1. 1 GEK1530 Frederick H. Willeboordse frederik@chaos.nus.edu.sg Nature’s Monte Carlo Bakery: The Story of Life as a Complex System

2. 2 Briefing and Introduction Lecture 0 This lecture aims to give an overview of the course and provide some background as with regards to its general philosophy.

3. GEK1530 3 Who am I? Frederick H. Willeboordse S12 #03-06 Dept. of Physics Specialized in Complex Systems Also ran a business for 5 years This picture was taken in 2371 on board of the starship Enterprise and is, due to time distortions, a bit blurry. Who would have thought I’d end up in Singapore!

4. GEK1530 4 The Complexity of Life I think so! Obviously, life is complex in the daily sense but here we’ll be talking about life as a complex system in the scientific sense. Is Life a Complex System?

5. GEK1530 5 Why the module? In order to gain an understanding of nature in a way that’s rather different from the traditional biology/chemistry centered approach. The amount of Mathematics will be very limited and not exceed Secondary School level. A different view! How about Math?

6. GEK1530 6 Workload A: 2 lecture hours per week B: 1 tutorial hour per week C: 0 lab work per week D: 3 hours for assignments per week E: 4 hours of preparation work per week The total workload for this GEM is 10 hours per week (on average). Of course, for this module, items D&E can overlap.

7. GEK1530 7 Course Schedule Lectures: 2 to 4 hours per week for a total of 26 lecture hours (these include the in-class quizzes) Tutorials: Small-group and In-class tutorials Discussion Sessions: Part of Small-group tutorials

8. GEK1530 8 Assessment All together there will be 10 quizzes with which you can earn 5 points each for a total of 50 points. The final exam will be open book and count for 50 points as well. Quizzes: 10 * 5 points Exam: 1 * 50 points

9. GEK1530 9 Lectures During most of the lectures, there will be a quiz. Usually, I’ll try to do the quiz around the middle of the lecture so that you won’t miss it if you come late. Discussion of Previous Quiz Discussion of Assignment First Part of the Lecture Quiz Second Part of the Lecture Lecture Applets and Animations

10. GEK1530 10 Tutorials & Discussion Sessions The goal of the tutorial is to have a free and open discussion. Talk! There are two types of tutorials: In-class tutorials and Small- group tutorials. Ask! The Small-group tutorials are mainly for discussions The In-class tutorials are mainly for Q&A

11. GEK1530 11 http://chaos.nus.edu.sg/cgi-bin/GEK1530/register.pl Tutorial Registration

12. GEK1530 12 You can see for which groups you friends signed up and the practical allocation once it's completed at this URL: http://chaos.nus.edu.sg/cgi-bin/GEK1530/display.pl Tutorial Registration Allocation is done by ballot as announced on the course web site.

13. GEK1530 13 Text Books All the lecture notes as well as other relevant material can be found on my web site at: http://chaos.nus.edu.sg/teaching/GEK1530 http://chaos.nus.edu.sg/teaching/GEK1530 Some good but optional text books are: F. Dyson: Origins of Life M. Eigen & R. Winkler: Laws of the Game J. Maynard Smith & E. Szathmary: The Origins of Life

14. GEK1530 14 Course Contents There are basically five interwoven aspects, illustrated with the metaphor of a bakery. I.Building Blocks and Recipes in Physics -General aspects of complex systems II.Building Block and Recipes in Chemistry III.Building Blocks and Recipes in Biology IV.Building Blocks and Recipes in Evolution V.Life as a complex system Does self-organization need intelligence?

15. GEK1530 15 I.Building Blocks and Recipes in Physics -General aspects of complex systems Chaos Fractals Cellular Automata Turing Machine Course Contents

16. GEK1530 16 II.Building Blocks and Recipes in Chemistry Phospholipids Turing Patterns DNA Course Contents

17. GEK1530 17 III.Building Blocks and Recipes in Biology DNA as a 'hard disk' The social amoebae Dictyostelium Cell-differentiation Course Contents

18. GEK1530 18 IV.Building Blocks and Recipes in Evolution The origin of life Multi-cellular life - replicate and modify! Population Dynamics Course Contents

19. GEK1530 19 V.Life as a complex system The search for Universalities Top-down versus the bottom-up approach Robustness of life Course Contents

20. GEK1530 20 Chance Distinction between Hardware and Software replication and metabolism are logically separable analogy between automata and living organisms John v. Neumann Replication of Basic Units Nucleotide monomers can give rise to nucleic acid polymers that replicate and mutate (without providing an RNA template but needs enzyme). Manfred Eigen Nucleotide monomers can polymerize into RNA (without the help of an enzyme but needs template). Leslie Orgel Key Concepts Building Blocks Permeates the living & non- living world Think of Quantum Mechanics, the comet that killed the dinosaurs Recipes Laws, rules Atoms, Molecules Nucleotides, Amino Acids Life

21. GEK1530 21 The Monte Carlo Bakery Building Blocks Recipes/Laws Chance Stretch & Fold Complexity

22. GEK1530 22 Broccoli Romanesco is a cross between Broccoli and Cauliflower. Examples Broccoli Romanesco Illustrates: Building Blocks, Fractals

23. GEK1530 23 Built from similar modified segments? Building Blocks in Paleontology Examples

24. GEK1530 24 The venous and arterial system of a kidney Examples Fractal Pathways Inside Us Deoxyribonucleic Acid Proteins Illustrates: FractalIllustrates: Building Blocks

25. GEK1530 25 Complexity is fun! Key Points of the Day Chance Laws Building Blocks Life!

26. GEK1530 26 Course Contents IV.Self-organization in Evolution The origin of life Multi-cellular life - replicate and modify! Population Dynamics