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Singularity University July 2010 diybio demo workshop

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Who invented the popular "arduino" microcontroller, and why? …

Who invented the popular "arduino" microcontroller, and why?

This presentation explores the development of several diybio kits and projects over 2010 and suggests that tools developed by and for non-professionals may be positioned to become disruptive innovations due to their low-cost, simple use, open design, and growing public documentation and examples.


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  • 1. why are you interested in biotech? tinkering business 29% 16% 1300+ amateur biologists around the world art 15% - scientists, inventors, artists, educators... research other - inventing “lo-fi” molecular biology 32% 8% - bridging the gap between science & society - broad interest in public, open work are you interested in working in public? reinforcing positive culture via diybio.org neutral - establish transparency & safety norms 5% interested uninterested - biosafey & legal tools, guidelines 84% 11% - support public lab & tool development - organize positive community projects (BWM) source: diybio 2010 survey
  • 2. 1. expert “biohackers” (5%) & “newbie” amateurs + hobbyists (95%) 2. entrepreneurs 3. artists 4. educators 5. journalists 6. policy makers 3 diybio mailing list users
  • 3. capabilities 94% talkers users (undergraduate level) DNA purification culturing 5% PCR mutagensis transformation part assembly 1% makers (grad level)
  • 4. May 2010 - http://diybio.org/local
  • 5. a growing community that wants to play with biotechnology developing lo-fi tools, techniques, and toys
  • 6. why ? science as new tools & culture techniques toys today, DNA is not scary. tools tomorrow; disruptive innovation.
  • 7. “ “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.”
  • 8. “ W. Brian Arthur: 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.
  • 9. why now ? Lab-as-a-Service Synthetic Biology DIY equiptment & CARLSON tools techniques 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. Heater Gel Electrophoresis Chamber SYNTHETIC 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 n this semi-log plot, DNA synthesis and sequencing productivity are both increasing at least as fast as Moore?s Law angles). Each of the remaining points is the amount of DNA that can be processed by one person running multiple ma- BIOLOGY 7 ne eight hour day, defined by the time required for pre-processing and sample handling on each instrument. Not in- ese estimates is the time required for sequence analysis. For comparison, the approximate rate at which a single mole- li DNA Polymerase III replicates DNA is shown (dashed horizontal line), referenced to an eight-hour day. rocessing time and cycle time per run for instruments in production are based on the experience of the scientific staff FOR ARTISTS & ular Sciences Institute and on estimates provided by manufacturers. ABI synthesis and sequencing data and Intel tran- ourtesy of those corporations. Pyrosequencing data courtesy of Mostafa Ronaghi at the Stanford Genome Technology eWriter data courtesy of Glen Evans, Egea Biosciences. Projections are based on instruments under development. sed in protein structure determination show nds (Figure 2), suggesting a general rapid im- sign new chips and the computational power of the chips used in the design process. dESIGNERS of biological technologies. As a reference, We can now see the beginnings of a similar effect in This was then centrifuged at room temperature for 3 minutes @ 8000 rpm. aw, which describes the doubling time of the the development of biological technologies. For exam- 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. transistors on microchips, is also shown in ple, enzymes optimized for laboratory conditions are 1 9 used in the preparation of DNA for sequencing, where ng anything to Moore’s Law is already a earlier sequencing technologies were part of characteriz- doing so remains a useful device to gauge our ing and modifying those enzymes. Recombinant proteins ns of how other technologies will affect so- are used every day to elucidate interactions between pro- ic change. This comparison starts with the ob- teins within organisms, and that information is already
  • 10. what’s going on now?
  • 11. $111? Hard to purchase w/o academic affiliation pGlo kit
