Evolution in Motion
Doug Fraser - Biology Nut
Matthew Allen
- Computer Nerd
· Graphing
· Glossary
Students can directly monitor the "gene values" of
the rover individuals and populations, gather data, and plot their reproductive
successes. In the Antibiotic Resistance simulation, students control the
exposure of the rover population to antibiotics and have the opportunity to
directly influence their evolutionary path.
The Evolution in Motion program does not predetermine the evolution of rovers in any way. The process is purely Darwinian - populations of genetically variable individuals live out their lives in a virtual environment. There is competition for limited food resources, and those individuals that happen to be better adapted to the environment are more successful, reproduce, and pass on their genes to the next generation.
Rover Biology
THE ENVIRONMENT
The virtual environment of Evolution in Motion consists of a large screen space containing food items. The screen space measures 120 by 75 positions. Each white dot represents a food item with a particular energy value. Rovers feed by moving around in the screen space and "eating" the food items they contact.
Food At the beginning of each simulation run, the program randomly drops 1000 food items into the environment. As the simulation continues, food items are steadily added and positioned at random within the environment (see Islands below). Each food item has an energy value of 45 units. Rovers accumulate energy as they obtain food.
Islands In the Speciation simulations the environment contains one (Darwin) or two (Darwin and Wallace) "islands." The environment of islands differs from that of the open space. These are very energy-rich environments in which the food drop-in rate is much higher than in the open space. Rovers that move onto islands have an opportunity to feed in this food-rich environment. In the One Island version, Darwin Island is located in the upper-left corner of the screen. In the Two Island version, the student has the option of placing Wallace Island anywhere on the screen.
Antibiotics In the Antibiotic Resistance simulation, the student can add low or high doses of antibiotic to the environment. These antibiotics are toxic to the rovers. When a rover hits a red dot of antibiotic it loses energy. The more dots it hits the more energy it loses (see Antibiotic Resistance Gene under Motion and Genes below). Each time the student clicks on a "dose" button the program randomly drops a predetermined dose of red antibiotic dots into the environment.
ROVERS
Rovers are digital organisms that live, reproduce, evolve, and struggle for survival in the virtual environments of Evolution in Motion. Their ability to survive and reproduce is directly influenced by their genetic makeup - their genes - as well as the environment in which they live. They are subject to the two primary mechanisms of evolution: genetic mutation and natural selection.
Energy, Feeding and Age The rovers move around the screen one move at a time. The age of a rover is the total number of moves it has made. Each move requires a single unit of energy. When rovers contact a food item, they obtain 45 units of energy - enough for 45 additional moves. An individual rover's energy reserves become depleted if it cannot obtain food frequently enough to meet its energy demands. When rovers run low on energy, they stop moving and die. If they successfully obtain large amounts of energy, they may have the opportunity to reproduce (See Reproduction and Mutation below).
Motion and Genes Rovers are able to move around the screen in a number of ways. During each cycle of the program, each rover makes one move. With each move, a rover has to choose from one of six different possible moves. The choices of moves are
Forward: the rover continues to move in the same direction that it did the previous move.
Spin Right: the rover moves in the same general direction it did the previous move but with a turn to the right.
Spin Left: the rover moves in the same general direction it did the previous move but with a turn to the left.
Flip Flop: the rover simply turns around and moves back to its immediately previous position.
Loop Right: the rover makes a sharp turn and steps to the right.
Loop Left: the rover makes a sharp turn and steps to the left.
Genes control the choice of moves that a rover makes. A different gene influences each choice. The gene value determines how influential any particular gene is. For example, if the forward gene value for a particular rover is 40%, then that particular rover will choose to move forward, on average, 40% of the time. Similarly, if the value of the flip-flop gene is only 5%, then on any given move the probability that the rover will flip flop is only 5%. Note that gene values only influence the probability of a particular move choice; they do not determine the movement. For example, a rover with a spin-right gene value of 10% would choose to make this move 10% of the time; however, it might spin right twice in a row and then not spin right for the next 20 moves. Out of 1000 moves, you would expect the rover to have chosen spin right about 100 times.
