DIYbio/FAQ

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Intro    In The News    Educational    Equipment    Projects    Kits    Methods    DIYbio.org    DIYbio googlegroup    FriendFeed - DIYbio    http://c.statcounter.com/5195189/0/1a5d59b0/1/0.png

DIYbio FAQ v1.5: "The biohacker's FAQ"

This FAQ for DIYbio is actively maintained by it's editors, and by you! Edit your contributions directly or email updates to the DIYbio email list, diybio@googlegroups.com.
Major contributors (in alphabetical order):
The contents of this FAQ are copyright under the OpenWetWare Copyright policy (Creative Commons Attribution-ShareAlike 3.0 Unported). When quoting any content of this FAQ elsewhere, include a full hypertext link back to the main FAQ page.


This Frequently Asked Questions document is for the DIYBio mailing list. This FAQ is now split into multiple topics for easier reading.


FAQ Revision History

  • 1.0 - copied on 4/7/2009 from heybryan.org...DIYbio_FAQ
  • 1.1 - some updates to clarify original version
  • 1.2 - new sections, reorg, + sections about DIY agar DOI:10.1007/BF00152620 --jcline@ieee.org
  • 1.3 - expand projects sections. Add Laboratory Basics section. --jcline@ieee.org
  • 1.4 - add 'Methods' section, move Laboratory Basics into 'Methods' --jcline@ieee.org

What is DIYbio, as an organization?

DIYbio is an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety. This will require mechanisms for amateurs to increase their knowledge and skills, access to a community of experts, the development of a code of ethics, responsible oversight, and leadership on issues that are unique to doing biology outside of traditional professional settings.


DIYbio is a distributed community of amateur or professional biologists, industry professional or amateur engineers, biomedical engineers, life scientists, computer scientists, etc. Our activities range across a broad spectrum, from molecular naturalism (sequencing part of your own genome or bacterial populations) to biological engineering to building low-cost, open-source alternative lab equipment (Gel Box 2.0) to writing open source software for biology, to creating open source hardware systems and manufacturing.

<html> <div style="float:left;"><object width="560" height="315"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=3454392&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=00ADEF&amp;fullscreen=1" /><embed src="http://vimeo.com/moogaloop.swf?clip_id=3454392&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=00ADEF&amp;fullscreen=1" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="560" height="315"></embed></object><br /><a href="http://vimeo.com/3454392">The DIYbio Community - Presented at Ignite Boston 5 (2009)</a> from <a href="http://vimeo.com/macowell">mac cowell</a> on <a href="http://vimeo.com">Vimeo</a>.<br /><br /></div> <object width="560" height="340" style="float:left;"><param name="movie" value="http://www.youtube.com/v/-IIWH6Hhcnc&hl=en&fs=1&rel=0"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/-IIWH6Hhcnc&hl=en&fs=1&rel=0" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object> <div style="clear:both"> </div><br /> </html>


What is DIYbio's mission?

""*The* goal of DIYBIO, for me, is to reduce as much as possible the specialized equipment handicap for those who choose not to take the degree track / academic institution approach. I can become a professor of electrical engineering, or computer science, or evolutionary biology, without ever getting a degree or attending a course below the PhD level. I can't currently say the same thing about biotechnology with much confidence unless I'm lucky enough to have access to a lab. [...] DIYbio is a hardware hacking endeavor at its core, and it's the hardware hackers working hand-in-hand with the protocol authors who are laying the groundwork for making this a field open to anyone with the drive to become great at it. ""

-- Len Sassaman, DIYbio google group

Are we moving to a future where everyone performs a little genetic engineering? Is genetic engineering safe? Are GMO's safe? Is genetic engineering safe for hackers or everyone to perform? Aren't there too many risks or unknowns? Is it legal or illegal?

Today, everyone performs a "little" computer use, whereas decades ago leaders in the computer field claimed regular people would never need a computer. Decades before that, leaders in the transportation field claimed regular people would never need a car or would never need high speed travel. Eventually these technologies became usable enough for everyone, and somewhat indispensable. Looking many decades ahead, genetic engineering will likely be a common place activity, as with any technology.

