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14<div id="__docusaurus"><div role="region" aria-label="Skip to main content"><a class="skipToContent_fXgn" href="#__docusaurus_skipToContent_fallback">Skip to main content</a></div><nav aria-label="Main" class="theme-layout-navbar navbar navbar--fixed-top"><div class="navbar__inner"><div class="theme-layout-navbar-left navbar__items"><button aria-label="Toggle navigation bar" aria-expanded="false" class="navbar__toggle clean-btn" type="button"><svg width="30" height="30" viewBox="0 0 30 30" aria-hidden="true"><path stroke="currentColor" stroke-linecap="round" stroke-miterlimit="10" stroke-width="2" d="M4 7h22M4 15h22M4 23h22"></path></svg></button><a href="https://avida-ed.github.io/Avida-ED4/" target="_blank" rel="noopener noreferrer" class="navbar__brand"><div class="navbar__logo"><img src="/img/avida-ed-logo.png" alt="Avida-ED Logo" class="themedComponent_mlkZ themedComponent--light_NVdE"><img src="/img/avida-ed-logo.png" alt="Avida-ED Logo" class="themedComponent_mlkZ themedComponent--dark_xIcU"></div><b class="navbar__title text--truncate">Launch Avida-ED 4</b></a><a aria-current="page" class="navbar__item navbar__link navbar__link--active" href="/">Home</a><a aria-current="page" class="navbar__item navbar__link navbar__link--active" href="/curriculum">Curriculum</a><a class="navbar__item navbar__link" href="/help">Help</a><div class="navbar__item dropdown dropdown--hoverable"><a href="#" aria-haspopup="true" aria-expanded="false" role="button" class="navbar__link">About</a><ul class="dropdown__menu"><li><a class="dropdown__link" href="/about/digital-evolution">Digital Evolution</a></li><li><a class="dropdown__link" href="/about/news-archive">News Archive</a></li><li><a class="dropdown__link" href="/about/vintage-archive">Vintage Archive</a></li><li><a class="dropdown__link" href="/about/team">About Us</a></li></ul></div></div><div class="theme-layout-navbar-right navbar__items navbar__items--right"><div class="navbarSearchContainer_Bca1"></div></div></div><div role="presentation" class="navbar-sidebar__backdrop"></div></nav><div id="__docusaurus_skipToContent_fallback" class="theme-layout-main main-wrapper mainWrapper_z2l0"><main class="container container--fluid margin-vert--lg"><div class="row mdxPageWrapper_j9I6"><div class="col col--8"><article><nav class="pageSubnav" aria-label="Curriculum page sections"><span class="pageSubnav__crumb" aria-current="page">Curriculum</span><a href="#avida-ed-lab-book">Lab book</a><a href="#model-lessons">Model lessons</a><a href="#publications-about-avida-ed-curricula">Publications</a></nav> 15<p>This page contains peer-reviewed <a href="#model-lessons" class="">model lessons</a>, including 16in-class, homework, and lab exercises, that instructors may download and modify 17for their own classes under a 18<a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank" rel="noopener noreferrer" class="">Creative Commons (Attribution, Non-commercial, Share-Alike) license</a>. 19For each model exercise, we also have instructor support materials with 20background information about the lesson, exercise variations, and answer keys 21that are available for registered instructors. We have included a few examples 22of the instructor support materials (with answer keys redacted). To find out 23how instructors can receive supplemental materials for other exercises, contact 24<code>[email protected]</code>.</p> 25<ul> 26<li class=""> 27<p>Avida-ED 4 Tutorial Videos</p> 28<ul> 29<li class=""><a href="https://www.youtube.com/watch?v=ue2FVhIV9bI" target="_blank" rel="noopener noreferrer" class="">App Intro</a></li> 30<li class=""><a href="https://www.youtube.com/watch?v=_pIjsatsI9Q" target="_blank" rel="noopener noreferrer" class="">Organism View</a></li> 31<li class=""><a href="https://www.youtube.com/watch?v=y1UFXkKFBGo" target="_blank" rel="noopener noreferrer" class="">Freezer Panel</a></li> 32</ul> 33</li> 34<li class=""> 35<p>Avida-ED <a href="https://qubeshub.org/community/groups/quant_bio_online/forum/general-discussions/resource-walk-through-discussions/9480" target="_blank" rel="noopener noreferrer" class="">Walk-through</a> 36with Cory Kohn and Louise Mead</p> 37</li> 38<li class=""> 39<p>Still using Avida-ED 3</p> 40<ul> 41<li class=""><a href="https://avida-ed.github.io/Avida-ED3/AvidaED.html" target="_blank" rel="noopener noreferrer" class="">Launch Avida-ED 3</a></li> 42<li class=""><a href="https://www.youtube.com/watch?v=x7pISK-eBE8&t=13s" target="_blank" rel="noopener noreferrer" class="">
