Singularity University July 2010 diybio demo workshop
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Transcript of Singularity University July 2010 diybio demo workshop
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1300+ amateur biologists around the world
- scientists, inventors, artists, educators...
- inventing “lo-fi” molecular biology
- bridging the gap between science & society
- broad interest in public, open work
other8%
art15%
business16%
tinkering29%
research32%
why are you interested in biotech?
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
reinforcing positive culture via diybio.org
- establish transparency & safety norms
- biosafey & legal tools, guidelines
- support public lab & tool development
- organize positive community projects (BWM)
uninterested11%
neutral5%
interested84%
are you interested in working in public?
source: diybio 2010 survey
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3
1. expert “biohackers” (5%) & “newbie” amateurs + hobbyists (95%)
2. entrepreneurs3. artists
4. educators5. journalists6. policy makers
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
diybio mailing list users
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capabilities
users (undergraduate level)DNA purification culturingPCRmutagensistransformationpart assembly
5%
makers (grad level)1%
talkers94%
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a growing community
that wants to play with biotechnology
developing lo-fi tools, techniques, and toys
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
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why ?
science asculture
new tools & techniques
DNA is not scary.toys today,
tools tomorrow;
disruptive innovation.
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“I see a close analogy between John von Neumann's blinkered vision
of computers as large centralized facilities and the public perception
of genetic engineering today as an activity of large pharmaceutical and
agribusiness corporations such as Monsanto. The public distrusts
Monsanto because Monsanto likes to put genes for poisonous
pesticides into food crops, just as we distrusted von Neumann
because he liked to use his computer for designing hydrogen bombs
secretly at midnight. It is likely that genetic engineering will
remain unpopular and controversial so long as it
remains a centralized activity in the hands of large
corporations.”
“
”
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We are attuned in the deepest parts of our being to nature, to our original surroundings and our
original condition as humankind. We have a familiarity with nature, a reliance on it that comes from
three million years of at-homeness with it. We trust nature.
When we happen upon a technology such as stemcell regenerative therapy, we experience hope. But
we also immediately ask how natural this technology is. And so we are caught between two huge
and unconscious forces: Our deepest hope as humans lies in technology; but our
deepest trust lies in nature. These forces are like tectonic plates grinding
inexorably into each other in one long, slow collision.
The collision is not new, but more than anything else it is defining our era. Technology is steadily
creating the dominant issues and upheavals of our time. We are moving from an era where machines
enhanced the natural—speeded our movements, saved our sweat, stitched our clothing—to one
that brings in technologies that resemble or replace the natural—genetic engineering, artificial
intelligence, medical devices implanted in our bodies. As we learn to use these technologies, we are
moving from using nature to intervening directly within nature. And so the story of this century will
be about the clash between what technology offers and what we feel comfortable with.
W. Brian Arthur:
“
”
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9
This was then centrifuged at room temperature for 3 minutes @ 8000 rpm.
Discard 900 micro ml of the supernatant and dissolve pellets in remaining 100 micro ml. Spreading helps ensure that you will be able to pick out a single colony.
These were then spread on LB Agar plates containing 100 micro grams per ml Ampicillin.
7
Put the gel along with the casting plate in a tank with TAE, EtBr at the same concentration can be added.
The gel must be completely covered by TAE and placed such that the wells are at the end electrode passing negative charge.
Procedure
molecular weight blue dye.
In the same way now inject the DNA samples mixed with the blue dye into the other wells.
Now a current is applied, about 100V for 30 minutes.
Lastly place the slab of gel on a UV light box and observe.
One can also capture a digital image of the same
Gel Electrophoresis Chamber
Heater
Lab-as-a-Service Synthetic Biology tools
DIY equiptment & techniques
nologies used in protein structure determination show
similar trends (Figure 2), suggesting a general rapid im-
provement of biological technologies. As a reference,
Moore’s Law, which describes the doubling time of the
number of transistors on microchips, is also shown in
Figure 1.
