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{{DIYbio:Top}}
{{DIYbio:Top}}
'''DIYbio FAQ v1.3''':  ''"The biohacker's FAQ"''
: Please '''update this FAQ mercilessly with Q&A !'''




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* 1.2 - new sections, reorg, + sections about DIY agar DOI:10.1007/BF00152620 --'''[[User:Jonathan Cline|jcline@ieee.org]]'''
* 1.2 - new sections, reorg, + sections about DIY agar DOI:10.1007/BF00152620 --'''[[User:Jonathan Cline|jcline@ieee.org]]'''
* 1.3 - expand projects sections.  Add Laboratory Basics section. --'''[[User:Jonathan Cline|jcline@ieee.org]]'''
* 1.3 - expand projects sections.  Add Laboratory Basics section. --'''[[User:Jonathan Cline|jcline@ieee.org]]'''
 
* 1.4 - add 'Methods' section, move Laboratory Basics into 'Methods' --'''[[User:Jonathan Cline|jcline@ieee.org]]'''
* 1.5 - Add 'News' section, move news articles there. [[User:Jonathan Cline|jcline@ieee.org]] 23:40, 23 May 2011 (EDT)
* 1.6 - Multiple updates to project section [[User:Jonathan Cline|jcline@ieee.org]] 00:20, 6 September 2012 (EDT)


= What is DIYbio, as an organization? =
= What is DIYbio, as an organization? =
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== What is DIYbio's mission? ==
== What is DIYbio's mission? ==
== 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? ==
 
{{DIYbio:Top}}
 
 
""*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.''
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:
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 unknowns in genetic engineering ("We don't know").
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* There are unknown risks if genetic engineering experiments escape into the wild ("We don't know").
* There are unknown risks if genetic engineering experiments escape into the wild ("We don't know").


'''Readers are encouraged to check out [http://www.macrovu.com/image/GMimg/infoMrlUnknwnsInGMv7.pdf "What we know--and what we don't know--about ecological risks of genetically engineered plants" as of 2001] knowledge map on risk from [http://www.stanford.edu/~rhorn/ Robert Horn at Stanford].'''
'''Readers are encouraged to check out [http://www.macrovu.com/image/GMimg/infoMrlUnknwnsInGMv7.pdf "What we know--and what we don't know--about ecological risks of genetically engineered plants" as of 2001] knowledge map on risk from [http://www.stanford.edu/~rhorn/ 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.


* ''If you have a more recent and easy-to-read summary of Risk than the paper from 2000/2001, then add it here.''
* 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
 
* 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.''
<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:
 
* 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
 
=== 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"? ==
== Who is a "biohacker"? ==
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There are other forums:  
There are other forums:  
*[http://biopunk.org/ biopunk.org]
*[http://biopunk.org/ biopunk.org]
*[http://diybioforum.org/ diybioforum.org]
*[http://www.sciencemadness.org/talk/ sciencemadness.org]
*[http://www.sciencemadness.org/talk/ sciencemadness.org]
*[http://www.roguesci.org/theforum/index.php roguesci.org]
*''please expand this list''
*''please expand this list''


== What are the Guidelines for Posting to the DIYBio mailing lists and/or Forums? ==
== Guidelines for Posting ==


''As the DIYBio mailing list membership grows, it is more important to follow good guidelines for easier readability within discussions.''   
'''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:
Please:
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     > > blubberblubber
     > > blubberblubber
     > laberlaber  
     > laberlaber  
    Your Thoughtful Reply Goes Here.
</pre>
</pre>


For complete information see [http://www.netmeister.org/news/learn2quote.html conventional netiquette].
For complete information on quoting, see [http://www.netmeister.org/news/learn2quote.html conventional netiquette].
** When quoting another author, keep the attribution line ("On such-and-such-date, Jonathan Cline wrote:").
* 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".
** 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.
*** Replace deleted text with "[...]" if it changes the placement of words or sentences in a paragraph.
* Trim all quoted text to be the minimum necessary to follow the discussion.
* ''Add your message below any quoted text.  This means "write your reply at the bottom".''
* ''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 when 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.
**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' of the email when the topic changes.
*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


There are many other resources available to learn about netiquette:
== Where can I see an archive of previous DIYbio discussions and questions? ==
* http://www.faqs.org/qa/rfcc-145.html
* http://www.idallen.com/topposting.html
* http://www.google.com/search?q="top+posting"
* in general please note that "top posting" is considered obscenely rude


== Where can I see an archive of previous DIYbio discussions and questions? ==
The [http://groups.google.com/group/diybio DIYbio google group mailing list] is hosted from Google Groups which allows reading prior discussions.
Right over [http://groups.google.com/group/diybio here].


