1. 1 Tutorial 3 Nature’s Monte Carlo Bakery: The Story of Life as a Complex System

2. GEK1530 2 Topics covered 1.Turing Machines 2.Reproduction versus Replication 3.Replication versus Metabolism 4.Summary on The Origin of Life 5.Genetic Drift

3. GEK1530 3 Turing Machine A Turing machine is a very simple machine, but, logically speaking, has all the power of any digital computer. It may be described as follows: What is Turing Machine? 1.There is an infinite tape with squares on it. 2.Each square may contain a symbol from a finite alphabet but there can be only finitely many non-blank square on the tape. 3.There is a read-write head which is positioned somewhere on the tape. 4.The machine is in one of a finite number of states. 5.There is a set of rules that tell the machine what to do given a certain state and a certain symbol read from the tape.

4. GEK1530 4 Turing Machine What is Turing Machine? The rule is of the following form: (current state, current symbol, new state, new symbol, left/right) This rule means that if the Turing machine is now in current state, and the symbol under the read/write head is current symbol, change its internal state to new state, replace the symbol on the tape at its current position by new symbol, and move the read/write head one square in the given direction (left or right). If a Turing machine is in a condition for which it has no rule, it halts.

5. GEK1530 5 Turing Machine 0 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) X Start with the symbol X on the tape and in state zero. Then apply the rules until the machine stops. > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, >

6. GEK1530 6 Turing Machine 0 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) X > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step In the beginning (this is also called the initial condition) we have: Step 0 - Read Apply rule 1.

7. GEK1530 7 Turing Machine 0 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 0 - Write State=0/Write=‘K’

8. GEK1530 8 Turing Machine 0 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 0 - Move Do not move

9. GEK1530 9 Turing Machine 0 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 1 - Read Apply rule 2

10. GEK1530 10 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 1 - Write State=1/Write nothing

11. GEK1530 11 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 1 - Move Right

12. GEK1530 12 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 2 - Read Apply rule 3

13. GEK1530 13 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 2 - Write State=1/Write=‘E’ E

14. GEK1530 14 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 2 - Move Do not move E

15. GEK1530 15 Turing Machine 1 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 3 - Read Apply rule 4 E

16. GEK1530 16 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 3 - Write State=2/Write nothing E

17. GEK1530 17 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 3 - Move Right E

18. GEK1530 18 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 4 - Read Apply rule 5 E

19. GEK1530 19 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 4 - Write State=2/Write =‘N’ E N

20. GEK1530 20 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 4 - Move Do not move E N

21. GEK1530 21 Turing Machine 2 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 5 - Read Apply rule 6 E N

22. GEK1530 22 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 5 - Write State=3/Write nothing E N

23. GEK1530 23 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 5 - Move Right E N

24. GEK1530 24 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 6 - Read Apply rule 7 E N

25. GEK1530 25 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 6 - Write State=3/Write=‘N’ E N N

26. GEK1530 26 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 6 - Move Do not move E N N

27. GEK1530 27 Turing Machine 3 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 7 - Read Apply rule 8 E N N

28. GEK1530 28 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 7 - Write State=4/Write nothing E N N

29. GEK1530 29 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 7 - Move Right E N N

30. GEK1530 30 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 8 - Read Apply rule 9 E N N

31. GEK1530 31 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 8 - Write State=4/Write=‘E’ E N E N

32. GEK1530 32 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 8 - Move Do not move E N E N

33. GEK1530 33 Turing Machine 4 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 9 - Read Apply rule 10 E N E N

34. GEK1530 34 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 9 - Write State=5/Write nothing E N E N

35. GEK1530 35 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 9 - Move Right E N E N

36. GEK1530 36 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 10 - Read Apply rule 11 E N E N

37. GEK1530 37 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 10 - Write State=5/Write=‘T’ E N E T N

38. GEK1530 38 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 10 - Move Do not move E N E T N

39. GEK1530 39 Turing Machine 5 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 11 - Read Apply rule 12 E N E T N

40. GEK1530 40 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 11 - Write State=6/Write nothing E N E T N

41. GEK1530 41 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 11 - Move Right E N E T N

42. GEK1530 42 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 12 - Read Apply rule 13 E N E T N

43. GEK1530 43 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 12 - Write State=6/Write=‘H’ E N E T H N

44. GEK1530 44 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 12 - Move Do not move E N E T H N

45. GEK1530 45 Turing Machine 6 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 13 - Read Apply rule 14 E N E T H N