42Avida-ED 3 Tutorial</a> to get started</li> 43</ul> 44</li> 45</ul> 46<hr> 47<h2 class="anchor anchorTargetStickyNavbar_Vzrq" id="avida-ed-lab-book">Avida-ED lab book<a href="#avida-ed-lab-book" class="hash-link" aria-label="Direct link to Avida-ED lab book" title="Direct link to Avida-ED lab book" translate="no">â</a></h2> 48<p><em>Wendy Johnson, Cory Kohn, Amy Lark, Louise Mead, Robert T. Pennock, Jim 49Smith, Michael Wiser</em></p> 50<p>Wondering where to begin? The Avida-ED lab book includes a sequence of model 51exercises used together in multiple courses. They introduce students to the 52mechanics of the software while also teaching core evolutionary concepts. The 53lab book also includes a background article about digital evolution, the 54Avida-ED quick-start user manual, and additional model exercises.</p> 55<ul> 56<li class=""><a href="/assets/files/Avida-ED_LabBook-a3587d9881426a07b2d98cc4f7014a97.pdf" target="_blank" class="">Avida-ED lab book - 2019 version</a></li> 57<li class=""><a href="/assets/files/Avida-ED_LabBook_Intro-cb4fb6558fcad86c1f7266b2117007c5.pdf" target="_blank" class="">Introduction</a></li> 58<li class=""><a href="/assets/files/Avida-ED_LabBook_Ex1-7f27d11cce47dc5e3c06dc0a90affe34.pdf" target="_blank" class="">Exercise 1 - The Introduction of Genetic Variation by Random Mutation</a></li> 59<li class=""><a href="https://mediaspace.msu.edu/media/Exercise+1+Explained+by+Mike+Wiser/1_snm2noyl" target="_blank" rel="noopener noreferrer" class="">Exercise 1: Video</a></li> 60<li class=""><a href="/assets/files/Avida-ED_LabBook_Ex2-d5bf710fe04684087d95d705a8f20cfb.pdf" target="_blank" class="">Exercise 2 - Exploring Random Mutation and Selection</a></li> 61<li class=""><a href="https://mediaspace.msu.edu/media/Exercise+2+Explained+by+Jim+Smith/0_z2buhpqb" target="_blank" rel="noopener noreferrer" class="">Exercise 2: Video</a></li> 62<li class=""><a href="/assets/files/Avida-ED_LabBook_Ex3-37f132f4c767f36e180c296af9ba61ef.pdf" target="_blank" class="">Exercise 3 - Exploring Fitness and Population Change under Selection</a></li> 63<li class=""><a href="https://mediaspace.msu.edu/media/Exercise+3+Explained+by+Jim+Smith/1_kws4c887" target="_blank" rel="noopener noreferrer" class="">Exercise 3: Video</a></li> 64<li class=""><a href="/assets/files/Avida-ED_LabBook_Ex4-c8cb3a6f5c8fe3a0bfc89df14fab6106.pdf" target="_blank" class="">Exercise 4 - Exploring Population Change without Selection</a></li> 65<li class=""><a href="/assets/files/Ex4.avidaedworkspace-5e5f7bea5ffc2585190357f46f8432f3.zip" target="_blank" class="">Exercise 4 Workspace (zip, for Avida-ED)</a></li> 66<li class=""><a href="https://mediaspace.msu.edu/media/Exercise+4+Part+1+Explained+by+Louise+Mead/0_oibj45c9" target="_blank" rel="noopener noreferrer" class="">Exercise 4: Video Part 1</a></li> 67<li class=""><a href="https://mediaspace.msu.edu/media/Exercise+4+Part+2+Explained+by+Louise+Mead/0_gbq2heph" target="_blank" rel="noopener noreferrer" class="">Exercise 4: Video Part 2</a></li> 68<li class=""><a href="/assets/files/Avida-ED_LabBook_IndRes-8b0a2e42e57981257f90127f730bfda0.pdf" target="_blank" class="">Independent Research - An Experimental Evolution Project</a></li> 69<li class=""><a href="https://mediaspace.msu.edu/media/Independent+Research+Explained+by+Rob+Pennock/0_x4hurcna" target="_blank" rel="noopener noreferrer" class="">Independent Research: Video</a></li> 70<li class=""><a href="/assets/files/Avida-ED_LabBook_Darwin-2e4882de338e6a597f6f1fbd78195945.pdf" target="_blank" class="">Discover: Testing Darwin</a></li> 71<li class=""><a href="/assets/files/Avida-ED_LabBook_QuickStart-bc8d4e210a5b367720e6727bdf3bc33a.pdf" target="_blank" class="">Quick Start User Manual</a></li> 72</ul> 73<hr> 74<a id="model-lessons"></a> 75<h2 class="anchor anchorTargetStickyNavbar_Vzrq" id="model-lessons">MODEL LESSONS<a href="#model-lessons" class="hash-link" aria-label="Direct link to MODEL LESSONS" title="Direct link to MODEL LESSONS" translate="no">â</a></h2> 76<p><strong>PLEASE NOTE</strong>: These exercises were designed for use with Avida-ED 1.0 and 772.0. They were not originally updated for the Avida-ED 3.0 web app. They can
78still be used, but screenshots and some interface descriptions differ slightly 79(for example, metabolic rate was renamed to energy acquisition rate).</p> 80<p>This page also includes <a href="#publications-about-avida-ed-curricula" class="">publications</a> specifically related to 81curriculum.</p> 82<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="understanding-the-introduction-of-genetic-variations-by-random-mutation">Understanding the Introduction of Genetic Variations by Random Mutation<a href="#understanding-the-introduction-of-genetic-variations-by-random-mutation" class="hash-link" aria-label="Direct link to Understanding the Introduction of Genetic Variations by Random Mutation" title="Direct link to Understanding the Introduction of Genetic Variations by Random Mutation" translate="no">â</a></h3> 83<p><em>Robert T. Pennock and Amy Lark</em></p> 84<p>This lesson focuses on mutations as a source of genetic variability and what it 85means to say that mutations occur randomly at some rate. Students make 86predictions about and observe the effects of random mutations on Avidian 87genomes.</p> 88<ul> 89<li class=""><a href="/assets/files/UnderstandIntroGenVar_Handout-b5a5d6cfb3f837ba9471a798dd4b330b.pdf" target="_blank" class="">Student handout</a></li> 90<li class=""><a href="/assets/files/UnderstandIntroGenVar_Instructor-b2e1c67ca8463b918498452dd4bf0e17.pdf" target="_blank" class="">Instructor support material (answer key redacted)</a></li> 91</ul> 92<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="from-genotype-to-phenotype-understanding-the-introduction-of-phenotypic-variations">From Genotype to Phenotype: Understanding the Introduction of Phenotypic Variations<a href="#from-genotype-to-phenotype-understanding-the-introduction-of-phenotypic-variations" class="hash-link" aria-label="Direct link to From Genotype to Phenotype: Understanding the Introduction of Phenotypic Variations" title="Direct link to From Genotype to Phenotype: Understanding the Introduction of Phenotypic Variations" translate="no">â</a></h3> 93<p><em>Robert T. Pennock</em></p> 94<p>Phenotype refers to observable traits that arise from interactions between 95genotype and environment. In this exercise, students investigate simple 96relationships between genotype and phenotype and observe how genomic changes in 97Avidians can change functional traits.</p> 98<ul> 99<li class=""><a href="/assets/files/GenotypeToPhenotype_Handout-6a4079b96d921ea79af5afc13b774e65.pdf" target="_blank" class="">Student handout</a></li> 100<li class=""><a href="/assets/files/MutationRateIndividuals_Instructor-a2ffaa8022285717c39b2836d5a86a35.pdf" target="_blank" class="">Instructor support material</a></li> 101</ul> 102<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="exploring-the-effects-of-mutation-rate-on-individuals">Exploring the Effects of Mutation Rate on Individuals<a href="#exploring-the-effects-of-mutation-rate-on-individuals" class="hash-link" aria-label="Direct link to Exploring the Effects of Mutation Rate on Individuals" title="Direct link to Exploring the Effects of Mutation Rate on Individuals" translate="no">â</a></h3> 103<p><em>Amy Lark</em></p> 104<p>This exercise is based on a 2012 study of butterflies near the Fukushima 105nuclear power plant after radiation release. Students evaluate whether increased 106mutation rate likely caused observed biological effects. An 107<a href="http://www.nabt.org/websites/institution/File/pdfs/american_biology_teacher/2014/ABT_Online_September_2014.pdf" target="_blank" rel="noopener noreferrer" class="">American Biology Teacher article</a> 108accompanies this lesson.