  • 12. DNA Explorer, $80? (Ages 10 and up) www.discovery.com no longer available :(
  • 13. bioweathermaps
  • 14. bioweathermaps • crowdsourced sampling + funding for metagenomics •volunteer microbial biosurveilance •Launched at GET2010 (April)
  • 15. culturing bioluminescent !"#$%&'#()%(*)+,$&,- !"#$%&'%(#)%*+,"# -,(,%.,/#01/,*#%#$* .)# >,&%2(.#31#&',#(2=,1.,#% D4%2(?#=%&'%(B%*+,"H /)0'#$,1'(."2.(&)0% ,%&2+,#$34431.#567 *,#',*,?#'&&@?AA=*,%&2+ B4%2(6=34#C#IJ2&&,*? 2&.-'% #8&&*2!0&2319#:'%*,%( #H31,&*0,=%&'%(9#H 2;,#<2=,1.,6 ,=34431.63*BA(2=,1. ,.A!"C.%A567A#D1E02* (%!.F*34F%!. ,#F3*#,G=,@&231.6 marine microbes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bit.ly/diybio-squid
  • 16. Rapid-Prototyped centrifuge spindle
  • 17. algae photobioreactor $50? spin-off from biofuel startup
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  • 55. Pearl Gel Box (v.2)- $499
  • 56. $100 2-axis microscope
  • 57. ... and DIY microfluidics
  • 58. $30 microbial fuel cell generates microamps @ 0.3 volts from natural soil microbes Great  educational  tool  for  kids  and  kids  at  heart! Dirt  Power! (Discounted  classroom packages  available,  including   educational  material  and  pre-­‐designed  curriculum) Key  Players: Microbial  Fuel  Cell  Kits Shewanella (aka    Mr.  Clean) find   Fill  it  up  with  dirt  from  your  backyard  and  whatever  you   in  your  refrigerator  and  see  how   much  powe r  you  can  get! Learn about  the  extraordinary  abilities  of  microbes  in  your  backyard. Shewanella can  be  found   almost  everywhere on  earth,  from   mountain  soils,  to  ocean   Compete in  our  International  Dirt  Power  Competition.   sediments.      It  has  an  ability  to   metabolize  a  wide  variety  of   elements  that  are  toxic  to  humans,   Develop the  technology  by  submitting  data  to  our  online  database. humans  or  other  animals.  It  even   has  the  ability  to  metabolize Uranium,  precipitating  it  out  of   contaminated  waters.     ed .    Your  name  w publicatio Get  Publishe  worldwith    our  online  ill  be  on  it!n,  presenting   Geobacter data  collected  all  around  th (aka  The  Iron-­‐breather) What  the  heck  is  a  microbial  fuel  cell? rness   Microbial  fuel  cells  (MFCs)   are  bio-­‐electrical  devices  that  ha the  natural  metabolisms  o f  microbes  to  produce  electrical  power   -­‐ ak  down   Known  as  the directly.    Within  the  MFC,  microbes  act  as  a  catalyst  to  bre ,  Geobacter species  have   sugars  and  other  nutrients  in  their  surrounding  environment  and   olecules   compounds  and  use  them  in  a  way   release  a  portion  of  the  energy  contained  within  those  m similar  to  the  way  humans  use   in  the  form  of  electricity. oxygen.
  • 59. SpikerBox $120 neuron recorder
  • 60. LavaAmp - $200 rapid pcr machine
  • 61. $400 open source PCR OpenPCR thermocycler
  • 62. 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
  • 63. who invents rapid prototyping toys?
  • 64. enables tinkering (rapid prototyping) with electronics
  • 65. enabling tinkering with biology
  • 66. two paths to new tools refactoring - cheaper existing tools - more open - more fun - simpler (more limited) inventing new tools (“toys”*) prioritizing tinkering play * over significance accuracy blinky LED new market for biotech tinkering tools tutorial
  • 67. 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.
  • 68. 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
  • 69. a growing community: that wants to play with biotechnology developing lo-fi tools, techniques, and toys
  • 70. a growing community: increasing human capital in biotechnology smoothing the interface between science society that wants to play with biotechnology increasing public awareness and understanding developing lo-fi tools, techniques, and toys protoyping tools disruptive technologies for biotechnology
  • 71. why are you interested in biotech? .org tinkering business 29% 16% art 15% - public blog research other - build safety legal resources 32% 8% - promote transparency outreach - organize positive community projects (BWM) are you interested in working in public? neutral want to collaborate? 5% interested uninterested contact@diybio.org 84% 11% source: diybio 2010 survey
  • 72. Bangalore Boston Chicago Los Angeles London New York City San Francisco Seattle Houston ... .org

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