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Drew Endy Stanford Bioengineering The BioBricks Foundation 12 September 2014 Lehigh University 1 Bio(technology) in the 21st century

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Page 1: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Drew Endy Stanford Bioengineering The BioBricks Foundation !!12 September 2014 Lehigh University

1

Bio(technology) in the 21st century

Page 2: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

2

Foods $110

billionStuff

$115 billion

Medicines $75 billion

10-15% past y.o.y. growth

Genetic engr. is >2% of US economy

Page 3: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Yet, most of biotechnology has not been imagined or made true.

3

Page 4: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

4

“Tetrahedral coordination of silica (SiO2), the basic building block of the most ideal glass former.”

http://en.wikipedia.org/wiki/Silicon_dioxide

~0.25nm

Page 5: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

5

Sponge biosilica

Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

500nm

Page 6: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

6Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

5,000nm

Laminated biosilica comprising sponge spicule

Page 7: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

7Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

25,000nm

Sponge spicule lattice junction

Page 8: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

8Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

20,000nm

Cross section of biosilica spicule composite beam

Page 9: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

9Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

100,000nm

Bracketed junctions of biosilica spicule composite beams

Page 10: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

10Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 2005

5,000,000nm (5mm)

Biosilica cage

Page 11: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

11Joanna Aizenberg et al., Science v.309 no.5732 pp.275-278, 8 July 20051cm

http://en.wikipedia.org/wiki/Venus%27_Flower_Basket

Page 12: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

What could we do with Menlo Park, now a California “Shangri La” ?

http://sjl.blogs.com/photos/sharon_park/

~16,000,000 pounds lawn & garden clippings per year...

Page 13: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

The living bridges of Cherrapunji, India are made from the roots of the Ficus elastica tree. (http://rootbridges.blogspot.com/)

13

Page 14: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Fungal Chair, c/o Phil Ross (www.philross.org)

14

Page 15: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Glycerol

Ar

5-Hydroxymethyl-

furfural

SG

Ferulic acid

Gallic acid

C6

C5

Higher alcohols

C2

Oxo synthesis

products

3-Hydroxy-

propionate

Lactic

Propionic acid

Malonic acid

Serine

Succinic acid

Fumaric acid

Malic acid

3-Hydroxy-

butyrolactone

Acetoin

Itaconic acid

Furfural

Levulinic acid

Glutamic acid

Xylonic acid

Xylitol/Arabitol

H2

Methanol

Mixed alcoholsBiobased

Syn Gas

Direct

Polymers & gums

TextilesCarpets, Fibers, fabrics, fabric

coatings, foam cushions, upholstery,

drapes, lycra, spandex

Safe Food SupplyFood packaging, preservatives,

fertilizers, pesticides, beverage

bottles, appliances, beverage can

coatings, vitamins

TransportationFuels, oxygenates, anti-freeze, wiper

fluids molded plastics, car seats, belts

hoses, bumpers, corrosion inhibitors

HousingPaints, resins, siding, insulation,

cements, coatings, varnishes, flame

retardents, adhesives, carpeting

RecreationFootgear, protective equipment,

camera and film, bicycle parts & tires,

wet suits, tapes-CD’s-DVD’s, golf

equipment, camping gear, boats

Health and HygienePlastic eyeglasses, cosmetics,

detergents, pharmaceuticals, suntan

lotion, medical-dental products,

disinfectants, aspirin

Iso-synthesis

products

Fischer-Tropsch

Liquids

C3

C4 Aspartic acid

Citric/Aconitic acid

Lysine

Gluconic acid

Sorbitol

Glucaric acid

Ammonia synthesis, hydrogenation products

Linear and branched 1º alcohols, and mixed higher alcohols

Methyl esters, Formaldehyde, Acetic acid, Dimethylether,

Dimethylcarbonate, Methyl amines, MTBE, olefins, gasoline

Olefin hydroformylation products: aldehydes, alcohols, acids

Iso-C4 molecules, isobutene and its derivatives

!-olefins, gasoline, waxes, diesel

Fermentation products, Propylene glycol, malonic, 1,3-PDO, diacids,

propyl alcohol, dialdehyde, epoxides

Acrylates, L-Propylene glycol, Dioxanes, Polyesters, Lactide

Acrylates, Acrylamides, Esters, 1,3-Propanediol, Malonic acid and

others

THF, 1,4-Butanediol, "-butyrolactone, pyrrolidones, esters, diamines,

4,4-Bionelle, hydroxybutyric acid

Unsaturated succinate derivatives (see above)

Hydroxybutyrates, epoxy-"-butyrolactone, butenoic acid

Methyl succinate derivatives (see above), unsaturated esters

Many furan derivatives

#-aminolevulinate, 2-Methyl THF, 1,4-diols, esters, succinate

EG, PG, glycerol, lactate, hydroxy furans, sugar acids

Amino diols, glutaric acid,substituted pyrrolidones

1,5-pentanediol, itaconic derivatives, pyrrolidones, esters

Numerous furan derivatives, succinate, esters, levulinic acid

Caprolactam, diamino alcohols, 1,5-diaminopentane

Dilactones, monolactones, other products

Gluconolactones, esters

Glycols (EG, PG), glycerol, lactate, isosorbide

Phenolics, food additives

polyhydroxyalkonoates

poyaminoacids

polysaccharides

Hydroxy succinate derivatives (above), hydroxybutyrolactone

Amino succinate derivatives (see above)