In the Antibiotic Resistance simulation, rovers have an additional antibiotic resistance gene that influences their resistance to antibiotics in the environment. This gene can provide them with a range of resistance from no resistance (a gene value of 0%) to complete resistance (a gene value of 100%). When a rover contacts an antibiotic red dot, it loses a set amount of energy. However, the greater the rover's antibiotic resistance, the less likely it is to lose this energy. With 100% resistance, a rover would never lose energy from contact with antibiotics, while at 50% resistance, the average energy loss would be half that of a rover with no resistance.
Reproduction and Mutation Rovers reproduce asexually, passing on their gene values to the next generation. Rovers must be at least 800 moves old before they are able to reproduce. After they have reached or passed the age of 800, they can and do reproduce as soon as they have accumulated 1000 units of energy. When they reproduce, they undergo fission, producing two new daughter rovers. The age of the two new rovers is one, and their energy reserves drop to one-half that of the parent rover. Each daughter rover inherits the gene values of the parent rover; however, each time a reproduction event takes place, there is a probability that a mutation will occur.
In Evolution in Motion, the chance that any individual daughter rover will have a mutation is 50%. When a daughter rover is first formed, the computer program "flips a coin" to determine whether or not the new rover will have a mutation. If the daughter rover is to experience a mutation the program then randomly chooses one of the six genes and then (at random) either increases or decreases the value of that gene. The values of the remaining genes are then adjusted accordingly.
Mutation Example A rover with gene values F 12%, SR 10%, SL 48%, FF 11%, LR 3%, and LF 16% reproduces. One of the daughter cells does not mutate and inherits the identical genome. The other daughter does mutate, and the computer program randomly selects the spin-left gene (SL) and decreases its value by 30%. The new value for the spin-left gene is 18% and each of the other gene values are increased by 6%. The genome for this new daughter rover is F 18%, SR 16%, SL 18%, FF 17%, LR 9%, LF 22%.
Note: the mutation of the antibiotic resistance gene does not affect either the motion of the rovers or the value of any other gene. When rovers reproduce in the Antibiotic Resistance simulation the value of this gene simply mutates up or down (at random) in 50% of the new daughter rovers.
Species and Crawlers Rovers do not reproduce sexually; therefore they cannot be classified as different species using the standard biological definition of a species as reproductively isolated populations. Instead, as modern biologists do with strains of bacteria and other asexual organisms, species are recognized and classified based on a set of distinct characteristics. The Evolution in Motion program defines a species as a population of individuals that share a gene value of 50% or more for any particular pattern of motion. So, for example all those individuals that have a forward gene value of 50% or more are classified as Prowlers while all those that have a flip-flop gene value of 50% or more are classified as Shakers. Note that no distinction is made between rovers based on the direction of their spin. For example, rovers that spin left over 50% of the time are placed in the same species (Gizmos) as those that spin right over 50% of the time. After viewing examples of these species in action, students might want to consider whether or not they think these rovers should be classified as different species or if they should remain subspecies.
|
Species |
Colour |
Gene Value |
|
Prowlers |
yellow |
forward gene value
50%+ |
|
Gizmos |
red |
Spin-right (or
spin-left) gene value 50%+ |
|
Shakers |
blue |
flip-flop gene
value 50%+ |
|
Quirks |
purple |
loop-right (or
loop-left) gene value 50%+ |
Note: Drifters (coloured green) have not been placed in a species category, as they do not represent a population with consistent shared characteristics. For example one Drifter could have gene values of F 40%, SR 20%, SL 30%, FF 0%, LR 0%, LF 0% while another Drifter could have very different values of F 0%, SR 0%, SL 0%, FF 2%, LR 48, LF 48%. Obviously it would be very misleading to present these two rovers as belonging to the same species.
DISPLAY SPECIES
The motions of Drifters and the four species of rovers can be viewed by selecting Display Species from the main menu. Note that the Display Species mode is intended only to illustrate the influence of gene values on the motion of rovers. No environmental parameters are monitored: rovers do not feed, age, die, or reproduce. When in the Display Species mode, students should change the All Rovers in the selection window to Individual. The student can temporarily slow down or stop the motion and then select a rover by clicking directly on that individual. The gene values, age, and energy level of that particular individual are then displayed.
