Assignment 3

1. Evolve a simple organism

Start with the Bacterium (Use File Open them choose bacterium).
Set the Global Mutation rate to 2. (Genes Mutation Rate)
Evolve an organism at least 30 steps using Evolve Breed. (You should try to make your selection in a consistent way. It may help to imagine an environment and how the structures you see will help the organism survive.)
Copy and paste it into your word processing file as #1. You can also just print it if that is easier, but label it #1 and with your name.
Add a short sentence saying what you were looking for when you made your selection and say how many generations you evolved your organism. (If you makes sure Fossil History under the Fossils menu is checked, and you hit new history when starting each of your organisms this will keep track of the number of generations for you.)
Save your organisms using File Save As. You will not hand these files in, but you will need it for number 7 below.

2. Add color and 3 more genes:

Start with the Bacterium again. (Use File Open then choose bacterium).
Go the Genes Special Genes Menu and turn on mutation for body color and three other genes (check the boxes). Record which other three you turn on in your answer.
Evolve an organism at least 30 steps using Evolve Breed. (You should try to make your selection in a consistent way. It may help to imagine an environment and how the structures you see will help the organism survive.)
Copy and paste it into your word processing file as #2. You can also just print it if that is easier, but label it #2 and with your name.
Add a short sentence saying what you were looking for when you made your selection and say how many generations you evolved your organism.

Save your organisms using File Save As. You will not hand these files in, but you will need it for number 7 below.

3. Make a fossil history.

Makes sure Fossil History under the Fossils menu is checked and hit new history.
when starting each of your organisms Look at your fossil history (before you quit!). Start with the Bacterium again. (Use File Open then choose bacterium). Go the Genes Special Genes Menu and turn on mutation for body color and three new genes (check the boxes and uncheck the ones you had checked for number 2). Record which other three you turn on in your answer.
Evolve an organism at least 30 steps using Evolve Breed. (You should try to make your selection in a consistent way. It may help to imagine an environment and how the structures you see will help the organism survive.)
Copy and paste it into your word processing file as #3. You can also just print it if that is easier, but label it #3 and with your name.
Add a short sentence saying what you were looking for when you made your selection and say how many generations you evolved your organism.
Go to Fossils Fossil History. Either copy each page in the fossil history and paste it into your answer or print it out. Make sure you do this before you quit. Fossil histories are not saved, when you save your organism.

Save your organisms using File Save As. You will not hand these files in, but you will need it for number 7 below.

4. Questions on Fossil History from #3

a. How many times in that history would you say there were new species?
Circle, Mark or otherwise identify on your fossil history each place you think there is a new species, .beginning with the bacterium and ending with the final organism?
b. How did you choose these points? What does it mean to say that these are separate species, according to the theory of evolution? How does this differ from the definition of a species for contemporaneous populations?
c. Could you tell that it was each stage you identified was a news species at the moment you evolved it? Is being a member of a certain species a property that a population has in virtue its existence or properties at any one moment? Explain. (You may want to peek at Dennett Chapter 4 to help answer these questions.)

5: Drift:

Go the the Evolve Engineer
Click in the white space near your organism. When you do the organism will change randomly. This is the same as if you made your choices randomly in breeding. Click this about 30 times or hit the repeat button to let it run a while on its own.

Copy and paste it into your word processing file as #5. You can also just print it if that is easier, but label it #5 and with your name.

aIs it as interesting as the ones you evolved? b. Why doesn't drift produce significant evolution?

6. Saltation (Hopeful monster)

Start with the Bacterium again
Go the the Evolve Engineer
Try Saltation (hopeful monster) a couple times? (click on the Hopeful button on the top right)

Copy and paste it into your word processing file as #6. You can also just print it if that is easier, but label it #6 and with your name.

a. What is saltation? (Look it up or look in the index of Dennett) b. If an organism is relatively well suited to its environment, what will saltation do to that adaptation? c. What does this show about how large mutations could have been involved in evolution?

7. Exploring Gene Space:

Use the Triangle menu to put the bacterium at the top of the triangle, and your organism from Number 3 at one of the other corners and your first organism at the other corner. You do this by reloading each organism using File Open then copying them and then using the Paste to command to paste them to one of the points on the Triangle.
Explore the design space between the bacterium and your organism #3. What is this space? What are you looking at when you move your mouse and make different organisms appear?
Copy the Screen and paste it into your answer, or print it out.
Is the sequence of organisms the same as your fossil history? Why not? How is the path taken by evolution different than the path you take from the bacterium to your organism on the triangle?
Explore the space around the path between the bacterium and your organism. Are there other interesting organisms nearby? Are they biologically possible according to Dennett? What does that mean?

8. Try doing some genetic engineering.

Above your organism are a line of numbers representing each of the genes. You can change them manually be right or left clicking on them to increase or decrease the values. Try to engineer one of the three organism you evolved in 1, 2, or 3.

Copy and paste your best attempt into your word processing file as #8. Make sure you say whether it is an attempt at 1, 2 or 3. You can also just print it if that is easier.
Figure out what at least 3 of the first 6 genes from the left do, and write them down.