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World Wide Web Based
Simulations for Teaching Biology
By Jeffrey R. Bell
The Biology Lab On-Line Project is
a component of the California State University System (CSU)
Integrated Technology Strategy (ITS), which calls for
anywhere, anytime access to information. The project
initially brought together biologists from throughout the
CSU system and the CSU Center for Distributed Learning (CDL)
to explore ways to use technology to improve learning in
introductory biology laboratories. Later, multimedia
developers from Addison Wesley Longman were added to the
development team. A major goal of the collaboration was to
allow students to learn as biologists do, i.e., by
actively designing experiments and interpreting their
results. Another goal was to extend student learning
opportunities by creating simulations of experiments that
they might not normally do because of expensive and/or
inaccessible lab equipment, lack of field opportunities,
time constraints, complexity, danger, or ethical problems.
Eliminating the time constraints of the traditional
experiment and two or three hour laboratory period gives
students the opportunity to design and interpret
experiments, learn from their mistakes, and to revise and
redo their experiments just like real scientists. The
simulations are not designed to replace the traditional "wet
labs" found in the normal biology course, but rather are
designed to extend the laboratory experience to subjects and
experiments that can not normally be done, or not done
enough, in a traditional laboratory. The simulations are
also not multi-media presentations, stand-alone
tutorials or on-line courses.
The project has produced five
different educational simulations covering the subjects of
evolution, Mendelian genetics, protein translation, human
population demography, and protein structure-function.
Current projects in progress and due to be finished by the
summer of 1999 will simulate human genetics, mitochondrial
electron transport, glycolysis, human female reproductive
physiology, and photosynthesis. While each of the
simulations is unique, all of them share many common
interface elements and functions. All of the simulations
have been designed so that the student can carry out many
different experiments, allowing the student to design and
interpret their own experiments. The flexibility of the
programs make well designed exercises an important part of
each laboratory. However, while sample exercises will be
included with each lab, instructors can easily design their
own exercises to meet the needs of their students.
The simulations have all been
created in the Java programming language, so that they can
be easily accessed over the web using any standard browser.
This solves the problem of widely disseminating the
applications, a common problem with most educational
software. The Java application provides the user interface
where students set the starting parameters for their
experiment and get graphical feedback on their current
settings. In some of the simulations the Java program also
calculates the results, while in others the input parameters
are passed back to the server, where the real calculations
take place. When the server is done it sends the results
back to the Java application, which presents the results to
the student.
The downside of using Java is that
only individuals and schools with fairly new computers and
software (Netscape 3 or better, etc.) and an internet
connection can use the software. Another disadvantage of
using Java is the inability of Java programs to save to disk
or print. This limitation has been overcome through the use
of a notebook that can be exported to a web page. All of the
data tables, such as numbers of different types of progeny,
or results of statistical calculations, can be imported
directly into the notebook. After typing in their comments
the student can export the notebook to a web page for
printing, or to email to themselves or an instructor. The
web page is temporarily stored on the server. Graphical
images such as graphs and charts produced by some of the
programs are also exportable to the notebook, where they can
then be printed.
All of the programs share some
common user interface elements, including a title bar with
links to an introduction to the lab, help, sample
assignments, the notebook, etc. While there is much
diversity in how the different labs operate, most of them
start in an input mode where the student designs their
experiment by adjusting different parameters. After
designing the experiment the student runs the simulation.
The program calculates the results of the experiment,
usually in a minute or less, and then presents the results
in the output mode. In this mode there is a tabbed interface
where the student chooses which type of output they wish to
view, a table of the data, a graph, the input values, etc.
After analyzing their results they can import them into the
notebook and then go back to the input mode to design
another experiment. This ability to quickly go back and
forth between the design of an experiment and the results is
one of the powerful advantages of a simulation approach to
teaching science.
Five of the programs are currently
available for beta testing and all ten should be finished by
the summer of 1999. Descriptions of each of the labs can be
found below. Current plans call for a $19.95 fee for access
to all ten of the simulations and a lab manual with printed
instructions and sample assignments. The fee is necessary to
support the servers and for maintenance of the various
programs as operating systems and computers change. Below is
a fairly complete description of EvolveIT along with brief
descriptions of the other simulations. However, the best way
to learn about these simulations is to go to the
CDL
site,
http://www.cdl.edu/html/biology.html, and try out some of
the five simulations currently available there.
