Avida-ED Sample Model Lessons

Note: These sample model lessons are provided temporarily for illustrative purposes. These will be replaced by edited versions after peer-review is completed. Avida-ED Sample Model Lessons.............................................1
Model In-Class Exercise 1.................................................................................3 Objectives:...................................................................................................3 Reading (before class):.................................................................................3 Zimmer (2005). Testing Darwin. Discover Magazine, 02-05-2005.................3 (Only an excerpt should be sufficient: the article is long, and the first part describes most of what is also relevant to Avida-ED).....................................3 Engagement in the classroom:.....................................................................3 Possible questions:.......................................................................................3 A. How are digital organisms in the Avida environment compare to living organisms in the natural world? ...................................................................3 B. Can we see evolution? Can we experiment with evolution? (elaborate)....3 Mini-lecture, Avida-ED demonstration:.........................................................3 Set up conditions for a basic test run, and run the software as the students observe/run it on their own computers..........................................................3 Questions and activity:.................................................................................3 - What do you expect to see if the test run is repeated multiple times, using the same parameters? Why?.........................................................................3 - Record and plot the results of an evolution experiment as in the following example:.......................................................................................................3 ....................................................................................................................4 Observe the population composition at two different time points (e.g., 200 updates and 600 updates) - look at both tabular data and graph - :..............5 - what is similar and different among the two populations? (same size, different phenotype frequencies, new phenotype - Nan - is present at 600 updates)........................................................................................................5 - how do you explain the differences?..........................................................5 - label the box-and-arrow model (next page) using the following concepts: Variation, Mutation, Inheritance, Fitness, Change in Population.....................5 ...................................................................................................................5 Population at 50 updates Population at 100 updates .................................................................................................5 Population at 200 updates Population at 600 updates..................................................................................................6 Testing Darwin.................................................................................................6 Digital organisms that breed thousands of times faster than common bacteria are beginning to shed light on some of the biggest unanswered questions of evolution...................................................................................6 Model In-Class Exercises 2...............................................................................9 Model Homework Exercise 1..........................................................................11 Model Homework Exercise 2..........................................................................13 Model Open-Ended Experiment Project..........................................................15 Model Lab Exercise 1.....................................................................................16 Model Lab Exercise 2.....................................................................................20

MODEL IN-CLASS EXERCISE 1

Objectives:
1. 2. Use Avida-ED as a model of evolution by natural selection. Apply the principles of random genetic mutation, phenotypic variation, heredity and fitness to explain how Avidian populations change over time.

Reading (before class):

Zimmer (2005). Testing Darwin. Discover Magazine, 02-05-2005 (Only an excerpt should be sufficient: the article is long, and the first part describes most of what is also relevant to Avida-ED)

Engagement in the classroom:

Possible questions: A. How are digital organisms in the Avida environment compare to living organisms in the natural world? B. Can we see evolution? Can we experiment with evolution? (elaborate)

Mini-lecture, Avida-ED demonstration:

Set up conditions for a basic test run, and run the software as the students observe/run it on their own computers.

Questions and activity:

- What do you expect to see if the test run is repeated multiple times, using the same parameters? Why? - Record and plot the results of an evolution experiment as in the following example: Mutation rate: 0.1% Available resources: ALL Time intervals: 100 updates World size: 30x30 (max. population size 900 Avidians) Updates 50 100 200 300 400 500 600 Population size 56 322 895 896 895 896 891 Not 0 29 269 414 495 518 553 Nan 0 7 38 61 137 289 Orn Ant 0 114 338 498 557 562 And 0 7 1 0 4 11

0 15 17 63 75

Avida-ED test run

Number of individuals performing given functions 600 500 400 300 200 100 0 0 100 200 300 Updates 400 500 600

Not Nan Orn Ant And

Observe the population composition at two different time points (e.g., 200 updates and 600 updates) - look at both tabular data and graph - : - what is similar and different among the two populations? (same size, different phenotype frequencies, new phenotype - Nan - is present at 600 updates) - how do you explain the differences? - label the box-and-arrow model (next page) using the following concepts: Variation, Mutation, Inheritance, Fitness, Change in Population.

Population at 50 updates updates

Population at 100

Population at 200 updates updates

From Discover Magazine (02.05.2005) TESTING DARWIN

Population at 600

Digital organisms that breed thousands of times faster than common bacteria are beginning to shed light on some of the biggest unanswered questions of evolution by Carl Zimmer If you want to find alien life-forms, hold off on booking that trip to the moons of Saturn. You may only need to catch a plane to East Lansing, Michigan. The aliens of East Lansing are not made of carbon and water. They have no DNA. Billions of them are quietly colonizing a cluster of 200 computers in the basement of the Plant and Soil Sciences building at Michigan State University. To peer into their world, however, you have to walk a few blocks west on Wilson Road to the engineering department and visit the Digital Evolution Laboratory. Here youll find a crew of computer scientists, biologists, and even a philosopher or two gazing at computer monitors, watching the evolution of bizarre new life-forms. These are digital organismsstrings of commandsakin to computer viruses. Each organism can produce tens of thousands of copies of itself within a matter of minutes. Unlike computer viruses, however, they are made up of digital bits that can mutate in much the same way DNA mutates. A software program called Avida allows researchers to track the birth, life, and death of generation after generation of the digital organisms by scanning columns of numbers that pour down a computer screen like waterfalls. After more than a decade of development, Avidas digital organisms are now getting close to fulfilling the definition of biological life. More and more of the features that biologists have said were necessary for life we can check off, says Robert Pennock, a philosopher at Michigan State and a member of the Avida team.

