Hands-on Activity: Engineering Digital Biodegraders for Biological Cleanup

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

Gloved hands hold two petri dishes with orange nutrient agar. One is covered in bacterial colonies and one has no colonies growing on it.
Traditional lab petri dishes with bacterial colonies.
Copyright © PublicDomainImage.com http://www.public-domain-image.com/science-public-domain-images-pictures/petri-dishes.jpg.html


A hypothetical scenario is introduced in which the class is asked to apply their understanding of the forces that drive natural selection to prepare a proposal along with an environmental consulting company to help clean up an area near their school that is contaminated with trichloroethylene (TCE). Students use the Avida-ED software application to test hypotheses for evolving (engineering) a strain of bacteria that can biodegrade TCE, resulting in a non-hazardous cleanup solution. Conduct this design challenge activity after completion of the introduction to digital evolution activity, Studying Evolution with Digital Organisms.
This engineering curriculum meets Next Generation Science Standards (NGSS).

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.

Pre-Req Knowledge

A basic understanding of evolution by natural selection is required. This activity should be introduced only after completing the introductory Evolution of Digital Evolution lesson and the Studying Evolution with Digital Organisms activity.

Learning Objectives

After this activity, students should be able to:

  • Explain how the process of natural selection leads to organisms that are well suited for the environment.
  • Discuss characteristics of the environment and organisms that influence the process of natural selection.
  • Develop and test a hypothesis and then use the data to draw conclusions.
  • Propose a protocol for critiquing proposed solutions to the problem.

More Curriculum Like This

Evolution of Digital Organisms

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Introduction to Evolutionary Computation

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Competing Evolved and Engineered Digital Organisms

Students engineer and evolve digital organisms with the challenge to produce organisms with the highest fitness values in a particular environment. They do this through use of the free Avida-ED digital evolution software application.

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Students observe natural selection in action and investigate the underlying mechanism, including random mutation and differential fitness based on environmental characteristics. They do this through use of the free AVIDA-ED digital evolution software application.

Educational Standards

Each TeachEngineering lesson or activity is correlated to one or more K-12 science, technology, engineering or math (STEM) educational standards.

All 100,000+ K-12 STEM standards covered in TeachEngineering are collected, maintained and packaged by the Achievement Standards Network (ASN), a project of D2L (www.achievementstandards.org).

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.

  • Use a computer simulation to model the impact of proposed solutions to a complex real-world problem with numerous criteria and constraints on interactions within and between systems relevant to the problem. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • The design process includes defining a problem, brainstorming, researching and generating ideas, identifying criteria and specifying constraints, exploring possibilities, selecting an approach, developing a design proposal, making a model or prototype, testing and evaluating the design using specifications, refining the design, creating or making it, and communicating processes and results. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • Biotechnology has applications in such areas as agriculture, pharmaceuticals, food and beverages, medicine, energy, the environment, and genetic engineering. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • Describe a reason for a given conclusion using evidence from an investigation. (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
  • Critique solutions to problems, given criteria and scientific constraints. (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?
  • Explain how natural selection leads to organisms that are well suited for the environment (differential survival and reproduction of chance inherited variants, depending upon environmental conditions). (Grades 9 - 12) Details... View more aligned curriculum... Do you agree with this alignment?
Suggest an alignment not listed above

Materials List

Each group needs:


Your school administrators want to buy an adjacent piece of property to build new athletic facilities. The property includes a large warehouse that has been used for various industrial purposes over the last 50 years. During the site inspection it was learned that the soil and water around the warehouse are contaminated by trichloroethylene (TCE), a hazardous chemical used as a spot remover in dry cleaning and as a degreaser for metal parts. The school board has asked our class to team up with an environmental consulting company to help cleanup the TCE so that our school can move ahead with purchasing and using the land.

(Continue by having students read aloud the complete hypothetical design challenge scenario as provided in the attached Evolving TCE Biodegraders Handout.)


Avida-ED: An educational version of the digital evolution software, Avida. Avida-ED is an award-winning educational application developed for undergraduate biology courses to help students learn about evolution and the scientific method by enabling them to design and perform experiments to test hypotheses about evolutionary mechanisms using evolving digital organisms.

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.


Before the Activity

  • Teacher to review the activities on in advance so that s/he can help direct students during class.
  • Prepare enough computers with Avida-ED installed for each pair of students.
  • Make copies of the Evolving TCE Biodegraders Handout, one per person. This handout provides the scenario, background information, and questions to guide students' experimental designs.

With the Students

  1. With student pairs each at computers that have Avida-ED installed, give each student a handout.
  2. As a class, read aloud the hypothetical design challenge scenario.
  3. Facilitate a class discussion to explore what students know about the problem and what they need to know about the problem.
  4. Read aloud the background information and the experimental design questions. Clarify any language in the questions so that the task is clearly defined—without providing any suggestions for how to solve the problem.
  5. Have students complete the experimental design questions, writing out their answers. Through this process, students:
    • develop hypotheses and predictions using the "if... then..." format
    • determine how much data to collect
    • write concise descriptions of their experimental design methods (including settings, replications, data collection, etc.) that are clear enough for replication by others
    • identify dependent and independent variables and the controls
    • organize their data into tables
    • determine the graph(s) for best data presentation
  1. Note: Students may choose to change one or more of the organism or environmental variables in order to influence the evolution of the "oro" function in the population. Students' protocols may go in a number of directions including changing only one variable at a time, changing multiple variables, evolving the "oro" function as quickly as possible using one set of parameters and then transplanting that organism to another environment to "clone" it, or using only one static set of parameters for the population. Permit students to pursue any of these options; as a group, discuss the pros and cons of each.
  2. Next, students collect data, documenting the parameters for each run and recording observations.
  3. Then students create graphs to display their results.
  4. Next, students describe how their results support/refute their hypotheses.
  5. Then students propose protocols for evolving bacteria to degrade TCE, including preparing short class presentations to explain their proposals.
  6. As a class, watch and listen to the group proposals.
  7. Facilitate a class discussion to determine which group proposal most effectively evolves efficient TCE degrading bacteria. Encourage students to critique the proposed protocols and come to a consensus about what should be presented to the environmental consulting company and why. Are there any unanswered questions? Do we feel confident submitting one of these proposals? Do we need to run more experiments? This should lead to a rich discussion about the nature of scientific inquiry and the engineering design process.



Activity Embedded Assessment

Handout Questions: Collect students' answers to the handout questions and/or the student-generated data and analysis as a source of formative assessment.

Data Summary Presentation: Grade the groups' oral class presentations, evaluating for subject matter comprehension, concise description of experimental design methodology, convincing presentation of proposed protocol to meet the design challenge, and overall clarity of communication. Alternatively, instead of oral presentations, have students create posters or other visual representations of the data.


Wendy Johnson; Amy Lark; Robert Pennock; Louise Mead


© 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


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: March 17, 2018