Lesson: Evolution of Digital Organisms

Contributed by: Bio-Inspired Technology and Systems (BITS) RET, College of Engineering, Michigan State University

A digital organism represented by a circle of 50 letters symbolizing computer commands.
A digital organism in Avida-ED.
copyright
Copyright © 2011 Rob Pennock, Michigan State University

Summary

Students are introduced to the concepts of digital organisms and digital evolution. They learn about the research that digital evolution software makes possible, and compare and contrast it with biological evolution.

Engineering Connection

Computer scientists and engineers work together to create software and hardware to model complex systems and create new technologies. The digital evolution software, Avida, was created by a group of computer scientists and software engineers interested in the experimental study of digital organisms in order to better understand how biological natural selection works and then to apply that knowledge to solving computational problems. Evolutionary computation methods can be applied to solve a wide range of engineering design problems, such as the design of self-managing computational systems, robot software, and even the morphological (form and structure) characteristics of robots.

Pre-Req Knowledge

A basic understanding of evolution by natural selection is required. While the concept of natural selection should have been introduced previously, the associated activities explore how the process works (including variation, inheritance, and selection).

Learning Objectives

After this lesson, students should be able to:

  • Compare and contrast digital evolution with biological evolution.
  • Discuss the strengths and limitations of using digital evolution software to study biological evolution.
  • Discuss how natural selection leads to adaptation both biologically and digitally.

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In the ASN, standards are hierarchically structured: first by source; e.g., by state; within source by type; e.g., science or mathematics; within type by subtype, then by grade, etc.

  • Systems thinking applies logic and creativity with appropriate compromises in complex real-life problems. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • Critique whether or not specific questions can be answered through scientific investigations. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • Summarize the major concepts of natural selection (differential survival and reproduction of chance inherited variants, depending on environmental conditions). (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
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Introduction/Motivation

(In advance, have enough computers for one per student pair, and the ability to download a free software application from the Internet. Alternatively, show the entire class the software with one computer and a projector. Also, make copies of the attached Discussion Questions Handout, one per student, or write the questions on the classroom board.)

What does it mean to be alive? What characteristics do all living things have in common? (Possible answers: Growing, transforming energy, metabolism, genetic information, reproduction, evolution by natural selection, etc.)

What is artificial life? (Possible answers: Inorganic, similarities to biological organisms.) What is a computer virus? (Answer: A computer program that can copy itself and infect a computer.) Is a computer virus alive? (Let students debate and suggest characteristics that are similar and dissimilar to living organisms.)

What do scientists mean when they use the word "evolution"? (Answer: Genetic change in populations over time or change in the proportions of traits in a population over time.) What is required for evolution to occur? (Answers: A variation, reproduction, selection and time.) How do we know that evolution has occurred? (Answers: Examining how a species has changed overtime through fossils.)

We are going to read an article from Discover Magazine that may cause us to change our minds about some of these ideas.

(Continue with the lesson by having students read the article, answer the discussion questions, download and open the software, before proceeding to conduct the two associated activities.)

Lesson Background and Concepts for Teachers

About Avida-ED

In advance, read the entirety of the "Testing Darwin" article by Carl Zimmer in Discover Magazine to become familiar with the Avida software and the questions for which it is being used to answer. (The article was published online on February 5, 2005 and is available at http://discovermagazine.com/2005/feb/cover.)

Avida-ED is a software program adapted from the Avida research software described in the Discover Magazine article. Both programs can be described as instances of evolution in a model environment. The evolution itself is real; the digital organisms are subject to the process of natural selection just as biological organisms are. For biologists, the main advantages of using digital organisms are that 1) the environment can be precisely controlled and manipulated and 2) the digital organisms reproduce much faster than any biological organisms. Avida-ED was created to give students the opportunity to learn about evolution by watching it in action. This powerful tool also enables students to design and perform their own experiments to test hypotheses about evolution in much the same way that researchers use Avida in their labs.

Have students download and install the Avida-ED software from http://avida-ed.msu.edu/ or have someone install it for them in advance.

With the Students

After conducting the Introduction/Motivation section, have students read the "Testing Darwin" article. Either have them read the article out loud as a class, or individually. The introductory section of the article is the main focus; it is followed by a series of six questions and discussions of how digital evolution software can be used to address each question. It is not necessary that the entire article be read, but everyone should read the introductory section. You may assign student groups to each read one of the six sections that follow, or assign for reading one or two of the sections that are most relevant to the course.

After reading the article, hold a class discussion using the following three questions, which are also provided in the attached Discussion Questions Handout. Either provide students with the handout so they can write down their ideas individually while reading the article, or have the students copy the questions from the board prior to reading. Have students hand in their answers for teacher review.

Discussion Questions to Consider about Artificial Life and Evolution of Digital Organisms

  1. Compare and contrast the digital organisms in the AVIDA environment to biological organisms in the natural world. In what ways are digital organisms similar to computer viruses?
  2. What do biologists mean when they use the word "evolution"? Can we observe evolution? Can we experiment with evolution? What are potential causes of evolution? Explain your answer and give examples from the article or prior knowledge.
  3. What makes AVIDA a useful tool for biologists? What are the strengths and limitations of such an approach?