Butanediols, butenols

Diols, ketone derivatives, indeterminant

Lactones, esters

Antifreeze and deicers

Fuel oxygenates

Green solvents

Phthalate polyesters

Plasticizers

Polyacrylates

Polyacrylamides

Phenol-formaldehyde resins

PEIT polymer

Polyhydroxypolyesters

Polyhydroxypolyamides

Chelating agents

Amines

Solvents

Nylons (polyamides)

Polyurethanes

Bisphenol A replacement

Polycarbonates

Reagents-building unit

EnvironmentWater chemicals, flocculants,

chelators, cleaners and detergents

Reagent, propionol, acrylate

Pharma. Intermediates

Polyvinyl acetate

Polyvinyl alcohol

Specialty chemical intermediate

Polyethers

Polypyrrolidones

Resins, crosslinkers

pH control agents

Emulsifiers

CommunicationMolded plastics, computer casings,

optical fiber coatings, liquid crystal

displays, pens, pencils, inks, dyes,

paper products

2-amino-1,3-PDO, 2-aminomalonic, (amino-3HP)

Threonine

IndustrialCorrosion inhibitors, dust control,

boiler water treatment, gas

purification, emission abatement,

specialty lubricants, hoses, seals

Intermediate

Platforms

Building

Blocks

Secondary

Chemicals

Products/UsesIntermediatesBiomass

Feedstocks

SugarsGlucose

Fructose

Xylose

Arabinose

Lactose

Sucrose

Starch

Starch

Cellulose

Lignin

Oil

Protein

Hemicellulose

Figure 3 – Analogous Model of a Biobased Product Flow-chart for Biomass Feedstocks

Food Energy Environment Agriculture Health Chemicals & Materials

Security

2004 DOE report lists 120 highvalue chemicals for biomanufacturing

15

Page 16: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

E.g., how much can we make with biology?

"The Game Plan" v1, S. Griffith et al.

Current energy sources (15-17TW)

Renewable energy sources

*Biology is ~90TW

16

Page 17: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

17

c/o Jon Hoekstra, Chief Scientist, World WildLife Fund

24% How$will$it$be$used?$

Page 18: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Could we make biology easy to engineer?

Self-mixing molecular systems

Atomic-scale thermal noise

Reproducing “machines”

High heterogeneity

Living ramifications

18

Page 19: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

19

Page 20: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

TAATACGACTCACTATAGGGAGA

DNA Construction = #1 Tech. of 21st Ctry.

From absract information to physical, living DNA designs.

2004: 10,000 bp 2010: 1,000,000 bp 2016: 100 million?

20

Page 21: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

21

Page 22: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

8 Bit Synchro. Counter

Abstraction barrier! Do not cross!

Abstraction barrier! Do not cross!

Abstraction barrier! Do not cross!

Systems = One or more devices encoding a human defined function(s). Note that my system becomes your device, and so on.

Devices = One or more parts encoding a human defined function(s).

Parts = Basic biological functions encoded via DNA.

DNA = Primary sequence and material.

Abstraction to enable engineered bio-simplicity!

TAATACGACTCACTATAGGGAGA

DNA Inversion Data Latch

22

Page 23: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

c.2012, Standard Promoters & UTRs, 2 genes

*unpublished BIOFAB data c/o Dr. Vivek Mutalik et al. of BIOFAB Emeryville, funded via NSF and several corporate gifts. 23

Page 24: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

1. Coordinate work over time

2. Coordinate work among parties

3. Enable the otherwise impossible

What do standards & abstraction enable?

BIOFAB

Page 25: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

MIT 2003

25

Page 26: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

iGEM 2010

26

Page 27: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

27

21st Century Biotech. via Tools RevolutionsDNA Sequencing

Read Out the Genetic Code

Recombinant DNA

Basic “Cut” & “Paste”

Polymerase Chain Reaction

Amplify & Make Simple Changes

First Gen.

Biotech=

...

Next Gen.

Biotech Adds New Tools

=

Page 28: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

3TANFORD�3%1�0HASE�)))��

Keep going for the next 70 years

28

Page 29: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

29

Get better at building DNA (time, reliability, cost) 4

Develop “rules” enabling functional composition 8

Populate genome-scale operating systems c/o rules 2

Refine sensors and actuators in accordance w/ rules 2

Develop libraries of molecular sensors to all primary and secondary metabolites

7-9

Develop reference materials for quantifying in vivo activities across time and place

4-8

Develop free-to-use data exchange standards for engineered genetic parts, devices, and systems 2-4

One engineer’s tools wish list

degr

ee o

f diffi

culty

(1=

easy

, 10=

impo

ssib

le)

Page 30: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

http://www.andyross.net/bill_joy.htm

“No matter who you are, most of the smartest people work for someone else” - Bill Joy

