But is it art?
Brandeis University
12.07.05
Panel of artists….
and their art…
Will the real artist please stand up?
Genetically-encoded Oscillator
Period is ~120’ (two doublings)QuickTime™ and a
TIFF (LZW) decompressorare needed to see this picture.
Time (minutes)
http://my.integritynet.com.au/purdic/oscillators.htm
Electronics 101
Hartley Oscillator Colpitts Oscillator
1. Motivation
why engineer biology?
1. Motivation
why engineer biology?
2. Plan
how to engineer biology?
1. Motivation
why engineer biology?
2. Plan
how to engineer biology?
3. Execution
state of the art (stupid bacteria tricks)
1. Motivation
why engineer biology?
2. Plan
3. Execution
… because we can
… because there’s so much to build
… because there’s so much to learn
Genetically-Encoded Digital Logic
“transfer function”
time at 42°C
transcript level
3’
heat shock promoter
heat shock response gene
Heat Shock Response: 32 induction
Straus, Walter, and Gross Nature (1987) 329: 347
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Genetically-Encoded Logic Functions
heat shock promoter
heat shock response gene
Genetically-Encoded Logic Functions
heat shock promoter
repressor gene
repressible promoter
heat shock response gene
Genetically-Encoded Logic Functions
heat shock promoter
repressor gene
repressible promoter
heat shock response gene
Genetically-Encoded Logic Functions
heat shock promoter
repressor gene
repressible promoter
heat shock response geneX
Logic Functions
Inverter input output
1 0
0 1
AND gate
ab
a b output
0 0 0
1 0 0
0 1 0
1 1 1
Programming with DNA: hiding the details
repressor gene
repressible promoter
Genetic InverterLambda cI, P22 c2, lacI, TetR…
PRM, PR, Plac, Ptet…
Programming with DNA: hiding the details
repressor gene
repressible promoter
Genetic InverterLambda cI, P22 c2, lacI, TetR…
PRM, PR, Plac, Ptet…
Programming with DNA: hiding the details
Genetic Inverter
Nature is source for code “Genetic Parts”
Synthetic Biology: programming with DNA
Make just about anything
Logically combined in a cell
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.nature.com/nature/comics/syntheticbiologycomic
“There is a great satisfaction in building good tools for other people to use.”
-Freeman Dyson
Biology Engineering
“There is a great satisfaction in building good tools for other people to use.”
-Freeman Dyson
Biology Engineering
“how can we help?”
“There is a great satisfaction in building good tools for other people to use.”
-Freeman Dyson
Biology Engineering
“Cells are tiny machines”
“OK then, build me a cell”
1. Motivation
why engineer biology?
2. Plan
3. Execution
1. Motivation
2. Plan
how to engineer biology?
3. Execution
1. Motivation
2. Plan
how to engineer biology?
3. Execution
…what foundational technologies are needed?
…are safeguards needed?
Works of Art
“A good scientist is a person with original ideas. A good engineer is a person who makes a design that works with as few original ideas as possible. There are no prima donnas in engineering.”
-Freeman Dyson
well characterized
predictable
modular
insulated
stable
Attributes for Foundational Technologies
well characterized
predictable
modular….
insulated
stable
Attributes for Foundational Technologies
http://parts.mit.edu
225 basic parts
454 composite parts
http://parts.mit.edu
Standard Assembly
Broadly consider two sources of risk
1. from the technology itself
2. from the people (hackers) who use it
http://biobricks.org/
G. Church, “Let us go forth and safely multiply” Nature (2005) 438:423
1. Motivation
2. Plan
how to engineer biology?
3. Execution
1. Motivation
2. Plan
3. Execution
state of the art
1. Motivation
2. Plan
3. Execution
state of the art …SB accomplishments
…undergrad. contributions
Nature (2005) 434: 1130
A new kind of biofilm: “coli-roid”
condition lacZ result
light low light color
dark high dark color
Light Dependent Gene Expression
Phytochromes from Synechocystis
Osmoregulation system from E. coli
LacZ reporter strain from literature (1979)
Light Dependent Gene Expression
Biofilm v2.0
mRFP
condition mRFP result
light high red
dark low not red
1. Motivation
why engineer biology?
2. Plan
how to engineer biology?
3. Execution
state of the art
Three comic strips to conclude
Worst case scenario: total failure
Three comic strips to conclude
Worst case scenario: total failure
Best case: total success, are we ready?
Three comic strips to conclude
Worst case scenario: total failure
Best case: total success, are we ready?
Biological Engineers, an oxymoron?
Credits
Tom Knight Drew Endy Randy Rettberg
the end