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E-grāmata: Evolution in Action: Past, Present and Future: A Festschrift in Honor of Erik D. Goodman

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This edited research monograph brings together contributions from computer scientists, biologists, and engineers who are engaged with the study of evolution and how it may be applied to solve real-world problems. It also serves as a Festschrift dedicated to Erik D. Goodman, the founding director of the BEACON Center for the Study of Evolution in Action, a pioneering NSF Science and Technology Center headquartered at Michigan State University. The contributing authors are leading experts associated with the center, and they serve in top research and industrial establishments across the US and worldwide.

 

Part I summarizes the history of the BEACON Center, with refreshingly personal chapters that describe Erik's working and leadership style, and others that discuss the development and successes of the center in the context of research funding, projects, and careers. The chapters in Part II deal with the evolution of genomes and evolvability. The contributions in Part III discuss the evolution of behavior and intelligence. Those in Part IV concentrate on the evolution of communities and collective dynamics. The chapters in Part V discuss selected evolutionary computing applications in domains such as arts and science, automated program repair, cybersecurity, mechatronics, and genomic prediction. Part VI deals with evolution in the classroom, using creativity in research, and responsible conduct in research training. The book concludes with a special chapter from Erik Goodman, a short biography that concentrates on his personal positive influences and experiences throughout his long career in academia and industry.

Part I The BEACON Center for Evolution in Action
1 2010: A BEACON Odyssey
3(16)
Richard E. Lenski
2 A Strong Director Facilitates the Successes of All BEACON Members: A Personal Example
19(14)
Kay E. Holekamp
3 BEACON: Using Diversity as an Evolutionary Tool for a High-Performing Science and Technology Center
33(12)
Judi Brown Clarke
Percy Pierre
4 Threading Together a Successful NSF-Funded Science and Technology Center: The Impact of Dr. Erik Goodman
45(8)
Patricia L. Farrell-Cole
Marilyn J. Amey
5 How BEACON Shaped my Research and Career Trajectory
53(4)
Connie A. Rojas
6 The Man Behind the Leader
57(6)
Constance James
Part II Evolution of Genomes and Evolvability
7 Limits to Predicting Evolution: Insights from a Long-Term Experiment with Escherichia coli
63(14)
Jeffrey E. Barrick
8 A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli
77(14)
Jeffrey E. Barrick
Daniel E. Deatherage
Richard E. Lenski
9 Experimental Evolution of Metal Resistance in Bacteria
91(16)
Joseph L. Graves Jr
Akamu J. Ewunkem
Misty D. Thomas
Jian Han
Kristen L. Rhinehardt
Sada Boyd
Rasheena Edmundson
Liesl Jeffers-Francis
Scott H. Harrison
10 Probing the Deep Genetic Basis of a Novel Trait in Escherichia coli
107(16)
Tanush Jagdish
J. Jeffrey Morris
Brian D. Wade
Zachary D. Blount
11 Fitness Costs and Benefits of Resistance to Phage Lambda in Experimentally Evolved Escherichia coli
123(22)
Alita R. Burmeister
Rachel M. Sullivan
Richard E. Lenski
12 Experimental Evolution of Human Rhinovirus Strains Adapting to Mouse Cells
145(14)
Bethany R. Wasik
Brian R. Wasik
Ellen F. Foxman
Akiko Iwasaki
Paul E. Turner
13 Normed Phase Space Model of Natural Variation in Bacterial Chromosomes
159(8)
Julius H. Jackson
14 Genome Size and the Extinction of Small Populations
167(20)
Thomas LaBar
Christoph Adami
Part III Evolution of Behavior and Intelligence
15 Temporal Niche Evolution and the Sensory Brain
187(18)
Barbara Lundrigan
Andrea Morrow
Paul Meek
Laura Smale
16 Time Makes You Older, Parasites Make You Bolder --- Toxoplasma Gondii Infections Predict Hyena Boldness toward Definitive Lion Hosts
205(20)
Eben Geringt
Zachary Laubach
Patricia Weber
Gisela Hussey
Julie Turner
Kenna Lehmann
Tracy Montgomery
Kay Holekamp
Thomas Getty
17 Behavioral Strategy Chases Promote the Evolution of Prey Intelligence
225(22)
Aaron P. Wagner
Luis Zaman
Ian Dworkin
Charles Ofria
18 A Hologenomic Approach to Animal Behavior
247(18)
Kevin R. Theis
Danielle J. Whittaker
Connie A. Rojas
19 Creative AI Through Evolutionary Computation
265(8)
Risto Miikkulainen
Part IV Evolution of Communities and Collective Dynamics
20 Subtle Environmental Differences have Cascading Effects on the Ecology and Evolution of a Model Microbial Community
273(16)
Justin R. Meyer
Richard E. Lenski
21 Ecological Context Influences Evolution in Host-Parasite Interactions: Insights from the Daphnia-Parasite Model System
289(20)
Katherine D. McLean
Meghan A. Duffy
22 Toward a Model of Investigating "Coordinated Stasis" Through Habitat Tracking in Communities of Digital Organisms
309(24)
Zaki Ahmad Khan
Faraz Hasan
Matthew R. Rupp
Jian-long Zhu
Tian-tong Luo
Gabriel Yedid
23 Major Transitions in Digital Evolution
333(18)
Heather Goldsby
Benjamin Kerr
Charles Ofria
Part V Evolutionary Applications
24 Rise of Evolutionary Multi-Criterion Optimization: A Brief History of Time with Key Contributions
351(18)
Kalyanmoy Deb
25 Doing Research at the Intersection of Arts and Science
369(16)
Francisco Fernandez de Vega
26 Making Better Use of Repair Templates in Automated Program Repair: A Multi-Objective Approach
385(24)
Yuan Yuan
Wolfgang Banzhaf
27 From Biological to Computational Arms Races - Studying Cyber Security Dynamics
409(14)
Una-May O'Reilly
Erik Hemberg
28 Small Implementation Differences Can Have Large Effects on Evolvability
423(12)
Jory Schossau
Arend Hintze
29 Surrogate Model-Driven Evolutionary Algorithms: Theory and Applications
435(18)
Subhrajit Dutta
Amir H. Gandomi
30 Mechatronic Design Automation: A Short Review
453(14)
Zhun Fan
Guijie Zhu
Wenji Li
31 Evolving SNP Panels for Genomic Prediction
467(24)
Ian Whalen
Wolfgang Banzhaf
Hawlader A. Al Mamun
Cedric Gondro
Part VI Evolution Education
32 Overcoming Classroom Skepticism with Evolution in Action
491(8)
J. Jeffrey Morris
33 How to Increase Creativity in Research
499(14)
Joan E. Strassmann
34 Student Learning Across Course Instruction in Genetics and Evolution
513(22)
Emily G. Weigel
Louise S. Mead
Teresa L. McElhinny
35 The Evolution of the Scientific Virtues Toolbox Approach to Responsible Conduct of Research Training
535(16)
Chet McLeskey
Eric Berling
Michael O'Rourke
Robert T. Pennock
36 The Influence of Instructor Technological Pedagogical Content Knowledge on Implementation and Student Affective Outcomes
551(20)
Amy M. Lark
Gail Richmond
Robert T. Pennock
37 Exploring Evolution in Action in the Classroom, through Human Genetic Diversity and Patterns
571(12)
Michael Wiser
Part VII The Evolution of Erik Goodman
38 Academic Biography of Erik D. Goodman
583(20)
Erik D. Goodman
Index 603