46. GEK1530 46 Turing Machine 7 Head State Tape Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) K > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 13 - Write State=7/Write nothing E N E T H N

47. GEK1530 47 Turing Machine Rules are defined in this format: (current state, current symbol, new state, new symbol, left/right) > = Right, - = write or do nothing Rules: 1) 0,’X’, 0, ‘K’, - 2) 0, ‘K’, 1, -, > 3) 1, -, 1, ‘E’, - 4) 1, ‘E’, 2, -, > 5) 2, -, 2, ‘N’, - 6) 2, ‘N’, 3, -, > 7) 3, -, 3, ‘N’, - 8) 3, ‘N’, 4, -, > 9) 4, -, 4, ‘E’, - 10) 4, ‘E’, 5, -, > 11) 5, -, 5, ‘T’, - 12) 5, ‘T’, 6, -, > 13) 6, -, 6, ‘H’, - 14) 6, ‘H’, 7, -, > Let us go through this algorithm step by step Step 13 - Move Right Fantastic! The function of this Turing machine is to print out my name! 7 Head State Tape K E N E T H N

48. GEK1530 48 Replication Reproduction versus Replication In biology, replication is the act or ability to make a copy. Mostly commonly meaning molecular replication. For a molecule, to replicate means to construct a precise copy of itself by a specific chemical process Reproduction For a cell, to reproduce means to divide into two cells with the daughter cells inheriting approximately equal shares of the cellular constituents, just like photocopying.

49. GEK1530 49 Reproduction versus Replication Cells can reproduce but only molecules can replicate! In modern times, reproduction of cells is always accompanied by replication of molecules, but this need not be the case in the past!

50. GEK1530 50 Metabolism Replication versus Metabolism Metabolism is the uptake and digestion of food, and the disposal of waste products in living organisms. Roughly, metabolism is the sum of a cell’s chemical reactions. In general, metabolism can be split into 2 groups of reactions: Catabolism, which breaks down molecules, releasing energy. Anabolism, which uses energy from ATP to synthesize large molecules, including macromolecules.

51. GEK1530 51 John von Neumann Replication versus Metabolism He observed that replication and metabolism are logically separable. He made the distinction between what is now called: HardwareSoftware process informationembody information Protein is hardware and is the essential component for metabolism. Nucleic acid is software and is the essential component for replication.

52. GEK1530 52 John von Neumann Replication versus Metabolism Introduced analogy between automata and living organisms. HardwareSoftware rulessymbols, states Automata metabolismreplication Organisms

53. GEK1530 53 Implication Replication versus Metabolism The separability between replication and metabolism implies: Possible to postulate organisms that are composed of pure hardware and capable of metabolism but incapable of replication. Possible to postulate organisms that are composed of pure software and capable of replication but incapable of metabolism.

54. GEK1530 54 Implication Replication versus Metabolism The basis functions of life: Replication and Metabolism. Two logical possibilities for life’s origin: Life began only once with the functions of replication and metabolism already present and linked together from the beginning. Life began twice, with separate kinds of creatures, one kind capable of metabolism without replication, the other kind capable of replication without metabolism.

55. GEK1530 55 Experiment: Synthesizing of Biological Building Blocks Summary on The Origin of Life Stanley L. Miller Juan Oró Showed that nitrogenous base in the nucleotide acid can be synthesized from naturally occurring molecules in a reducing environment. Demonstrated that amino acids are easy to synthesize from naturally occurring molecules in a reducing environment. Problem: The environment of the early Earth was not reduced!!

56. GEK1530 56 Experiment: RNA polymerization Summary on The Origin of Life Manfred Eigen Leslie Orgel Showed that nucleotide monomers can polymerize into RNA given a suitable template without any enzyme. Demonstrated that nucleotide monomers can polymerize into RNA using an enzyme but without any template. Problem: RNA is made using both templates and enzymes in living cells!!

57. GEK1530 57 Theories: Alexander I. Oparin Summary on The Origin of Life The order of events in the origin of life: cells  enzymes  genes. He observed that oil liquid in water form a stable mixture called a coacervate. He proposed that life began by successive accumulation of more and more complicated molecular populations within the droplets of a coacervate. This became the physical framework of the cell. Enzymes came in later to organize the random population of molecules within the droplet into metabolic cycles. Lastly, the genes came in.

58. GEK1530 58 Theories: Manfred Eigen Summary on The Origin of Life The order of the events in the origin of life: genes  enzymes  cells He believed that life began with self-replicating RNA. Enzymes appearing soon afterwards to build with the RNA a primitive form of the modern genetic transcription apparatus, and cells appearing later to give the apparatus physical cohesion.