Comparing anything to Moore’s Law is already a
cliché, but doing so remains a useful device to gauge our
expectations of how other technologies will affect so-
cioeconomic change. This comparison starts with the ob-
servation that chip doubling times are a consequence of
the planning intrinsic to the semiconductor and computer
industry.3 Moore’s Law is primarily a function of the
capital cost and resource allocation necessary to build
chip fabrication plants. In addition, for much of the last
thirty years there was feedback between the ability to de-
sign new chips and the computational power of the chips
used in the design process.
We can now see the beginnings of a similar effect in
the development of biological technologies. For exam-
ple, enzymes optimized for laboratory conditions are
used in the preparation of DNA for sequencing, where
earlier sequencing technologies were part of characteriz-
ing and modifying those enzymes. Recombinant proteins
are used every day to elucidate interactions between pro-
teins within organisms, and that information is already
being used to design and build new protein networks. En-
zymes are directly used in a process known as Pyrose-
CARLSON2
3Moore, G. Cramming more components onto integrated cir-
cuits. Electronics 1965. 38(8).
FIG. 1. On this semi-log plot, DNA synthesis and sequencing productivity are both increasing at least as fast as Moore?s Law
(upwards triangles). Each of the remaining points is the amount of DNA that can be processed by one person running multiple ma-
chines for one eight hour day, defined by the time required for pre-processing and sample handling on each instrument. Not in-
cluded in these estimates is the time required for sequence analysis. For comparison, the approximate rate at which a single mole-
cule of E. coli DNA Polymerase III replicates DNA is shown (dashed horizontal line), referenced to an eight-hour day.
Sample processing time and cycle time per run for instruments in production are based on the experience of the scientific staff
of the Molecular Sciences Institute and on estimates provided by manufacturers. ABI synthesis and sequencing data and Intel tran-
sistor data courtesy of those corporations. Pyrosequencing data courtesy of Mostafa Ronaghi at the Stanford Genome Technology
Center. GeneWriter data courtesy of Glen Evans, Egea Biosciences. Projections are based on instruments under development.
1
SYNTHETIC
BIOLOGY
FOR
ARTISTS &
dESIGNERS
why now ?
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what’s going on now?
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pGlo kit
$111?
Hard to purchase w/o academic affiliation
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DNA Explorer, $80?
(Ages 10 and up)
www.discovery.com
no longer available :(
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bioweathermaps
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bioweathermaps• crowdsourced sampling + funding for metagenomics
•volunteer microbial biosurveilance
•Launched at GET2010 (April)
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".00-%8./%-.'6%78%4.,:%,")4%#,%#$%".=)(%,"#$%&'#()%5#11%*,%1)*$,%)4,)/,*#46%[email protected]
culturing bioluminescentmarine microbes
bit.ly/diybio-squid
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Rapid-Prototyped centrifuge spindle
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algae photobioreactor
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$50? spin-off from biofuel startup
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Pearl Gel Box (v.2)- $499
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$100 2-axis microscope
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... and DIY microfluidics
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$30 microbial fuel cellgeneratesmicroamps @0.3 voltsfrom natural soil microbes
Known as the -‐
, Geobacter species have
compounds and use them in a way
similar to the way humans use
oxygen.
Shewanella can be found
almost everywhere on earth, from
mountain soils, to ocean
sediments. It has an ability to
metabolize a wide variety of
elements that are toxic to humans,
humans or other animals. It even
has the ability to metabolize
Uranium, precipitating it out of
contaminated waters.
Microbial Fuel Cell KitsDirt Power!
Fill it up with dirt from your backyard and whatever you find
in your refrigerator and see how much power you can get!
Great educational tool for kids and kids at heart!
Shewanella(aka Mr. Clean)
Geobacter(aka The Iron-‐breather)
Microbial fuel cells (MFCs) are bio-‐electrical devices that harness
the natural metabolisms of microbes to produce electrical power
directly. Within the MFC, microbes act as a catalyst to break down
sugars and other nutrients in their surrounding environment and
release a portion of the energy contained within those molecules
in the form of electricity.
