Lesson 6. Lesson 6: Natural Selection

Sugat Dabholkar, Kevin Hall, Philip Woods, Connor Bain
Biology
45-90 min
Introductory High School Biology
v2

Overview

The teacher first introduces the new model. Students then design and perform computational experiments to explore how selective advantage because of different behaviors (due to a physical trait – flagella number) affect the outcomes of natural selection in population of virtual bacteria. Students present their initial results to the class and the class discusses possible explanations for why these different conditions yield different shifts in the distribution of trait variations from natural selection. Groups return to their experimentation and develop their explanations further, and report these out at the end of their experimentation. At the end of class, the teacher develops class consensus on the big ideas regarding the conditions necessary for natural selection and revises the scientific principle from the last lesson.

This lesson uses the same model as the previous lesson of a population of bacteria with different types. However, there are some important differences. In this model, there is an advantage of having higher number of flagella and there is cost associated to having flagella. 

[Note: Computational scientists use variations of a model to study different but related phenomena. Though the model in this lesson looks similar to the one in previous lesson, it has important differences.] 

Standards

Next Generation Science Standards
  • Life Science
    • [HS-LS2] Ecosystems: Interactions, Energy, and Dynamics
    • [HS-LS4] Biological Evolution: Unity and Diversity
  • NGSS Crosscutting Concept
    • Patterns
    • Systems
    • Stability and Change
  • NGSS Practice
    • Analyzing Data
    • Using Models
    • Conducting Investigations
Computational Thinking in STEM
  • Data Practices
    • Analyzing Data
    • Manipulating Data
    • Visualizing Data
  • Modeling and Simulation Practices
    • Using Computational Models to Find and Test Solutions
    • Using Computational Models to Understand a Concept
  • Computational Problem Solving Practices
    • Troubleshooting and Debugging
  • Systems Thinking Practices
    • Investigating a Complex System as a Whole
    • Thinking in Levels
    • Understanding the Relationships within a System

Credits

Unit designed/developed by Dabholkar, S., Hall K., Woods P., & Bain C.

Acknowledgement

CODAP is developed and built by The Concord Consortium at https://codap.concord.org/  

Lesson 7 is based on the lesson Evolution in Action: The Galápagos Finches Authored by Paul Strode for Howard Hughes Medical Institute based on data collected by Peter and Rosemary Grant, Princeton University.

This work is supported by the National Science Foundation (grants CNS-1138461, CNS-1441041 and DRL-1020101) and the Spencer Foundation (grant 201600069). Any opinions, findings, conclusions, and/or recommendations are those of the investigators and do not necessarily reflect the views of the funding organizations.

Activities

  • 1. Natural Selection Model 1: Predation
  • 2. Natural Selection Model 2: Environmental Conditions
  • 3. Natural Selection Model 2: Make a prediction
  • 4. Natural Selection Model 2: Test the prediction
  • 5. Exploring effects of energy cost on natural selection
  • 6. BehaviorSpace Experiment
  • 7. Discoveries

Student Directions and Resources


In this activity students engage in simulated natural selection to discover how natural selection emerges from mechanisms: a) variation in heritable traits in a population and b) interactions in the environment give individuals with some variations a competitive advantage over other individuals. Another purpose  of this lesson is to describe the outcome of natural selection as an increase in the proportion of individuals with advantageous heritable trait variations in a population over multiple generations.

1. Natural Selection Model 1: Predation


Let's look now at a different version of the bacteria flagella model that we used in the last lesson. 

In this model, you are a predator. You can kill bacteria by moving the mouse cursor over and clicking.

Make sure to choose "none" from the VISUALIZE-PHENOTYPE menu, then set up the model and click on the button "run one minute experiment". The model will run for one minute. Try to kill as many bacteria as you can in that one minute.  After the time is up, choose "flagella and color" from the VISUALIZE-PHENOTYPE menu. And click on "visualize" button. 

Note your observations in the space provided below after you finish the experiment.

 


Question 1.1

Repeat the experiment twice. Write the number of bacteria of each variation at the end of the simulation run.



Question 1.2

What pattern do you notice in your results?  Explain your observations.

2. Natural Selection Model 2: Environmental Conditions


Purpose

Find different environmental conditions that generate different trends in which number of flagella become more common over time due to natural selection.  For example, what conditions favor lots of flagella?  What conditions favor few flagella?

With a partner, discuss possible experimental conditions (in terms of %-resource-distribution or resource-location) that might generate these outcomes in the model. 

Use the model to test your ideas with at least three environmental conditions. 

[* If the model is runs very slowly in your browser, use this NATURAL SELECTION MODEL for completing this lesson. You MUST have NetLogo installed on your computer to use the downloaded version of the model.]


Question 2.1

How did the %-resource-distribution and/or resource-location affect the average number of flagella of the bacteria?  Describe what you saw in each of the three conditions that you tested.



Question 2.2

Based on your observations from the model, why do you think this was the case?