</p> 109<ul> 110<li class=""><a href="/assets/files/MutationRateIndividuals_Handout-19a3c839268909509dae0edeca231045.pdf" target="_blank" class="">Student handout</a></li> 111<li class=""><a href="/assets/files/@allfunctions.avidaedfreezeritem-dd2dd92725c67c49de43431dcd1c2e8d.zip" target="_blank" class="">Organism file: @allfunctions</a></li> 112<li class=""><a href="/assets/files/MutationRateIndividuals_Instructor-a2ffaa8022285717c39b2836d5a86a35.pdf" target="_blank" class="">Instructor support material (answer key redacted)</a></li> 113</ul> 114<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="exploring-the-effects-of-mutation-rate-on-populations">Exploring the Effects of Mutation Rate on Populations<a href="#exploring-the-effects-of-mutation-rate-on-populations" class="hash-l
114ink" aria-label="Direct link to Exploring the Effects of Mutation Rate on Populations" title="Direct link to Exploring the Effects of Mutation Rate on Populations" translate="no">â</a></h3> 115<p><em>James Smith and Amy Lark</em></p> 116<p>Two important population characteristics are average fitness and population 117size. In this exercise, students test whether these characteristics are affected 118by mutation rate and in what ways.</p> 119<ul> 120<li class=""><a href="/assets/files/MutationRatePopulations_Handout-259b81e4e03505d8f6f7e30e90a8cdb6.pdf" target="_blank" class="">Student handout</a></li> 121<li class=""><a href="/assets/files/MutationRatePopulations_Instructor-7c2708fff8729246b870743ab794cad6.pdf" target="_blank" class="">Instructor support material (answer key redacted)</a></li> 122</ul> 123<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="artificial-selection-evolution-in-practice">Artificial Selection: Evolution in Practice<a href="#artificial-selection-evolution-in-practice" class="hash-link" aria-label="Direct link to Artificial Selection: Evolution in Practice" title="Direct link to Artificial Selection: Evolution in Practice" translate="no">â</a></h3> 124<p><em>Rett Weber, Wendy Johnson, and Amy Lark</em></p> 125<p>Students are presented with a hypothetical scenario where they use artificial 126selection to evolve an organism with a target trait.</p> 127<ul> 128<li class=""><a href="/assets/files/ArtificialSelection_Handout-c6a55e1c6ea4147f32a397c817f4db58.pdf" target="_blank" class="">Student handout</a></li> 129<li class=""><a href="/assets/files/ArtificialSelection_Instructor-a99ac95dbd2ce104c04538d4e2fb77cf.pdf" target="_blank" class="">Instructor support material</a></li> 130</ul> 131<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="exploring-selection-and-fitness">Exploring Selection and Fitness<a href="#exploring-selection-and-fitness" class="hash-link" aria-label="Direct link to Exploring Selection and Fitness" title="Direct link to Exploring Selection and Fitness" translate="no">â</a></h3> 132<p><em>Amy Lark and Robert T. Pennock</em></p> 133<p>In this exercise, students perform experiments to determine relationships among 134variation, selection, and fitness. From their data, students develop a 135hypothesis about how bacteria evolve antibiotic resistance.</p> 136<ul> 137<li class="">Student handout (legacy reference)</li> 138<li class="">Instructor support material (legacy reference)</li> 139</ul> 140<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="experimental-evolution-project-with-evolving-digital-organisms">Experimental Evolution Project with Evolving Digital Organisms<a href="#experimental-evolution-project-with-evolving-digital-organisms" class="hash-link" aria-label="Direct link to Experimental Evolution Project with Evolving Digital Organisms" title="Direct link to Experimental Evolution Project with Evolving Digital Organisms" translate="no">â</a></h3> 141<p><em>Robert T. Pennock and Amy Lark</em></p> 142<p>This open-ended assignment asks students to propose an evolutionary hypothesis 143that can be tested with Avida-ED, design and conduct an experiment, analyze 144their data, and write a research report.