Does this, does that, does this. Metabolism? Maybe not quite yet, but getting pretty close. One thing the digital organisms do particularly well is evolve. Avida is not a simulation of evolution; it is an instance of it, Pennock says. All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If thats central to the definition of life, then these things count. It may seem strange to talk about a chunk of computer code in the same way you talk about a cherry tree or a dolphin. But the more biologists think about life, the more compelling the equation becomes. Computer programs and DNA are both sets of instructions. Computer programs tell a computer how to process information, while DNA instructs a cell how to assemble proteins. The ultimate goal of the instructions in DNA is to make new organisms that contain the same genetic instructions. You could consider a living organism as nothing more than an information channel, where its transmitting its genome to its offspring, says Charles Ofria, director of the Digital Evolution Laboratory. And the information stored in the channel is how to build a new channel. So a computer program that contains instructions for making new copies of itself has taken a significant step toward life. A cherry tree absorbs raw materials and turns them into useful things. In goes carbon dioxide, water, and nutrients. Out comes wood, cherries, and toxins to ward off insects. A computer program works the same way. Consider a program that adds two numbers. The numbers go in like carbon dioxide and water, and the sum comes out like a cherry tree. In the late 1990s Ofrias former adviser, physicist Chris Adami of Caltech, set out to create the conditions in which a computer program could evolve the ability to do addition. He created some primitive digital organisms and at regular intervals presented numbers to them. At first they could do nothing. But each time a digital organism replicated, there was a small chance that one of its command lines might mutate. On a rare occasion, these mutations allowed an organism to process one of the numbers in a simple way. An organism might acquire the ability simply to read a number, for example, and then produce an identical output. Adami rewarded the digital organisms by speeding up the time it took them to reproduce. If an organism could read two numbers at once, he would speed up its reproduction even more. And if they could add the numbers, he would give them an even bigger reward.Within six months, Adamis organisms were addition whizzes. We were able to get them to evolve without fail, he says. But when he stopped to look at exactly how the organisms were adding numbers, he was more surprised. Some of the ways were obvious, but with others Id say, What the hell is happening? It seemed completely insane. On a trip to Michigan State, Adami met microbiologist Richard Lenski, who studies the evolution of bacteria. Adami later sent Lenski a copy of the Avida software so he could try it out for himself. On a Friday, Lenski loaded the program into his computer and began to create digital worlds. By Monday he was tempted to shut down his laboratory and dedicate himself to Avida. It just had the smell of life, says Lenski. It also mirrored Lenskis own research, launched in 1988, which is now the longest continuously running experiment in evolution. He began with a single bacteriumEscherichia coliand used its offspring to found 12 separate colonies of bacteria that he nurtured on a meager diet of glucose, which creates a strong incentive for the evolution of new ways to survive. Over the past 17 years, the colonies have passed through 35,000 generations. In the process, theyve become one of the clearest demonstrations that natural selection is real. All 12 colonies have evolved to the point at which the bacteria can replicate almost twice as fast as their ancestors. At the same time, the bacterial cells have gotten twice as big. Surprisingly, these changes didnt unfold in a smooth, linear process. Instead, each colony evolved in sudden jerks, followed by hundreds of generations of little change, followed by more jerks.

Similar patterns occur in the evolution of digital organisms in Avida. So Lenski set up digital versions of his bacterial colonies and has been studying them ever since. He still marvels at the flexibility and speed of Avida, which not only allow him to alter experimental conditions with a few keystrokes but also to automatically record every mutation in every organism. In an hour I can gather more information than we had been able to gather in years of working on bacteria, Lenski says. Avida just spits data at you. With this newfound power, the Avida team is putting Darwin to the test in a way that was previously unimaginable. Modern evolutionary biologists have a wealth of fossils to study, and they can compare the biochemistry and genes of living species. But they cant look at every single generation and every single gene that separates a bird, for example, from its two-legged dinosaur ancestors. By contrast, Avida makes it possible to watch the random mutation and natural selection of digital organisms unfold over millions of generations. In the process, it is beginning to shed light on some of the biggest questions of evolution. ()

FULL-TEXT ARTICLE AVAILABLE AT: http://discovermagazine.com/2005/feb/cover

MODEL IN-CLASS EXERCISES 2 BIOL 391: Evo Modeling In-Class Project 1: Familiarization with the Avida-ED Platform
The variables we can control are on the Settings screen. Thats where we set up the conditions for evolutionary runs. First in-class exercise: Using all default settings, turn off all rewards by unchecking the appropriate boxes in the rewards list on the Settings screen. Flip to the Petri Dish screen and click the Start button. Monitor the average fitness graph for 250 Updates. Click the Pause button as close to 250 updates as you can. Discussion Questions: 1. What is the form of the curve on the average fitness graph? 2. Why would the curve take that form? 3. Click the graph to Number of Organisms. Is the grid full? In the Petri Dish screen click on Control in the menu bar and click Start New Experiment. Click Start New Experiment on the popup (well look at freezing (saving) an evolved Petri Dish later). Second in-class exercise: On the Settings Screen select just the two boxes associated with Not and Nand. Uncheck all the other boxes. Flip back to the Petri Dish screen and click the Start button. Run for 250 Updates, monitoring the Average Fitness graph. Click the Pause button as close to 250 updates as you can. Discussion Questions: 1. What is the form of the curve on the average fitness graph? 2. Why would the curve take that form? Why is it different from the first exercise? 3. Click the graph to Number of Organisms. Is the grid full? 4. In the table titled Population Statistics how many organisms are performing Not and Nand? Why arent all organisms performing both tasks? Click Start New Experiment again to reset to the default values.

Third in-class exercise: On the Settings Screen use the Mutation Rate slider to set the Mutation Rate to zero. Leave everything else at the default settings. Flip back to the Petri Dish and click the Start button. Run it for 200 updates and click the Pause button. Discussion Questions: 1. Why is the grid a uniform color? 2. Why is the Average Fitness curve flat? Click Start New Experiment again to reset to the default values. Fourth in-class exercise: On the Settings Screen use the Mutation Rate slider to get as close to a 10% mutation rate as you can adjust the slider (+/- 0.5% is OK). Leave everything else at the default settings. Flip back to the Petri Dish screen and click the Start button. Let it run for 500 Updates and then pause the run. Discussion Questions: 1. How does the form of the Average Fitness curve differ from the first two? 2. Why does it look like that? 3. On the menu below the graph select Number of Organisms. On the first two runs the grid filled completely within 250 updates, but with a high mutation rate it has not filled at 500 updates. Why is it not filled? How would you test your answer in Avida-ED?

