What is Synthetic Biology?

ELECTRICAL engineering solution

water = weight water<weight

MECHANICAL engineering solution

BIOLOGICAL engineering solution

BIOLOGICAL engineering solution

BIOLOGICAL engineering solution

A biological machine

The instructions for the machine

Figure 20.1 An overview of how bacterial plasmids are used to clone genes

Genetic engineering involves moving existing genes from one organism to another.

Synthetic biology involves constructing new genetic systems and turning cells into biological machines

A bacterial photograph

Bacteria engineered to change color based on light

A LIVING HOUSE -

Terreform’s Fab Tree Hab

Or…

Bacteria that can test for Arsenic in water

Bacterial computers

Bacteria that detect mines

Yogurt that cleans teeth

These are not possible by evolution

Engineered bacteria to change color based on light.

Evolution didn’t do this!Engineers did…

And they have…

Synthetic biology is engineering

How is engineering different from science?

PCR

Genetic Engineering

Synthetic Biology

Sequencing

rDNA

Synthesis

Abstraction

Standardization

A+A+C+T+T…

• Abstraction -- a term borrowed from software engineering to indicate the management of complexity inherent to biological parts and the systems made with them. Abstraction simplifies components by hiding, or "black boxing" information, facilitating their use and re-use

Abstraction Hierarchy

Part -- a nucleic acid-encoded biological function

Parts

promoter

Ribosome binding site

• Device -- an engineered genetic object that produces a human-defined function under specified conditions. Devices are produced by combining one or more standard biological part

Eau d’coli

• System- an engineered genetic object that produces a human-defined function under specified conditions. Systems are produced by combining one or more standard biological Device.

Standardization

a series of assembly andcharacterization rules. In time, thesestandards may allow the reliablephysical and functional assembly ofgenetic parts into devices, anddevices into systems

Standard Assembly

Std functional assembly???

An engineering paradigm

• What precisely is the problem or opportunity you are focusing on?

• How clear are you on an approach to make a dent in the problem?

• What if your project is fully successful? How big a difference could it make? What concerns will it raise?

• What other technologies can be used/have been used to address this area?

• What don't you know? How big are the gaps in what you know? How much is completely unknown or unknowable?

•iTune: the test part of the paradigm

•Characterizing the device

•Can we tune it to the output we want?

•Why would we want to do this?

• We can increase or decrease the output of a gene by affecting:

• The promoter• Which alters the rate of transcription

• The RBS– Which alters the rate of translation

LacZ codes forBeta-Galactosidase

promoter RBSORFLacZ

GlucoseGalactose

If given lactose

promoter RBSORFLacZ

Galactose o-nitrophenol, (yellow)

If given ONPG

• Yellow color is proportional to the o-nitrophenol

• Which is proportional to the amount of LacZ expression (Beta-galactosidase)

• Which is controlled by the Promoter and RBS

• Activity is measured in Miller units

PCR

Genetic Engineering

Sequencing

rDNA