diybio faq for biohackers

This Frequently Asked Questions document is for the DIYbio mailing list and ##hplusroadmap freenode IRC channel.

This document is split into multiple sections.

  • educational - books and things to read
  • projects - various known biohacking projects
  • methods - some basic protocols for manipulating lab materials
  • kits - glowpop culture
  • equipment - basic lab equipment introduction
  • software - software for biology, chemistry, physics
  • news - a list of articles in the news about diybio, biohacking, and biopunk
  • groups - places to hang out around the world, also some hackerspaces
  • better-questions - questions directly extracted from the diybio mailing list

What is DIYbio.org?

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.

Are there any easy, cheap projects I can do to get started?

See kits.

What is the goal of do-it-yourself biology?

"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 (1980 - 2011)

Is it safe for everyone to be biohacking?

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.

"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; Open-Source Biology And Its Impact on Industry, Rob Carlson, IEEE Spectrum, 2001.)

"[..] 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." (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/Diffusionofsynthetic_biology.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)." (IRGC 2008. Concept note: Synthetic Biology. Risks and opportunities of an emerging field. International Risk Governance Council, Geneva. http://www.synbiosafe.eu/uploads/pdf/IRGCConceptNoteSyntheticBiologyFinal30April.pdf)

Ethical and social implications

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

Some papers

Webcasts on social implications

  • 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/MonsantoCanadaInc.v.Schmeiser

Are there historical precedents or prior cases which have demonstrated similar issues?

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 mailing list

Recent example where a homebrew chemistry project runs into danger due to an accident, perhaps causing larger scrutiny for others in the future. This was in Arizona in 2009.

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

What's a biohacker in general?

How can I contribute?

Many ways! Here's a brief overview:

  • Join the mailing list. Also be sure to see the discussion on the list's standards (like for netiquette).
  • IRC (Internet Relay Chat). There are some active communities on the irc.freenode.net server in ##hplusroadmap and #diybio, #biopunk, and #biohack. Users unfamiliar with IRC are encouraged to try connecting with mibbit or the Chatzilla for Firefox plugin or AndroIRC for Android. The ##hplusroadmap channel has been active since 2008 and focuses on biohacking, open source hardware, nootropics (smart drugs), human enhancement, and advanced technologies. Channel logs can be found at gnusha.org/logs. Historically, the ##hplusroadmap channel existed prior to the #diybio channel and this might explain why there has been a history of greater activity there.
  • Join a local group. See the later section on this.

So far, we mainly communicate through the mailing list. Many of us communicate through the mailing list by email, although some users choose to use the Google Groups web interface. Jake Stewart created a mail2forum gateway on phpBB once, so that users can participate from a phpBB forum, but unfortunately he discontinued this service. There is a very low volume (unused) mailing list for announcements only.

Here is a list of mailing lists for local groups.

There are also a few forums, although so far they seem to be low traffic for biohacking:

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.

View a larger map, or to add yourself or your group to the map. 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.

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

What does a garage lab look like?

4044058001<em>71291f7196</em>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?

See In The News for a significant list of articles.

What are some educational resources for DIYbio and biology?

See educational See /wiki/diybio/faq/educational for educational resources.

What equipment do I need?

See equipment.

What is open source hardware?

http://p2pfoundation.net/Opensourcehardware

"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 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

See projects.

Please add your own project info to the projects page.

Contributing to this document

Edit your contributions to this wiki over the web like a regular wiki. Register to edit here and see other commands. You must register prior to editing. When editing, please remember to include commit messages to describe your changes to onlookers.

You can also email your contributions to Bryan Bishop, Jonathan Cline, or the DIYbio mailing list (diybio@googlegroups.com). You can also optionally use git to edit this wiki:

git clone git://diyhpl.us/diyhpluswiki.git

Note to push changes you must push with your registered account:

git push username@diyhpl.us:/srv/git/diyhpluswiki.git master

You can make this easier by updating the remotes:

git remote set-url origin username@diyhpl.us:/srv/git/diyhpluswiki.git

Now "git push" should work without debilitating complaint.

There is a historical copy on OpenWetWare. However, unlike a traditional wiki, users must be registered and approved by a system administrator. Some individuals have complained about this in the past. Also, the revision history is likely to diverge since the markup formatting is different. But, since nobody has kept that version up to date, it doesn't seem to be a big deal anyway.

Copyright

The contents of this FAQ are copyright under the Creative Commons Attribution-ShareAlike 3.0 Unported license. When quoting any content of this FAQ elsewhere, include a full hypertext link back to the main FAQ page. This link seems to presently be http://diyhpl.us/wiki/diybio/faq although there are historical alternatives.

FAQ Revision History

  • v1.0 - copied on 2009-04-07 from http://heybryan.org/mediawiki/index.php/DIYbio_FAQ to OpenWetWare here.
    • Also, there was a version on Nathan McCorkle's diybioforums.org mediawiki installation for a while.
  • v1.1 - some updates to clarify original version
  • v1.2 - new sections, reorg, + sections about DIY agar DOI:10.1007/BF00152620 -- jcline@ieee.org
  • v1.3 - expand projects sections. Add Laboratory Basics section. -- jcline@ieee.org
  • v1.4 - add 'Methods' section, move Laboratory Basics into 'Methods' -- jcline@ieee.org
  • v1.5 - Add 'News' section, move news articles there. jcline@ieee.org 23:40, 23 May 2011 (EDT)
  • v1.6 - Revision history rebased on top of original revision history from hplusroadmap wiki, and then merged into diyhpluswiki.git. The revision numbers should be replaced with the git commit id, except for tagged releases, of which there are presently none. The previous versioning could be considered to be tags maybe. (2012-08-01)

Appendix 1: List of synthetic biology companies

Appendix 2: List of equipment suppliers

See equipment for new/used/refurbished equipment suppliers.

Appendix 3: Laboratory basics

See methods for basic lab technique, including sterilization, using animals, etc.