Biology Question



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Please see the attached document to answer the questions

You have to do the three excerices to be able to answer the questions.For number 8 and 15, you have also to look at the Manuel which is attached too. The most important thing, no plagiarism please

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For these exercises, you will be using Avida-ED (Links to an external site.) to simulate evolution of digital organisms called Avidians. Please read the introductory material for this Activity before attempting these exercises, and familiarize yourself with the Avida-ED Workspace Areas. The following exercises are meant to be completed in order, and you will have the best success completing them if you do so. Be sure to read all of the text boxes and follow the bulleted instructions. We will be using Avida-ED off-and-on throughout the semester. Exercise 2.1: Observe an Avidian undergoing reproduction • Navigate to the Organism viewer, and the lab bench will display a large rectangle with a set of navigation buttons at the bottom. • Drag the “@ancestor” from the Freezer to the genetic code box near the top of the lab bench area. • After a second or two, the genome will load. • Select “Run”, and observe the organism’s genome being executed.The curved lines or execution path within the genome represent the instructions being executed and their height (increasing towards the center of the genome) represents the number of times that instruction has been executed. Eventually the organism will begin reproducing – its offspring’s genome will take shape on the right. • Use the slider and/or the “Back” and “Forward” buttons to observe the genome being executed at the position and pace you wish to explore. • While paused or at the end of the reproduction process, you can display the genomic position (number) of any instruction by selecting it. After exploring an Avidian reproducing, please respond to the following questions: Question 1: Which position of the Avidian genome is the first to be executed? Question 2: Which position(s) of the Avidian genome are responsible for reproduction? (Hint, what does the execution path, and its height, represent? Storing An Avidian in the Freezer and Examining An Offspring’s Genome • Select “End” to skip to the very end of the reproduction process. A genetic code symbol will appear within the offspring’s genome. • To freeze the offspring for later use, drag its genetic code symbol directly on top of an organism already listed in the Organisms section of the Freezer. Another method is to simply choose “Save Offspring Organism” in the Freezer menu. • A prompt will appear to name the Avidian. You may use any name you like, but for future use we suggest a descriptive name of some sort. Items saved in the freezer may be renamed or deleted by right-clicking on the freezer item. • You can now examine the offspring by placing it in the Organism viewer. Practice freezing your offspring Avidian, placing it in the Organism viewer, and then deleting it from the Freezer. You will need to apply these skills in the following sections. Exercise 2.2: Observing mutations that occur during Avidian reproduction • While still in the Organism viewer, select Settings above the Lab Bench area. • Set the Per Site Mutation Rate to 10% by entering “10” in the box next to the slider. • Drag the “@ancestor” from the Freezer to the genetic code box. • Select “Run” then “End” to skip the animation. The number line and slider track the current location within the entire set of commands being executed. Notice that the total number of instructions executed (far right number line value) is greater than the Avidian genome length of 50. Some instructions may be executed many times (very high curved execution paths) and others might not be executed at all (the execution path jumps those instructions). The number of executed instructions required to complete reproduction is termed Offspring Cost. • Observe the mutations that occur in the offspring’s genome. A mutation is highlighted with a black outline around the instruction circle. In Avida-ED, mutations only occur during the reproduction process, and appear in the offspring of an ancestral Avidian. After observing reproduction with a 10% mutation rate, respond to the following: Question 3: In your own words, provide a brief (i.e., 2-3 sentence) description of how an Avidian reproduces. Question 4: How many mutated sites did you observe your Avidian’s offspring to have? Question 5: Briefly describe how the offspring’s genome compares to the parent’s genome. Question 6: If a mutation occurred in the sequence of instructions responsible for reproduction what do you predict would happen to the mutated offspring’s ability to reproduce? Question 7: After recording this prediction, perform the experiment. If your current offspring does not have one or more mutations in the set of reproduction