Running a Simulation
Evolution in Motion permits students to simulate three different evolutionary scenarios. The simulations include: Cumulative Selection, in which an initial population evolves in a single, large environment; Speciation in which an initial population evolves in a variable environment; and Antibiotic Resistance, in which an initial population evolves in the presence or absence of antibiotics. In each case, students are able to monitor and document the evolutionary history of the population and witness natural selection in action. In both the Speciation and Antibiotic Resistance simulations, the students are able to influence the environmental conditions and thereby influence the course of evolution.
CUMULATIVE SELECTION
The
purpose of this simulation is to observe, record, and assess the effects of
random mutation and natural selection. The simulation begins with an initial
population of Drifters living within a large environment. The gene values for
the initial population are uniform, with each gene having an equal value - no
one motion is more likely to occur than any other. As the population moves,
feeds, ages, dies, and reproduces, changes in the population gene values may be
observed. Some changes may be the result of genetic drift, while others may be due
to the forces of natural selection.
Cumulative selection results when many small mutational changes result in a gradual but dramatic change in the genetic makeup and observed characteristics of a population. In this simulation cumulative selection typically results in the evolution of the initial Crawler population into that of a specialized species.
Cumulative Selection Default Values
Initial population size: 10 Drifters
Initial amount of food: 1200
Food value added: approximately 10 energy units per cycle
Initial gene values: 16.7% (all genes)
Note: Clicking the Main Menu button ends the simulation run.
SPECIATION
The purpose of this simulation is to observe, record, and assess the effects of evolution in a patchy environment. The varied nature of the environment can result in disruptive selection and may lead to the evolution of two or more species. In this simulation, one (Darwin) or two (Darwin and Wallace) islands are positioned on the screen within the large open environment. These islands are small but are very rich in food, each having a much greater energy supply than the entire large screen environment. Note that there is limited room on each island, and spaces already occupied with food cannot receive additional food.
When students select "Darwin Island" from the pop-up window, Darwin Island will appear in the upper-left portion of the screen and will rapidly become filled with coloured food. Rovers that move onto the island will obtain large energy supplies, but they have no way of controlling their motion other than by the effects of the inherited gene values. In other words, no matter how beneficial the environment, rovers have no mechanism for directing their motion or their evolution.
When students select "Darwin and Wallace Islands" from the pop-up window, an orange rectangle and cursor arrow will appear in the screen. The student has the option of placing Wallace Island anywhere on the screen by moving the cursor and left clicking the mouse. With the option of positioning Wallace Island anywhere on the screen, students can compare and contrast evolution on two remote islands instead of two neighbouring islands. The Founder effect and genetic drift may result in a variety of outcomes and the evolution of two, three, or more species within even a single simulation run.
Speciation Default Values
Initial population size: 10 Drifters
Initial amount of food: 1200
Food value added: approximately 10 energy units per cycle (full screen environment)
Initial gene values: 16.7% (all genes)
Note: Clicking the Main Menu button ends the simulation run.
Darwin Island
Size: 14 ´ 14
Initial amount of food: a small fraction of the initial 1200
Food value added: approximately 40 energy units per cycle
Location: Fixed upper left corner of screen.
Wallace Island
Size: 24 ´ 10
Initial amount of food: a small fraction of the initial 1200
Food value added: approximately 40 energy units per cycle
Location:
user defined.
Evolution in Motion is purely Darwinian having no preprogrammed outcomes. It is therefore highly recommended that the student run these simulations a number of times to see if evolutionary "history repeats itself."
ANTIBIOTIC RESISTANCE
The purpose of this simulation is to model the evolution of antibiotic resistance in bacteria. In this case, the model uses a population of Prowlers that have been given an additional gene, one that influences its resistance to antibiotics (See Rover (above)). The environment is rich in food supply and is able to support a relatively large population of Prowlers.
