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