Some of our favorites ("member picks") include discussions on ..
Some of our favorites ("member picks") include discussions on ..
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== Are there any videos from regional groups? ==
== Are there any videos from regional groups? ==
=== 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 ===
=== DIYbio-NYC: Shot glass DNA extraction ===
<youtube align="left">s2HPVs25HlY</youtube> <html><div style="clear:both;"></div></html>
<youtube align="left">s2HPVs25HlY</youtube> <html><div style="clear:both;"></div></html>
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<youtube align="left">oQ3BRKAsG0I</youtube> <html><div style="clear:both;"></div></html>
<youtube align="left">oQ3BRKAsG0I</youtube> <html><div style="clear:both;"></div></html>


---
=== 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? ==


== Has DIYbio been in the news? ==
http://farm3.static.flickr.com/2478/4044058001_71291f7196_m.jpg
Yes.


* 2009-08-01: [http://www.the-scientist.com/2009/08/1/17/1/ Am I a biohazard?] (The Scientist)
:'''Post pictures of your own home laboratory setup, and view some: http://www.flickr.com/groups/diylabs/ '''
* June 2009 issue of [http://hplusmagazine.com/ hplusmagazine]
::-- From Raymond McCauley, DIYbio google group
* June 2009 issue of Gourmet magazine [http://groups.google.com/group/diybio/msg/9bda9e3d613a18c6]
* 2009-05-18: [http://weekinideas.wordpress.com/2009/05/18/in-attics-and-closets-%e2%80%98biohackers%e2%80%99-prove-the-spirit-of-thomas-edison-endures/ In attics and closets, "biohackers" prove the spirit of Thomas Edison endures]
* 2009-05-12: [http://online.wsj.com/article/SB124207326903607931.html In Attics and Closets, 'Biohackers' Discover Their Inner Frankenstein]
* 2009-03-18: [http://www.guardian.co.uk/technology/2009/mar/19/biohacking-genetics-research The Geneticist in the Garage]
* 2009-01-19: [http://www.wired.com/medtech/genetics/magazine/17-02/ff_diygenetics?currentPage=all DIY DNA: One Father's Attempt to Hack His Daughter's Genetic Code]
* 2009-01-07: [http://www.newscientist.com/article/mg20126881.400-genetic-manpulation-now-becoming-a-hobby.html?full=true&print=true Rise of the garage genome hackers]
* 2008-12-30: [http://www.pbs.org/newshour/bb/science/july-dec08/diybio_12-30.html Students, Scientists Build Biological Machines (transcript)] (Lehrer on PBS) ([http://www.youtube.com/watch?v=-IIWH6Hhcnc video])
* 2008-12-25: [http://iht.nytimes.com/articles/ap/2008/12/25/america/Do-It-Yourself-DNA.php Amateurs are trying genetic engineering at home] ([http://science.slashdot.org/article.pl?sid=08/12/25/1833211 Slashdot])
* 2008-12-18: [http://www.publico.es/ciencias/184626/biohackers/reventar/reinventar/biologia/garajes Público: Biohackers: reventar y reinventar la biología desde los garajes]
* 2008-12-11: [http://seedmagazine.com/news/2008/12/the_biohacking_hobbyist.php The Biohacking Hobbyist]
* 2008-09-15: [http://www.boston.com/news/science/articles/2008/09/15/accessible_science/ Hackers aim to make biology household practice]
* many, many other occurences- keep sending them in
** also, there have been many news stories from the pre-DIYbio era which should be in this list


== Has DIYbio been in the news? ==
Yes.  Frequently!  '''See [[DIYbio/FAQ/News|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? =
= What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing? =
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See [http://openwetware.org/wiki/DIYbio/FAQ/Educational DIYBio FAQ: Education & Resources]
See [http://openwetware.org/wiki/DIYbio/FAQ/Educational DIYBio FAQ: Education & Resources]