</p> 145<ul> 146<li class=""><a href="/assets/files/ExpEvoProject_Handout-416fe4154cc7d68f70826ee2fb0a3bc9.pdf" target="_blank" class="">Student handout</a></li> 147<li class=""><a href="/assets/files/ExpEvoProject_Instructor-85f3967f76970961781827ea22fccc8e.pdf" target="_blank" class="">Instructor support material</a></li> 148</ul> 149<h3 class="anchor anchorTargetStickyNavbar_Vzrq" id="more-coming-soon">MORE COMING SOON<a href="#more-coming-soon" class="hash-link" aria-label="Direct link to MORE COMING SOON" title="Direct link to MORE COMING SOON" translate="no">â</a></h3> 150<hr> 151<h2 class="anchor anchorTargetStickyNavbar_Vzrq" id="publications-about-avida-ed-curricula">PUBLICATIONS about Avida-ED Curricula<a href="#publications-about-avida-ed-curricula" class="hash-link" aria-label="Direct link to PUBLICATIONS about Avida-ED Curricula" title="Direct link to PUBLICATIONS about Avida-ED Curricula" translate="no">â</a></h2> 152<ul> 153<li class="">James J Smith; Wendy R Johnson; Amy M Lark; Louise S Mead; Michael J Wiser, 154Robert T. Pennock. <a href="/assets/files/Smithetal2016-5817349847b01e94a2a923f2bd513179.pdf" target="_blank" class="">An Avida-ED digital evolution curriculum for 155undergraduate biology</a>. 156<em>Evolution: Education and Outreach</em> (2016, 9(1), 1-11; DOI 15710.1186/s12052-016-0060-0)</li> 158<li class="">Amy Lark, Gail Richmond, Robert T. Pennock. <a href="http://www.nabt.org/websites/institution/File/pdfs/american_biology_teacher/2014/ABT_Online_September_2014.pdf" target="_blank" rel="noopener noreferrer" class="">Modeling Evolution in the 159Classroom: The Case of the Fukushima 160Butterflies</a>. 161<em>American Biology Teacher</em> (2014, 76(7):450-454)</li> 162<li class="">Elena B. Speth, Tammy Long, Robert T. Pennock and Diane Ebert-May. <a href="https://msu.edu/~pennock5/research/papers/EvoEdOut09_UsingAvida-ED.pdf" target="_blank" rel="noopener noreferrer" class="">Using 163Avida-ED for teaching and learning about evolution in undergraduate 164introductory biology 165courses</a>. 166<em>Evolution Education & Outreach</em> (Vol. 2, No. 3, pp. 415-428, 2009)</li> 167<li class="">Cory Kohn, Robert T. Pennock, Jim Smith, Michael J Wiser, and Louise S Mead. 168A Digital Technology-based Introductory Biology Course Designed for 169Engineering and Other Non-life Science STEM Majors. <em>Computer Applications in 170Engineering Education</em> (2018; DOI: 10.1002/cae.21986)</li> 171<li class="">Amy M Lark; Gail Richmond; Louise S Mead; James J Smith; Robert T. Pennock. 172<a href="/assets/files/ABT_Exploring_Relationship__Understanding_Acceptance_Evo-2ce81cd8d81d641a00c834baa561f667.pdf" target="_blank" class="">Exploring the relationship between experiences with digital evolution and 173students' scientific understanding and acceptance of 174evolution</a>. 175<em>American Biology Teacher</em> (2018, 80(2):74-86; DOI 10.1525/abt.2018.80.2.74)</li> 176<li class="">Wendy R. Johnson and Amy Lark. <a href="/assets/files/ABT_Online_Feb_2018-f7bb5e8d47de12829e2b9395e7752f4f.pdf" target="_blank" class="">Evolution in Action in the Classroom: 177Engaging Students in Science Practices to Investigate and Explain Evolution by 178Natural 179Selection</a>. 180<em>American Biology Teacher</em> (2018, 80(2):92-99)</li> 181</ul> 182<hr> 183<p>© Robert T. Pennock</p> 184<p><img decoding="async" loading="lazy" alt="National Science Foundation logo" src="data:image/gif;base64,R0lGODdhQABBAPcAAAAAAAAAVQAAqgAA/wAkAAAkVQAkqgAk/wBJAABJVQBJqgBJ/wBtAABtVQBtqgBt/wCSAACSVQCSqgCS/wC2AAC2VQC2qgC2/wDbAADbVQDbqgDb/wD/AAD/VQD/qgD//yQAACQAVSQAqiQA/yQkACQkVSQkqiQk/yRJACRJVSRJqiRJ/yRtACRtVSRtqiRt/ySSACSSVSSSqiSS/yS2A
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