Regarding whether genetic engineering is safe for hackers or for everyone, the group invites discussion. There are the key points:

  • There are many unknowns in genetic engineering ("We don't know").
  • There are many more unknowns than we currently know are unknown ("We don't know what we don't know").
  • There are methods to contain genetic engineering experiments to a clean laboratory with only small amounts of risk ("We can reduce the possibility of problems during experimentation").
  • There are unknown risks if genetic engineering experiments escape into the wild ("We don't know").

Readers are encouraged to check out "What we know--and what we don't know--about ecological risks of genetically engineered plants" as of 2001 knowledge map on risk from Robert Horn at Stanford. If you have a more recent and easy-to-read summary of Risk than the paper from 2000/2001, then add it here.

Readers are encouraged to watch the documentary, "The Future of Food" on Hulu: http://www.hulu.com/watch/67878/the-future-of-food

  • Open-Source Biology And Its Impact on Industry, Rob Carlson, IEEE Spectrum, 2001.
""Technology based on intentional, open-source biology is on its way, whether we like it or not. Distributed biological manufacturing is the future of the global economy and will occur as inexpensive, quality DNA sequencing and synthesis equipment becomes available to anyone. In 2050, garage biology hacking will be well under way. Fear of potential hazards should be met with increased research and education, rather than closing the door on the profound positive impacts that distributed biological technology will have on human health, human impacts on the environment, and increasing standards of living around the world. "" http://www.kurzweilai.net/articles/art0613.html?printable=1
""[..] more and more people outside the traditional biotechnology community will create self-replicating machines (life) for civil and defence applications, ‘‘bio-hackers’’ will engineer new life forms at their kitchen table; and illicit substances will be produced synthetically and much cheaper. Such a scenario is a messy and dangerous one, and we need to think about appropriate safety standards now. ""
""Suggestions have also been made for dealing with biosafety issues to do with the accidental (rather than purposeful) release of synthetic organisms. Tucker and Zilinskas (2006), for example, think that the precautionary principle should be adopted with respect to synthetic biology saying that it may be necessary to ban all uses in the open environment until a robust risk assessment can be conducted for each proposed application (p.44). Others think that this step would make research expensive and restrict synthetic biology to a few labs (Garfinkel et al. 2007). ""


What are the social, ethical, legal/patent implications of DIY Bio or home genetic engineering? How might it be best to create more social, ethical, legal/patent discussion?

These issues are discussed very well in the publications of SYNBIOSAFE, which includes discussion of DIYbio itself.

<html><center><iframe src='http://video.economist.com/linking/index.jsp?skin=oneclip&ehv=http://audiovideo.economist.com/&fr_story=706e536c2a60f103f23adcc3f0c0c76150dfbe6b&rf=ev&hl=true' width=402 height=336 scrolling='no' frameborder=0 marginwidth=0 marginheight=0></iframe></center></html>

  • Webcasts
    • Patenting Synthetic Biology: A Transatlantic Perspective. http://www.synbioproject.org/events/archive/6384/ ( Go to the link and click "View Webcast".) Investments in synthetic biology research have been ramping up and the field holds significant promise across areas ranging from medicine to renewable energy. As synthetic biology moves forward, it is critical for researchers, technology developers, investors, and public policy makers to understand how the European Patent Office and the U.S. Patent and Trademark Office will react and respond to the applications covering synthetic biology inventions. This is a unique opportunity to discuss factors influencing EU and U.S. policies on the evolution of intellectual property protection for synthetic biology with experts from both sides of the Atlantic. John LeGuyader, Director TC 1600, U.S. Patent and Trademark Office; Berthold Rutz, Examiner, Directorate 2.4.01, Biotechnology, European Patent Office
    • Bioethics: The Presidential Commission for the Study of Bioethical Issues, The Ritz-Carlton, Washington, D.C., July 8-9, 2010. http://www.tvworldwide.com/events/bioethics/100708/default.cfm . Drew Endy, Bonnie L. Bassler, Robert Carlson, J. Craig Venter, George Church, Kristala L. J. Prather, Allison Snow, Jim Thomas, Nancy M.P. King, Gregory Kaebnick, Allen Buchanan, David Rejeski, Markus Schmidt, Paul Root Wolpe, Amy Patterson, Michael Rodemeyer, Edward H. You.