MODEL HOMEWORK EXERCISE 1

AVIDA-ED HW #1

Understanding the Introduction of Genetic Variations by Random Mutation Background The basic components of the Darwinian evolutionary mechanism are variation (V), inheritance (I), natural selection (S) and time (T). This exercise focuses on variation and how it can arise. Natural selection acts upon phenotypic variations in a population of organisms. Variations can arise in a population in several different ways. Here we will look only at variations introduced by genetic mutationsrandom changes in an organisms genomeand not at other processes such as recombination, horizontal transfer, etc. Genetic mutations may be point mutations (changes from one instruction to a different one), insertions (additions of an instruction into the genome), or deletions (deletions of an instruction from a genome). For simplicity, this version of AVIDA-ED allows only point mutations, not insertions or deletions in an orgs genome. In real organisms, heritable phenotypic variation is in part determined by differences in genotype. For instance, a strain of bacteria may have the ability to metabolize some sugar (e.g. Glu+) because it produces a particular functional enzyme. Such an enzyme is coded for and produced by some sequence of instructions in the organisms DNA. In AVIDA-ED as well, phenotypic variation (e.g. Nan+, And-) depends upon genotypic variations, i.e. the different sequences of instructions in the orgs genome that can produce different functions. Your goal in this exercise is not to look at what exactly makes a sequence of instructions functional, but just to understand how mutations produce varieties of genetic sequences and that these can affect the sequences functionality. There are several common misconceptions people have about how random mutations work in the evolutionary process and these experiments should help you learn to avoid them. Assignment Tasks Preparation. Download AVIDA-ED software from <www.avida-ed.msu.edu>. Go to the Download page and then click the Mac or PC link to get the appropriate version of the software for your computer. You can also download the user manual, which is the same for both versions. Pilot study: Use the Organism Viewer to see how point mutations change the genomes of

organisms. (i) Flip to settings. Set the per site mutation rate to 10%. Keep repeatability mode set to Experimental. Flip back to viewer. (ii) Drag in the @ancestor from the freezer and click play to watch it run. (iii) Record the changes in the offsprings genome after replication. (For this exercise, it will be sufficient just to list the mutated instructions. Do that in clockwise order starting from the 3 oclock position on the circular genome). - Observations Run #1: Predict: What do you expect to see if you repeat this several times using the same ancestor with the same mutation rate? - (1) Will the number of mutations always be the same? Yes / No - (2) Why? - (3) Will the specific mutations always be the same? Yes / No - (4) Why? Test: Repeat steps (ii) and (iii) from the Demo at least three times (but not until AFTER you have written down your predictions above). - Observations Run #2: - Observations Run #3: - Observations Run #4: Results: Were your predictions confirmed or disconfirmed? Discussion: What do your tests above reveal about how genotypic variations arise in a population?

Future research: Do specific mutations arise because they are the ones that the organism needs in a given environment? Given your observations above, what would be your hypothesized answer to this question? Then describe a simple experiment that could test your hypothesis. (Give your answers on the back of this sheet.)

MODEL HOMEWORK EXERCISE 2

10/26/2006 09:49 AM AVIDA-ED Page 1 of 2 http://www.msu.edu/course/lbs/144/f06/hw3_avida.html

LBS144 F06 October 26, 2006 Homework #3 (20 pts.) AVIDA-ED Introduction
Evolutionary theory is widely misunderstood and even rejected by a majority of Americans. To help address this problem, we are working to adapt an artificial life research platform, "AVIDA", as an educational tool. Organisms in this system, Avidians, are digital organisms that self-replicate, mutate, and adapt by natural selection to a computational environment. In this homework exercise, you will use the computer program, AVIDA-ED, to test hypotheses about the evolution of Avidians. We will develop a set of hypotheses about the effect of mutation rate on the overall fitness of a population. We will each run AVIDAED under a specified set of conditions, and then create a data set based on everyone's results. We will then explore the class data in lecture and try to understand what the data are telling us. Homework Tasks 1. (5 pts.) Download the AVIDA-ED software from Angel. On "My Page" in Angel, go to, "My ANGEL Groups", and in "Find a Group", search for AVIDA under, "Keywords". Enroll in this group, and then download the appropriate version of AVIDA-ED for the computer that you are using. 2. (5 pts.) Write two sets of hypotheses and corresponding null hypotheses regarding what will happen when the mutation rate increases drastically and decreases drastically. (We will do a preview exercise of this in class on Thursday Oct. 26th.)
10/26/2006 09:49 AM AVIDA-ED Page 2 of 2 http://www.msu.edu/course/lbs/144/f06/hw3_avida.html

Then, on your own, do three runs of AVIDA using the following conditions: World Size = 60 X 60; Pause Run at 200 updates, Starting Organism = @ancestor; Mutation Rate = 0.2%, 2.0% and 20%. For each of these three runs: Record or make a graph showing fitness as a function of update. Record the Population Size and Average Fitness for your population at Update 200. Briefly describe the visual image of the Petri plate. (I.e., are there a lot of different colors? Are the different colors grouped together? , Etc.) Are there similarities and differences between the three runs? 3. (5 pts.) Submit your fitness and population size data from each run in Part 2 to Kristin Bott (kristin.bott@gmail.com) by Sunday, Nov. 5th at 11:59 pm. Kristin may have additional instructions on how these data should be submitted. We will explore the class data in lecture on Thursday, Nov. 9th. 4. (5 pts.) After we go over the class data, write a paragraph about what happened. Explain whether the data support or contradict the hypotheses, and why. 5. Turn in the following, on paper, in class Tuesday Nov. 14th: Your two sets of hypotheses and corresponding null hypotheses; Your graphs showing fitness as a function of update for the AVIDA-ED runs at mutation rates of 0.2%, 2.0% and 20%;

Your brief descriptions of your Petri plates from these three runs; and Your paragraph about the class data.