With the Students

After discussing the questions, introduce the students to the Avida-ED software by having them download and install it on computers. Or, if it already installed, have them open the program or watch the teacher open it via projector.

Avida-ED is a software program adapted from the Avida research software described in the Discover Magazine article. Both programs can be described as instances of evolution in a model environment. The evolution itself is real; the digital organisms are subject to the process of natural selection just as biological organisms are. For biologists the main advantages of using digital organisms are that the environment can be precisely controlled and manipulated and the fact that digital organisms reproduce much faster than any biological organisms. Avida-ED was created to allow students the opportunity to learn about evolution by watching it in action. This powerful tool also allows students to design and perform their own experiments to test hypotheses about evolution in much the same way that researchers use Avida in the lab.

We are going to acquaint ourselves with the Avida-ED software so that you can use it to investigate how natural selection works and how it can be used to solve real-world problems in subsequent activities. Point out the three main panels (navigation, freezer and lab bench) of the Avida-ED program, as described in the quick Avida-ED tour (below). Then proceed to conduct the two associated activities.

A screenshot shows three boxed areas with different background colors : Lab Bench (analysis; most of screen), Navigation (upper left corner box) and Freezer (lower left corner box)
Figure 1: Panels of the Avida-ED home screen.
copyright
Copyright © 2011 Rob Pennock, Michigan State University

Quick Avida-ED Tour

Avida-ED has three panels (see Figure 1).

  1. Navigation (select the Lab Bench view)
  • Population - to view organisms evolving
  • Organism - to view individual organisms
  • Analysis - to analyze results
  1. Freezer (for saved materials)
  • Configured dishes - settings, no organisms
  • Full petri dishes - settings and organisms
  • Organisms - individual organisms
  1. Lab Bench (this is where things happen)

Vocabulary/Definitions

Avida-ED: An educational version of the digital evolution software, Avida.

digital evolution: An instance of evolution wherein self-replicating digital organisms are subject to random mutation that is acted on by natural selection.

digital organism: A small self-replicating computer program.

evolution: The change in the genetic composition of a population from generation to generation.

natural selection: A process in which organisms with certain inherited characteristics are more likely to survive and reproduce than are organisms with other characteristics; the main driving force of evolution.

Associated Activities

  • Studying Evolution with Digital Organisms - Students observe natural selection in action through a guided inquiry activity using the Avida-ED software application as they investigate the role of random mutation and the environmental characteristics on fitness and selection.
  • Evolving TCE Biodegraders - Students apply their understanding of the forces that drive natural selection to help a (hypothetical) environmental consulting company engineer bacteria to biodegrade trichloroethylene (TCE) for non-hazardous clean-up of property near their school. They use the Avida-ED software application to do this. Conduct this activity after completion of the introduction to digital evolution activity, Studying Evolution with Digital Organisms.

Lesson Closure

Computer scientists and engineers work together to create software and hardware to model complex systems and create new technologies. The digital evolution software, Avida, was created by a group of computer scientists and software engineers interested in the experimental study of digital organisms in order to better understand how biological natural selection works and then to apply that knowledge to solving computational problems. Evolutionary computation methods can be applied to solve a wide range of engineering design problems, such as the design of self-managing computational systems, robot software, and even the morphological (form and structure) characteristics of robots. In the coming days you are going to get the opportunity to use the Avida-ED software to investigate the process of natural selection.

Attachments

Assessment

Writing & Reflection: After reading the article, hold a class discussion guided by the three questions provided in the attached Discussion Questions Handout. Either provide students with the handout so they can write down their ideas individually while reading the article, or have the students copy the questions from the board prior to reading. Have students turn in their written answers to the discussion questions before moving on to conduct the associated activities.

References

McKinley, Philip, Betty H.C. Cheng, Charles Ofria, David Knoester, Benjamin Beckmann, and Heather Goldsby. January 2008. "Harnessing Digital Evolution." IEEE Computer Society. 41 (2008) pp. 54-63. (In digital evolution, self-replicating computer programs—digital organisms—experience mutations and selective pressures, potentially producing computational systems that, like natural organisms, adapt to their environments and protect themselves from threats. Such organisms can help guide the design of computer software.) http://www.cse.msu.edu/~mckinley/digital-evolution.pdf

Zimmer, Carl. "Testing Darwin." Published online February 5, 2005. Discover Magazine, Kalmbach Publishing Co. Accessed May 30, 2012. http://discovermagazine.com/2005/feb/cover

Contributors

Wendy Johnson; Robert Pennock; Louise Mead

Copyright

© 2013 by Regents of the University of Colorado; original © 2011 Michigan State University

Supporting Program

Bio-Inspired Technology and Systems (BITS) RET, College of Engineering, Michigan State University

Acknowledgements

The contents of this digital library curriculum were developed through the Bio-Inspired Technology and Systems (BITS) RET program under National Science Foundation RET grant no EEG 0908810. However, these contents do not necessarily represent the policies of the NSF and you should not assume endorsement by the federal government.

Last modified: July 20, 2017

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