Simulating the evolution of antibiotic resistance requires the program to model both the benefits and the costs of resistance. When bacteria encounter antibiotics in nature, they often suffer damage caused by interference with a metabolic pathway. Evolution in Motion models this damage by having the rover experience a loss in energy. This loss is set at 75 units of energy, but is subject to a rover's degree of antibiotic resistance. In nature, resistance to antibiotics is usually the result of the synthesis of a unique protein product. The protein is able to prevent the damage normally associated with coming in contact with a particular antibiotic molecule. The synthesis of such a protein requires both cellular resource and energy. Similarly, in Evolution in Motion, antibiotic resistance is not entirely beneficial. Each time a Prowler moves, it must expend a set amount of energy to maintain its current level of resistance. The greater the gene value, the greater the resistance, but also the greater the energy cost per move. For example, with an antibiotic resistance of 50%, the cost of each move increases by 15% (from 1 to 1.15 units of energy). Rovers with 100% resistance expend 30% more energy with each move (1.3 units per move) than rovers with no resistance.
After selecting the Antibiotic Resistance
simulation, the student simply clicks on the "low dose" or "high dose"
antibiotic buttons. Each time a button is clicked, a number of red dots are
placed at random within the environment. When Prowlers contact these antibiotic
dots, they lose energy: the amount of energy lost depends on their genetic
resistance. The less resistance they have, the more energy they lose. If they
survive an accumulate energy, the Prowlers can and will reproduce, at which
time their antibiotic resistance gene may mutate.
Students can vary the dose rate to explore the relationships between the presence of and the concentration of antibiotic in the environment and the evolution of antibiotic resistance in the population. In addition, students should examine the long-term selective pressure and evolution that results after antibiotics are no longer added to the environment. Note that, in this simulation, the motion genes of the Prowlers are set and do not mutate. This has no significant effect on the population, as their motion is well adapted to the open environment.
Antibiotic Resistance Default Values
Initial population: 30 Prowlers
Initial amount of food: 300
Food value added: approximately 30 energy units per cycle
Initial motion gene values: Forward 85%, all others 3%. (no mutations)
Initial antibiotic resistance gene values: 5% (all Prowlers)
Antibiotic cost: 75 units (on contact)
low dose: 250 antibiotic particles
high dose: 1000 antibiotic particles
Antibiotic Resistance benefit: reduces antibiotic injury (reduction determined by the gene's value)
Antibiotic Resistance cost: maximum 30%
Note: Clicking the Main Menu button ends the simulation run.
Screen Display Options
MAIN MENU
The Main Menu permits the user to choose from instructions, running one of three simulations or displaying the motion of rover species.
To begin Evolution in Motion, click on one of the choices and press "RUN." The quit the program, return to the Main Menu and press "EXIT."
SIMULATION SCREEN
When running a simulation, a number of displays and options are accessible as follows:
Toolbar
Main Menu: click to return to the Main Menu.
Refresh: click to redraw the screen. This is used to redisplay the food items after the screen has been shrunk or temporarily hidden from view. Note that it is not necessary to refresh the screen in order for the program to function properly. Refreshing the screen during a simulation is used to redraw the screen for the benefit of the user.
Graph: clicking on this button opens a graph window that displays changes in each species population size since the beginning of a simulation run. The program continues to run while viewing the graph. For more information on graphing, including updating the graph, refer to Graphing (below).
Help: opens the help text window containing this User Manual.
Rover Selection Window (default "All Rovers")
This window is used to select and monitor the gene values and/or age and energy levels of rover species or individuals.
All Rovers: displays the average gene values of all rovers. Does not display age or energy data.
Individual: used to display the gene values, age, and energy level of a selected rover. To select an individual rover, set the speed to 0 and then click directly on the rover of interest: it will be highlighted in light blue. After the rover has been selected, the speed can be altered and the program can run normally.
Prowlers (Gizmos, Shakers, or Quirks): use the arrows to select a particular rover species. Once selected, the program displays the average gene values for all individuals of that species. It does not display age or energy data.
Gene, Age and Energy
Values
When "All Rovers" or a species is selected in the Rover Selection Window, the average values of each gene are displayed, but no age or energy data are shown. If an individual rover is currently selected, these windows display the specific gene, age, and energy values of the individual. If the selected rover dies, the displays go blank. If the selected rover reproduces, the values for one of the daughter rovers are displayed.