MODEL OPEN-ENDED EXPERIMENT PROJECT

Spring 2007 Experimental Evolution with Evolving Digital Organisms Project Tasks: Hypothesize: Propose an evolutionary hypothesisa simple one will dothat you can test using Avida-ED. Design an Experiment: Work up an experimental protocol to follow to test your hypothesis. You should consider what the relevant variables are, what data to take, and how many replications are needed. Say what predicted observations will confirm or disconfirm your hypothesis. Run Your Experiment & Analyze your data: Follow the protocol and record the appropriate data. Perform statistical tests to as needed to analyze your data. Write up a report: Write up your experiment as a standard scientific paper. This should include (i) introductory background information and statement of your hypothesis, (ii) methods, (iii) results, and (iv) conclusions and discussion. The complete report should be no more than 5 pages long.

MODEL LAB EXERCISE 1 LBS-145 Stream II Lab Exercise and Homework #1: Evolving TCE Biodegraders
The soil and water on the corner of Grand River and Hagadorn are contaminated (as reported last semester in the State News). One of the contaminants is trichloroethylene (TCE), a hazardous chemical used as a spot remover in dry cleaning. Since bacteria in the soil are decomposers, theoretically they should be able to break down the toxic chemical to non-toxic elements (i.e., chloride, water, CO2). Assume an environmental consulting company visited our LBS-145 class to ask for help cleaning up the trichloroethylene (TCE). Each year the company spends millions of dollars on similar spills all over Michigan. Current methods to remove TCE are expensive and require that contaminated soil be removed and disposed in hazardous waste dumps. The environmental consulting company is interested in spiking the soil with bacteria that biodegrade (break down) TCE. Your goal is to evolve a bacterial strain that can biodegrade TCE so the soil can be cleaned up on-site instead of dumped into hazardous waste landfill. 1) What do you know or think you know about this problem? List below:

2) What things do you not know about this problem? List below:

3) What would you like to know, but cant know to solve this problem? List below:

Background information: Objective: For your exercise you will use Avida-Ed (an environment for artificial bacterial evolution) to find the most efficient method to evolve an organism to degrade TCE. Researchers use models to test hypotheses when an experiment would take too long to perform, be difficult to manage, or be too expensive to conduct. For this project we are using a artificial bacterial organisms in a Petri dish (Avida-Ed). In real life, bacterial populations can double as fast as every 30 minutes. In Avida-Ed, doubling times are about 1 second. Problem: TCE in Avida-Ed The or function of Avida-Ed degrades TCE (or is an enzyme). Your job is to evolve organisms that make or. On the back of the Petri dish change the environment for evolving organisms by 1) changing the mutation rate, 2) changing the world size (maximum population size) or 3) adding or removing the reward for functions (Figure 1). If a function is checked, organisms that make the function are rewarded with a higher reproductive rate. Organisms that make more functions have higher fitness.

Figure 1: Some features may have changed a little bit in the latest version of the software.

If an organism in Avida-Ed can make the enzymes that degrade TCE, a number will appear next to the function or in the organism info and population info panels. The organism highlighted in Figure 2 can make the functions not and ornot. The population info panel shows what all organisms in the Petri dish can do. In the example, organisms can make 766 not, 651 nand and 536 ornot functions. Use the population info panel to determine if any of the organisms can make or, which consumes TCE.

Figure 2. Some features may have changed a little bit in the latest version of the software. Downloading Avida-ED software for your own computer: We set up an Angel guest account that you can access to download the software. The page also has a discussion section that you can use to post comments. Complete the Avida-ED laboratory assignment individually or in pairs: Put Group Name and Names on the hard copies.

Write up the text part of this homework (word process) Use a spreadsheet to make graphs (Excel) or hand draw your graphs on carbonless paper

1. Get Avida-Ed: a. Download Avida-Ed [PC ( zip 13 meg or executable 78 meg), Mac ( dmg 22 meg) ] from the Angel group website. If you don't know how to unzip a file, download the executable. To start Avida-Ed, just double click on the executable.

b. Complete the tutorial. It is short. This tutorial will quickly familiarize you with Avida-Ed and how to use it. You may also download the Avida-Ed user manual for more detailed information. 2. Design the experiment: 1. Write a hypothesis to test an idea about the most efficient method to evolve a TCE degrading bacteria. To do so, change variables on the back side of the Petri dish. The changeable variables include mutation rate, population size, and function rewards. 2. Write a description of an experimental design to test your hypothesis using Avida-Ed. The dependent variable will be the number of updates to evolve TCE (or) biodegradation. In your description, state how the conditions you selected test your hypothesis. The description should be clear enough that another group can replicate your experiment. The design must include at least 5 runs for each treatment. 3. Write a prediction based on the hypothesis before you run the simulation Remember, a hypothesis does not have to be correct, but your experiment must be designed to logically test it. 2. Simulations: Collect data. For each run, write down the parameters you changed and the number of updates it took to evolve or. During and after each run record observations that you think might be important, but that are not included in the experimental design. Use these observations to help you explain the results. 2. Data Analysis: o Plot graphs of the results. What are the independent and dependent variables? Label the axes? 3. Discussion: o Write a description of how your results support or refute the hypothesis. Use the readings, observation, notes, and information from the model to explain your results with regard to your hypothesis. o Propose a protocol for evolving bacteria to degrade TCE based upon the results. o o