instruction positions, select “Reset” then “Run” and “End” to observe another reproduction replicate. Continue until there’s an appropriate offspring genome; freeze and examine using the Offspring viewer. Were your predictions from Question 6 above upheld? Question 8: What is happening to its ability to reproduce? (Hint, compare the Avida-ED terms “viability” and “death” in the Glossary of the Avida-ED Quick Start User Manual Actions Exercise 2.3: Comparing Avidian genomes and phenotypes • While still in the Organism viewer, drag the “@all functions” organism from the Freezer to the genetic code box. • Select “Run”, and observe the Avidian’s genome being executed. • While it is executing, notice the numbers directly above the number line. At each of these points during its execution, the organism performs a logic function. Each number corresponds to a function listed in the Details window at the top right. Notice that the number of Times Performed indicated here should increase by one at each of the indicated points above the number line. The performance of a function is a phenotype of the Avidian, as is the ability to reproduce. The sequence of instructions in the genome is the genotype of the Avidian. • The labeled arrays of yellow and blue squares describe in computer science terms how the organism’s genome (computer program) is working. Selecting “Instruction Details” will display a description of the instruction (simple programing command) just executed as well as the instruction about to be executed. All of these computer science details can be ignored unless the user is particularly curious. After observing its ability to perform functions, compare the “@all functions” organism to the “@ances- tor” organism investigated in previous sections: Question 9: How do the genotypes and phenotypes of the “@all functions” and “@ancestor” organisms compare? Question 10: The “@all functions” organism is a descendant of the “@ancestor” organism. How do you think it became so different? Question 11:How does the execution path of the “@all functions” and “@ancestor” organisms compare? Question 12: What accounts for the Offspring Cost difference between the “@all functions” and “@ancestor” organisms? Question 13: How is Avidian genetics different from biological genetics? Exercise 2.4: Evolving a Population of Avidians Avidian populations grow in the Virtual Petri Dish (or Map), similar in many ways to how bacterial populations grow when plated on a medium in a Petri dish. The Map is divided into a grid in which each cell contains one Avidian. When an Avidian reproduces, the offspring is placed in a cell adjacent to its parent (the default setting) or randomly on the Map. As we saw previously, if there is mutation, the resulting offspring Avidian will not be identical to its parent. • Drag “@ancestor” from the Freezer to the Ancestral Organism(s) box. • Set the following parameters: Dish Size 30x30; 2% Per Site Mutation Rate; Place Offspring Near their parent; Uncheck all resources; Repeatability Mode Experimental; Pause Run Manually. [Note: each resource available in the environment provides increased energy, which alters the Energy Acquisition Rate of Avidians performing the corresponding function. Since Fitness equals Energy Acquisition Rate divided by Offspring Cost, relative fitness also changes. • Select “Map” to return to Map view. Below the Map, confirm that the viewing Mode is set to “Fitness”; Avidians on the Map will be colored according to the continually adjusting Fitness color scale. The slider on the left will increase the Map view size. • Select “Run” below the Map and watch as the ancestor organism and its descendants multiply. Notice changes within the Population Statistics panel at the top right and the graph below. • Select “Pause” to halt population growth when there are no empty (black) cells. • View an organism’s details by selecting its Map cell, outlining it in white. Information for the Avidian in this cell will be displayed in the Selected Organism Type panel (Figure 2.4). Select a few other Avidians and notice how their details differ. Continue the experiment by selecting “Run”. Notice the Y-axis options for the graph on the lower right and view each in turn while the experiment is in progress. • • • Pause the experiment when there have been about 500 updates, as indicated below the Map on the left. (An update is a unit of time in Avida-ED.) Identify an individual organism with a relatively high fitness for the population. To do so, select organisms in turn and check the Selected Organism Type panel. If there is enough variation in the population, the Fitness color scale may also be helpful. • • Practice saving an Avidian to the Freezer. With your identified high fitness organism selected, select “Freeze” beneath the Map. Choose “Organism” from the displayed options, and enter a name. For future experimental use we suggest a descriptive name that is meaningful to you, for example “org fitness0.55”. Practice saving a populated dish to the Freezer. Select “Freeze” beneath the Map and choose “Population”. Again, use a descriptive name. We suggest using a labeling system that denotes important experimental variables, for example “2%mut 30x30 no-res @anc” for this experimental setup. (Note: the Freezer menu can also be used to store items in the freezer.) Question 14: What distinguishes the Avidian in a grey cell from an Avidian in any other (non- black) colored Map cell, AND how does an organism become like this? Question 15: Describe how fitness is measured and how it can change (Hint – Quick Start User Manual Actions .) Question 16: Choose two viable Avidians in your population with different fitness values and explain how differences in these Avidians contribute to differences in their fitness. Final thoughts: Why might Avida-ED be a good model system? What can we study with these model systems? What are the limitations of a system like Avida-ED? That is, what can’t you study using a system like this? Homework: 1. As precisely and thoroughly as possible, define the following concepts with specific reference to Avida-ED and its digital organisms: • • • • Genome Fitness Mutation Rate Offspring Cost 2. dentify the area (and the mode, if applicable) of the Avida-ED workspace or interface you would go to when you want to do the following: A. “Save” or “restore” a particular organism genome “snapshot” to use as ancestors in different evolutionary runs. B. Examine or execute the “genome” of an avidian digital organism. C. Set up the experimental conditions and variables of a particular evolutionary scenario. D. Collect and save data from a finished experiment. Avida-ED Quick Start Manual v.3.2 Avida-ED Quick Start User Manual I. General Avida-ED Workspace Viewer chooser Lab Bench Freezer (A) Viewer chooser buttons Switch between lab bench views (B) Lab bench Three lab bench options: 1. Population View Lab Bench (Petri dish & stats viewpanes) © Robert T. Pennock -1- Avida-ED Quick Start Manual v.3.2 2. Organism View Lab Bench (Genetiscope) 3. Analysis View Lab Bench (Data graphing & analysis) (C) The Freezer • Storage shelves for: - Configured Petri dishes (environmental settings but no organisms) - Individual organisms removed from a Petri dish - Populated Petri dishes (environment settings and frozen organisms) • Drag and drop freezer items to or from an open lab bench. • Right-click (Ctrl-click) or double-click item in freezer (except default items) to rename, delete or export it. • Click a disclose triangle to hide or show lists of items • Export selected item. [MENU File -> Export Freezer Item…] © Robert T. Pennock -2- Avida-ED Quick Start Manual v.3.2 II. Lab Benches (1) Population Viewer (“Petri Dish” & environment settings) Functionality - Evolve a population in a Petri dish - Click on an individual organism and observe its stats - Observe whole population stats in real time - Graph population stats in real time Basic Controls - Drag a Petri dish (configured or populated) or one or more organisms into the Petri dish bench from the freezer to begin a new run. - Setup/Map button: Switch between Petri dish front view and its environment settings. - Export data to comma-delimited file. [MENU File -> Export Data…] - Save images of population or graph in viewer [MENU File -> Export Graphics…] - Import or Export a dish or organism. [MENU File -> Import/Export Item…] Organism clicked on stats report Dish viewpane (front) Population statistics panel Population data graph Buttons to flip to Petri dish front map and to hide/show side stats panel Dish viewpane (rear) Environment settings © Robert T. Pennock -3- Avida-ED Quick Start Manual v.3.2 Dish viewpane (front) Population icon & name Switch over to environmental setup controls; Hide/show stats panel Petri dish grid Pull down menu to change what information is being displayed Color scale legend Zoom level & control Update # Freeze dish/organism button New Experiment and Run/Stop buttons - Population icon & name: Drag icon to freezer to save either the populated dish or just the dish environmental configuration. Click name to rename. - Setup button: Go to environmental settings for this Petri dish. - Stats button: Hide/reveal stats side panel for this dish. - Petri dish map: More or less of the map is visible depending upon the size of the grid. Use scroll bars and/or zoom control if grid extends beyond window. - Color Scale Legend: During a run, the color scale will automatically adjust as numbers increase or decrease. [“Rescaling” will appear in parentheses.] The spectrum will thus always show relative values, but particular colors will represent different absolute values as a population evolves. Special colors: Black indicates an empty cell and white indicates a cell whose value is above the maximum portrayed on the scale (as the scale readjusts to accommodate this new value it will be colored appropriately). Grey indicates that