Hint: when new species are starting to evolve, their presence can often be detected by monitoring the average gene values for ALL rovers while the program is running in Turbo mode (see below).
Generations
This window monitors the number of complete generations that have passed. The generation counter changes during a simulation with the first reproduction event. Following the first reproduction event, the counter adds 1 to the generation count after every 1000 cycles.
Monitoring the generation display is an excellent way to objectively judge the relative amount of time (and evolutionary history) that has elapsed. When running Evolution in Motion on computers with wide-ranging CPU speeds, the generation count can be used as a basis for fair comparison between different machines. Regardless of machine, speed generation counts are equivalent!
Turbo On/Off
The turbo mode can be used to increase dramatically the speed of the program. This is accomplished by temporarily suspending the screen display. On turbo mode, the speed of the rovers is a blur and thus the display only slows down the program and acts as a distraction. While in turbo mode all other components of the program function normally. Students can use the turbo mode to enhance the evolution rate while still monitoring the numbers of individual species as well as gene values.
The turbo mode does not operate when the rover speed is set to 0. To return to the normal mode simply click "Turbo Off." It is particularly useful to use the turbo mode when examining long-term trends in species numbers, the evolution of species on islands, and/or for completing multiple trials of a given simulation.
Rover Speed (window/scroll bar)
The Rover Speed window displays a value along a scale from 0-1000. This speed can be adjusted using the scroll bar under the window. Adjusting the speed may be necessary to slow down the motion of the rovers to examine more easily their movement patterns or to stop the rovers for the purpose of selecting an individual rover (See Rover Selection Window above).
Computers may vary considerably in their CPU speed and therefore the Rover Speed window values cannot be used to compare simulation times on different computer platforms. However, generation values (as collected in graphing data) are consistent across platforms and can be used to directly compare the simulation runs on different computers.
Rover Numbers
The number of each species of rover, as well as the number of Drifters and the total number of rovers, is displayed and continuously updated on the simulation screen.
Hint: The evolution of new species can often be detected by monitoring rover species numbers while running the program in turbo mode.
DROP ANTIBIOTICS (LOW
DOSE/HIGH DOSE)
When conducting an antibiotic resistance simulation, the user can alter the environment by adding antibiotics using the Low and High dose buttons. When the user clicks one of these buttons, a predetermined dose of red antibiotic dots are placed at random within the environment.
Default settings: low dose: 250; high dose: 1000
Reminder: When conducting an antibiotic resistance simulation, only Prowlers are present.
Graphing
Evolution in Motion provides two methods of graphing. From the toolbar, the user can click the graph button. The program then displays a graph of the simulation run and also simultaneously creates (or updates) data files that are placed on the desktop.
These files can be opened using a spreadsheet such as Microsoft Excel and used for graphical analysis and presentation. The displayed graphs can be used to examine long-term trends in evolution over many generations.
In the Cumulative Selection and Speciation simulations the displayed graphs document changes in the population sizes of the distinct rover species - Prowlers, Gizmos, Shakers, and Quirks. Drifter numbers are not displayed, as they typically include a very heterogeneous group of individuals.
During the Antibiotic Resistance simulation the graph displays the average value for the antibiotic resistance gene for the entire population as well as the total dose of antibiotics given since the last data were gathered. For example, if the particular graph plots a point after every two generations, then the antibiotic values represent the total dose administered during the previous two generations.
You may notice that the most recent generation data are not included in an updated graph. If the program has been running for a large number (hundreds) of generations, the graph data are only being collected and tallied after perhaps 10 or more generations have passed.
Note: the Refresh button on the graph window toolbar must be used to update the graph. Once a graph has been created, it can only be updated using the Refresh button. It is not updated by clicking the graph button on the Simulation Screen toolbar.
Glossary
age: The number of moves a rover has made since it was produced in a reproduction event.
antibiotic: Red dots on the screen. When a rover contacts an antibiotic dot it may lose energy, depending on the value of its antibiotic resistance gene.
antibiotic resistance gene: The greater the value of the antibiotic resistance gene, the less energy a Prowler will lose when it contacts an antibiotic dot.
Darwin Island: A small very energy-rich environment. Food drop-in rates on the island are much higher than in the open environment.