Other Papers:

""A code of ethics and standards should emerge for biological engineering as it has done forother engineering disciplines. [...] Above all, outreach is required. Genetically modified products, including crops and gene-therapy drugs, have been opposed for reasons that go beyond worries about scientific uncertainties. Citizens who will gladly take recombinant-DNA drugs (such as interferon, insulinand erythropoietin) are reluctant to eat foods containing even trace amounts of recombinant DNA. Can synthetic biology gain greater public trust? We should learn from past cases; in the case of foods generated by synthetic biology, for example, we need to recognize that stakeholders include not just the farmers, but their neighbours and grocery shoppers also. [...] In addition to a code of professional ethics for synthetic biologists, we need to watch for the rare cases when they transgress. This requires not just laws, but also monitoring compliance. [..] Discussions about this have begun, including one funded by the Sloan Foundation ('Study to explore risks, benefits of synthetic genomics'). But any actions that penalize the legitimate manufacturer or user are likely to backfire, and having laws without government-mandated surveillance will be ineffective. Finally, the community needs to discuss the benefits of synthetic engineering to balance the necessary, but distracting, focus on risks. From now on, each small step towards engineering enzymatic pathways for cheaper pharmaceuticals, smart biomaterials and large-scale integrated genetic circuits should be celebrated. ""
  • ""Monsanto Canada Inc. v. Schmeiser [2004] 1 S.C.R. 902, 2004 SCC 34 is a leading Supreme Court of Canada case on patent rights for biotechnology. The court heard the question of whether growing genetically modified plants constitutes "use" of the patented invention of genetically modified plant cells. It ruled that it does. The case drew worldwide attention."" http://en.wikipedia.org/wiki/Monsanto_Canada_Inc._v._Schmeiser

Are there Historical Precedents or Prior Cases which have Demonstrated these Issues?

U.S.

DIY/homebrew chemistry is already adversely affected by the War on Drugs via government regulations intended to limit manufacture of methamphetamine. 

 There is a really interesting parallel between potential DIYbio
 regulations and attempts to quash meth production in America. Biotech-
 commentator Robert Carlson published an article in 2008 (
 http://www.springerlink.com/content/n211746672413507/ ) which confirms
 the point you mention--mom and pop (drug-manufacturing) outfits changed into cartels across
 the US border when the DOJ/DEA tried to crack down by controlling
 access to DIY-meth materials. On his blog,
 http://www.synthesis.cc/2009/08/and-the-innovation-continuesnow-for-shake-and-bake-meth.html 
 and in his new book, he predicts a similar phenomenon will befall
 biological engineering and DIY-biology if the government tries to
 restrict access to materials. Luckily for DIYbio enthusiasts, Carlson
 is also involved in some public policy and expert panels.
-- Marshall Louis Reaves, DIYbio google group


Arizona, 2009

Recent example where a homebrew chemistry project runs into danger due to an accident, perhaps causing larger scrutiny for others in the future. 