EvolveIT
Although evolution is the unifying
theme of the biological sciences, it is perhaps one of the
most misunderstood and difficult concepts to convey in a
laboratory setting. The study of evolution is especially
suited to computer simulations because evolution normally
occurs over very long time intervals, large data sets are
usually needed to understand it, and there are usually a
number of important parameters that are difficult to control
in real experiments. EvolveIT (http://www.cdl.edu/EvolveIT), is a web based, interactive computer
simulation designed to teach the basic concepts of natural
selection and to convey the importance of time in the
evolutionary process.
Students using EvolveIT observe
evolutionary changes in bird beak morphology in hypothetical
populations of birds isolated on two islands. In the
simulation students can set the annual rainfall on island(s)
containing finch populations, and then observe the effect of
this environment on the evolution of the finch's beaks.
Students may also change several other properties of the
bird populations, such as initial mean beak size, beak size
variability, beak size heritability and mean clutch size, to
determine their effect on beak evolution.
To help students clearly see the
effects of changes in the different variables, the
simulation uses two islands with independent and isolated
populations. A student can either directly compare two
different sets of conditions, or do a duplicate run where
both populations have identical starting conditions. As many
students will also be unfamiliar with some of the variables,
the program gives extensive feedback on what is being
changed with each alteration of one of the initial
variables. For instance, when the slider for mean beak size
is moved to the right a picture of a finch head shows the
finch beak growing larger, or when variability is increased
a graph of the current distribution of beak sizes spreads
out.
The program creates several hundred
different virtual "birds" using the initial parameters
entered by the student. These birds then go through a round
of natural selection where each bird's probability of
survival is a function of the seed distribution (determined
by the setting for rainfall) and that bird's beak size.
After the selection step the surviving birds are randomly
mated to one another. They then produce offspring based on
the values for heritability and variability entered by the
student. This new population of birds becomes the starting
population for the next year. This repeats for each year of
the simulation. Because of the random selection and mating
each simulation run is unique and will produce a different
result than any other run, even one that starts with exactly
the same starting parameters. The program produces several
different outputs: a scrolling table with the mean beak
size, the variability and the population size for every year
of the simulation, for both populations; a series of
histograms showing what proportion of birds of different
beak sizes survived, for each year of the simulation; a plot
of the mean beak size versus time for both populations; and
a plot of the population size versus time for both
populations. The final output is a table with the initial
values for the simulation.
The student can rerun the
simulation with the same initial values, revise the
experiment, or start over with the default values and design
a new experiment. Students can study the effects of
different amounts of rainfall on the evolution of beak size
to get a feel for how natural selection works. They should
be able to determine that large beaks are favored in low
rainfall, the optimum beak size for different amounts of
rainfall, the effect of varying the severity of the
selection, and the importance of the environment in
determining the direction of selection. Similar experiments
can be done in which only population variability or beak
size heritability is manipulated to study how these
parameters affect beak evolution. Changes in island size
affect the carrying capacity of the island and allow the
student to investigate the stochastic effects that can
result from small population size. Variations in clutch size
permit the student to investigate the consequences of
different fecundities on the capacity of different species
to evolve. Some aspects of population dynamics can also be
investigated using this parameter (rate of exponential
growth, boom bust population cycles, etc.)
While the simulation is based on
Darwin's finches, changes in the species variables such as
mean beak size, variability, heritability and clutch size
create virtual species that can have properties similar to
many other wild species. Students can investigate the
parameters that are more likely to lead to the extinction of
endangered species, see why some species might evolve faster
than others, and examine many other facets of evolution. The
program generates large data sets, one run can produce 600
data points, so students can learn how to analyze and
interpret large amounts of data, unlike the situation in a
typical lab. The great flexibility of the program should
allow individual instructors to tailor student assignments
to their particular preferences and provide students with a
real opportunity to design their own experiments. Actively
engaging students in exploring and studying evolution
through this simulation will provide another avenue for
students to learn about evolution in addition to the
traditional text and lecture explanations.
Virtual Fly Lab
Two genetics labs are currently
planned. One is a simulation of classical fruit fly genetics
while the other one lets the student study human genetics by
analyzing pedigrees. The Virtual
Fly Lab (http://www.cdl.edu/Flylab) simulation is an update to the Virtual Fly
Lab originally created by Bob Desharnais. In the Virtual Fly
Lab students design their own fruit flies by choosing from
many different possible phenotypes for characteristics such
as eye color, wing shape, body color, etc. They then mate
their flies and analyze the progeny to determine the rules
of inheritance for different traits. Each experiment is
unique and students can have up to 10,000 progeny produced
from one mating. Offspring can also be mated so a wide range
of different experiments are possible. There are 29
different traits that can be studied in isolation or in
various combinations so the number of possible experiments
is in the millions. The traits are all represented
graphically so the student can observe the phenotypes
directly. For instance, if the student selects the white eye
mutation for the female parent their picture of the female
parent will change to have white eyes. After the mating they
will get a picture of the different progeny, along with
numbers beside each picture to indicate the number of
progeny of that type (number of females with white eyes,
females with red eyes, etc.) The program includes a Chi
Square calculator for doing statistical tests of the
students hypotheses, and a notebook for recording results,
observations, hypotheses and conclusions. Students can
import the numerical results from their crosses and
statistical tests directly into the notebook.