59. GEK1530 59 Theories: Cairns-Smith Summary on The Origin of Life The order of the events in the origin of life: clay  enzymes  cells  genes He believed that the beginning of life was a natural clay crystal directing the synthesis of enzyme molecules absorbed to its surface. The clay and enzymes learned to make cell membranes and became encapsulated in cells. The cells contained clay crystals performing in a crude fashion the functions in a modern cell by nucleic acids. Later on, a cell discovered that RNA is a better genetic material than clay and hence the RNA-based life survived.

60. GEK1530 60 Theories: Freeman Dyson’s Conclusion Summary on The Origin of Life The Cairns-Smith theory is a double-origin theory. It has the first origin of life mainly concerned with the building of a protein metabolic apparatus. The second origin of life is the replacement of the clay component by an efficient replicative apparatus made of nucleic acids. Cairns-Smith supposed that the two origins of life to be separated by a long period of biochemical evolution so that cells could have highly organized with protein enzymes and lipid membranes.

61. GEK1530 61 Theories: Freeman Dyson’s Conclusion Summary on The Origin of Life Both Oparin theory and Eigen theory were single-origin theories. Each of them supposes the origin of life to have been a single process. Oparin places primary emphasis on metabolism and barely discusses replication. Eigen places primary emphasis on replication and imagines metabolism falling into place rapidly as soon as replication is established.

62. GEK1530 62 Freeman Dyson’s Double-Origin Hypothesis Summary on The Origin of Life The life began twice, with two separate kinds of creatures, one kind capable of metabolism without exact replication and the other kind capable of replication without metabolism. The spontaneous emergence of protein structure and of nuclei acid structure out of molecular chaos are BOTH unlikely. It would be easier to imagine two unlikely events occurring separately over a period of time than occurring simultaneously!

63. GEK1530 63 Freeman Dyson’s Double-Origin Hypothesis Summary on The Origin of Life The first beginning must have been with proteins and the second beginning with nuclei acids. The first protein creatures might have existed independently for a long time, eating and growing and gradually evolving a more and more efficient metabolic apparatus. The nucleic acid creatures must have been parasites from the start, preying upon the protein creatures and using the products of protein metabolism to achieve their replication. Dyson believes that hardware should come before software!

64. GEK1530 64 Genetic Drift Genetic drift refers to random changes in the gene frequencies of a population from generation to generation as a result of sampling error. In each generation, some individuals may, just by chance, leave behind a few more descendents (and genes of course) than other individuals. The genes of the next generation will be the genes of the “lucky” individuals, not necessarily the healthier or “better” individuals.

65. GEK1530 65 Genetic Drift – Sampling Error Genetic Drift Imagine a game in which you have a bag holding 100 marbles, 50 of which are brown and 50 green. You are allowed to draw 10 marbles out of the bag. Now imagine that the bag is restocked with 100 marbles, with the same proportion of brown and green marbles as you have just drawn out. The game might play out like this: It’s clear that the ratio of brown to green marbles “drifts” around (5:5, 6:4, 7:3, 4:6...).

66. GEK1530 66 Genetic Drift This process causes gene frequencies in a population to drift around over time. Some genes may even “drift out” of a population (i.e., just by chance, some gene may reach a frequency of zero). In general, genetic drift has the effect of decreasing genetic variation within a population. Due to many random factors, the genes in one generation do not wind up in identical ratios in the next generation, and this is evolution. While this is evolution, it is evolution due to chance, not selection.

67. GEK1530 67 Genetic Drift Imagine that our random draws from the marble bag produced the following pattern: 5:5, 6:4, 7:3, 4:6, 8:2, 10:0, 10:0, 10:0, 10:0, 10:0... Why did we keep drawing 10:0? Because if the green marbles fail to be represented in just one draw, we can’t get them back—we are “stuck” with only brown marbles.

68. GEK1530 68 Genetic Drift The 10:0 situation illustrates one of the most important effects of genetic drift: it reduces the amount of genetic variation in a population. And with less genetic variation, there is less for natural selection to work with. Selection cannot increase the frequency of the green gene, because it’s not there for selection to act on. Selection can only act on what variation is already in a population; it cannot create variation.

69. GEK1530 69 Genetic Drift Genetic drift acts faster and has more drastic results in smaller populations. This effect is particularly important in rare and endangered species. In general, genetic drift would not result in changes that are more adaptive. Genetic drift is an evolution due to chance!!