the organism in the cell is not viable. - Time - Avida internal time; in number of updates since the beginning of a run. This is a constant internal time; it does not correspond to external time because updates take longer for larger populations. © Robert T. Pennock -4- Avida-ED Quick Start Manual v.3.2 - Mode menu: Pull down menu to select a feature of the population to indicate by color. Options: Fitness, Offspring Cost, Energy Acquisition Rate, Ancestor Organism. - New button: Ends the current run (after offering to discard or save it) and then resets the Petri dish for a new experiment. - Run/Stop button: Starts and temporarily stops a run. - Freeze button: Save the population and/or environmental settings to the freezer. - Zoom: Set the zoom level for the Petri dish. Use scroll bars if zooming in causes the grid to extend beyond window. Shortcuts: - Click on an organism in the Petri Dish and drag it to the Freezer to save it. - Click on an organism in the Petri Dish or the Freezer and drag it to the Organism Viewer icon in the Viewer Chooser to open it directly in the Organism Viewer. - Click on an organism in the Petri Dish to select it. Use arrow keys (up, down, left or right) to select a neighboring organism. - Click on the Petri Dish icon in the Petri Dish and drag it to the Freezer to save it. - Click on the Petri Dish icon in the Petri Dish or on the name of a populated dish in the Freezer and drag it to the Analyze Viewer icon in the Viewer Choose to view it directly in the Analyzer without having to save it to the Freezer first. - Click on an item in the Freezer and drag it to the trash can icon to delete it. © Robert T. Pennock -5- Avida-ED Quick Start Manual v.3.2 Stats viewpanes Selected Organism Type Statistics Report Name: Upon initial replication, Avida-ED automatically assigns temporary placeholder names to new varieties of Avidians as they evolve in a population. (New kinds of organisms that have not replicated, perhaps because they are not viable, are listed as no_name.) The square’s color matches the color of the selected Avidian in the current Petri dish grid. Basic Statistics: The listing of stats related to the selected organism are updated as the population is running: Fitness, Energy Acquisition Rate, Offspring Cost, Age (updates), Ancestor, and Viability. Functions list: Metabolic functions, listed in ascending order of complexity, that the organism may have evolved the ability to perform. If “Times Performed” is “0” the organism has not performed that function yet in this lifetime (or never does). Organisms get more energy (SIPs) if they perform more complex functions. © Robert T. Pennock -6- Avida-ED Quick Start Manual v.3.2 Population statistics Click buttons to highlight orgs in dish that have these phenotypes - These are the same functions as in the Org. Clicked on Report, but data is given for the population as a whole. - Click a single function button to highlight organisms in the dish that have the given function. Clicking two or more function buttons highlights organisms that have ALL the selected functions. Population data graph Pull down menu for property to graph - Pull down property menu: Pick the property of the population to graph in real time. Options include: Average Energy Acquisition Rate, Average Fitness, Average Offspring Cost, and Number of Organisms in the population. - Vertical axis: Units change depending upon property being graphed. The scale dynamically changes during a run to accommodate the evolving population. - Time axis: Time, in updates, since beginning of run of this population. © Robert T. Pennock -7- Avida-ED Quick Start Manual v.3.2 Buttons to show Petri dish map; show/hide stats side panel Environmental settings & controls Petri Dish size setting Per Site Mutation Rate & slide control Ancestral seed organism(s) Offspring placement setting Environmental resources settings Exact repeatability control Pause Run setting - Per site mutation rate: This rate reflects the percent chance that an instruction is incorrectly copied. So, if the per site mutation rate is 1%, there is a 1% chance that when an instruction is copied, it will end up as any one of the 26 possible instructions (one of which is itself, so it could ‘mutate’ back to itself). With a 1% per site mutation rate, if 100 instructions are copied one of them will be mutated on average (although this number could be higher or lower in any instance). - Dish size: Sets the maximum number of Avidians that can exist in the population. The two numbers specify the number of Avidians per row, and per column. So, 10 x 10 = a population of 100 organisms. - Ancestral seed organism(s): The organism(s) the population begins from. Drag in or out additional organisms at the beginning of a run. If seed organisms are added to the dish using this setting they are automatically placed in a set pattern on the Petri Dish (e.g. in the exact ce ...
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