30

Page 31: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

“No matter who you are most of the smartest biological engineers work for someone else”

“No matter who you are most of the smartest biologists work for someone else”

“No matter who you are most of the best bio. parts you need will be discovered & refined by someone else”

“No matter who you are, most of the needs & opportunities for what you can engineer exist somewhere else”

“No matter who you are, most of the aspects & issues arising from what you engineer ramify somewhere else”

“No matter who you are, most of the best biotechnology ideas will be imagined and made true somewhere else”

Joy’s Law meets engineering biology

31

“No matter who you are, most of the best bioterrorists & bioweaponeers work for someone else”

Page 32: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

So, what can we do about it?“... globalization is best understood in terms of a power inherent in social relations, which he (Grewal) calls network power. Using this framework, he demonstrates how our standards of social coordination both gain in value the more they are used and undermine the viability of alternative forms of cooperation. A wide range of examples are discussed, from the spread of English and the gold standard to the success of Microsoft and the operation of the World Trade Organization, to illustrate how global standards arise and falter.”

Could we realize the future of biotech by developing tools that lead the scaling of particular communities?

32

Page 33: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Prevent remilitarization of biological tech (globally). 5

Define and lead strategy for biological security. 8-10

Get biology recognized as a technology. 4

Increase and sustain support for improved fundamental engineering tools (many free-to-use)

3

Enable application areas that are beneficial, reasonably threatening, & that need improved tools.

5

Better public/private partnerships in biotech (open). 3

degr

ee o

f diffi

culty

(1=

easy

, 10=

impo

ssib

le)

Lead and partner globally with others. E.g., NIST et al. to establish open “network power.”

5

We can find many such opportunities

33

Page 34: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

34

Page 35: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

35

Page 36: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

36

Page 37: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

37

Page 38: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Who will lead biosafety into the future? 4

What is our strategy for biological security? 8-10

How much can we make in partnership with biology? 2-8

What is the best balance of private and common wealth?

4-6

Who will choose what problems and opportunities are explored, pursued, and realized?

7-9

How can we best work together? ?

... to benefit all people & the planet?

degr

ee o

f diffi

culty

(1=

easy

, 10=

impo

ssib

le)

How can we invigorate new schools of engineering and art? Not just about industrialization.

4-6

Page 39: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

39

Page 40: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Left to right: Philip Sharp, David Baltimore, unidentified (c/o US NAS Archives)

c/o http://cr4.globalspec.com/blogentry/8698

E.g., biosafety ~1975 Asilomar

Page 41: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

41http://www.cdc.gov/od/ohs/biosfty/bmbl4/bmbl4toc.htm

Biosafety Level 1 practices, safety equipment, and facility design and construction are appropriate for undergraduate and secondary educational training and teaching laboratories, and for other laboratories in which work is done with defined and characterized strains of viable microorganisms not known to consistently cause disease in healthy adult humans. Biosafety Level 1 represents a basic level of containment that relies on standard microbiological practices with no special primary or secondary barriers recommended, other than a sink for handwashing.!!Biosafety Level 2 practices, equipment, and facility design and construction are applicable to clinical, diagnostic, teaching, and other laboratories in which work is done with the broad spectrum of indigenous moderate-risk agents that are present in the community and associated with human disease of varying severity. With good microbiological techniques, these agents can be used safely in activities conducted on the open bench, provided the potential for producing splashes or aerosols is low. Hepatitis B virus, HIV, the salmonellae, and Toxoplasma spp. are representative of microorganisms assigned to this containment level. !!Biosafety Level 3 practices, safety equipment, and facility design and construction are applicable to clinical, diagnostic, teaching, research, or production facilities in which work is done with indigenous or exotic agents with a potential for respiratory transmission, and which may cause serious and potentially lethal infection. Mycobacterium tuberculosis, St. Louis encephalitis virus, and Coxiella burnetii are representative of the microorganisms assigned to this level. Primary hazards to personnel working with these agents relate to autoinoculation, ingestion, and exposure to infectious aerosols. At Biosafety Level 3, more emphasis is placed on primary and secondary barriers to protect personnel in contiguous areas, the community, and the environment from exposure to potentially infectious aerosols. !!Biosafety Level 4 practices, safety equipment, and facility design and construction are applicable for work with dangerous and exotic agents that pose a high individual risk of life-threatening disease, which may be transmitted via the aerosol route and for which there is no available vaccine or therapy. Agents with a close or identical antigenic relationship to Biosafety Level 4 agents also should be handled at this level. When sufficient data are obtained, work with these agents may continue at this level or at a lower level. Viruses such as Marburg or Congo-Crimean hemorrhagic fever are manipulated at Biosafety Level 4. The primary hazards to personnel working with Biosafety Level 4 agents are respiratory exposure to infectious aerosols, mucous membrane or broken skin exposure to infectious droplets, and autoinoculation. All manipulations of potentially infectious diagnostic materials, isolates, and naturally or experimentally infected animals, pose a high risk of exposure and infection to laboratory personnel, the community, and the environment.

