Team:Carnegie Mellon/Fish
From 2014.igem.org
Purpose
Outline
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
• 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:
Mature male fish store estrogen at a slower rate. A male fish is defined as mature when its age is greater than or equal to the age it is old enough to reproduce. The rate of estrogen storage for a mature male fish is captured by the formula below:
The model updates the state of each agent each tick. A tick is essentially representative of all the life functions an agent needs to carry out. In a tick each organism will consume food, increment its age, move, reproduce, and determine whether or not it needs to die.
Each tick, the model of a male fish will call a function that uses a random number generator (RNG) to determine whether or not they are feminized. The chance for a male fish to be feminized is captured by the formula below:
The RNG then generates a floating point number between 0 and 1.0. If said number is less than the feminization chance of a particular male fish, then that particular male fish will become feminized. Thus fish with high amounts of estrogen accumulated in their body (representing a prolonged exposure to estrogen) and placed in a very estrogenic environment will have a high chance of becoming feminized. The reproduction function for both the fish and birds follow the same exact principles (they differ in only the parameters they use). The fish reproduction function will be explained below, and the reasoning will be the exact same for the bird reproduction function. Essentially each female fish that is above the reproduction age will call a reproduction function that uses RNG to determine whether or not it successfully creates offspring. The chance that a female reproduces is based on the following formula below:
Thus the chance any female can successfully reproduced varies as a function of the number of fertile males of reproduction age. If there are only a few males in the lake relative to the size of the lake, adding more males will greatly increase the chance that the eggs of a female are fertilized. Conversely if there are a large number of males in the lake additional males will not really affect the rate at which eggs are fertilized. The constant fish- find-egg represents the number of males after which additional males will not greatly affect the rate at which eggs are fertilized.
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
If there is no estrogen added, the ecosystem is in dynamic equilibrium. Essentially the ecosystem follows the classic predator prey relationship described in the section titled 'Outline'.
INSERT GRAPHS
Code
References:
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.
Wilensky, U. (1999). NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.