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MCB 135
Introductory Systems Biology
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Emergent behavior: a property of the
whole not found in any of the parts
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E. coli – 1 fL cell contains:
•! 1 genome (5 million base
pairs, 4400 genes)
•! 200,000 RNA molecules
•! 3 million protein molecules
•! 20 million lipid molecules
•! 60 million ions
•! 20 billion water molecules
Your body has ~10 trillion human cells…and 100 trillion more
from microorganisms on and within it!
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To understand emergent behavior,
start by reducing the problem
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Alan
Hodgkin
Andrew
Huxley
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After finding a minimal system,
you could…
Loss-of-function mutants and knockouts:
the workhorses of molecular and cellular
biology
Start removing parts and see what breaks
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After finding a minimal system,
you could…
Techniques from biochemistry and
structural biology often study “single parts”
The crystal structure of DNA
suggested the mechanism
of its replication (later
confirmed by Meselson and
Stahl)
Study each part in isolation
After finding a minimal system,
you could…
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Study the interactions between parts
The Rules of Life
The Rules of Life
Played on an
infinite 2D grid
Played on an
infinite 2D grid
Most squares
are ”dead” (dark)
Most squares
are ”dead” (dark)
A few squares
are “alive” (light)
A few squares
are “alive” (light)
Played in rounds
Rules tell us when
a square will die
or come to life
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The Rules of Life
The Rules of Life
Live squares
“survive” in the
next round if they
had 2 or 3 live
neighbors in the
last round
Squares are “born”
in the next round
if they had exactly
3 live neighbors in
the last round
These squares
will die in the
next round
These squares will
be born in the
next round
Round one
The Rules of Life
This pattern is
called a “blinker.”
It’s one of many
that oscillate
indefinitely.
Round two
These simple rules produce
complex behaviors
Other patterns
travel along the
grid, like this
“glider.”
Round three
Glider motion
(simulated in Golly)
Understanding emergent behaviors
in GoL: the dot matrix printer
In a sense, you already understand how the printer
works: you know the initial pattern
and the rules for its changes with time.
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An alternative explanation of how
the dot matrix printer works
An alternative explanation of how
the dot matrix printer works
7
There are seven vertical
rows of “dots” in the
message.
5
4
3
2
1
There are seven similar printing units,
each of which is responsible for generating
the spaceship pattern in one row.
Each “dot” is a spaceship (similar to
a glider, but it moves straight)
An alternative explanation of how
the dot matrix printer works
An alternative explanation of how
the dot matrix printer works
3
Within each printing unit,
gliders travel around an
infinite loop, bouncing off
of reflectors.
1
C
M
An alternative explanation of how
the dot matrix printer works
5
Within each printing unit,
gliders travel around an
infinite loop, bouncing off
of reflectors.
This is the “memory tape”
for when dots should be
printed.
B
A duplicator
in one
corner
makes a
copy of each
passing
glider
6
M C B
1 3 5
An alternative explanation of how
the dot matrix printer works
The original
glider stays in
the loop
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An alternative explanation of how
the dot matrix printer works
Take-home lessons
•! In Life, emergent behaviors can be explained
with multiple levels of abstraction
•! A complete understanding of the rules may
not be necessary or even helpful for
explaining some phenomena
•! Focusing on interactions between
appropriately-chosen parts (a systems
approach) can give a clear understanding
The copy
heads towards
a “converter”
that turns
gliders into
spaceships
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•! Finding interactions
between biological parts is
hard (but getting easier)
•! Important phenomena are
occurring at levels from
single molecules to
populations
•! Understanding systems
with many parts requires
simulation and/or analysis
Human Protein
Interaction Network
One field by many names
•!
•!
•!
•!
•!
Von Bertalanffy’s General Systems Theory
Norbert Wiener’s Cybernetics
“New Cybernetics”
Systeomics
Systems Biology
… now has departments
at many schools (but few
undergraduate programs)
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What We’ll Cover
in MCB 135
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Course Logistics
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Next Time:
Logic and Computability
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