Transcript Introduction - Frederick H. Willeboordse

Nature’s Monte Carlo Bakery:
The Story of Life as a Complex System
GEK1530
Frederick H. Willeboordse
[email protected]
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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.
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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!
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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.
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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.
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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.
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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
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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
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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
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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!
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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
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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.
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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
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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?
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Course Contents
I.
Building Blocks and Recipes in Physics
-General aspects of complex systems
Chaos
Fractals
Cellular Automata
Turing Machine
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Course Contents
II. Building Blocks and Recipes in Chemistry
Phospholipids
Turing Patterns
DNA
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Course Contents
III. Building Blocks and Recipes in Biology
DNA as a 'hard disk'
The social amoebae Dictyostelium
Cell-differentiation
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Course Contents
IV. Building Blocks and Recipes in Evolution
The origin of life
Multi-cellular life - replicate and modify!
Population Dynamics
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Course Contents
V.
Life as a complex system
The search for Universalities
Top-down versus the bottom-up approach
Robustness of life
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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
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The Monte Carlo Bakery
Building Blocks
Recipes/Laws
Chance
Stretch & Fold
Complexity
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Examples
Broccoli Romanesco
Illustrates: Building Blocks, Fractals
Broccoli Romanesco is a cross between Broccoli and Cauliflower.
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Examples
Building Blocks in Paleontology
Built from similar
modified segments?
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Examples
Fractal Pathways Inside Us
Illustrates: Fractal
Illustrates: Building Blocks
Proteins
Deoxyribonucleic Acid
The venous and arterial
system of a kidney
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Key Points of the Day
Chance
Life!
Laws
Building Blocks
Complexity is fun!
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Course Contents
IV. Self-organization in Evolution
The origin of life
Multi-cellular life - replicate and modify!
Population Dynamics
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