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Do you teach a biology lab that has been disrupted by the coronavirus outbreak?

Entry #842: 01 Apr 2020; 8:56 am; 0 comments

This March 29 guest blog post on Rich Lenski's Telliamed by Rob Pennock describes AvidaEd, an online evolution simulation. AvidaEd is free online and has supporting educational materials openly available on their website. It can be found in the collections on this site.

Do you teach a biology lab that has been disrupted by the coronavirus outbreak? If so, you may want to consider using the Avida-ED experimental evolution platform as a virtual replacement.

To limit the spread of the coronavirus, many colleages and universities have suspended in-person classes, and instructors have had to scramble to replace them with on-line instruction. Biology faculty who teach laboratory-based courses find it especially difficult or impossible to do their planned lab exercises. Avida-ED may provide a valuable substitute for some classes.

Avida-ED is an award-winning educational application developed at Michigan State University for undergraduate biology courses. It is aimed at helping students learn about evolution and the scientific method by allowing them to design and perform actual experiments to test hypotheses about evolutionary mechanisms using evolving digital organisms. Funded by the NSF, Avida-ED is the educational version of a model system used by researchers to perform evolution experiments–including many that have been published in leading scientific journals (see some examples below). Avida-ED is not a simulation, but an instantiation of the evolutionary mechanisms and process that allows for real experiments. Avida-ED produces copious data that can be analyzed within the application or exported for statistical analysis. Avida-ED has been used in classrooms across the country and around the world for over a decade.

Here are more reasons that Avida-ED may provide a useful, quick replacement for your lab:

Avida-ED is free.
Avida-ED requires no special registration or configuration.
Avida-ED is accessible on-line and runs locally in your web browser.
The user-friendly interface requires little technical training to use.
It includes ready-to-use exercises to teach a variety of evolutionary concepts.
It can also be used for open-ended labs where students design and perform their own experiments.
It can be used to teach principles of experimental design and scientific method.

See the Avida-ED web site for:

Link to the Avida-ED application launch page.
Model exercises (under the Curriculum link).
The Avida-ED lab book.
Quick start user manual.
Background information about digital evolution.
Articles about Avida-ED, including effectiveness studies.

The Avida-ED team is working to provide instructional videos for the core exercises from train-the-trainer workshops that we have offered in previous summers, where we teach faculty how to use the software in their own classes. We can also provide instructor support materials for some exercises offline for certified instructors. A mirror of the Avida-ED site is available in case the primary site goes down.

*****

Lenski, R. E., C. Ofria, T. C. Collier, and C. Adami. 1999. Genome complexity, robustness and genetic interactions in digital organisms. Nature 400: 661-664.

Wilke, C. O., J. Wang, C. Ofria, R. E. Lenski, and C. Adami. 2001. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331-333.

Lenski, R. E., C. Ofria, R. T. Pennock, and C. Adami. 2003. The evolutionary origin of complex features. Nature 423: 139-144.

Ofria, C., and C. O. Wilke. 2004. Avida: A software platform for research in computational evolutionary biology. Artificial Life 10: 191-229.

Chow, S. S., C. O. Wilke, C. Ofria, R. E. Lenski, and C. Adami. 2004. Adaptive radiation from resource competition in digital organisms. Science 305: 84-86.

Ostrowski, E. A., C. Ofria, and R. E. Lenski. 2007. Ecological specialization and adaptive decay in digital organisms. American Naturalist 169: E1-E20.

Clune, J., R. T. Pennock, C. Ofria, and R. E. Lenski. 2012. Ontogeny tends to recapitulate phylogeny in digital organisms. American Naturalist 180: E54-E63.

Goldsby, H. J., A. Dornhaus, B. Kerr, and C. Ofria. Task-switching costs promote the evolution of division of labor and shifts in individuality. Proceedings of the National Academy of Sciences, USA 109: 13686-13691.

Covert, A. W. III, R. E. Lenski, C. O. Wilke, and C. Ofria. 2013. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences, USA 110: E3171-E3178.

Goldsby, H. J., D. B. Knoester, C. Ofria, and B. Kerr. 2014. The evolutionary origin of somatic cells under the dirty work hypothesis. PLoS Biology 12: e1001858.

Fortuna, M. A., L. Zaman, C. Ofria, and A. Wagner. 2017. The genotype-phenotype map of an evolving digital organism. PLoS Computational Biology 13: e1005414.

Canino-Koning, R., M. J. Wiser, and C. Ofria. 2019. Fluctuating environments select for short-term phenotypic variation leading to long-term exploration. PLoS Computational Biology 15: e1006445.

About the author

Kristin Jenkins

I am the Executive Director of TIDES at UT Austin. I earned my Bachelors at the University of California San Diego, in Biochemistry and Cell Biology. A high point of my undergraduate career was studying abroad at LaTrobe University in Melbourne, Australia for a year. I earned my PhD in Molecular and Cellular Biology at the University of Arizona, where I worked on RNA metabolism. After a short stint in industry at a start up biotech company, I moved into education. I have been fortunate to have a variety of experiences including teaching high school, as well as at a small college, an R1 and a community college. I ran a McNair Program at Concord College in West Virginia, and worked for BCSC before taking a position at the National Evolutionary Synthesis Center (NESCent). From NESCent, I moved to a position in future faculty development at the University of Wisconsin. In 2015I became the Executive Director of BioQUEST where I led the transition to a non-profit organization and played a key role in the development of QUBES.

My goal in science education is promoting success for all students and I use the Universal Design for Learning framework to support this outcome. I am particularly interested in teaching evolution, nature of science and quantitative reasoning skills. Projects I have been involved in to achieve these goals include Quantitative Biology at Community Colleges (https://qubeshub.org/community/groups/qbcc), which brings together a community of mathematics and biology faculty at two year institutions to develop Open Education Resources for teaching quantitative skills in a biology context, the BioQUEST UDL Initiative, which is focusing on bringing Universal Design for Learning practices to higher education, and EVOKE, an EU coalition focused on improving evolution education for everyone.

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