Transcript Digitally Programmed Cells

Building Biological Systems
from Standard Parts
Tom Knight
MIT Computer Science and
Artificial Intelligence Laboratory
IGEM Headquarters
Ginkgo Bioworks Inc.
A Scientist discovers that which
exists;
an Engineer creates that which never
Maxwell / Darwin
Physics / Biology
1900’s / 2000’s
Science ~ 1870
Science ~ 1960
Electrical engr. ~ 1905
Synthetic biology ~ 2000
Major ideas: modularity,
hierarchy, information,
black box behavior,
feedback, design &
synthesis, control of
materials, technological
substrate
Major ideas: modularity,
hierarchy, information,
black box behavior,
feedback, design &
synthesis, control of
materials, technological
substrate
Perfect devices
Perfect behavior
Major societal problems
• Energy & raw materials
• Environmental protection and cleanup
• Health & aging
• Defense against natural and unnatural events
Science and Engineering
Knowledge & understanding
Excellent models
Science
Systems Biology
Natural organisms
Engineering
Synthetic Biology
Engineered organisms
Science and Engineering
Science &
Systems Biology
of natural
organisms
Knowledge & understanding
Excellent models
Parts
Repository
De novo DNA
synthesis
Engineered organisms
Revised
knowledge
and new
techniques
Engineering &
Synthetic Biology
using standard
parts
Systems Biology
vs.
Synthetic Biology Based on Standard
Parts
Systems Biology
Synthetic Biology Based on Parts
- Models of natural systems
- New discoveries from data
analysis and fusion
- Understanding of noise and
other effects in natural systems
- Success measured in match
of the model to nature
- Embrace natural complexity
- Parts designed for use by others
- Engineering design tools
- Simulators
- Industrial development of good parts
and devices
- Simple organisms to hold designs
- iGEM team success is based on parts
- Registry is the primary catalog of parts
- Success measured in generality and
utility of parts, systems and protocols
-Remove natural complexity
Powerful tools of
engineering design
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abstraction
hierarchy
modularity
standardization
isolation, separation of concerns
flexibility
Abstraction model
catabolism
anabolism
Real world
complexity
Constructed
complexity
Small core of standard parts
Design
information
Abstraction model
catabolism
anabolism
Living
systems,
waste
Food
Metabolic intermediates
AAs, NTPs, core metabolites
genome
Abstraction model
Abstraction barrier
Requirements
Implementations
Abstraction layers
Part
Standard interfaces
Contracts
Abstractions
Abstraction layer
Abstractions in electronics
User
Application software
Operating system, user interface
Programming language
Instruction set architecture
Virtual machine
Computer hardware design
Functional computing units
Logic synthesis
Logic gates
Circuit design
Transistors
Mask geometry
Fabrication technologies
Semiconductor physics
Quantum physics
State change,
abstract behavior
1E9 components
Differential equations:
KCL, KVL, device models,
network theory
Types of designers
User
Application software
Operating system, user interface
Tall, thin
designer
Programming language
Instruction set architecture
Virtual machine
Computer hardware design
Functional computing units
Broad, deep designer
Logic synthesis
Logic gates
Circuit design
Transistors
Mask geometry
Fabrication technologies
Semiconductor physics
Quantum physics
Carver Mead, 1980
Mead & Conway,
Introduction to
VLSI Design
Standards & Design Rules
User
Application software
Operating system, user interface
Programming language
Instruction set architecture
Virtual machine
Computer hardware design
Functional computing units
Logic synthesis
Logic gates
Circuit design
Transistors
Mask geometry
Fabrication technologies
Semiconductor physics
Quantum physics
Run Microsoft software
Fanout rules
Signal restoration rules
Spacing rules
Carver Mead, 1980
Mead & Conway,
Introduction to
VLSI Design
Complexity Reduction
User
Application software
Operating system, user interface
Programming language
Instruction set architecture
Virtual machine
Computer hardware design
Functional computing units
Logic synthesis
Logic gates
Circuit design
Transistors
Mask geometry
Fabrication technologies
Semiconductor physics
Quantum physics
100’s of OS calls
100 statements
100’s of instructions
10’s of units
10’s of gate types
4 types of transistors
15 mask layers
6 materials
Complexity Reduction
• Good News:
Biology is modular and abstract
 Evolution needs modular design as much as we do
 We can discover the modular designs, modify them,
and use them
Learn New Engineering
Principles from Biology
Coping with errors
Design with unreliable components
Design with evolution
Self organization
Self repair
Molecular scale construction
Biology is the nanotechnology which works
Role of Standards in Engineering
• Simplified thinking about interfaces: Design rules
 Composition: Structural / Functional
• Reusable Parts
• Contracts and commercial access
• Independent evolution of components and technologies
• Facile comparison of results
“The good thing about standards is that
there are so many to choose from”
“In this country, no organized attempt has yet been made to
establish any system, each manufacturer having adopted whatever
his judgment may have dictated as best, or as most convenient for
himself.”