MODEL LAB EXERCISE 2

ArtificialLife&Evolution
Objectives: Toexploreevolutionwithevolvingdigitalorganisms. Totestevolutionaryhypotheses. Totryoutdifferentevolutionaryscenarios. Toaddressseveralmisconceptionsaboutevolution. Introduction: Lifeonlyevolvedonceonearth.Inaddition,formostorganisms, evolutionhappensveryslowlyonahumantimescale.Asaresult,itisdifficult toexploreevolutionexperimentallytoaddressquestionslikeWhatwould havehappenedif?orDiditnecessarilyhavetohappenthisway? InthePopulationGeneticslab,yousimulatedevolutionforasingle simplegenewithtwoalleles.Althoughthisisimportant,itdoesnotcapture muchofthecomplexityofevolutioninthewild. Toexploreevolutioninmoredetail,youneedorganismswithamore complexgenotypethatcanreproducerapidly.Manyresearchersstudythe evolutionofmicroorganismsforthesereasons.Inthislab,youwillexplorethe evolutionofsimpledigitalmicroorganismsastheyevolveinthecomputer simulation,AVIDA. InAVIDA,theorganismsareshortcomputerprogramsthatcarryout onlyonefunction:theyreplicatethemselves.Theyaresimilartocomputer viruses,whichreproducebycopyingthemselvesfromonecomputertoanother. Sincecomputervirusescopythemselvesexactly,theydonotevolve;anychanges areduetohumanintervention.TheorganismsinAVIDAaresubjecttorandom mutationandnonrandomselection,sotheydoevolvelikeorganismsinthereal world. AVIDAwasdevelopedbyresearchersasatooltostudyavarietyof evolutionaryprinciplesandhasresultedinseveralinterestingfindings.Youcan findlinkstotheseontheAVIDAwebpage;thereisalinktothispageontheOn LineLabManualforthislab.WewillbeusingAVIDAEd(AVIDAfor

Education)developedbyRobertPennockandothers.AVIDAEdisfullfeatured AVIDAwithauserfriendlyuserinterface.AlinktotheAVIDAEdhomepage canalsobefoundontheOnLineLabManualpage. Thebasicrequirementsforevolutionare: 1. Genomes .Organismsmusthaveagenome,acompletesetofgenetic instructionsformakingthemselves. 2. Selfreproducingorganisms .Organismsmustbeabletomakecopiesof themselves,includingcopiesoftheirgenome. 3. Mutation .Thecopyingin(2)isnotalwaysperfect,sogenomescan change. 4. LimitingResources .Thereisonlyenoughspace,resources,etc.forafinite numberoforganisms,sosomeorganismsreproducelessfrequentlythan others. Giventhesefourconditions,theorganismswillevolvetheywilladapttotheir environmentbyaprocessofnaturalselection.Themorefitvariantswillout competethelessfitvariantsandthepopulationwillchangeovertimetoadaptto thegivenenvironment. AVIDAsimulatesaworldthatsatisfiesthesefourrequirementsfordigital organismscalledAvidans.TheAVIDAprogramsimulatestheworldthatthe Avidanslivein;itsimulatesfeedingtheAvidans,replicatingthem,and removingthemwhentheydie.Inordertounderstandhowthisoranyother simulationworks,youneedtoconsidereachofthefourrequirementsinthree differentways: A. Howtheseissuesmanifestthemselvesintherealworld.Thiswillbe showninitalictype. B. Howisthisshowninthesimulation.Thiswillbeshowninboldtype. C. Theunderlyingmechanismthatthesimulationusestosimulatethis behavior.Thiswillbeshowninregulartype. Herearethefourrequirementsindetail:

1. Genomes .Intherealworld,mostorganismshaveaDNAgenome.This sequenceofDNAdeterminesthegeneticpropertiesofthatorganismandcontains instructionsformakingthatorganism.Itisnotasetofinstructionslikea computerprogram,butitresultsintheproductionofasetofproteins,etc.that arecapableofreplication,behavior,etc.Avidanshavegenomesthatcontain geneticinformation.ThisgeneticinformationtellstheAVIDAsoftware howtoreplicatetheorganism.EachAvidanhasashortcirculargenome, likeaDNAmolecule.InAvidans,thereare26differentkindsofbases intheirDNA,representedbythelettersathroughz.Eachdifferent base(athroughz)correspondstoaparticularinstructionfortheAVIDA

programtoexecuteasitsimulatesthecreaturecontainingthatinstruction. AgivenAvidansgenomeisalways50baseslong.Theparticular arrangementofthesebasesdeterminesif,andhow,theAvidanwill reproduceandbehave.AsampleAvidangenomeisshownbelow: Eachsmallcircleisabase.Thedifferentlettersarethedifferent instructionsinthe Avidansgenome.Theyformasimplecomputerprogramthatisexecuted bythe AVIDAsoftware. 2. Selfreproducingorganisms .Intherealworld,organismsmakecopiesof themselves;theyreproduce.InBio112,wehavelookedatbothasexualand sexualreproduction.Avidansreproduceasexuallylikebacteriaandother microorganisms.ThesimplestviableAvidangenomecontainsjustthe sequenceofbasesnecessarytoreproduceitself.Itdoesnothingmore thancopyitself.Inthisway,itisthesimplestpossiblelivingthingin

theAVIDAworld.TheAVIDAprogramreadsthegenomeofeach Avidanandexecutesthesequenceofcommandslistedinthegenome. ThesimplestviableAvidansgenomeisjustthesequenceofinstructions neededtotelltheAVIDAprogramtomakeonecopyofitself.Thus,in onegeneration,asingleviableAvidangivesrisetoacopyoftheAvidan; sonowtherearetwoAvidans.Inthenextgeneration,eachofthetwo producesadaughter,givingatotaloffourAvidans,etc. 3. Mutation .Intherealworld,DNAreplicationisnotperfect;daughtercellshave genomesthatdifferslightlyfromthoseoftheirparents.Thisgivesrisetothe variationthatisnecessaryforevolution.WhenAvidansreplicate,their genomesaresubjecttomutation.Youcancontrolthechanceof mutationwhenyousetupanAVIDAexperiment.EachtimetheAVIDA programcopiesaninstructionfromaparentAvidantoadaughter Avidan,thereisasmall(andadjustable)chancethatthecopied instructionwillbedifferentfromtheoriginal(forexample,changingan atoane).Thisresultsinamutationthatwillbepassedtothe offspringofthedaughter. 4. LimitingResources .Intherealworld,thereisnotenoughspace,food,light, etc.forallorganismsthatareborntosurvive.Asaresult,someorganisms reproducemorethanothers,sosucceedinggenerationshaveahigherfrequencyof advantageousalleles.IntheworldsimulatedbyAVIDA,thereisplentyof food,butspaceislimiting.Therefore,onlyafixednumberofAvidans canbealiveatanygiventime.Thisnumberisadjustable,butit defaultsto900.WhenanAvidanisborn(copiedfromparentto daughter),itreplacesarandomlychosenneighborofitsparent.Open spacesresultwhenAvidansdie.Avidansarechosenrandomlyfordeath independentofgenotype.Avidansaredeletedrandomlyfromthepetri dish. Inthislab,youwillexploretheevolutionofAvidansandmake connectionsbetweenthissimulatedworldandevolutionintherealworld.