Using this program students can
discover or study most of the important principles of
Mendelian genetics, including dominant and recessive
alleles, sex-linkage, lethal alleles, independent
assortment, epistasis, linkage, gene order, linkage groups,
and linkage maps. More importantly, students can discover
these principles by doing the same sort of experiments as
the original researchers, only much faster. The program is
appropriate for a wide range of biology courses as the
assignment determines the level of difficulty. Students can
do statistical tests, but this is not required. Students can
do complicated crosses with multiple traits, or simple
crosses with only one trait at a time. If a student is
confused by a complicated cross, they can always do some
additional simpler crosses to try to figure out what is
going on. They can also do additional crosses with the
progeny from their crosses, and their progeny, etc. This
ability to devise their own experiments and try many
different permutations is a major strength of the
FlyLab.
PedigreeLab
PedigreeLab will generate numerous
pedigrees for a particular genetic disease. The student can
examine the pedigrees to determine the inheritance pattern
of the particular disease. In addition, the student will be
able to examine various molecular markers and determine
whether they are linked to the genetic disease. This is a
key process in the current search for human genetic disease
genes and is normally very difficult to explain to students.
Having them actually go through the process should
significantly improve their learning of these difficult
concepts.
TranslateIT
So far, the Biolabs project has
produced two molecular biology simulations. The first,
TranslateIT, http://www.cdl.edu/TranslateIT, simulates some of the original experiments
used to crack the genetic code, one of the key discoveries
in molecular biology. These experiments rely on radioactive
materials and difficult to produce RNA templates so they
can't be done in the normal biology lab. Students design and
create simple RNA molecules in the simulation that they then
translate in a virtual in
vitro translation mix. The
program shows a simple animation of the techniques that
would be used to analyze the products of the translation and
then gives them the amino acid sequence of any proteins
produced in their experiment. The student must logically
analyze the results of multiple experiments to deduce the
properties of the genetic code, just as the original
researchers did, only with the advantage of being able to do
experiments in minutes that normally take months to carry
out. Various properties of the code that can be determined
using this simulation are the triplet nature of the code,
that the code is non-overlapping, codon assignments for
particular amino acids, and the existence and identity of
stop codons.
HemoglobinLab
In the second molecular biology
simulation, the HemoglobinLab, http://www.cdl.edu/HemoglobinLab, students investigate various aspects of
the molecular biology of hemoglobin, using case studies. The
goal is for the student to learn how changes in the
nucleotide sequence of a gene may effect
the protein sequence, which may effect
the structure of the protein, which may effect
the function of the protein, which may effect
the properties of the cell, which may in turn
effect the physiology of the individual. Students choose a
case by selecting a patient from a pull down menu with a
list of over a dozen patients. For each case the students
can examine the doctors notes about the symptoms and medical
history of the patient, examine the color of a vial of the
patients blood, examine the blood under a microscope to see
if there are changes in the red blood cells, run a sample of
the blood on an electrophoresis gel to determine if there
are physical changes in the globin protein, and, finally,
the student can determine the amino acid sequence of the
patients globin protein. Having determined the sequence of
the protein the student can go to the DNA sequence editor
and try to alter the DNA sequence of the normal gene to see
what type of DNA mutation would cause the changes found in
the patient they are examining. The patients have a variety
of mutations in the globin gene ranging from simple point
mutations that change one amino acid, such as in sickle cell
anemia, to deletions and insertions causing frameshifts,
such as some of the thallasemias. The mutations cause many
different patient phenotypes, such as anemia, brown blood,
polycythemia (too many red blood cells), and purple skin
color.