Page 42: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

42

NIH

StanfordCAB

http://mit.edu/cab/

Page 43: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University
Page 44: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University
Page 45: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

http://www.mercurynews.com/breaking-news/ci_20531408/meningitis-claims-san-francisco-va-lab-worker

Page 1 of 2 16/05/2012 10:39 AM

Deadly infection claims San Francisco VA lab workerBy Matt O'Brien Bay Area News Group San Jose Mercury NewsPosted: MercuryNews.com

State and federal health officials are investigating how a rare and virulent bacteria strain appears to have killed ayoung researcher at a VA Hospital's infectious diseases lab in San Francisco, setting off alarms that the man's friendsand fellow researchers also may have been exposed.

The 25-year-old laboratory researcher at San Francisco Veterans Affairs Medical Center died Saturday morningshortly after asking friends to take him to the hospital. For the week and months before his death, he had beenhandling a bacteria linked to deadly bloodstream infections at the VA Hospital's Northern California Institute forResearch and Education, said Peter Melton, a spokesman for the California Occupational Safety and HealthAdministration.

The man, whose name has not been released, was working with fellow researchers to develop a vaccine for abacterial strain that causes septicemia and meningitis. Hours after he left work, however, the germ that he wasstudying took his own life.

"He left the lab around 5 p.m. (Friday)," said Harry Lampiris, chief of the VA Hospital's infectious diseases division."He had no symptoms at all."

Two hours later, however, the Treasure Island resident reported to his girlfriend he was feeling sick with a headache,fever and chills, Lampiris said. Not until Saturday morning did the symptoms grow worse with a body rash. Heasked friends to take him to the hospital but fell unconscious in the car and had no pulse by the time he arrived. Hedied later in the morning.

"It starts out so non-specifically, people don't think it's anything serious," Lampiris said. "Obviously, he didn'tsuspect it."

The San Francisco Department of Public Health is trying to identify everyone who had close contact with the workerduring the time he was infected, said city health spokeswoman Eileen Shields.

His friends and co-workers are getting preventive antibiotics, as are some 60 health workers who treated him at thehospital, Shields said.

The bacteria spreads through respiratory exposure such as sneezing and coughing or kissing.

Cal-OSHA confirmed Wednesday that it is investigating the lab worker's death and whether the lab where he workedfollowed safety protocols.

The federal Centers for Disease Control and Prevention also is helping state and city authorities to determine whatoccurred, a spokeswoman said.

"We're not certain how this death happened, but hopefully the investigation will turn up some answers to helpprevent it from ever happening again," CDC spokeswoman Alison Patti wrote in an email.

A state laboratory has confirmed that the San Francisco worker was infected with the Neisseria meningitidisbacterium, the same germ he had been handling at the laboratory for weeks and months before his death. It alsoconfirmed that the rare strain he and fellow researchers were studying -- Serogroup B -- was the same one found inhis body.

The germ can cause two separate but equally deadly conditions. One is septicemia, a bloodstream inflammation thatcauses bleeding into the skin and organs and is believed to be the cause of the man's death.

The other is meningitis, which inflames the thin layer of tissue surrounding the brain and spinal cord and can lead to

Page 46: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

Can you catalyze a renewal of biosafety leadership?

Who will lead biosafety in 2020?

Page 47: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

What’s the difference between safety & security?

47

Hint: Safety belts vs. security locks in a car.

Page 48: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

48

1. Databases populated with sequence information.

2. The internet.

3. Early improvements in automated DNA construction technology.

4. Overnight shipping.

5. Expanded concern re: active misapplication of biotech.

What’s changed since the 1970s?

Page 49: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

http://en.wikipedia.org/wiki/2001_anthrax_attacks

Page 50: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

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

Page 51: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

SynthesisSequencing

Material (Physical DNA)

Information (DNA Sequence)

Page 52: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University
Page 53: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University
Page 54: Bio(technology) in the 21st centuryinbios21/PDF/Fall2014/Endy_09122014.pdf · Drew Endy! Stanford Bioengineering! The BioBricks Foundation!!! 12 September 2014! Lehigh University