Procedure PartI:WarmupExercises 1)StartupAVIDAEdfromthedock.Ittakesalittlewhiletogetstarted. 2)Youwillseesomethinglikethis: Viewer chooser buttons Petri dish viewpane Panel Changer Button Statistics viewpane

Petri Dish: Avidans live here.

Freezer

ThisistheviewyouwillobserveasyourpopulationofAvidansevolves. Younowneedtosetupthepetridishenvironment,addastartingAvidan,and runasimulation.

3)ClickthePanelChangerButton(itisattheupperrightofthePetriDish ViewpaneandismarkedFliptoSettingstogettothesettingspanel.You shouldseethisinthecenterpanel:

Thisallowsyoutosettheenvironmentalparametersforthesimulationrun.The are: Persitemutationrate:Thisratereflectsthepercentchancethataninstruction isincorrectlycopied.So,ifthepersitemutationrateis1%,thereisa1% chancethatwhenaninstructioniscopied,itwillendupasanyoneofthe26 possibleinstructions(oneofwhichisitself,soitcouldmutatebacktoitself). Witha1%persitemutationrate,if100instructionsarecopiedoneofthem willbemutatedonaverage(althoughthisnumbercouldbehigherorlower inanyinstance).

Worldsize:SetsthemaximumnumberofAvidiansthatcanexistinthe population.ThetwonumbersspecifythenumberofAvidiansperrow,and percolumn.So,10x10=amaximumpopulationof100organisms. Ancestralorganism(s):Theorganism(s)thepopulationbeginsfrom.Dragin organismsfromtheFreezeratthebeginningofarun. EnvironmentalResourceSettings:Avidianscanreceiveextraenergyand haveincreasedfitnessiftheyevolvetheabilitytometabolizenutrients. Hereyoucansetwhatnutrientsareavailableintheenvironment. ExactRepeatability:ManystepsinanAvidaevolutionaryrunhappen randomly(e.g.whatmutationswilloccurinthegenome,intowhatcellanew organismwillbeplacedatdivision),soeachrunwillbeslightlydifferent evenwiththesamegeneralenvironmentalvalues,asinnature.Thisisthe defaultsetting.However,ifyouneedtorepeatarun(e.g.fora demonstration)youcanswitchthistoexactlyreplicatethesequencewiththe samemutationsandvalues. Offspringplacement:Whenanoffspringisborn,itcaneitherbeplaced(at random)inanyoftheeightcellsadjacenttoitsparent,oranywhere(at random)inthepopulation.Ifthecellisalreadyoccupiedtheorganismthere isoverwritten. PauseRunManually/Automatically:Ifyousetaspecificnumberaheadof time,therunwillpausewhenthismanyupdateshavepassed.Ifyousetthe runtostopmanually,itwillcontinueindefinitelyuntilitispausedusingthe buttonunderthePetridish. FreezePetriDishButton:Pushsnowflakebuttontosaveeitherjustthe environmentalconfiguration(bysavinganempty)Petridish,orelsethe environmentplustheorganisms(bysavingafullPetridish).

Forthislab,themostimportantoneistheEnvironmentalResource Settings.Thismodelsdifferentresourcesavailableinnatureandallowsyoutoseehow evolutionwouldproceedifconditionsweredifferent.Someoftheseresourcesaremore nutritiousthanothers.AlthoughallAvidansinthepetridishreceivesufficient nutrition,iftheyareabletometabolizecertainadditionalnutrientsugars (notose,nanose,etc.)theyreceiveasubstantialincreaseinfitness.For example,anAvidanthatcanusenotosehastwicethefitnessofanotherwise identicalAvidanthatcannot.Othersugarshaveevenhigherfitness rewards;thesearelistedabovethebuttonsinthispartofthepane.Avidans

thataremorefitreproducemoreoftenthanthosethatarelessfit.Inthe AVIDAsystem,anAvidanisabletouseasugarifitcanperformaparticular simplenumericalcalculation.TheAVIDAsystemtriestosendanumbertoeach Avidan,ifthatAvidancanreadinthatnumberandsendbackanappropriately modifiednumber,thenAVIDAgivesthatAvidanafitnessboost. Importantly,itiseasiertoevolvetheabilitytoutilizesomesugarsthanothers. Thatis,ittakesmorealterationsofthestartingAvidantoallowittoutilizeequosethan toallowittousenotose.Intherealworld,somenutrientsourcesrequiremoreenzymes, ormorehighlymodifiedenzymes,tobeutilizedbyanorganism.TheancestorAvidan cannotuseanyofthesugarsintheEnvoironmentalResourceSettings.Some mutantversionsoftheancestorcanusesomeorallofthesesugars.Itrequires onlyafewmutationstomakeanAvidanthatcanusenotose;itrequiresmany independentmutationstouseequose.Inordertouseanysugar,theAvidan mustincludeinstructionsforgettinganumberfromAVIDAandreturningitto AVIDA.Itmustalsoincludeinstructionsfortheparticularmathematical manipulation.Somemanipulationsaresimple,liketheonefornotose,andtake onlyafewmoreinstructions;othersaremorecomplex,liketheoneforequose, andtakemanyadditionalinstructions. Youshouldleavealltheothersettingsattheirdefaultvaluesinthispartof thelab.YoumaywanttoplaywithsomeoftheminPartII. 4)Forthisfirstrun,youshouldturnonallofthesugarsintheEnvironmental ResourceSettingthisisthedefault.Inthisstate,Avidansthathavetheability tousesugarsaremorefitthanthosethatdonot. 5)LoadanancestorAvidanintothepetridish.IntheFreezer,lookunder Organisms.Clickon@ancestoranddragitintotheAncestralOrganisms panedescribedabove.Youshouldseethisinthepane:

Nowyouarereadytorunasimulationandlettheseorganismsevolve. 6)ClickontheFliptoPetriDishbuttonintheupperrightofthe EnvironmentalSettingsPanel.Thiswilltakeyoubacktothepetridishview. 7)Startthesimulation.AtthebottomofthePetriDishviewpane,youwillsee thesebuttons:

Start/Pause Button

Be sure this is set to Fitness.