3. Natural Selection Model 2: Make a prediction


Flagella help a bacterium to move and thus increase its chances of being near food before its eaten by other other bacteria. However, a bacterium has to incur some cost in terms of energy that it needs to spend to make and maintain a flagellum.

Make a prediction about which phenotype will survive after you run the model with limited resource conditions.


Question 3.1

Which of the following phenotypes will survive if you run the model (with 40% resource distribution around the central point) until only one phenotype survives?

You may choose more than one options if you think that the results will be different in each simulation run.

  Phenotype with 1 flagellum
  Phenotype with 2 flagella
  Phenotype with 3 flagella
  Phenotype with 4 flagella
  Phenotype with 5 flagella
  Phenotype with 6 flagella


Question 3.2

Explain the reason for your answer.

4. Natural Selection Model 2: Test the prediction


Set the given values for the following parameters: 

 #-PHENOTYPES   6
 INITIAL-#-BACTERIA-PER-PHENOTYPE   8
 RESOURCE-LOCATION   'around a central point'
 RESOURCE-DISTRIBUTION  40%

 

 

 

 

Click setup and run the model until only one phenotype survives. Repeat the experiment 5 times and note your results in the table below.   Make sure you uncheck the "view updates" box at the top of the model.  This will still allow you to see the plots update, and will make the model run much more quickly.


Question 4.1

Fill in the table below:



Question 4.2

Describe any patterns you observe in the results of the previous computational experiment.



Question 4.3
In this environment, the bacteria face selection against extremely small and extremely large numbers of flagella.  This is an example of stabilizing selection, which reduces the amount of variation in a population.  Stabilizing selection typically occurs when the environment isn't changing much.  Why is there selection against a small number of flagella?  Why is there selection against a large number of flagella?

 

5. Exploring effects of energy cost on natural selection


In the previous experiment you must have observed that the phenotype with maximum number of flagella is not always successful in terms of its survival. This is because of the energy cost per flagellum. 

Let's investigate the effect of the energy cost per flagellum on the process of natural selection. 


Question 5.1

Set ENERGY-COST-PER-FLAGELLUM to 0.10. Make sure that all the other parameters are at their original default values. Run the experiment till 5000 ticks. What is the average number of flagella in the population? 



Question 5.2

What will happen if you increase the ENERGY-COST-PER-FLAGELLUM and run the experiment again? Explain your answer.



Question 5.3

Design a series of computational experiments to systematically investigate the effect of ENERGY-COST-PER-FLAGELLUM on the process of natural selection. Describe your dependent variable and your independent variable. 

6. BehaviorSpace Experiment


Download this Bacteria Food Hunt - Natural Selection NetLogo Model. You MUST have NetLogo installed on your computer to use the downloaded version of the model.

The software that you are using to explore the phenomenon of natural selection, NetLogo, has a feature called BehaviorSpace that can be used to conduct such experiments. 

In this part you will use BehaviorSpace to conduct an experiment for investigating the effect of ENERGY-COST-PER-FLAGELLUM on 'avg. # of flagella' in the population after a certain time period. 

  • Go to "Tools" at the top of the screen and click "BehaviorSpace"
  • Create a new experiment.
Vary variables as follows

["trace-paths?" false]
["#-phenotypes" 6]
["resource-location" "around a central point"]
["visualize-phenotype" "flagella and color"]
["energy-cost-per-flagellum" [0.1 0.1 0.7]]
["initial-#-bacteria-per-phenotype" 8]
["resource-distribution" 40]
Repetitions 5
Run combinations in sequential order Checked
Measure runs using these reporters mean [phenotype] of bacteria
Measure runs at every step Unchecked
Setup commands setup
Go commands go
Time limit 5000

 

  • The independent variable in this experiment will be the energy-cost-per-flagellum. In order to vary the energy-cost-per-flagellum, you will use the the BehaviorSpace tool. The format below is for varying this parameter systematically. 

["energy-cost-per-flagellum" [energy-cost-in-the-first-run step-size energy-cost-in-the-final-run] ]

  • Press OK and run the experiment.
  • Select "Table output".
  • Uncheck "Update view" and "Update plots and monitors" to run the experiment faster. 
  • The output will be in the form of a "csv" file. You will open it in Excel to analyze your data.

[* In case if you have problems using the BehaviorSpace experiment, use this data for your analysis.]


Question 6.1

We are using the code  "mean [phenotype] of bacteria" to generate desired output after each run. Explore the 'code' tab of the NetLogo Model above and explain how this code will give us the desired value of the dependent (output) variable. 



Question 6.2

In the spreadsheet file, create a plot of your dependent variable vs your independent variable. Upload the spreadsheet file here.

Upload files that are less than 5MB in size.
File Delete
Upload files to the space allocated by your teacher.


Question 6.3

Describe and explain your observations from the BehaviorSpace computational experiment that you just performed and analyzed.

7. Discoveries


How does natural selection change populations over time?


Question 7.1

In your words, describe the process of 'natural selection'. Explain how populations evolve because of natural selection.