DIYbio/FAQ

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
 * 1.5 - Add 'News' section, move news articles there. jcline@ieee.org 23:40, 23 May 2011 (EDT)

= 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.

 The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

   


 * DIYBio blog
 * DIYBio friendfeed
 * DIYBio twitter feed

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


 * Schmidt M, 2008. Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthetic Biology. Vol.2(1-2):1-6. http://www.markusschmidt.eu/pdf/Diffusion_of_synthetic_biology.pdf
 * ""[..] 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. ""


 * IRGC 2008. Concept note: Synthetic Biology. Risks and opportunities of an emerging field. International Risk Governance Council, Geneva. http://www.synbiosafe.eu/uploads/pdf/IRGC_ConceptNote_SyntheticBiology_Final_30April.pdf
 * ""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.


 * SYNBIOSAFE publications: Safety, Security and Ethical Aspects of Synthetic Biology. http://www.synbiosafe.eu/index.php?page=resources
 * Schmidt et al. 2009. A priority paper for the societal and ethical aspects of synthetic biology. Systems and Synthetic Biology. Vol.3(1-4):1-2 http://www.synbiosafe.eu/uploads/pdf/Schmidt_etal-2009-SSBJ.pdf
 * Kelle A. 2009. Ensuring the security of synthetic biology—towards a 5P governance strategy. Systems and Synthetic Biology. Vol.3(1-4): 85-90  http://www.synbiosafe.eu/uploads/pdf/Kelle-2009-SSBJ.pdf
 * Schmidt M, Torgersen H, Ganguli-Mitra A, Kelle A, Deplazes A, Biller-Andorno N. 2008. SYNBIOSAFE e-conference: online community discussion on the societal aspects of synthetic biology. Systems and Synthetic Biology. http://www.markusschmidt.eu/pdf/SSBJ-SYNBIOSAFE_e-conference.pdfVol.2(1-2):7-17

<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>
 * Rob Carlson on THE ECONOMIST
 * http://audiovideo.economist.com/?fr_story=706e536c2a60f103f23adcc3f0c0c76150dfbe6b&rf=bm Rob Carlson on synthetic biology.  You can do a lot in your garage. A professor of biosynthesis on open-source biology, buying DNA online and the problem with patents.


 * 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:


 * Selgelid M. 2007. The tale of two studies: Ethics, Bioterrorism, and the Censorship of Science. Hastings Center Report 37, no. 3:35-43. http://www.synbiosafe.eu/uploads///pdf/Tale%20Two%20Studies%20Final%20Printed.pdf
 * Rai A, and Boyle J. 2007. Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons. PLoS Biol. 13;5(3):e58 http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.0050058


 * Church G., 2005, Let us go forth and safely multiply. Nature, Vol. 438: 423. http://www.nature.com/nature/journal/v438/n7067/pdf/438423a.pdf
 * ""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

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"?

 * What do people think of when they think of a typical biohacker?
 * probably in the sense of the subculture (more broadly, Hacker culture)
 * combines the hacker ethic of biologists, programmers, DIY enthusiasts, etc.
 * Hacker ethic of the Homebrew Computer Club
 * Free software movement
 * people who enjoy "hacks".
 * GNU is a hack: a recursive acronym for "GNU is Not Unix".
 * might be somewhat related to biopunk.

How can I find out more and contribute?
Many ways! Here's a brief overview:
 * mailing list (most activity) (note the discussion on the list's standards)
 * IRC (#diybio on irc.freenode.net)
 * local groups

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:


 * San Francisco
 * Chicago
 * New York (city)
 * London
 * Boston.
 * The main list is (as mentioned above) DIYBio mailing list

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

There are other forums:
 * biopunk.org
 * sciencemadness.org
 * please expand this list

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:

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

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:
 * http://www.faqs.org/rfcs/rfc1855.html

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 ..
 * Public perception
 * your favorite thread here

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.

<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">

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 screenshot of how to add a new point on the map</a>.

You may also be interested in other local science groups around the world:
 * dorkbot group ("people doing strange things with electricity")
 * hackerspace.
 * please expand this list

DIYbio MCR
Manchester, UK group. Some photos of SwabFest plates and participants, courtesy of Hwa Young Jung. "Find out more about what we do at diybio.madlab.org.uk #diybiomcr"
 * http://www.flickr.com/photos/madlabuk/collections/72157626528280829/

DIYbio-NYC: Shot glass DNA extraction
s2HPVs25HlY

DIYbio-SF: Tito's food coloring electrophoresis
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DIYbio-boston: diybio visits the fablab
oQ3BRKAsG0I

---

Bio-Artist Multimedia

 * BIO:FICTION Science, Art & Film festival 2010, Museum of Natural History, Vienna, Austria
 * Bio:Fiction is the world's first synthetic biology film festival. Our call for submissions in 2010 triggered 130 short film entries from 25 countries. 52 films were shortlisted and judged by an international jury composed of filmmakers and synthetic biology scientists. Several award categories will honour the best short films, covering science documentaries, science fiction films and plain fictional narratives.
 * http://bio-fiction.com/videos

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. Frequently! See In The News for a significant list of articles.

= 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
 * Open Source Everything project, adciv.org
 * Open Source Ecology (Factor E Farm, openfarmtech, etc.)
 * ToolBook (just some links to other articles about ToolBook) (infrastructure)


 * How do I put an invention into the public domain?
 * The State of Open Source Hardware in 2008
 * Open source hardware for fun and profit (re: Arduino)
 * Open source hardware gift guide
 * Open source hardware gets public introduction
 * Best open source licenses for hardware?
 * What is open source hardware?
 * other slashdot.org threads about OSH

Open Source Ecology
Open source hardware includes large systems.

This is Chris Fornof with Open Source Ecology, http://opensourceecology.org We're attempting to create a Global Village Construction Set (GVCS, with the aim of creating a "civilization starter kit".  See the TED talk, http://www.ted.com/talks/marcin_jakubowski.html

= 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 =
 * Amyris Biotechnologies
 * ATG:biosynthetics
 * Blue Heron Biotechnology, Inc.
 * DNA2.0
 * febit synbio gmbh
 * GENEART
 * Ginkgo BioWorks
 * LS9, Inc.
 * Sloning Biotechnology
 * Synthetic Genomics, Inc.
 * Mr.Gene GmbH

= 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.