SetthecolorcodeselectorshownabovetoFitness. ClickontheStart/pausebuttonandthesimulationwillstart. Youwillthenseeseveralthingshappening: ColoredsquareswillstartappearinginthepetridishtheseareAvidans beingborn. TheTime(Updates)willstarttoincreasetoindicatethatthesimulationis running. ThegraphatthelowerrightoftheStatisticsWorkpanewillstartbeing drawntoshowtheaveragefitnessoftheAvidansinthepetridish. ThePopulationStatisticsnumbersattheupperrightoftheStatistics

Workpanewillstarttochange. Thearrowbuttonwillchangetoa||pausebutton.

8)Quicklypausethesimulationbyclickingthepausebuttonafterabout50 updates. 9)Youshouldlookatthevariousdisplaysanddiscussasaclasswhattheymean: TheAverageFitnessGraph.Theancestorhasafitnessof0.25.Youwill notethattheaveragefitnessofthepopulationfallsbrieflybeforerising. Provideaplausibleexplanationforthisobservation.

TheColorScaleLegendtherainbowstripejustbelowthepetridish. ThisisthecolorcodefortheAvidansinthepetridishtheircolor dependsontheirfitness.Thisisusefulbecause,inadditiontoshowing thefitnessofeachAvidan,itisconstantlyupdatedasthefitnessofthe creaturesincreases.Therefore,ifyoulookatthemaximumvalueofthis legend,itgivesyouthefitnessofthemostfitAvidancurrentlyinthepetri dish.ClickonanAvidanwithalowfitnessandlookintheStatistics WorkpaneunderOrg.ClickedonReporttofindtheexactfitnessofthe Avidanyouclickedon.

10)Clickthestart(arrow)buttontocontinuethesimulation.Letitrununtilthe petridishisfullandthePopulationSizeisabout900andthenclickthepause button.Fromthemenuunderthegraph,chooseNumberofOrganismsandyou willseeagraphofthenumberoforganismsovertime.Whatkindofgrowth doesthatshow(linear,exponential,logistic)?Why?

11)Runthesimulationforawhilelongeruntilthehighestfitness(shownbythe numberattherightendofthecolorcodebarabovethestart/pausebutton)gets toabout100ormore.PausethesimulationandclickontheAvidanwiththe highestfitness.LookintheOrg.ClickedonReportandyouwillsee somethinglikethis: Whatisitsfitness?Whatsugarscanituse?Howdoesthisexplainits highfitness? Intheexampleattheright: Fitness=277.69 ItcanuseOrose,Antose,andNorose Thehighfitness=(basefitness)X(bonusfromeachsugar) thebasefitnessis0.25 inthiscase: 0.25x8x8x16=256whichiscloseto277.69

PartII:MisconceptionsaboutEvolution YouwillnowuseAvidatoexplorefourimportantmisconceptionsabout evolution. MisconceptionI:Mutationsalwaysreducethefitnessoforganisms.Infact, mutationscanbeneutral,advantageous,ordisadvantagous. MisconceptionII:Thepresenceofaselectiveagentcausesadvantageousmutationsto occur.Infact,themutationsoccurrandomlyindependentoftheselection; selectionthenfavorstheadvantageousmutations. Youwilladdressthesetwomisconceptionsthroughthefollowing experiments:

1)ChooseStartNewExperimentfromtheControlmenu.ClickDiscard andstartnewexperiment. 2)Draginasingle@ancestorasyoudidbefore. 3)Forthisfirstrun,youshouldturnoffallofthesugarsintheEnvironmental ResourceSettings.Clickthecheckboxesonallofthemuntiltheyareall unselected.Inthisstate,allAvidansreceiveminimalnutritionandthereisno addedfitnessassociatedwithbeingabletouseanyofthesugars. 4)BesurethedisplayissettoshowFitness. 5)Clickthestartbuttonandletthesimulationrununtilabout300 updateshavepassed,thenclickthepausebutton.Lookinthe PopulationStatistics,youshouldseesomethinglikethis(your numberswillbedifferent): ThisdisplayshowsthenumberofAvidansinthepopulation thatareabletouseeachofthedifferentsugars.Youcanclickon thebuttonstoidentifytheorganismsthatareabletousethatsugar. IfyouclickononeoftheidentifiedAvidans,youwillseethatits fitnessisnothighereventhoughitisabletousethesugar.You shoulddiscussthefollowingquestionsasaclass:

a) WhyisitthattheAvidansthatcanusenotosedonothavesignificantly higherfitnesshere?Whatdoesthishavetodowithevolutioninthereal world?

b) HowisitpossiblethattheseAvidanshaveevolvedtousethesesugars eventhoughthesugarsarenotpresent?Whatwouldyouhaveexpected ifMisconceptionIIwerecorrect?

c) PooltheclassresultsofhowmanyAvidanscoulduseeachofthesugars intoatableontheblackboard(onecolumnforeachgroup;onerowfor eachsugar).Whyarentthenumbersthesameforallgroups?Whatdoes thishavetodowithevolutionintherealworld?

d) Whatistherangeoffitness(lowesttohighest)oftheorganismsinyour population?

e) NotetheAverageFitness;wewillusethisdatalater.