 A super interesting case study of this behavior(*) is homebrew bio-diesel in Arizona.   
 [ * - Referring to social issues and/or government regulation stemming
  from bad media portrayals or accidents in homebrew experimentation. -- JC ]
 Without going into too much detail, homebrewers use chemicals that can
 mostly be purchased at swimming pool supply stores (lots of those in
 the desert) including methanol and NaOH. Last summer, a homebrewer's
 oily rags ignited methanol in his garage. An explosion and house fire
 followed. A local news article about the blast:
 http://www.google.com/search?q=Fumes+from+biodiesel+kit+cause+house+explosion+in+Surprise&btnI=745
 You should note how demonized and terrifying making the bio-diesel
 seems. The paragraphs essentially alternate between indicating safety
 and overblown fears.
 ""We knew about (Spreadbury) doing the biodiesel but we didn't think
 he was a danger to us," said neighbor Shannon Daron.
 When asked if she now felt differently, Daron replied "absolutely."
 The fire never spread beyond the garage and Spreadbury and his family
 were not injured.
 A spokesperson for the Surprise Fire Department said Sunday they're
 concerned more people will turn to alternative fuels like biodiesel
 with the rising price of gas.
 Asst. Chief Kevin Pool worries, if not installed and maintained
 properly, they could see more fires started by people making biodiesel
 at home.
 "You might make one little mistake like this and there could be a
 tragedy," said Pool.  "It's at your own risk and your neighbor's
 risk."
 "We just bought this house," said Daron.  "We don't want it
 jeopardized or our children.""
 It seems like an almost nonsensical work of journalism. Homebrew
 doesn't seem to get a fair play in the slightest. This was a serious
 black-eye for homebrew.
 Some cities in the Phoenix valley (Phoenix is a collection of
 independent cities) lashed back. A  "Bio-diesel Task Force" was
 formed, and some jurisdictions deemed homebrewing bio-diesel as
 "industrial activity" and therefore illegal in residential zones. A
 very easy "fix" for overzealous authorities. I'm not sure if searches
 or arrests/fines occurred. This could be a similar weapon used against
 DIYbio'ers, since many materials including simple enzymes could be
 "industrial" in nature. On the brighter side, some cities have adopted
 a pro-homebrewer stance by taking into account safety and zoning
 codes: http://tinyurl.com/ProBDcode  Throughout the state, chemicals
 are incredibly difficult to acquire, even in small amounts. The Meth-
 trade in Arizona doesn't help either.
 Although opinions differ--there are some very smart and well-
 positioned advocates of homebrew bio-diesel in Arizona--with one vital
 key to all of this is a separation of "safe" from "unsafe" practices.
 This is something that DIYbio'ers often seem to work towards. But the
 codification of best practices and vigorous dissemination of them
 seems to be working in homebrewers favor when talking with regulators:
 http://216.104.40.250/~biodcom1/greenbeat/soybenz/b101man/
 When people ask questions of safety, can DIYbio'ers point to a "Bible"
 of sorts to ask if it is a sin? This is especially important to
 separate the *good* parts of DIYbio from a more dangerous fringe if
 such a group exists now or in the future: We are good, they are the
 bad because they violate rules X, Y, and Z. Otherwise, the whole group
 gets labeled as bad, dangerous, or whatever, and this obviously leads
 to being outlawed.
 I know lots of people speculate about lots of futures of regulation
 and public perception, but I think that lessons can be learned form
 homebrew bio-diesel. A great resource is a the Desert Biofuels Blog at
 http://desertbiofuels.blogspot.com
-- Marshall Louis Reaves, DIYbio google group

Who is a "biohacker"?

How can I find out more and contribute?

Many ways! Here's a brief overview:

So far, we mainly communicate through the mailing list. There is also a lower volume DIYbio announce mailing list, which occassionally has announcements that the community might be interested in. Also, there are groups for:

You're welcome to subscribe to the mailing lists- in fact, we encourage it.

There are other forums:

Guidelines for Posting

As the DIYBio mailing list membership grows, it is more important to follow good guidelines for easier readability within discussions. This is called Netiquette.

Please:

  • Follow proper quoting rules:
 One should reply using the standard technique:

    User C. wrote:
    > User B. wrote:
    > > User A. wrote:
    > > > blablabla
    > > blubberblubber
    > laberlaber 

    Your Thoughtful Reply Goes Here.

For complete information on quoting, see conventional netiquette.