== How can I grow and engineer yeast? How can I grow and engineer bacteria? ==
See [http://openwetware.org/wiki/DIYbio/FAQ/Projects DIYBio FAQ: Projects]


= What equipment do I need to perform DIYBio-related projects? =
= What equipment do I need to perform DIYBio-related projects? =
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* [http://www.google.com/search?hl=en&client=opera&rls=en&hs=078&num=100&q=site%3Aslashdot.org+open+source+hardware&btnG=Search other slashdot.org threads about OSH]
* [http://www.google.com/search?hl=en&client=opera&rls=en&hs=078&num=100&q=site%3Aslashdot.org+open+source+hardware&btnG=Search 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 =
= Projects =
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= Appendix 2 - List of Equipment Suppliers =
= Appendix 2 - List of Equipment Suppliers =


== New Equipment ==
See [http://openwetware.org/wiki/DIYbio/FAQ/Equipment DIYBio FAQ: Equipment] for new/used/refurbished equipment suppliers.
 
* ''please expand this list''
 
 
=== In the United Kingdom ===
 
====Microscopy====
 
* Brunel Microscopes: http://www.brunelmicroscopes.co.uk/
 
Brunel Microscopes Ltd has many years professional experience in all aspects of microscopy and specimen preparation. They stock a wide range of light microscopes, stereomicroscopes, accessories, prepared slides, stains and reagents that are suited to the professional and amateur microscopist, as well as educational establishments, industry and research.
 
* Used Microscopes UK: http://www.usedmicroscopes.co.uk/index.html
 
Used Microscopes UK is a Brunel Microscopes website dedicated to preowned microscopes, accessories and ex-demonstration equipment.
 
====Educational lab kits====
 
* National Centre for Biotechnology Education: http://www.ncbe.reading.ac.uk/menu.html
 
Since its establishment in 1984-5, the NCBE has gained an international reputation for the development of innovative educational resources.  The NCBE sells enzymes, microcentrifuges, pipettes, electrophoresis kits, transformers and other science kits.
 
=== In the United States of America ===
 
====Chemical Suppliers====
 
*  Chemsavers: http://www.chemsavers.com
 
From the website: "Chemsavers is a distributor of laboratory chemicals. We stock many different types of chemicals and often hard to find and one of a kind chemicals. We offer below retail prices and free shipping. How can we do this? We make special purchases on sale items, bulk items and close outs. As far as most of the basic lab chemicals go, we keep them in stock as we purchase directly from the manufacturers to increase the savings to you"
 
Their international shipping policies are not known.
 
*  The Lab Depot Inc: http://www.labdepotinc.com/
 
Cory Tobin notes: "Lab Depot sells pouches of pre-mixed TBE powder.  For $22.71 you get enough to make 1L of 10x TBE.  The usual working concentration of TBE is 1/2x, so this makes 20L of buffer.  They don't mention only shipping to academic/commercial addresses so I suppose they will send the stuff to your apartment."
 
====Culture Media====
 
* Sunrise Science Products: http://www.shop.sunrisescience.com
 
A recent question was asking where to find a supplier of amino acids for media. Sunrise Science Products (www.shop.sunrisescience.com) is good,         
primarily focused on basic yeast media. They also ship to residential addresses. Likely better purity than one would find at a GNC type store       
where there is no assurance of the actual content of any bottle.                                                                           
                                                   
====Educational and kit suppliers====
 
* American Science & Surplus: http://www.sciplus.com/
 
From the website : "Here at American Science & Surplus we are fascinated by discovery and invention. And we are dedicated to having fun along the way. We offer an eclectic range of products, many with a science or educational tilt to them, others simply handy or amusing. Value is important, and whenever we can, we carry surplus at prices well below retail. We love closeouts, inventory overruns, mis-manufactures, and items whose time has not come.
 
A word of caution: When a surplus item is gone, it is gone. So if you see something you love, best get it now since we may not have it tomorrow. When we can't find surplus, we may carry regular merchandise which we think those interested in learning and tinkering will find appealing, but only if we feel it is good quality at a fair price."
 