Williams Sellers “On a Uniform System of Screw Threads”
Franklin Institute April 21, 1864
Several Standards
• Standard components & interfaces
• Standard composition
• Standard function & interfaces
• Standard measurements
• Standard chassis
Biobricks:
Standard Biological Parts
• Snap together Lego block assembly
 Mechanical compatibility
• Output of one component suitable as input of
next component
 Functional compatibility
 Input Sensors
 Computational Devices
 Output Actuators
Naturally Occurring Sensor and
Actuator Parts Catalog
Actuators
Sensors
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Light (various wavelengths)
Magnetic and electric fields
pH
Molecules
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Autoinducers
H2S
maltose
serine
ribose
cAMP
NO
Internal State
 Cell Cycle
 Heat Shock
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Chemical and ionic membrane
potentials
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Motors
 Flagellar
 Gliding motion
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Light (various wavelengths)
Fluorescence
Autoinducers (intercellular
communications)
Sporulation
Cell Cycle control
Membrane transport
Exported protein product
(enzymes)
Exported small molecules
Cell pressure / osmolarity
Cell death
Standard Component Form
gca GAATTC gcggccgc t TCTAGA g
t ACTAGT a GCGGCCG CTGCAG gct
cgt CTTAAG cgccggcg a AGATCT c
a TGATCA t cgccggc GACGTC cga
EcoRI
XbaI
SpeI
X
S
E
No internal sequences of the form
EcoRI:
XbaI:
SpeI:
PstI:
GAATTC
TCTAGA
ACTAGT
CTGCAG
PstI
P
Assembly 3-Way
vector origin
antibiotic resistance
E
P
X
E X
S
S P
t A
a TGATC
SpeI
CTAGA a
T t
XbaI
t ACTAGA a
a TGATCT t
mixed
E
X
S
P
DARPA Biocomp Plasmid
Distribution 1.0 May 2002
• Standard vectors, components, protocols
• Very limited coverage –
 Plac, ECFP, EYFP, lacZ, T1
 Assembled compound structures
• Enough to get started
• More coming soon
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Lux systems from V. fischeri and P. luminescens
cI, p22-C2, tetR, luxR
Antibiotic resistance, pACYC & pSC101 ori
Autoinducer systems from V. fischeri, P. aeruginosa
Some toy experiments
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Plac
Plac
Plac
Plac
Plac
Plac
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–
–
–
–
–
ECFP
EYFP
ECFP – EYFP
EYFP – ECFP
ECFP – T1 – EYFP
EYFP – T1 – ECFP
• Need standardized measurement techniques
• Need good modeling tools
MIT Synthetic Biology, IAP Class 2003
Laura Wulf, MIT News Office c.2003
Grace
June-Wha
Maia
Connie
Louis
Alex
Danny
Jose
Reshma
Vinay
Ty
Samantha
Neel
Voichita
Brian
Peter
Kenney
Rhee
Mahoney
Tao
Waldman
Wissner-Gross
Shen
Pacheco
Shetty
Mahajan
Thomson
Sutton
Varshney
Marinescu
Chow
Carr
6/7
6/7
6
6
2/6
6/8/18
6
10/14
BE
BE
BE
BE
HST
HST
MAS
MAS
2006
2006
2005
2004
2005
2003
2005
2003
G
G
G
G
G
G
G
RS
No prerequisites, no credit, consumes most of January… 13 waitlisted students
Four project teams, shared components
sixty fabricated components – Blue Heron
Key Ideas
• Build system out of standard parts
 Pre-optimized for assembly
• Use standard techniques to assemble them
 No surprises
 Routine
 Robot assembly
• Network effects on the size of the library
 6 -> 5500
• Couple functional and physical designs
 Parts have a logical function, not random DNA fragments
• Measured and characterized for modeling
 First time success
• Part collections of similar interchangeable parts
Standard Plasmids
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pSB1A3
 pSB “synthetic Biology”
 1 -> high copy number origin (pUC19 e.g.)
 A -> Ampicillin resistant
 3 -> Biobrick cloning site with up and downstream terminators
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Available antibiotics
 A ampicillin (orange) 100 ug/ml
 C chloramphencol (green) 35 ug/ml
 K kanamycin (red) 50 ug/ml
 T tetracycline (yellow) 15 ug/ml
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Available origins - pSC101, p15A, inducible
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We need parts returned to the Registry in 1 series plasmids if possible
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VF2, VR sequencing primer locations
Resources
• IGEM home pages: igem.org
 Past team project wikis, posters, presentations
• Registry of standard biological parts:
 Partsregistry.org
• Openwetware: openwetware.org
 Searching the literature
• IGEM headquarters [email protected]
• Me: [email protected]
Synthetic Biology
• An Engineering technology based on biology
 which complements rather than replaces standard
approaches
• Engineering synthetic constructs will
 Enable quicker and easier experiments
 Enable deeper understanding of the basic mechanisms
 Enable applications in nanotechnology, medicine and
agriculture
 Become the foundational technology of the 21st century
Simplicity is the ultimate
sophistication