranes. You can also adjust the
speed of the sim.
Role in a Lesson: This is a level 3
sim: detailed, malleable, and open to experimentation and
investigation. A sim like this would be excellent for the explore
portion of a lesson introducing students to membrane channels; its
user interface is simple and intuitive, but the mechanics of fluids
and membranes aren't grossly simplified, as you see in many other
sims.
It would work well as the "day
one" exercise of the two-day lesson proposed in my review of the
Action Potential sim. Students would be given a list of scenarios to
test in the sim; after doing so, they would describe what happened,
and explain which of the fundamental principles of cross-membrane
flow caused it to happen. The model also contains all the necessary
parts to simulate action potential membrane flow. After going over
action potentials, you could have students come back to the sim and
use it to reconstruct the inner membrane of a axon. then have them
demonstrate how their model represents the firing of a neuron.
Eating and Exercise Sim
Level 3
Overview: A very intricate sim; so
intricate, in fact, that at first it's a bit difficult to see what is
being simulated. After setting parameters for a human being (height,
weight, gender, daily activity, etc.), you determine what they eat
and how much they exercise each day by dragging icons representing
foods and strenuous activities onto a plate and a "fitness log,"
respectively.
When you activate the sim, it plots,
over the course of several years, their weight, calories consumed,
and calories burned, under the assumption that they're doing these
activities every day. For instance, if you drag two pieces of pizza
onto the plate and "15 minutes of biking" onto the fitness
log, they will eat two slices of pizza and bike for 15 minutes each
day, and their weight over time reflects their habits. From what I
understand, the goal of this game is to get the individual's diet and
habits into a healthy equilibrium for their body type. This isn't
clear at first, however, due to the sim's unintuitive interface,
which sacrifices legibility and ease-of-use for a misguided attempt
at "kid-friendly" graphical representation.
Role in a Lesson: This is a level 3
simulation, in that it provides a complex representation of a real
phenomena and has enough options to allow for investigation and
experimentation. However, unlike the other level 3 sims reviewed, the
complexity of this sim presents an obstacle against classroom use.
Dragging random clipart images onto a haphazard stack is not
intuitive interface design, and there's no indication that these
items are the "daily diet--" confused students might try to
continuously drag foods onto the plate, assuming that their human
needs something new to eat every day. Using this lesson would require
a significant amount of class time devoted to simply explaining how
the sim works, and much more time after the fact clearing up
misconceptions and nonsensical results acquired from using the sim
incorrectly.
Were you to use this sim in a
classroom, it would preferably be with a more advanced class; it
would be appropriate as an activity for AP Biology students, or 9th
grade Biology students in a class with a less urgent schedule. I'm
hesitant to recommend the usual approach for inquiry-based teaching
with a simulator-- give the students scenarios to set up and test,
have them make sense of the results and devise their own
experiments-- because the simulator only represents weight, not other
aspects of human health. If you ask students to devise an effective
weight loss regime, for example, the easiest way to do so with this
sim is just to eliminate food and increase exercise until weight
reaches the desired level-- even though that would be devastating for
a normal human being. Lastly, the sim allows for an absurd situation
where the human subject starves to death by reaching a weight of 0
lbs.
All in all, I would recommend against
using this sim in a classroom.
Color Vision Sim
Level 1
Overview: The sim has two "tabs:"
one with a set of three lights (red, green and blue), one with a
single light that can shine white (multi-wavelength) or monochromatic
colored light. These lights are shined into the eye of a cartoon
character; a thought bubble over his head shows the color that he is
currently perceiving.
The purpose of the first tab is to show
the user the way multiple colors of light interact. This is different
from the way paint colors interact, which is often taught in
elementary school; red and green light combine to make yellow, for
example. The other tab has a screen between the light and the man's
eye; the viewer can adjust the color of the screen, allowing only
photons of the same color wavelength to pass through. The color of
the light can be adjusted to show how this isn't a binary
relationship; a cyan light and a cyan screen of slightly different
hues will still allow a few photons to pass through into the man's
eye.
Role in a Lesson: This is a fairly
simple sim; a potential user could see everything it has to offer
within about five minutes of experimentation. One might say that the
material it covers is too rudimentary for a middle school or high
school science lesson, but in my experiences, even 9th
grade biology students can have misconceptions about how colored
lights combine or how the eye parses light. A sim like this would
help such students understand that the eye absorbs light without
"releasing" it (a surprisingly common misconception), and
visualising light as a continuous stream of particles with unique
wavelengths.
Because of its brevity and simplicity,
this lesson would be best as the Engage of a more involved lesson on
the eye, giving students a foundation of information before getting
into the specifics of vision. It would also work well in a physics
class; it's one of the simulations listed on PhET's website as
"biology" that straddles multiple fields of science.
Lac Operon Sim
Level 2
Overview: Like the protein expression
sim, this one models the mechanism by which the lacI and lacZ operons
go from genome to protein, and the way they interact with lactose
molecules. The user has a bar filled with transcription and
translation enzymes on the bottom of the screen, which they can drag
into the sim space to enact their various functions-- promoters
trigger transcription, the operons bind lactose, et cetera. Unlike
the other sim, this deals with material that students won't be
getting into until AP Biology.
Role in a Lesson: This too is a level 2
sim: it provides a detailed model of its content, but it lacks the
interactivity required for investigation or experimentation. However,
the material it covers is much more in-depth than the other sim.
Exactly what is going on during the sim is also less
self-explanatory; some context is required to make sense of its
results.
Because you would be using a sim like
this in an AP Biology class, the students would hopefully be able to
understand that context. This sim would best be used to demonstrate
operon functions after students had gone through lessons on
transcription, translation, promoters and the like. The teacher could
lead the students in going through the steps of the simulation, and
task them with explaining the details of the different processes
involved.
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