Beginners Interactive NetLogo Dictionary (BIND)
Farsi / Persian
NetLogo Models Library:
This model allows for the exploration and comparison of two different mechanisms of evolution: natural selection and genetic drift. It models evolution in a population of asexually reproducing bacteria, E. coli.
It starts with different types of E. coli, each with a different types (trait values) represented by different colors. When ‘natural selection’ is off, the model shows that competing types of E. coli, each reproducing with equal likelihood on each turn, will ultimately converge on one type without any selection pressure forcing this convergence. This is called genetic drift, an idea explained in more detail in Dennett's Darwin's Dangerous Idea that explains that genetic drifts can occur without any particular purpose or 'selecting pressure'. When ‘natural selection’ is on, one of the type of E. coli cells has a selective advantage. It gains more energy from sugar in a given time unit. This results in faster reproduction by that type of cells. An important thing to note is this model includes one mechanism of natural selection called r-selection.
The model starts with different colored E. coli cells, randomly distributed across the world. The user can select the number of different colors (types) of cells to start with. The cells can then move randomly across the world. Then,
When Natural Selection is OFF:
Each turn, each E. coli moves randomly around the world, eats sugar if the patch it is at contains sugar. Eating sugar increases energy of E. coli cell, whereas movement and basic metabolic processes decreases energy. An E. coli cell reproduces when its energy doubles, to form to two daughter cells of its type (of the same color). If energy of an E.coli cell reduces to zero, the cell dies. The increase in energy by eating sugar is identical for each type (color) of E. coli cell. By statistical advantage, a dominant color becomes more likely to ‘win’ and take over the population. However, because the process is random, there will usually be a series of dominant colors before one color finally wins.
When Natural Selection is ON:
A user can select which type (color) has a selective advantage in this world, causing it to gain more efficiently digest sugar and gain more energy from sugar at each time step. The cells with selective advantage are represented as cells with blue outline in the model.
This in terns causes that particular type of E. coli reproduce faster. The % advantage slider sets the percentage increase in energy gain by the cells with selective advantage. Through this selective advantage, a dominant color becomes more likely to 'win. However, if the selective advantage is low, statistical advantage might still cause another color to 'win.
Note that once a color dies out, it can never come back.
The SETUP button initializes the model.
The GO button runs the model.
Use the NUMBER-OF-TYPES slider to select the number of competing colors.
Use the ECOLI-WITH-SELECTIVE-ADVANTAGE chooser to select the color (type) of E. coli that has a selective advantage.
Use the %-ADVANTAGE slider to set % increase in energy gain of "Faster reproducing E. coli" as compared to others.
Use the MAX-INITIAL-POPULATION to set maximum population of all types of E. coli bacteria at the beginning of the simulation.
Use the CARRYING-CAPACITY chooser to chose the carrying capacity that is the maximum number of individuals that survive in the given environment. This chooser changes sugar availability (rate of addition of sugar per tick) in the model.
Notice that the E. coli cells with selective advantage often wins the race when the % selective advantage is high. When the % selective advantage is low, statistical advantage in favor of any of the other colors might result in different outcomes. Check if there is any tipping point above which % selective advantage always makes the color win.
Notice the effect of change in the carrying capacity on the natural selection process.
In each simulation, the time required for a single type to become dominant varies. Check to see if an increase or decrease in the carrying capacity has any effect on how fast a color wins. Now check this same phenomenon in the presence and absence of natural selection.
The type of natural selection incorporated in this model is r-selection. The other possible type is k-selection. Think about how you could incorporate k-selection in this model.
This model uses the
runresult primitive in order to convert your color selection (a
string) into a NetLogo color (a number).
If you mention this model or the NetLogo software in a publication, we ask that you include the citations below.
For the model itself:
Please cite the NetLogo software as:
To cite the GenEvo Systems Biology curriculum as a whole, please use:
Copyright 2016 Uri Wilensky.
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