CGGACACACAAAAAGAAAAAAGGTTTTTTAAGACTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAGTTTAAGATATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTAACTTTCCCTGGTTGTGACAATTGAATCAGTTTTATCTATTACCAATTACCATCAACATGGTATGTCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAGCTCTGAATCCATTTTGCGAGAAGTTCATCCAAACGACCCAGTGTCTGAAAATACAAAAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTGATTGGGAAGATCAAGGAAACAATTTGTTCCAATAATATCGTACATCTTGACTAAGTCGAACAAGGGGAAGTCGATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTTACTGTTCAACAGGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGACTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACGGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCCGCACTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGTATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAATTGTCAAAACCGTTCTTGATCATATTCTGCAAAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGGGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCGGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTTAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTGGACGATCAGGAAAGAAGAATACTAATGAACTTCCATCAGAAGAAAAACGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCTAAATTAACAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAGACAAGACGACGGCAATGAAATACCGTTCCCTGGGCCTATAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCTAGAGACTCCAGAGACACCATCATTCCTAATGGTGCAATTGACCCCGAGGATGGTGATTTTGAAAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCCTGTTCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGGACAGCTCGCCACAATCCCAAAGGGAAATAGAGAGAGAAAGATTAATTCATCCACCCCCAGGCAACAACAAGGACGACAATCGAGCCTCAGACAACAATCAACAATCAGCAGATTCTGAGGAACAAGGAGGTCAATACAACTGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGCACGAAGAGGACACCCTTATGGATCAAGGTGATGATGATCCCTCAAGCTTACCTCCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGAATGAAGACCCTGATATCGGTCAATCAAAGTCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAAGCCATCAATTATTATCACATGATGAAGGATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAAAGAGAATCGCTACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAGTCCCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTTAAGACTTGACCGATTCATCTACAAAAACTAATCCATTATAACTTATTAGTGCTACTTTTCTATAAGTGATTCTTAATCTAAGGCCATTAAGAGTTTAAGTAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTGATTTGAACATAGTCATAAGGGGATAAATAATACTTTATATTTCTGATTGTGGATTGACCCATTCTGCTTAAAATGCTTCGCCCATTGAAAATGTGATCTAATAGATAGCCCTGACTAGACAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCGCCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAATTTGGAAATATCCTACCTTAGGACCATTGTCAAGAGGTGCATAGGCATTACCACCCTTGAGAACATGTACAATAATAAATTGAAGGTATGTTCAGGCCCAGAAACGACTGGATGGATTTCTGAGCAACTTATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAAATGGAAGTCCGACTCAAACCATCATCAAGGAGCTCAACAAGAACTTGTACAAGTAGCAGTCAGACGGAGGTCAACTATGTACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAATGCCACCAGTCGTCAGAATGCTGCAATCGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGTGCCGAAATGGTTGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGATGCGTATTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCGTTGTATGAAGAGAATGCGCTTAAAGGAAAAATCGATGATCCAAACAGCTATGTACCAGATGCTGTGCAAGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCTAAAGACCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTTTTGGACACAATCCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGGGTCCCAATCTTTCAGGATGTGCCGCCCCCGATAATCCATATTAGATCCCGTGGTGACATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAATTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGAATCAAGATTTATTTAACAAGGCAAGCCACAACCTTAGATGGAACCTCAGCCAGACTATTGAACTATTGACGCTGTTGATGATAATATATAATTAATGGTCTTATTTGAATATGACAACATCTTGCTTCTTGTTCTGCCTTGTAGCTCTTTGAATTGGAAGATCATTCCAAACTTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAACAAGTGATGAAGATTAAGAAAAACCAGTCGGTATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATATTTTATCATCAAAAAATGAGGCGCGGAGTGTTACCAACGGCTCCTCCAGCATATAATGATATTGCATACCCTATGAGCATACTCCCAACCCGACCAAGTGTCATAGTCAATGAGACCAAATCAGATGTACTGGCAGTGCCAGGGGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTGGAAGCTACAGTGAATGTAATTTCGGGAACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATATACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAACCCGCTGGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTTCTTCCACCAGTCCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGCTCTTCGTCCTGGGCTCTCACTCCATCCCAAGCTTCGTCCAATTCTCCTGCCGGGGAAGACAGGAAAGAAAGGACATGCTTCAGACTTAACATCACCTGACAAGATTCAAACAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAACCAAGAACATAGTTGGAATTGAGGTTCCAGAATTACTAGTTCAAAGGCTGACCGGCAAAAAACCACAACCCAAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGACTTGATCCTATATCGCCAGGGGACTTAACTATGGTTATCACCCAGGATTGTGATTCATGCCACTCTCCAGCCAGCCATCCGTATCACATGGACAAGCAGAATAGTTACCAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATTCCGACGGGATCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATCAAGCAGAGGCAACAGACTCACAGCTTACGCCTAGATAACTAATATTAAGGAGTTTTTTAATCTAATTTTCCAGTCTTGAGTAATAATCATTTCTTTTGTAATTAATTATGCATTTGTTAACTTATCGGTGCGAGATTTCCTTGAGAACCCGGCGGAGCTTCTACTATCTGCAGTAACCAGAAGAGAAGTTCAACCCAGTCAAAACTAAACCAAGCAATATTCTGAATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAAGATTTCAATGACTCGTTAACAATCGCTAGTAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAACGAGCCGAAACTTCATCTCTTTTAAAGATCTAACATTATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATTGTAAGCTGCTATTTCTTACCTCCCCAAATTACCTATACAACATGGGGTCAGGATATCAACTTCTCCAATTGCCTCGGGAACGTTTTCGTAAAACTTCGTTCTTAGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGACAAATAGCACTCTCAAAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCTGTGGGGCTGAATCTGGAAGGAAATGGAATTGCAACCGATGTCCCATCAGCAACAAAACGCTGGGGATTTCGTTCAGGTGTGCCTCCCAAGGTGGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAGTGAATGCCTCCCTCTCCCTCCCGACGGTGTACGAGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCTTGTCCTGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTCATCTACCGAGGGACAACTTTTGCTGAAGGTGTCGTAGCTTTTTTAATTCTGTCAGAGCCCAAGAAGCATTTTTGGAAGGCTACACCAGCTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATGACCCTGACACTCAGCTACGAGATGTCAAATTTTGGGGGCAATGAAAGCAACACCCTTTTTAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATCGCCTTAGCAACAGTACAGGGAGATTGACTTGGACATTGGATCCTAAAATTGAACCAGATGTTGGTGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAACTTGCATTTCCAAATTCCATCAACCCACACCAACAACTCCTCAGATCAGAGCCCGGCGGGAACTGTCCAAGGAAAAATTAGCTACCACCCACCCGCCAACAACTCCGAGCTGGTTCCAACGGATTCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCTAACCAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGCCCCAAGTCCAACCATGACAAGCGAGGTTGATAACAATGTACCAAGTGAACAGCCGAACAACACAGCATCCATTGAAGACTCCCCCCCATCGGCAAGCAACGAGACAATTTACCACTCCGAGATGGATCCGATCCAAGGCTCGAACAACTCCGCCCAGAGCCCACAGACCAAGACCACGCCAGCACCCACAACATCCCCGATGACCCAGGACCCGCAAGAGACGGCCAACAGCAGCAAACCAGGAACCAGCCCAGGAAGCGCAGCCGGACCAAGTCAGCCCGGACTCACTATAAATACAGTAAGTAAGGTAGCTGATTCACTGAGTCCCACCAGGAAACAAAAGCGATCGGTTCGACAAAACACCGCTAATAAATGTAACCCAGATCTTTACTATTGGACAGCTGTTGATGAGGGGGCAGCAGTAGGATTGGCATGGATTCCATATTTCGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACCCAGGCTCTTCAATTATTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGTACCTGTCGAATCCTAGGACCATCTTGTTGCATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAGAAAAATCTCAGGGTTACTCTAAGGAGAAATATTATTTTTAAAATTTACTTGAATGCTGACCACTTATCTTAAATGAGCAATTAATAATATGTTTTTCTGCTTCTTTGCTTGATTTACAATATGATATTTCTCTTAATAATGATTAATATATTAAGAAAAACTTATGACGAAGATTAAAGGAGAGGATCGTTAACGGGAAAACCTCCCATCTCGTTCGTCGAAGCCACGTTGGTGGTGCTTGCAGCTGAGAACAACTCCAGAGATTGTAGGTAGAAAGGACCAACATTTATAGGTAGGGGTCAGAAAGCAACAATAACCATAAAAGGAGAGCCTGACATTGCTATTTAATATCCTAGAACCTGATTTCTAGGTTCTAGCTTTAAAATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGACAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATAGTTCCTCCGGCTCCTAAAGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGCAAATTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGGTTAGCGAATCCAACAGCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGGGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAGTCATTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGATACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATTGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGAATAGAAAACCACTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGAGTTCCATTTAGTAATAATGATTCTTAAAACAATCTACTATCGCAATTATCGATGGATCTACCCTATTTGACGGTACATGACTTGAATGTAATAAGGTAAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATCGTATGTCTAGCAAATTATCAATAGCAAAGTTAAATTCTCCTAACCTCATATTTTGATCAAGTAATCATGATTTTATGATAATTCTTTTCAGATTATCGGTTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCTTGGGTATCCAAGTTTATGAATAGAGCTAGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAAACCAGTAATGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACTTTAGTTCCTTAAGGCCTCGTCCGAATCTTCATCAGTTCGTAAGTTCTTTTATAGAAGTCATTAGCTTCTAAGGTGATTATATTTTAGTATTAAATTTTGCTAATTGCTTGCTATAAAGTTGAAATGTCTAATGCTTAAATGAACACTTTTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAATTAGAGCGTCCTTGAAGTCTGGCATTGACAGTCACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAAAAGAGGTCCCAGAGAGTCCCAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCGGCTCGACCAAGACTGTAAGCGAGTCGATTTCAACTAAAAAGATTATTTCTTGTTGTTTAAACAAATTCCTTTTGTGTGAGACATCCTCAAGGCACAAGATGGCTAAAGCCACAGGCCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGACTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTTTTCCCACATCTGTTCCAGAACCCAAATTCGGTTATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGAGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGACCAGCTTAGTCTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACTTCTACACACACAATCATTATAACTCGTACAAATATGGGTTTTCTCGTGGAAGTTCAAGAGCCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCACAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGTTTGTTGGCAATTTAACAAGGTAATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTATCTAGCATTGTTGAGTTAACTATCTAATCTATTTTCGCTAATTGCATTGAGCACTGCTAATAGGTTTGTATCACGTTAAAGATTTAGAGTGTATGAATTGTGCAGATTTAAACTTGGGTTTTGCCTTATGCTTCATAGGTGGTCTTTTTGAAATGGAGATTATCAGCATTTCTTAAATGGGAGGAGTTAGCAATCAGAAATTGGAGATAAATGGACATCGGGATAGAACAATGCCTAACTATTGGGCGGCTTCCATTTTTACATGTGTATATAACCAATCTTTTCCTATCTTTGCTTATATTGGTGTAACTTTATTTTAATAACATGTCAATGCTATACTGTTAAGAGAAGGTCTGAGGAAGATTAAGAAAAAGGCCTCGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGGTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGTTTATCCTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCAATGTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTAAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCATTGACCCCGACTTGCAATCAATTCCTTGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGTGCACAGGACCATTTGACAAACATTGCAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGATTATGTCCATCAATTGTTCTTCTGGCATGACCTTTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCAGTTACTATAGACGGGGTCCCACACGCAGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCATAGCCAAATCCTATCTGTGTCAACAGCTGAAATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCAAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTTGGCTCAGAGGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGAGATTTTCACAAAATATTATTACAATTGCAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATCTTTGAGACATATTGTGTATTCAAGTACAATATTGCCAAGCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGACAGGAATTTAACTCCAGGACTCAACTCCTTCATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAAGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCTCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAAGAGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGAATTACATTATTTATTACCACAGAATAGGAATTTTTCCTTTTCTCTCAAAGAAAAGGAATTAAATATTGGACGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCTCTGTTAGCAGATGGACTGGCCAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAAGAGAGCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGTGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGGCACTTAGGAGGCATAGAGGGATTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTTCCACTTAAAACAGACCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGATGAGACATTTGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCACCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGACAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAACTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTTAACATGAAAGACCTATTTTGTCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAAATCGTTAGGCGTAGTATTACCCTAACTGCTAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAGTGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTGCAGCGGATATTTTTTCCAGGACACCGAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTGGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAAATTAGTTGCACGGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGATCATTGATCGGAGCGACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAGGACAATATGAACCTTGTCCAGAATGTCTCAACAAAAAAGGCTCAAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCTATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGAGGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTGGAAGCGAGAGTCAACCTTAGTGTCAGTGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACGACCAATACAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTTTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACAAACACCTCTGATATAAGGCATAATAGGGCTCATCTTCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTGACATATACAAGTGCACTTAATCTGGATTTAAGCCGTTATCGTGATAATGAACTAATATATGACTCAAATCCACTGAAGGGAGGATTGAACTGCAATTTAACAATAGATAGTCCTTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCATCTCAGACAATAGCAACTCATCAACAGATCCAATCAGTAGCGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTACCCTCAGATTGGCCTTCTTTACAGTTTCGGAGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTACGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTTTTTAAACCAACATTTAAGCATGCCAGTGTGATGTCCCGATTAATGGAAATTGATTCTAACTTCTCAATTTATATTGGCGGGACATCTGGAGATCGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATCGCGAGTTTTTTACAATTTCTTAAAAGCTGGATCATCGATCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAATCCATCAATGAATTTCTACATAAAATTTTGGGTCTGCTCAAACAAGGCCCCAAAAGTATTCCAAAGGAGGTCAGCATCCAAAATGATGGACATTTGGATTTGGCAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAGAAGTAGGAAATCTCGGAAAACTCAAGACCATAATGATTTCTCAAGAGGGGATGGAACACTTACAGAACCCGTGCGTAAGTTTTCAAGCAATCATCAGTCAGATGAAAAGTACTACAATGTGACATGTGGAAAGTCACCGAAGCCGCAAGAACGCAAAGACTTCTCGCAATACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCCTGCAAAATGTTAATGGAGAGTCAAAGGGGAACTGTTCTAACAGAGGGTGACTACTTTCAAAACAATACTCCACCAACAGATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAACCATGCACATGATCAAGATGCCCAAGAATTGATGAATCAAAATATTAAACAGTACCTACATCAGCTAAGGTCTATGTTGGACACCACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATAGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAAAAATATAGTACAAGGTTATTATTTTTGAACACATTGGCAACAGAACACAGTATAGAATCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAGTCACTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTATGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGTCTTGGTGTTATCAGAGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATGCTACAAAGAATCTCCATTGTGAATACATAGGCCTTGGTTTCCCATCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTTGATACTGGACTCGGTCCATTGTCGTCAGTTATTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTAGATTATAACCTGATGAGGGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAGTTAGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCACTCAAAAATAATTCTTCTTGGTATACTGAGCTTAAAAAATTACCTGAGGTTATTAATGTGTGTAATCGATTTTATCATACTCACAATTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAACGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGAAGGGTTAATATATTCCAATCACACATAGGTACTAAATCATCATAGTATGAGGAATAAGATAATGATAATTCCTGACGACAGTTTTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATCTTAATTGTTAGAGGTAACAAGCTATTAGTTATTACTTATTGATAAGAATACACTTTATCATAGCGTAACACATCATAACTTTATAACGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTACCAGAGAAATGACCCCAGTTCCTATCTTTAAATAATGATTGTGTGTATTAAATTATTAGTTTATTAGGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTATGTAGATAGGTAATCTAACACTGAATCACCCATCTGATGTCACCATATCCAAATGTTGTGCTAGTCGCATTTAAACATGCTATCTTCAGTTAAGTAACATAGACTGAAAATGCTAAGAAGAGATTGGAGTAAAAGTATAAAATAAATTTAATTAAACTTCAAAGTGATTAAATGATAATGATCTTGGGAACTCGATATGACCTCAAGTCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTGATAATGTAAATTTTGATAACTAACTAGCTTTAGTAGTTAAGATCAAATGCAAACATTATAAGAATGTTAAGCGCACACAAAAACATTATAAAAAACCAATTTTTTCCTTTTTGTGTGTCC

