1. Endy, MIT BE, 20 May 2004 1 Application Struggle, Limited Success, Struggle… System?? Devices? Design & Fabrication

2. Endy, MIT BE, 20 May 2004 2 Application Struggle, Success, Predictable Success Systems Parts & Fabrication Design Applications Tools Registries Synthesis Measurement

3. Endy, MIT BE, 20 May 2004 3 Standardization of Components –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, 1900s Decoupling Design & Fabrication –Rules insulating design process from details of fabrication –Enable parts, device, and system designers to work together –VLSI electronics, 1970s Enabling Biological Engineering

4. Endy, MIT BE, 20 May 2004 4 Abstraction Hierarchy Devices Parts Systems

5. Endy, MIT BE, 20 May 2004 5 Parts Zif268, Paveltich & Pabo c. 1991

6. Endy, MIT BE, 20 May 2004 6 Devices cI-857 O Lac RBS T CI LacI CI

7. Endy, MIT BE, 20 May 2004 7 Devices LacI  CI inverter CI LacI

8. Endy, MIT BE, 20 May 2004 8 Systems Inverter.2Inverter.3Inverter.1

9. Endy, MIT BE, 20 May 2004 9 Interfaces Devices Parts Systems Inv.2Inv.3Inv.1 Zif268, Paveltich & Pabo c. 1991 LacI  CI inverter CI LacI

10. Endy, MIT BE, 20 May 2004 10 Parts/Device Interface Devices Parts Zif268, Paveltich & Pabo c. 1991 LacI  CI inverter CI LacI XX A  B inverter B A

11. Endy, MIT BE, 20 May 2004 11 Device/System Interface Devices Systems Inv.2Inv.3Inv.1 A  B inverter B A C  D inverter D C E  F inverter F E

12. Endy, MIT BE, 20 May 2004 12 Device/System Interface Devices Systems E  FC  DA  B inverter B A C  D inverter D C E  F inverter F E X X X

13. Endy, MIT BE, 20 May 2004 13 Device/System Interface Devices Systems E  FC  DA  B inverter B A C  D inverter D C E  F inverter F E A  D X X X

14. Endy, MIT BE, 20 May 2004 14 Device/System Interface cI-857 O Lac RBS T cI LacI cI-857 RBS T cI O PoPS in PoPS out LacI cI PoPS out PoPS in

15. Endy, MIT BE, 20 May 2004 15 cI RBS T O PoPS OUT PoPS IN cI PoPS OUT INVERTER PoPS OUT PoPS IN Polymerase Per Second = PoPS!

16. Endy, MIT BE, 20 May 2004 16 Device/System Interface Devices Systems BCA A B C PoPS IN PoPS OUT X

17. Endy, MIT BE, 20 May 2004 17 Interfaces Devices Parts Systems PoPS Inv.2 PoPS Inv.3 PoPS Inv.1 Zif268, Paveltich & Pabo c. 1991 PoPS Inv.1 PoPS

18. Endy, MIT BE, 20 May 2004 18 E.colibrator, Polkadorks @ IAP 2004

19. Endy, MIT BE, 20 May 2004 19 Device-Level System Diagram

20. Endy, MIT BE, 20 May 2004 20 Parts- and Device-Level System Diagram

21. Endy, MIT BE, 20 May 2004 21 DNA Layout

22. Endy, MIT BE, 20 May 2004 22 System-Level Timing Diagram

23. Endy, MIT BE, 20 May 2004 23 Population-Level Simulations

24. Endy, MIT BE, 20 May 2004 24 Trigger Test Circuit Characterization and Debug

25. Endy, MIT BE, 20 May 2004 25 MIT Registry of Standard Biological Parts http://parts.mit.edu/

26. Endy, MIT BE, 20 May 2004 26 DNA Synthesis Year Bases of DNA Per Person Day Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)

27. Endy, MIT BE, 20 May 2004 27 Hacking the Living World?

28. Endy, MIT BE, 20 May 2004 28 Risk Biological Risk: Background Technology Classes Relevant to Biological Risk (current relative capabilities) Manipulation Analysis Response Detection

29. Endy, MIT BE, 20 May 2004 29 Biological Risk: Tactics as “Strategy” Maginot Line France, 1940 Ciprofloxacin Smallpox vaccine Anthrax vaccine SARS assay VHF therapy (under construction) Plague vaccine (under construction)

30. Endy, MIT BE, 20 May 2004 30 Biological Risk: Future Strategy Risk Technology Classes Relevant to Future Biological Risk (needed capabilities) Detection Analysis Response Manipulation

31. Endy, MIT BE, 20 May 2004 31 Biological Risk: Suite of Solutions Number of Individuals Individual’s Intent honorable dishonorable Bin Laden Genetics, Inc. Disgruntled Researcher Garage Bio-Hacker Basic Researcher

32. Endy, MIT BE, 20 May 2004 32 A Constructive Society

33. Endy, MIT BE, 20 May 2004 33 D23L AvrII D24L EcoRI D26L BamHI D27L EagI D28L SacII D30L SalI D22L BstEII D22RD23RD24RD26RD27RD28RD30R ø2.5 32.8 ø3.8 3.53.8R3.8 D25L XmaI D25R 2.5 D29L PciI D29R 1.82 BglII 175209357234384644787530675 FspIAvrII D50L BsiWI D51L PvuI D53L SacII D54L BamHI D55L XmaI D57L HindIII D50RD51RD53RD54RD55RD57R ø9 10ATøTø12 D52L EcoRI D52R 9 D56L ApaI D56R 8 PacI 1611351038354647359123823 ø10 11 DraIRsrII XbaI BssHIIAatIIAvaIBspHIEciINsiI NdeI AseI D57L HindIII D59L EcoRI D58L PfoI D57R D58R 1213 PacI 2382624173 ø13 R13 D60L BsiWI D62L EagI D59RD60RD62R 16 D61L PvuI D61R 15 ApaLI 59122443520437 14 NciI ScaI BstBIAvaI D64L HindIII D65L BamHI D67L ApaI D68L EcoRI D69L BsiWI D71L SalI D63L SacII D63RD64RD65RD67RD68RD69RD71R ø17 18.5/18.718 E 19/19.2/19.319.5R18.5 D66L XmaI D66R 17.5 D70L PstI D70R 17 35166220427053460176135150 øOR SRR/TR 160 KasIBspDIFspI BglI BlpIDraIIIAcvIAciIKpnI

34. Endy, MIT BE, 20 May 2004 34 Kuroda-Kawaguchi et al., Nature Genetics 29:279 (2001)

35. Endy, MIT BE, 20 May 2004 35 Responsibility “Men have forgotten this truth,” said the fox. “But you must not forget it. You become responsible, forever, for what you have tamed.” Saint-Exupéry, Le Petit Prince (1943)