carlson, pace & proliferation of biological technologies , biosec. & bioterror. 1(3) :1...

1Endy, DB May 2005

Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)

2Endy, DB May 2005

Application

Struggle, Limited Success, Struggle…

System??Devices?Design &

Fabrication

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Struggle, Success, Predictable Success

SystemsParts & Fabrication

DesignQuickTime™ and a

Video decompressorare needed to see this picture.

Applications

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• Decoupling– Rules insulating design process from details of fabrication– Enable parts, device, and system designers to work together– VLSI electronics, 1970s

• Standardization– Predictable performance– Off-the-shelf– ME, 1800s

• Abstraction– Insulate relevant characteristics from overwhelming detail– Simple artifacts that can be used in combination– From Physics to EE, 1800s

Enabling Biological Engineering

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Abstraction

Devices

Parts

Systems

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Parts

Zif268, Paveltich & Pabo c. 1991

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Devices

cI-857OLac RBS T

CILacI

LacI

CI

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Devices

LacI CI inverter

CILacI

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Systems

Inverter.2 Inverter.3Inverter.1

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Interfaces

Devices

Parts

SystemsInv.2 Inv.3Inv.1


LacI CI

inverterCILacI

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Parts/Device Interface

Devices

Parts


LacI CI

inverterCILacI

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Stories“In 1910, I was in Mexico, in the state of Yucatan, when an invasion of locusts occured; the Indians reported to me that in a certain place the ground was strewn with the corpses of these insects. I went there and collected sick locusts, easily picked out since their principal symptom was an abundant blackish diarrhoea. This malady had not as yet been described, so I studied it. It was a septicaemia with intestinal symptoms, It was caused by bacteria, the locust coccobacilli, which were present almost in the pure state in the diarrhoeal liquid. I could start epidemics in columns of healthy insects by dusting cultures of the coccobacillus on plants in front of the advancing columns: the insects infected themselves as they devoured the soiled plants…

In the course of these researches, at various times I noticed an anomaly, shown by some cultures of the coccocacillus which intrigued me greatly, although in fact the observation was ordinary enough, so banal indeed that many bacteriologists had certainly made it before on a variety of cultures. The anomaly consisted of clear spots, quite circular, two or three millimeters in diameter, speckling the cultures grown on agar.”

From The Bacteriophage by Dr. Felix d'Herelle, Science News 14: 44-59 (1949). (Translation by J. L. Crammer)

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Parts/Device Interface

Devices

Parts


LacI CI

inverterCILacI

X X

A B inverter

BA

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Device/System Interface

Devices

Systems Inv.2 Inv.3Inv.1

A B inverter

BA

C D inverter

DC

E F inverter

FE

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Devices

Systems E F C DA B

A B inverter

BA

C D inverter

DC

E F inverter

FE

X X

X

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Devices

Systems E F C DA B

A B inverter

BA

C D inverter

DC

E F inverter

FE

A D

X X

X

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cI-857OLac RBS T

cILacI

cI-857RBS T

cI

O

PoPSin

PoPSout

LacI

cIPoPSout

PoPSin

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cIRBST

O

cI

PoPSIN

Polymerase Per Second = PoPS!

cIRBST

O

PoPSOUT

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cIRBST

O

PoPSOUT

PoPSIN

cI

PoPSOUTPoPSIN

Polymerase Per Second = PoPS!

INVERTER

PoPSOUTPoPSINPoPSOUT

PoPS Source (Any)

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Devices

Systems

XA B

inverterBA

C D inverter

DC

E F inverter

FE

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Devices

SystemsB CA

A

B

C

PoPSIN

PoPSIN

PoPSIN

PoPSOUT

PoPSOUT

PoPSOUT

X

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‘I need a few DNA binding proteins.’

‘Here’s a set of DNA binding proteins, 1N, that each recognize a unique cognate DNA site, choose any.’ ‘Get me this DNA.’

‘Here’s your DNA.’

‘Can I have three inverters?’

‘Here’s a set of PDP inverters, 1N, that each send and receive via a fungible signal carrier, PoPS.’

TAATACGACTCACTATAGGGAGA DNA


Parts

PoPSNOT.1PoPS PoPS Devices

PoPS NOT.2

PoPS NOT.3

PoPS NOT.1

Systems

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Device-Level System Diagram

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Parts- and Device-Level System Diagram

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DNA Layout

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Trigger Test Circuit

Characterization and Debug

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Registry of Standard Biological Parts

http://parts.mit.edu/

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From: XXXXSubject: Endy LetterDate: January 6, 2005 9:45:17 AM ESTTo: [email protected]

Dr. Endy,

I am a sophomore at XXXXX High School in Connecticut and have recently taken an interest in Synthetic Biology.I am writing to ask for your help because i am having difficulty in obtaining information,and understanding some of the information i already have. Anything you can send my way would be greatly appreciated…

…I will soon begin working on a proposal to create a BioBrick, any information you can send me on their creation would be excellent.

-Sincerely, XXXX XXXX XXXX High School -Grade 10

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Education Driving Research

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A Constructive Society

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c/o Jeff Tabor

UT 2004 SB Competition Team

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Photons

PoPS

Light PoPSReceiver

PoPS ColorConverter

BBa_I15010BBa_R0082

BBa_B0034BBa_E0033BBa_B0015

c/o Jeff Tabor


33Endy, DB May 2005

Lens ripped off of overhead projector

Casserole dishPile of cells/agar

Thermostable chassis

c/o Jeff Tabor


34Endy, DB May 2005

c/o Jeff Tabor


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