Thesis ID: CBB241773141

Replaying Life's Virtual Tape: Examining the Role of History in Experiments with Digital Organisms (2021)

unapi

Lenski, Richard E. (Advisor)
Jason Nyerere Bundy (Author)


Lenski, Richard E.
Michigan State University
Publication date: 2021
Language: English


Publication Date: 2021
Physical Details: 173

Evolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not everyone was convinced. Some believed that chance was the primary driver of evolutionary change, while others insisted that natural selection was the most powerful influence. Since then, “replaying life’s tape” has become a core method in experimental evolution for measuring the relative contributions of adaptation, chance, and history. In this dissertation, I focus on the effects associated with history in evolving populations of digital organisms—computer programs that self-replicate, mutate, compete, and evolve in virtual environments. In Chapter 1, I discuss the philosophical significance of Gould’s thought experiment and its influence on experimental methods. I argue that his thought experiment was a challenge to anthropocentric reasoning about natural history that is still popular, particularly outside of the scientific community. In this regard, it was his way of advocating for a “radical” view of evolution. In Chapter 2—Richard Lenski, Charles Ofria, and I describe a two-phase, virtual, “long-term” evolution experiment with digital organisms using the Avida software. In Phase I, we evolved 10 replicate populations, in parallel, from a single genotype for around 65,000 generations. This part of the experiment is similar to the design of Lenski’s E. coli Long-term Evolution Experiment (LTEE). We isolated the dominant genotype from each population around 3,000 generations (shallow history) into Phase I and then again at the end of Phase I (deep history). In Phase II, we evolved 10 populations from each of the genotypes we isolated from Phase I in two new environments, one similar and one dissimilar to the old environment used for Phase I. Following Phase II, we estimated the contributions of adaptation, chance, and history to the evolution of fitness and genome length in each new environment. This unique experimental design allowed us to see how the contributions of adaptation, chance, and history changed as we extended the depth of history from Phase I. We were also able to determine whether the results depended on the extent of environmental change (similar or dissimilar new environment). In Chapter 3, we report an extended analysis of the experiment from the previous chapter to further examine how extensive adaptation to the Phase I environment shaped the evolution of replicates during Phase II. We show how the form of pleiotropy (antagonistic or synergistic) between the old (Phase I) and new (Phase II) habitats was influenced by the depth of history from Phase I (shallow or deep) and the extent of environmental change (similar or dissimilar new environment). In the final chapter Zachary Blount, Richard Lenski, and I describe an exercise we developed using the educational version of Avida (Avida-ED). The exercise features a two-phase, “replaying life’s tape” activity. Students are able to explore how the unique history of founders that we pre-evolved during Phase I influences the acquisition of new functions by descendent populations during Phase II, which the students perform during the activity.

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Authors & Contributors
Daylight, Edgar G.
Grave, Kurt De
Baber, Robert L.
Ensmenger, Nathan Lee
Epstein, Bob
Grad, Burton
Journals
IEEE Annals of the History of Computing
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences
Publishers
Lonely Scholar Scientific Books
Basic Books
Johns Hopkins University Press
LIT Verlag
Concepts
Computers and computing
Software
Technology
Computer science
Engineering
Computer industry
People
Babbage, Charles
Dijkstra, Edsger Wybe
Gould, Stephen Jay
Grad, Burton
Heaviside, Oliver
Johnson, Luanne
Time Periods
20th century, late
20th century
21st century
19th century
Places
United States
Tunisia
Institutions
Rockefeller Foundation
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