  • When quoting another author, keep the attribution line ("On such-and-such-date, Jonathan Cline wrote:").
    • Delete portions of the paragraph which do not pertain to the new reply. This is known as Trimming the post.
    • Trim all quoted text to be the minimum necessary to follow the discussion.
      • Replace deleted text with "[...]" if it changes the placement of words or sentences in a paragraph.
  • Add your message below any quoted text. This means "write your reply at the bottom".
    • Do not "top post". "Top posting" is when the reply is added above the quoted text. This is not as easy to read wen there are many replies in a thread. For this reason, do not "top post", only add the reply at the bottom. Many mail programs have a setting to "reply at top" or "reply at bottom" -- always set it to "Reply at bottom" or manually perform this action yourself. "Top posting" is considered rude by many readers.
  • Change the Subject when the topic changes.
  • Do not "bump" messages. Bumping is purposely replying and quoting an old message purely for the intention of bringing attention to the message (usually with a single line of text, consisting of "Bump!"). If there is new information, then group members will reply. If there are no replies, then wait at least two weeks before bringing up the topic again, or until there is something "new" to add to the original post.

Please see the following Internet reference for complete information:

Where can I see an archive of previous DIYbio discussions and questions?

The DIYbio google group mailing list is hosted from Google Groups which allows reading prior discussions.

Some of our favorites ("member picks") include discussions on ..


Is there a group in my area?

There's probably a group nearby- maybe at least somebody somewhat interested in getting together for lunch or maybe sitting down over a bench and doing serious experiments- at any rate, you can find out about those near you by checking out the map below or diybio.org/local.

<html> <iframe width="575" height="350" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;ll=42.358163,0.0&amp;z=1&amp;spn=0,0&amp;msid=117373025318808082442.00045fd549f07830e0465&amp;output=embed&amp;s=AARTsJqk9drOPzgJzPIckjwHnoC0bQwDAA"></iframe><br />

<a href="http://maps.google.com/maps/ms?ie=UTF8&amp;hl=en&amp;msa=0&amp;ll=42.358163,0.0&amp;z=2&amp;spn=0,0&amp;msid=117373025318808082442.00045fd549f07830e0465&amp;source=embed">View a larger map, or to add yourself or your group to the map.</a> You'll need to sign into your Google account in order to add a new point. Here's a <a href="http://skitch.com/jasonmorrison/bycdy/add-a-point.png-png-image-864x494-pixels-scaled-70">screenshot of how to add a new point on the map</a>. </html>

You may also be interested in other local science groups around the world:

Are there any videos from regional groups?

DIYbio-NYC: Shot glass DNA extraction

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DIYbio-SF: Tito's food coloring electrophoresis

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DIYbio-boston: diybio visits the fablab

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What does a Garage Lab look like?

http://farm3.static.flickr.com/2478/4044058001_71291f7196_m.jpg

Post pictures of your own home laboratory setup, and view some: http://www.flickr.com/groups/diylabs/
-- From Raymond McCauley, DIYbio google group


Has DIYbio been in the news?

Yes.

What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing?

See DIYBio FAQ: Education & Resources


What equipment do I need to perform DIYBio-related projects?

See DIYBio FAQ: Equipment


What is open source hardware?

http://p2pfoundation.net/Open_source_hardware

"Open Source Hardware is hardware that keeps its designs available in a way similar to the open source in software." There is no defacto license for open source hardware yet. Some websites (like ponoko, thingiverse, unptnt) put hardware CAD files under a "Creative Commons" license. However, it's still unknown how this is likely to interface with the legal systems around the world (i.e., patents). And it's not necessarily true that putting something directly into the public domain is the best way to go either. So, the future is presently unclear- in terms of legal issues.

DIYbio has many big supporters of standardized packaging formats (like .tar.gz, .deb, .tar, .rpm, etc.) for automatic downloading of hardware components and instructions on how to build the components. There are some sites that almost implement this (but not quite) such as instructables, ponoko, thingiverse, odesigns, unptnt, etc.

'Slashdot discussions


Projects

What Projects has DIYBio completed? What projects are DIYBio contributors working on now? Who is working on what? Who do I contact to offer to collaborate on a project?

See DIYBio FAQ: Projects.

Please add your own project info to the DIYBio FAQ: Projects topic!


Appendix 1 - list of Synthetic Biology Companies

Appendix 2 - List of Equipment Suppliers

See DIYBio FAQ: Equipment for new/used/refurbished equipment suppliers.

Appendix 3 - Laboratory Basics

See DIYBio FAQ: Methods for basic lab technique, including sterilization, using animals, etc.

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