Drifter: Rovers with no single-motion-gene value greater than or equal to 50%.
energy: Rovers use energy to move. Each move requires one unit of energy. Rovers obtain energy from their food.
environment: The virtual space in which rovers evolve in Evolution in Motion.
flip-flop gene: Causes the rover to move back to its immediate previous location.
food energy value: Each food item has an energy value of 55 units.
forward gene: Causes the rover to continue in the same direction as its previous move.
gene value: The probability that the individual will move according to a particular motion gene on any given move.
generation: 1000 moves; the minimum age before a rover can reproduce.
Gizmo: A rover that spins (left or right) at least 50% of the time.
graph button: Used to display and create a graph of the simulation run.
high dose: A large number of antibiotic dots are added to the environment.
individual (select): Choosing "Individual" in the Rover Selection window permits the user to click on and display the gene values, age, and energy of a particular rover.
loop (right/left) gene: causes the rover to make a sharp turn to the right or left.
low dose: A relatively small number of antibiotic dots are added to the environment.
motion: The movements of the rovers. Evolution in Motion models the role of mutation and natural selection in the evolution of motion patterns in virtual organisms.
mutations: When a rover reproduces, each of the new daughters has a 50% chance of mutating. Mutations result in an increase (or decrease) in the value of a gene selected at random.
Prowler: A rover that moves forward at least 50% of the time.
Quirk: a rover that loops (left or right) at least 50% of the time.
refresh button: Used to update the Simulation Screen display. Also used to update the Graph Display and the graph data files.
reproduction: Rovers reproduce when they meet two conditions. They must be 1000 or more generations in age and have an energy value of at least 800.
rover(s): Digital organisms that
live, reproduce, evolve and simply struggle for survival in the virtual
environments of Evolution in Motion.
rover selection window: Used to choose the species or individual for displaying gene, age, and energy data.
rover speed: The rover speed scale ranges from 0-1000. It can be adjusted with a scroll bar. Rover speed is not comparable between different computers.
Shaker: A rover that flip flops at least 50% of the time.
spin (right/left) gene: Causes a rover to move in the same general direction with a turn toward the right (or left).
turbo On/Off: Used to accelerate the simulation. The screen is not visible in turbo mode.
Wallace Island: Similar to Darwin Island but can be positioned by the user.
Acknowledgments
Evolution in Motion was inspired by the excellent software program Simulated Evolution created by Mike Palmiter (copyright 1985). His elegant DOS-compatible program employed the same mathematical modelling system to explore the evolution of one or two species. Our program enhances and extends this modelling system using a more visually powerful, interactive, and student-friendly interface. The graphing capabilities and the inclusion of an antibiotic resistance simulation provide students with data files and an STSE connection.
It is hoped that Evolution in Motion will provide students with a better insight into that most beautiful of biological processes - evolution - the simple but elegant mechanism that has produced the rich diversity of life on Earth. We are forever indebted to Charles Darwin, Alfred Russell Wallace, Richard Dawkins, and Stephen Jay Gould for introducing us to the beauty of evolutionary biology.
Doug Fraser and Matthew Allan
Timiskaming District Secondary School
90 Niven Street
New Liskeard, ON P0J 1P0
Please send comments to: dfraser@ourniche.net
The full version of Evolution in Motion CD provides graphing capabilities in all simulations, the ability to observe multiple speciation events on two islands (Darwin and Wallace), and the complete antibiotic resistance simulation in which students can manipulate the environment to model the evolution of highly resistant pathogens.
Bonus Mini Lessons include the "Chaos Game" and "Me thinks it is like a weasel."
The full version of the Evolution in Motion CD also includes student lesson and Teacher Support materials.
Single
User Licence: $US 14.95 ($24.95 CDN)
Secondary School Site Licence: $US 29.95 ($49.95 CDN) University/College Licence: $US 49.95 ($74.95 CDN) All prices include shipping. Taxes may apply. For information about purchasing Evolution in Motion
or receiving a demo version, please contact:
Ourniche Software Box 36 Haileybury, ON P0K 1K0 705-672-2257 or e-mail: dfraser@ourniche.net