carlson, pace & proliferation of biological technologies , biosec. & bioterror. 1(3) :1...
DESCRIPTION
Carlson, Pace & Proliferation of Biological Technologies , Biosec. & Bioterror. 1(3) :1 (2003). Struggle, Limited Success, Struggle…. Devices?. System??. Design & Fabrication. Application. Struggle, Success, Predictable Success. Applications. Systems. Parts & Fabrication. Design. - PowerPoint PPT PresentationTRANSCRIPT
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1Endy, DB May 2005
Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)
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2Endy, DB May 2005
Application
Struggle, Limited Success, Struggle…
System??Devices?Design &
Fabrication
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3Endy, DB May 2005
Struggle, Success, Predictable Success
SystemsParts & Fabrication
DesignQuickTime™ and a
Video decompressorare needed to see this picture.
Applications
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4Endy, DB May 2005
• 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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5Endy, DB May 2005
Abstraction
Devices
Parts
Systems
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6Endy, DB May 2005
Parts
Zif268, Paveltich & Pabo c. 1991
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7Endy, DB May 2005
Devices
cI-857OLac RBS T
CILacI
LacI
CI
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8Endy, DB May 2005
Devices
LacI CI inverter
CILacI
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9Endy, DB May 2005
Systems
Inverter.2 Inverter.3Inverter.1
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10Endy, DB May 2005
Interfaces
Devices
Parts
SystemsInv.2 Inv.3Inv.1
Zif268, Paveltich & Pabo c. 1991
LacI CI
inverterCILacI
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11Endy, DB May 2005
Parts/Device Interface
Devices
Parts
Zif268, Paveltich & Pabo c. 1991
LacI CI
inverterCILacI
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12Endy, DB May 2005
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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13Endy, DB May 2005
Parts/Device Interface
Devices
Parts
Zif268, Paveltich & Pabo c. 1991
LacI CI
inverterCILacI
X X
A B inverter
BA
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14Endy, DB May 2005
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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15Endy, DB May 2005
Device/System Interface
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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16Endy, DB May 2005
Device/System Interface
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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17Endy, DB May 2005
Device/System Interface
cI-857OLac RBS T
cILacI
cI-857RBS T
cI
O
PoPSin
PoPSout
LacI
cIPoPSout
PoPSin
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18Endy, DB May 2005
cIRBST
O
cI
PoPSIN
Polymerase Per Second = PoPS!
cIRBST
O
PoPSOUT
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19Endy, DB May 2005
cIRBST
O
PoPSOUT
PoPSIN
cI
PoPSOUTPoPSIN
Polymerase Per Second = PoPS!
INVERTER
PoPSOUTPoPSINPoPSOUT
PoPS Source (Any)
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20Endy, DB May 2005
Device/System Interface
Devices
Systems
XA B
inverterBA
C D inverter
DC
E F inverter
FE
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21Endy, DB May 2005
Device/System Interface
Devices
SystemsB CA
A
B
C
PoPSIN
PoPSIN
PoPSIN
PoPSOUT
PoPSOUT
PoPSOUT
X
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22Endy, DB May 2005
‘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
Zif268, Paveltich & Pabo c. 1991
Parts
PoPSNOT.1PoPS PoPS Devices
PoPS NOT.2
PoPS NOT.3
PoPS NOT.1
Systems
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23Endy, DB May 2005
Device-Level System Diagram
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24Endy, DB May 2005
Parts- and Device-Level System Diagram
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25Endy, DB May 2005
DNA Layout
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26Endy, DB May 2005
Trigger Test Circuit
Characterization and Debug
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27Endy, DB May 2005
Registry of Standard Biological Parts
http://parts.mit.edu/
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28Endy, DB May 2005
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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29Endy, DB May 2005
Education Driving Research
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30Endy, DB May 2005
A Constructive Society
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31Endy, DB May 2005
c/o Jeff Tabor
UT 2004 SB Competition Team
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32Endy, DB May 2005
Photons
PoPS
Light PoPSReceiver
PoPS ColorConverter
BBa_I15010BBa_R0082
BBa_B0034BBa_E0033BBa_B0015
c/o Jeff Tabor
UT 2004 SB Competition Team
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33Endy, DB May 2005
Lens ripped off of overhead projector
Casserole dishPile of cells/agar
Thermostable chassis
c/o Jeff Tabor
UT 2004 SB Competition Team
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34Endy, DB May 2005
c/o Jeff Tabor
UT 2004 SB Competition Team