DemographyLab
The DemographyLab, http://caldera.calstatela.edu/DemoLab, models human population growth in several
different countries around the world. Students can use this
lab to investigate how differences in population size,
age-structure, and age-specific fertility and mortality
rates affect human population growth. Default values for
seven countries have been incorporated into the program to
allow comparisons between nations with very different
demographics, such as Japan and Nigeria. In addition,
students can change any of the parameters to create their
own experiments. The proportion of males and females in each
five year age group, the total population size, the
mortality rate for males and females in each five year age
group and the birth rate per female in each five year age
group can all be set by the student using a simple graphical
interface. After running the simulation for 100, 200 or 300
years, students get summary statistics for the population at
the end of the time interval, such as life expectancy, birth
rate, population growth rate, etc. They can view a line
graph of population numbers over the course of their
experiment, see a graphical representation of the population
structure for every five years of the experiment, or examine
the number of males and females in each age group for each
five year period. Using the program a variety of demographic
phenomena can be demonstrated, such as exponential growth
and decline, stable age structure, zero population growth,
demographic momentum, dependency ratios, sex ratios and
marriage squeezes.
MitochondriaLab
Three biochemistry and cell biology
labs currently in development are MitochondriaLab,
GlycolysisLab, and PlantLab. MitochondriaLab will simulate
electron transport, proton gradients and oxidative
phosphorylation in mitochondria. Students will be able to
recreate the classic experiments that established the
chemiosmotic theory as the mechanism for energy production
in the cell. They will add various substrates and inhibitors
to their virtual mitochondrial extracts and then measure the
consumption of oxygen over time. From their results they can
work out some of the steps in the pathway and the mechanism
by which the chemical energy is converted into ATP
molecules.
GlycolysisLab
In GlycolysisLab students will
study the enzymatic reactions of the glycolysis pathway and
the kinetics of biochemical reactions by varying quantities
of substrates and cofactors and then measuring reaction
rates.
PlantLab
The PlantLab will simulate the
photosynthetic reactions in leaves. Students will vary
wavelength and intensity of light, CO2 and
oxygen concentrations, temperature, etc. and then measure
the consumption of CO2 and the
production of sugar in their simulated leaves.
ReproductionLab
The tenth and last lab currently
under development is ReproductionLab. This lab will simulate
the human female reproductive cycle. Students will be able
to inject various hormones, alter diet and exercise, and
remove organs in their virtual subjects and then can track
hormonal changes and various physiological responses over
time. Student experiments should lead to a greater
understanding of hormone action, positive and negative
feedback loops, homeostasis, reproductive cycles and
physiological pathways. Understanding this physiological
cycle is obviously of great importance to the students and
will also teach them many important physiological
concepts.
Assessment
The precursor to all of these labs
is the original virtual Fly Lab. This simulation of fruit
fly genetics is now used in biology classes all over the
world, and has created so much demand on the server hosting
the program that there are now five different mirror
servers. The Virtual Fly Lab, EvolveIT and TranslateIT have
been field tested in an upper division genetics course with
encouraging results. 98% of the students in this course
considered their Virtual Fly assignments useful in learning
genetics, 83% found EvolveIt to be useful and 93% found
TranslateIt useful. Some sample comments from the students
are:
"Excellent 3 part demonstration of
Mendelian genetics - each lesson built on the previous one -
excellent practice for the tests. Also includes repetition
of important concepts (X linkage, etc.)"
"Liked best - actually enjoyed!
(what a concept) Virtual Fly I, II, and III. These were
great fun to puzzle out - someone's going to hate me for
saying this"
"TranslateIt was enjoyable because
it requires the student to investigate and solve the
problem."
"Virtual Fly and TranslateIt were
the assignments I got the most out of. I liked the way it
made you systematically think to solve the problems."
"I liked the Virtual fly and
EvolveIt activities because they allowed you to do some
investigation on your own and they made you think about what
was really happening, which made you understand the material
better."
There were only a few negative
comments, usually having to do with the difficulty of
getting on-line and using the programs. Students who are
uncomfortable with computers are at a disadvantage when
using these simulations and special care must be taken to
make sure they get the most out of the simulations. The only
other negative comment was, "I liked TranslateIt the least
because it made my head hurt." While this is unfortunate, if
the BioLabs project can produce more simulations that cause
some students heads to hurt, then the project will be
producing simulations that change, for the better, the way
biology is taught.
Acknowledgements: The
following individuals contributed to the development of
these simulations, their contributions are gratefully
acknowledged: Bob Desharnais, Steve Wolf, Zed Mason, Ron
Quinn, Terry Frey, David Hanes, Judith Kandel, Nancy Smith,
Sally Veregge, Abbe Barker, Michelle LaMar, Chuck
Schneebeck, Rachel Smith, Lou Zweier, Scott Anderson, Peilin
Nee and Anne Scanlan-Rohrer. Partial support was provided by
U.S. National Science Foundation grant DUE 9455428 to Bob
Desharnais.
This document is maintained by:
Jeffrey R. Bell
Last Update: Thursday, October 29,
1998
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