6)Nowitistimeforanewrun.SelectStartNewExperimentfromtheControl menu(orhitappleR)andclickDiscardandStartNewExperiment.Thepetri dishwillclear. 7)ClicktheFliptoSettingsbutton. 8)Setupforyournextrun: Startwithone@ancestorasinstep(2). Settheenvironmenttocontainoneandonlyonesugar:notose(upperleft ofthelist).Besurethatnotoseandonlynotoseisselected. ClicktheFliptoPetriDishbutton. 9)Clicktherun(arrow)buttonandletthesimulationrunforabout300updates andthenclickthepausebutton.Youshouldthenanswerthefollowing questionsasaclass: a) WhatistheAverageFitness?Howdoesitcomparetotheaveragefitness youobservedinStep(5e)?Provideaplausibleexplanationforthisresult. WhatwouldyouhaveexpectedifMisconceptionIwerecorrect?

b) Whatistherangeoffitnessvaluesinyourpopulation?Doesitdifferfrom youranswerto(5d)?Provideaplausibleexplanationforthisresult.

c) PooltheclassresultsofhowmanyAvidanscoulduseeachofthesugars intoatableontheblackboard(onecolumnforeachgroup;onerowfor eachsugar). o Howdothesenumbersdifferfromthoseyousawin(5c)?Provide aplausibleexplanationforthisresult.Whatdoesthishavetodo withevolutionintherealworld?

o Whyarentthenumbersthesameforallgroups?

d) HowdotheseresultsaddressMisconceptionsIandII?

MisconceptionIII:Becausemutationsarerandom,theycannotleadtotheorderly progressthatisevolution.Infact,althoughmutationsarerandom,selection providestheguidethatleadstoanorderlychange. Toaddressthismisconception,youwillneedtopooltheclasssdata. 1)Startanewrunwith@ancestorandallsugarspresent. 2)StopthesimulationwhenanAvidanappearsthatcanuseanewsugar.Note thetimeatwhichthisnewfeatureevolvedandthesugarinvolved.Then continuetherunandlogwhentheabilitytouseothersugarsevolves.For example,youmightfindthat: Time Event 10 firstAvidanthatcouldusenotose 50 firstAvidanthatcouldusenanose etc. 3)Dothisforseveralrunsandpoolyourresults. Isthereanypatterntotheorderandtimingofappearanceofthedifferent typesofAvidans?

Provideaplausibleexplanationforthispattern.

WhatwouldyouhaveexpectedifMisconceptionIIIweretrue?

MisconceptionIV:Complexfeatures(forexampleaneye)cannotevolvebecauseeither: theyaretoocomplextoarisefromonemutation orifyoutriedtoevolveacomplexfeatureinseveralintermediatesteps,there wouldbenoadvantagefortheintermediates(forexample,alenswithouta retina),sotheywouldneverevolve. Infact,itistruethatcomplexfeaturesareunlikelytoevolveinonestep. However,complexfeaturesdoevolvebecausetheintermediates(forexample, primitiveeyesratherthanpartialeyes)doconfersomeselectiveadvantage.You canlookatitlikethis:althoughyoucantjumptothetopofacliffinonejump, youcangetthereifthereisastaircaseofintermediatestepsandjumpfromone totheother. Addressingthismisconceptionwillalsorequirepoolingoftheclasss

data.

Inthiscase,thecomplexfeaturewillbetheabilitytouseoneofthe difficultsugarsonethattypicallyevolveslaterthantheothers.Inthiscase, ornose.Youwillcomparetwodifferentscenarios: a) Allinonejumpyouwillonlyprovideornose.Inthiscase,the Avidanswillhavetoevolvetheabilitytouseornosewithoutany intermediatesteps.Althoughtheymayhappentoevolvetheabilityto usesimplersugarsalongtheway,therewillbenoadvantageforthis. Theyonlygetafitnessboostiftheygetallthewaytoornose. b) Upthestaircaseyouwillprovideallthesugarsinadditiontoornose. Thatway,Avidanswhomaketheeasystepofbeingtouseanysugarwill getatleastasmalladvantage.TheseAvidanswillbeataselective advantageandtakeoverthepopulation.Fromthisnewpopulation,it willtakefewermutationstogettothenextsugarandfinallyontoornose. Theothersugarsprovideaselectiveadvantageforpartialuseofornose stepsontheladdertoornose. Youwillcomparethesetwoscenariosintermsoftheamountoftimeit takestoevolvetheabilitytouseornose.Halfoftheclassshouldsetupscenario (a)andtheotherhalfscenario(b).Eachshoulddomanyrunsandtallythetime ittookforthefirstAvidancapableofusingornosetoappear.Sincetherewillbe awiderangetothesetimes,youwillneedtodomanyrepeatedrunsandpool yourdata.

NOTE:ifyouaredoingscenario(a),youwillneedtoturnoffallsugars exceptornoseeverytimeyousetupanewrun.Besuretodothis,sincethe programdefaultstoincludingallsugarsineveryrun.

Afteryouhavecollectedyourdata,answerthefollowingquestions:

Whataretheresults?Whichscenarioallowsthemorerapidevolutionof thiscomplextrait?

Howdoesthisrelatetoevolutionintherealworld?

WhatwouldyouhaveexpectedifMisconceptionIVwerecorrect?

LabReport Mustbetyped;handdrawngraphsareacceptable. Dueatthestartoflabduringtheweekindicatedonthesyllabus;thisisafirm deadline. Yourlabreportmustbeinyourownwords. Yourlabreportmustinclude: Chooseanyoneofthefourmisconceptionsdescribedinthelabmanualand answerthefollowingquestionsaboutthatmisconception. 1)Whichmisconceptiondidyouchoose? 2)Althoughmisconceptionsarenotcorrect,theyoftenseemreasonableifyou dontknowallthedetails.Explainwhatmightleadsomeonetothinkthatthe misconceptionyouchosewasplausible. 3)Explainhowthedatayoucollectedinlabshowsthatthemisconceptionyou choseisincorrect. 4)Askepticcouldargue,Avidaisjustacomputersimulation.Ithasnothingto dowithrealorganisms.Anyconclusionsyoudrawfromitarenotrelevantinthe realworld.Howwouldyouarguethat,althoughAvidaisacomputer simulation,theresultsfromitarestillrelevanttothemisconceptionyouchose? Inotherwords,InwhatrelevantwaysisAvidasimilartotherealworldsoasto allowonetodrawmeaningfulconclusionsaboutthismisconception?