This game was developed for the Young Leaders in STEM summer program led by the Cambridge Science Club for Girls.

It was developed as part of a 3-day lesson on bacteria and the human microbiome to teach concepts about mutation, diversity, selection, and evolution.

It can be simulated using this code or played with a classroom of students.

Run python play_game.py.

You can change the starting sequence (-s), the number of students in the class (-n), the number of rounds of mutation in Part 1 (-m), the number of rounds of mutation/selection in Part 2 (-x), and the number of die (-d) from the command line.

You can change whether and how a base pair is mutated in load_p_mut and the selection rules in load_selection_dict in load_data.py.

• Students, to be divided into 3 groups
• 2 6-faced die per student
  • Game can also be played with 3 die. This makes the evolutionary dynamics different. Empirically (from this code), I prefer using 2 die.
• Writing materials

All students start with the same 12 base pair sequence. I've tested this code with the starting sequence ATGGTACGATCG and it seems to work pretty well.

Have each student roll their die twice.

• The first roll indicates which base pair location will be mutated.
• The second roll decides what happens to that base pair. Use the following table to determine what happens to the base pair:

After each mutation, have the students translate their DNA sequence into a protein.

After 10 rounds of mutation, ask the students to write their sequences on the board and ask them to count how many unique sequences now exist.

• How rare are these mutations? How much diversity did they lead to? Is this what you would have expected?
  • Even though mutations are relatively rare, they lead to a lot of diversity!
• How does the DNA sequence diversity compare to the protein diversity?
  • There can be more DNA diversity than protein diversity, because the DNA --> protein code is redundant!

Before starting Part 2, talk to your students about how DNA codes for proteins and show them a DNA codon table.

Split the class into three groups, and place each group into soil, ocean, or gut environments.

Have the students translate their sequences into proteins. Have them use the following tables to determine whether their microbe can survive in its new environment. If any of the codons are the STOP codon, the bacteria does not survive.

If a student's bacteria does not survive, have her replace her sequence with one from her group which did survive. If no bacteria in the entire group (environment) survived, have them make one up that would survive and go with that.

Go through N more rounds of mutation and selection. Like in Part 1, have students roll the die to decide the location and type of mutation to happen. Have them translate the sequence into amino acids, and determine the fate of their new bacteria.

After enough rounds, ask the students to again write the surviving bacterial (amino acid) sequences on the board, separated by environment. Discuss patterns that they noticed.

• What was the difference between parts 1 and 2?
  • Part 1 didn't have any selection, so all mutations survived. Part 2 added selection, so that some mutations were helpful and some were harmful.
• How does this game relate to evolution? What other aspects of evolution are missing in this game?
  • It demonstrates the principles of evolution! Mutations lead to diversity, selection selects for organisms which can survive.
  • *Competition between organisms is missing."
• Does it take more or less time for diversity to be generated when you add selection? Why?
  • More time, because much of the diversity generated in each round does not survive
• Which protein locations seem to be most diverse? Which ones are least diverse? Why?
  • Proteins which provide bacteria an essential function are least diverse, because if a microbe is missing that specific protein then it dies and does not reproduce.
  • Proteins which give bacteria an additional function (i.e. can save it from death due to a lacking protein elsewhere) are intermediately diverse - in most cases, they don't matter, but in some, they matter a lot.

• Environments with selective pressures limit the types of organisms that can survive
• Diversity is still generated, but at a much slower rate than just random mutations
  • The most diverse proteins are those that have non-essential functions
  • Or ones that give the bug an advantage
• Bonus question: how do we define bacterial species?

$ python play_game.py
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ROUND ONE - MUTATION
---------------------
After 1 rounds of mutation, there are 3 unique sequences
After 2 rounds of mutation, there are 4 unique sequences
After 3 rounds of mutation, there are 5 unique sequences
After 4 rounds of mutation, there are 5 unique sequences
After 5 rounds of mutation, there are 6 unique sequences
After 6 rounds of mutation, there are 8 unique sequences
After 7 rounds of mutation, there are 10 unique sequences
After 8 rounds of mutation, there are 10 unique sequences
After 9 rounds of mutation, there are 10 unique sequences
After 10 rounds of mutation, there are 10 unique sequences
---------------------
ROUND TWO - SELECTION
---------------------
After 0 rounds of selection, this is what we have:
        gut: MERS, MVRS
        soil: MVRC
        ocean: MVRS, MVPP, MVCS
After 1 rounds of selection, this is what we have:
        gut: IVRS, MERS, MVRS
        soil: MVRC
        ocean: MVRS, MVPP, MVCS
After 2 rounds of selection, this is what we have:
        gut: IVRS, MERS, MVRS
        soil: MVRC, MVPC
        ocean: MVRS, MVPP, MVCS
After 3 rounds of selection, this is what we have:
        gut: IVRS, MERS, MVRS, KERS
        soil: MVRC, MVPC
        ocean: MVRS, MVPP, MVCS
After 4 rounds of selection, this is what we have:
        gut: IVRS, MERP, MVLS, MVRS, KERS
        soil: MVRC, MVPC, MLRC
        ocean: MVRS, MVPP