What the heck is a microbial fuel cell?
Learn
Compete
Develop
Get Published
in our International Dirt Power Competition.
the technology by submitting data to our online database.
with our online publication, presenting
data collected all around the world. Your name will be on it!
Key Players:(Discounted classroom packages available, including
educational material and pre-‐designed curriculum)
about the extraordinary abilities of microbes in your backyard.
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SpikerBox $120 neuron recorder
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LavaAmp - $200 rapid pcr machine
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OpenPCR $400 open source PCR thermocycler
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what’s happened?mostly hardware development
- open source & patented
- several startups formed - $10,000+ in crowdsourced funding
fun & easy wetware
- bioluminescent microbes
- yogurt-hacking - genotyping
one academic conference (Jan 2010)
formation of several public lab spaces
lots of news
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rapid prototyping toys?
who invents
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enables tinkering (rapid prototyping)
with electronics
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enabling tinkering with biology
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
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two paths to new tools
refactoring existing tools
- cheaper
- more open
- more fun
- simpler (more limited)
inventing newtools (“toys”*) prioritizing
tinkering & play
over significance & accuracy
blinky LED tutorial
new market for biotech tinkering tools
*
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negative framing by the media“Many a computer business has started in a garage or a teenager's bedroom. So, though, has many a computer virus. And where computing led, biotechnology may follow.” Economist, Sept. 2, 2006
“The Dr. Strangelove of the 21st century may well be a biohacker.” The Sunday Telegraph, December 24, 2006.
“…with DNA hacking far more widespread, what if your friendly local terrorist decided to take up the hobby?” The Times (London), Sept. 16, 2006.
“Welcome to the age of synthesized life, built from scratch. Soon, it may be so cheap and simple a teen hacker could do it. Or a terrorist.” 2005 The Globe and Mail (Canada)
“What's available to idealistic students, of course, would also be available to terrorists.” 2009, The New Yorker
What kinds of organisms will scientists, terrorists and other creative individuals make? 2007, Washington Post
“The ability to create nasty pathogens like your hybrid rabies virus in your bathroom is becoming easier and easier…this is much easier than trying to get enough fissile material to make a nuclear bomb…” 2009, Homeland Security Today.
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diybio.org + Woodrow Wilson International Center for Scholars (synbioproject.org)
1-year grant to develop a long-term roadmap to a positive culture of safety within diybio worldwide, funded by Alfred P. Sloan foundation.
objectives (want to help?)
1) define the diybio community
- define a baseline to track +/- trends & control hype
2) inventory existing ethical codes of conduct
- hobbyist & “maker” codes; hacker ethic; igem, RCR
3) identify potential risks posed by diybio
- to amateurs, mainstream science, and public at large
4) develop preliminary biosafety guidance
- adapted from EHS, NIH and other professional sources
5) mobilize & celebrate biosafety “champions” within community
- work with existing groups to build & demonstrate safety ethic
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a growing community:
that wants to play with biotechnology
developing lo-fi tools, techniques, and toys
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
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a growing community:increasing human capital in biotechnology
smoothing the interface between science & society
that wants to play with biotechnologyincreasing public awareness and understanding
developing lo-fi tools, techniques, and toysprotoyping tools & disruptive technologies
for biotechnology
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
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other8%
art15%
business16%
tinkering29%
research32%
why are you interested in biotech?
- public blog
- build safety & legal resources
- promote transparency & outreach
- organize positive community projects (BWM)
uninterested11%
neutral5%
interested84%
are you interested in working in public?
source: diybio 2010 survey
want to collaborate?
! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
.org
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BangaloreBostonChicago
Los AngelesLondon
New York CitySan Francisco
SeattleHouston
...! " # $ " % % & ' ( " ) *
+ " # , % - & + & # . " ) $ + , % /
.org
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