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Nature’s Monte Carlo Bakery: The Story of Life as a Complex System GEK1530 Frederick H. Willeboordse [email protected] 1 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. 2 GEK1530 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! 3 GEK1530 The Complexity of Life Is Life a Complex System? 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. 4 GEK1530 Why the module? A different view! In order to gain an understanding of nature in a way that’s rather different from the traditional biology/chemistry centered approach. How about Math? The amount of Mathematics will be very limited and not exceed Secondary School level. 5 GEK1530 Workload The total workload for this GEM is 10 hours per week (on average). 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 Of course, for this module, items D&E can overlap. 6 GEK1530 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 7 GEK1530 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 8 GEK1530 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 Assignment Discussion of Previous Quiz First Part of the Lecture Quiz Second Part of the Lecture Applets and Animations 9 GEK1530 Tutorials & Discussion Sessions The goal of the tutorial is to have a free and open discussion. There are two types of tutorials: In-class tutorials and Smallgroup tutorials. The Small-group tutorials are mainly for discussions The In-class tutorials are mainly for Q&A Ask! Talk! 10 GEK1530 Tutorial Registration http://chaos.nus.edu.sg/cgi-bin/GEK1530/register.pl Name as on Matriculation Card: Frederick H. Willeboordse Matriculation Number: 15473A Email: [email protected] Faculty: Science First choice: Group 1, Wednesdays 9:00-11:00 Second Choice: Group 2, Wednesdays 14:00-16:00 Third Choice: Group 3, Thursdays 9:00-11:00 Fourth Choice: Group 4, Thursdays 14:00-16:00 Fifth Choice: Group 5, Fridays 9:00-11:00 Register 11 GEK1530 Tutorial Registration 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 Sort by Name Frederick H. Willeboordse 15473A [email protected] Sort by Matriculation Number Science 1 3 Sort by Group 5 2 6 tba tba Mon Jan 7 08:32:45 2002 tba = to be announced when the balloting has been completed Allocation is done by ballot as announced on the course web site. 12 GEK1530 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 Some good but optional text books are: F. Dyson: J. Maynard Smith & E. Szathmary: M. Eigen & R. Winkler: Origins of Life The Origins of Life Laws of the Game 13 GEK1530 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? 14 GEK1530 Course Contents I. Building Blocks and Recipes in Physics -General aspects of complex systems Chaos Fractals Cellular Automata Turing Machine 15 GEK1530 Course Contents II. Building Blocks and Recipes in Chemistry Phospholipids Turing Patterns DNA 16 GEK1530 Course Contents III. Building Blocks and Recipes in Biology DNA as a 'hard disk' The social amoebae Dictyostelium Cell-differentiation 17 GEK1530 Course Contents IV. Building Blocks and Recipes in Evolution The origin of life Multi-cellular life - replicate and modify! Population Dynamics 18 GEK1530 Course Contents V. Life as a complex system The search for Universalities Top-down versus the bottom-up approach Robustness of life 19 GEK1530 Key Concepts Recipes Laws, rules Building Blocks Atoms, Molecules Nucleotides, Amino Acids Life Replication of Basic Units Manfred Eigen Nucleotide monomers can give rise to nucleic acid polymers that replicate and mutate (without providing an RNA template but needs enzyme). Leslie Orgel Nucleotide monomers can polymerize into RNA (without the help of an enzyme but needs template). Chance Permeates the living & nonliving world Think of Quantum Mechanics, the comet that killed the dinosaurs Distinction between Hardware and Software John v. Neumann replication and metabolism are logically separable analogy between automata and living organisms 20 GEK1530 The Monte Carlo Bakery Building Blocks Recipes/Laws Chance Stretch & Fold Complexity 21 GEK1530 Examples Broccoli Romanesco Illustrates: Building Blocks, Fractals Broccoli Romanesco is a cross between Broccoli and Cauliflower. 22 GEK1530 Examples Building Blocks in Paleontology Built from similar modified segments? 23 GEK1530 Examples Fractal Pathways Inside Us Illustrates: Fractal Illustrates: Building Blocks Proteins Deoxyribonucleic Acid The venous and arterial system of a kidney 24 GEK1530 Key Points of the Day Chance Life! Laws Building Blocks Complexity is fun! 25 GEK1530 Course Contents IV. Self-organization in Evolution The origin of life Multi-cellular life - replicate and modify! Population Dynamics 26