From 2014.igem.org
Carousel Template · Bootstrap
Purpose The fish model allows users to see the effects of different concentrations of estrogen on a freshwater ecosystem containing algae, fish, and birds. The model attempts to capture the long-term effects of estrogen on male fish, and demonstrates how sensitive a freshwater ecosystem can be to various concentrations of estrogen. The model is stochastic and it was written in NetLogo, an agent-based modeling language which allows users to view and analyze complex interactions between agents and their environment. A stochastic model employs probability to determine the behavior of its components, thus it is the best type of model to capture the randomness of an ecosystem. The model was also demonstrated to local public school teachers so that they could help their students visualize interactions between different organisms and organisms and their environment. The current lake we are simulating is fictional, however, the code has been developed in such a way that one could substitute the parameters in our model with parameters they have received from a particular lake they wish to test.
Outline
The fish model follows a simple tropic pyramid structure. The algae is the food source of the fish, which
in turn are the food source for the birds. If no estrogen is introduced into the environment, the ecosystem is
stable and the model simulates what is essentially the predator-prey interaction. Initially there is a relatively
high amount of fish, and relatively low amounts of birds and algae. This puts a strain on the fish population,
while simultaneously making it easy for the birds to find prey due to the combination of a large food source
and low competition for that food source. Thus this leads to a dip in the fish population and a peak in the bird
population. The dip in the fish population also leads to a peak in the algae population, as the algae can grow
without being consumed as fast due to the lack of fish. This scenario puts a strain on the bird population as
there is now too much competition for a smaller food source, while simultaneously making it easy for the fish
to find food due to the combination of a large food source and low competition for that food source. Thus the
population is back to the initial starting conditions, and the model continues to cycle through these scenarios ad
infinitum. The user can tamper with the ecosystem by adding varying concentrations of estrogen. The estrogen
leads to the feminization of male fish, with higher concentrations of estrogen corresponding to an increased
likely hood of feminization. Feminized male fish cannot reproduce, which leads to more frequent dips in the
fish population and can throw the entire ecosystem out of the equilibrium that was described above.
To run the model simply go to the interface tab, hit setup, and then run.
Each fish in the model represents a school of 100 fishes.
The Parameters
The parameters do not entirely reflect reality. For example both the max age of the fish and birds are the same
in the model, even though in actuality birds typically live much longer than fish. However, the parameters
are organized in such a way that the math for the model works out in a manner which is easy to program.
Essentially the most important thing for the model to do is capture the effects of estrogenic on a freshwater
ecosystem, which is what the default parameters do.
Parameter
Value (if applicable)
Reasoning (if applicable)
water-color
blue
Aesthetic purposes. Static value.
male-fish-color
cyan
Aesthetic purposes. Static value.
female-fish-color
pink
Aesthetic purposes. Static value.
feminized-fish-color
yellow
Aesthetic purposes. Static value.
bird-color
orange
Aesthetic purposes. Static value.
algae-color
green-scale
Aesthetic purposes. Static value. Darker green squares correspond to more algae.
fish-stride
0.8
The distance traveled each tick. Static value.
bird-stride
0.5
The distance traveled each tick. Static value. Birds should be a little slower than the fish so that the fish are not decimated.
fish-size
0.8
Relative size of the fish. Static value.
bird-size
1.2
Relative size of the birds. Static value. Birds should be bigger than their prey.
fish-reproduction-age
20
The age at which a fish is mature enough to reproduce. Static value.
bird-reproduction-age
20
The age at which a bird is mature enough to reproduce. Static value.
fish-max-age
100
The age at which a fish will die of old age. Static value.
bird-max-age
100
The age at which a bird will die of old age. Static value.
max-fish-offspring
2
Maximum number of offspring a female fish can produce each time she successfully reproduces. Static value. DO NOT CHANGE as the value must
always be greater than the max number of offspring a bird can produce but almost all computers cannot handle a value of > 2.
max-bird-offspring
1
Maximum number of offspring a female bird can produce each time she successfully reproduces. Static value. DO NOT CHANGE as the value must
always be less than the max number of offspring a fish can produce but almost all computers cannot handle a value of > 1.
male?
true/false
Assigned when an agent is born. Static at birth. 50% chance of being true.
energy
≤ 100
Initialized to 100 when an agent is born. If it is less than or equal to 0, then the agent dies. Increases as the agent consumes food, up
to a max value of 100. Decreases by a fixed amount each tick.
current-age
0-100
The age of an agent. Initialized to 0 when an agent is born. Incremented by one each tick.
estrogen-concentration
≥ 0
Initialized to 0. Represents the current concentration of estrogen (ppt) in the water. Decreases over time and as fish are feminized. Can
be increased by the user.
estrogen-resistance
200
The ability of a male fish to resist feminization. Static value. Higher number corresponds to higher base resistance (different types of
fish resist estrogen to various extents so the model can be used to simulate different freshwater sources).
estrogen-accumulated-max
0.1
Essentially captures how much estrogen can be accumulated in the fat tissue of a male fish over time. Static value.
estrogen accumulated
≤ estrogen-stored-max
The current amount of estrogen accumulated in a male fish due to exposure to estrogen from environment. As this number increases the chance
a male fish is feminized also increases.
algae-energy
0-100
The amount of algae present in a square. If it equals 0, then there is no algae present in the square and the square is blue.
algae-growth-rate
10
The amount of energy an algae tile gains each time it reproduces. Static value.
algae-growth-delay
15
The amount of time the algae needs to wait before it can reproduce. Static value.
algae-max-energy
100
The maximum amount of algae that can be located in a tile. Static value.
fish-survival
0.30
Probability that a fish makes it out of infancy. Static value.
bird-survival
0.15
Probability that a bird makes it out of infancy. Static value.
fish-find-egg
10
The more male fish there are the greater the chance is that an egg is fertilized. Increasing this number increases the number of male fish
needed to fertilize eggs (a large body of water will have a greater value for this parameter).
bird-egg
1
The more male birds there are the greater the chance is that an egg is fertilized. Increasing this number increases the number of male
birds needed to fertilize eggs (a large body ecosystem will have a greater value for this parameter).
Insight
In the following section we explain the reasoning behind the two stochastic processes employed in the model:
• Feminization of the male fish
• Reproduction of the birds/fish.
All male fish accumulate estrogen in their bodies when exposed to high levels of estrogen in their environment.
Juvenile males will be more affected by exposure to estrogen, thus they will store it at a faster rate than sexually
matured males. The rate of estrogen storage for a juvenile male fish is captured by the formula below:
Results
The most important thing to take away from the model is how fickle the organisms at the top of the food chain
are to changes in the chemical composition of the water. Even though the estrogen directly affects the fish by
feminizing them, the birds are the species which are more prone to dying out first if the estrogen level is too
high as they are highly responsive to even slight dips in the population of their food source, due to the fact that
they are a trophic level higher than the fish.
Scenario 1: No Estrogen Added Scenario 2: Low Concentrations of Estrogen (ppt 0 – 20) Scenario 3: Medium Estrogen Concentrations (21 – 39 ppt) Scenario 4: High Estrogen Concentrations (≥ 40 ppt) Code
A commented, working version of the code can be found at Feminized Fish Model
References 1. Novak, M. and Wilensky, U. (2011). NetLogo Bug Hunt Predators and Invasive Species model. http://ccl.northwestern.edu/netlogo/models/BugHuntPredatorsandInvasiveSpecies. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
2. Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.
"