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Don’t exist

Unknown reservoir

Locked-up

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Should the DNA sequences encoding human pathogens be freely available online?

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Property rights are important

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The first U.S. patent, issued to Samuel Hopkins on July 31, 1790, for an innovative way of making "pot ash and pearl ash" -- source, Wikipedia

2. Define and scale relationships among parties

3. Support investment and returns

1. Disclose how to do something useful.

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Such rights can be licensed to others in order to make money.

Current practice in biotech.

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“Method” or “utility” patents provide ownership of exclusive rights to the practice of research processes, or uses of genetically encoded functions, respectively.

Patent-based rights can be used to protect an investment for a period of time (e.g., your future startup company).

Public domain also used to support giving things away.

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rDNA method patent generated $200+ million in licensing revenue for Stanford and UCSF.

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Costs of patent based framework

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Patents take time and money to obtain (~$25k and 18-36 months).

Patent claims often disputed and not resolved until trial years later (i.e., more time and money).

What a patent claim covers often not 100% clear.

Searching patent claims not trivial (e.g., machine readable but not machine knowable).

Patents can be used to restrict access to methods and functions that others could benefit from.

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Restrictive access to technologies can lead to public anger and rejection of tools and technologies.

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1. 2008 iGEM budget worldwide ~$4 million

2. Utility filings on all 2008 parts would cost ~$37.5 million

4. iGEM and the parts collections continue to grow (geometric)

2008 iGEM competition resulted in 1,500 new BioBrick parts being developed, produced by ~1000 students across 30 countries.

3. Commercial freedom to operate unclear (e.g., competing claims?)

For example, standards-based sharing

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E.g., designer genomes

Quick, do a freedom to operate search on 1000 genes in your company’s designer genomes...

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A company (real but anonymous) can make ~5000 engineered strains of microbes per week to support internal R&D. !Suppose each strain has, on average, 5 heterologous genetic functions. !How will their lawyers search for claims on 25,000 functions per week? 1,250,000 per year... !How will they license the uses as needed?

E.g., automated engineering

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Changes in foundational tools... !

Stress, strain, and swamp existing systems (capital costs, turn times, giving up)

Vitalize new venues?

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“Proprietary software divides the users and keeps them helpless, and that is wrong.”

Richard Stallman, Free Software Foundation72

“The first Unix application would be a word-processing program to be used by AT&T's patent-writing group.”

http://www.spectrum.ieee.org/print/1571 http://www.time.com

http://www.boycottnovell.com/2009/03/14/

Early 1970s Mid 70s to Mid 90s

Free, Open Tools

“Who can afford to do professional work for nothing? ... Nothing would please me more than being able to hire ten programmers and deluge the hobby market with good software.” Bill Gates, Microsoft, Inc.

Today

Ownership, sharing, and innovation frameworks can “evolve.”

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The Copyright Act of 1976 stipulates (section 102): ! (b) In no case does copyright protection for an original work of authorship extend to any idea, procedure, process, system, method of operation, concept, principle, or discovery, regardless of the form in which it is described, explained, illustrated, or embodied in such work. !Congress attempted to clarify the situation for computer programs (Rep. No. 473, 94th Cong., 1st Sess. 54 (1975)): ! Section 102(b) is intended, among other things, to make clear that the expression adopted by the programmer is the copyrightable element in a computer program, and that the actual processes or methods embodied in the program are not within the scope of the copyright law. !and the National Commission on New Technological Uses of Copyrighted Works (CONTU), wrote in its final report (1978): ! Where could a meaningful line of demarcation be drawn? Between flow chart and source code? Between source code and object code? . . . The Commission believes that none of these is appropriate. The line which must be drawn is between the expression and the idea, between the writing and the process which is described.

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E.g., copyright law was extended to cover software decades ago. More recently software patents have been pursued.

From MIT Course 6.805/STS085: Software and copyright law

And, changes in property rights law can be critical

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What do we want to become true?

>50% browsers

Free Software

>90% HPC

>80% servers

>60% smart phones

12 of 15 languages

“Just” the DNA Dictionary + Rules of Grammar

I.e., for me (DE) I want to see a future in which the “operating systems for life” are free to use.

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http://i.pbase.com/u47/hodero/large/30691408.jungle.jpg

OpportunitiesEnable all constructive

biotechnology.Renew humanity in

partnership with nature.

DreamsMake biology easy to engineer (tools).

Understand life.

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