Note: does NOT ship outside of US territories
 
== Surplus/Auction Equipment ==
 
* [http://www.equipnet.com equipnet]
* [http://ebay.com/ ebay]
* [http://www.go-dove.com/ go-dove]
* [http://labx.com/ labx]
* ''please expand this list''


= Appendix 3 - Laboratory Basics =
= Appendix 3 - Laboratory Basics =


== USING PHYSICAL AGENTS TO CONTROL MICROORGANISMS ==
See [http://openwetware.org/wiki/DIYbio/FAQ/Methods DIYBio FAQ: Methods] for basic lab technique, including sterilization, using animals, etc.
 
::This section is quoted from [http://student.ccbcmd.edu/courses/bio141/labmanua/lab19/lab19.html BIOL 230 MICROBIOLOGY LABORATORY MANUAL by Dr. G.E. Kaiser, Copyright © Gary E. Kaiser, Updated: March 4, 1999]
 
 
A. INTRODUCTION TO THE CONTROL OF MICROORGANISMS
 
Control of microorganisms is essential in order to prevent the transmission of diseases and infection, stop decomposition and spoilage, and prevent unwanted microbial contamination.
 
Microorganisms are controlled by means of physical agents and chemical agents. Physical agents include such methods of control as high or low temperature, desiccation, osmotic pressure, radiation, and filtration. Control by chemical agents refers to the use of disinfectants, antiseptics, antibiotics, and chemotherapeutic antimicrobial chemicals.
 
Basic terms used in discussing the control of microorganisms include:
 
1. Sterilization
Sterilization is the process of destroying all living organisms and viruses. A sterile object is one free of all life forms, including bacterial endospores, as well as viruses.
 
2. Disinfection
Disinfection is the elimination of microorganisms from inanimate objects or surfaces.
 
3. Decontamination
Decontamination is the treatment of an object or inanimate surface to make it safe to handle.\
 
3. Disinfectant
A disinfectant is an agents used to disinfect inanimate objects but generally to toxic to use on human tissues.
 
4. Antiseptic
An antiseptic is an agent that kills or inhibits growth of microbes but is safe to use on human tissue.
 
6. Sanitizer
A sanitizer is an agent that reduces, but may not eliminate, microbial numbers to a safe level.
 
5. Antibiotic
An antibiotic is a metabolic product produced by one microorganism that inhibits or kills other microorganisms.
 
6. Chemotherapeutic antimicrobial chemical
Chemotherapeutic antimicrobial chemicals are synthetic chemicals that can be used therapeutically.
 
7. Cidal
An agent that is cidal in action will kill microorganisms and viruses.
 
8. Static
An agent that is static in action will inhibit the growth of microorganisms.
 
B. TEMPERATURE
 
Microorganisms have a minimum, an optimum, and a maximum temperature for growth. Temperatures below the minimum usually have a static action on microorganisms. They inhibit microbial growth by slowing down metabolism but do not necessarily kill the organism. Temperatures above the maximum usually have a cidal action, since they denature microbial enzymes and other proteins. Temperature is a very common and effective way of controlling microorganisms.
 
1. High Temperature
 
Vegetative microorganisms can generally be killed at temperatures from 50°C to 70°C with moist heat. Bacterial endospores, however, are very resistant to heat and extended exposure to much higher temperature is necessary for their destruction. High temperature may be applied as either moist heat or dry heat.
 
a. Moist heat
 
Moist heat is generally more effective than dry heat for killing microorganisms because of its ability to penetrate microbial cells. Moist heat kills microorganisms by denaturing their proteins (causes proteins and enzymes to lose their three-dimensional functional shape). It also may melt lipids in cytoplasmic membranes.
 
1. Autoclaving
 
Autoclaving employs steam under pressure. Water normally boils at 100°C; however, when put under pressure, water boils at a higher temperature. During autoclaving, the materials to be sterilized are placed under 15 pounds per square inch of pressure in a pressure-cooker type of apparatus. When placed under 15 pounds of pressure, the boiling point of water is raised to 121°C, a temperature sufficient to kill bacterial endospores.
 
The time the material is left in the autoclave varies with the nature and amount of material being sterilized. Given sufficient time (generally 15-45 minutes), autoclaving is cidal for both vegetative organisms and endospores, and is the most common method of sterilization for materials not damaged by heat.
 
2. Boiling water
 
Boiling water (100°C) will generally kill vegetative cells after about 10 minutes of exposure. However, certain viruses, such as the hepatitis viruses, may survive exposure to boiling water for up to 30 minutes, and endospores of certain Clostridium and Bacillus species may survive even hours of boiling.
 
b. Dry heat
 
Dry heat kills microorganisms through a process of protein oxidation rather than protein coagulation. Examples of dry heat include:
 
1. Hot air sterilization
 
Microbiological ovens employ very high dry temperatures: 171°C for 1 hour; 160°C for 2 hours or longer; or 121°C for 16 hours or longer depending on the volume. They are generally used only for sterilizing glassware, metal instruments, and other inert materials like oils and powders that are not damaged by excessive temperature.
 
2. Incineration
 
Incinerators are used to destroy disposable or expendable materials by burning. We also sterilize our inoculating loops by incineration.
 
c. Pasteurization
 
Pasteurization is the mild heating of milk and other materials to kill particular spoilage organisms or pathogens. It does not, however, kill all organisms. Milk is usually pasteurized by heating to 71.6°C for at least 15 seconds in the flash method or 62.9°C for 30 minutes in the holding method.
 
2. Low Temperature
 
Low temperature inhibits microbial growth by slowing down microbial metabolism. Examples include refrigeration and freezing. Refrigeration at 5°C slows the growth of microorganisms and keeps food fresh for a few days. Freezing at -10°C stops microbial growth, but generally does not kill microorganisms, and keeps food fresh for several months.
 
 
 
C. DESICCATION
 
Desiccation, or drying, generally has a static effect on microorganisms. Lack of water inhibits the action of microbial enzymes. Dehydrated and freeze-dried foods, for example, do not require refrigeration because the absence of water inhibits microbial growth.
 
D. OSMOTIC PRESSURE
 
Microorganisms, in their natural environments, are constantly faced with alterations in osmotic pressure. Water tends to flow through semipermeable membranes, such as the cytoplasmic membrane of microorganisms, towards the side with a higher concentration of dissolved materials (solute). In other words, water moves from greater water (lower solute) concentration to lesser water (greater solute) concentration.
 
When the concentration of dissolved materials or solute is higher inside the cell than it is outside, the cell is said to be in a hypotonic environment and water will flow into the cell (Fig. 1). The rigid cell walls of bacteria and fungi, however, prevent bursting or plasmoptysis. If the concentration of solute is the same both inside and outside the cell, the cell is said to be in an isotonic environment (Fig. 2). Water flows equally in and out of the cell. Hypotonic and isotonic environments are not usually harmful to microorganisms. However, if the concentration of dissolved materials or solute is higher outside of the cell than inside, then the cell is in a hypertonic environment (Fig. 3). Under this condition, water flows out of the cell, resulting in shrinkage of the cytoplasmic membrane or plasmolysis. Under such conditions, the cell becomes dehydrated and its growth is inhibited.
 
The canning of jams or preserves with a high sugar concentration inhibits bacterial growth through hypertonicity. The same effect is obtained by salt-curing meats or placing foods in a salt brine. This static action of osmotic pressure thus prevents bacterial decomposition of the food. Molds, on the other hand, are more tolerant of hypertonicity. Foods, such as those mentioned above, tend to become overgrown with molds unless they are first sealed to exclude oxygen. (Molds are aerobic.)
 
E. RADIATION
 
1. Ultraviolet Radiation
 
The ultraviolet portion of the light spectrum includes all radiations with wavelengths from 100 nm to 400 nm. It has low wave-length and low energy. The microbicidal activity of ultraviolet (UV) light depends on the length of exposure: the longer the exposure the greater the cidal activity. It also depends on the wavelength of UV used. The most cidal wavelengths of UV light lie in the 260 nm - 270 nm range where it is absorbed by nucleic acid.
 
In terms of its mode of action, UV light is absorbed by microbial DNA and causes adjacent thymine bases on the same DNA strand to covalently bond together, forming what are called thymine-thymine dimers (see Fig. 4). As the DNA replicates, nucleotides do not complementary base pair with the thymine dimers and this terminates the replication of that DNA strand. However, most of the damage from UV radiation actually comes from the cell trying to repair the damage to the DNA by a process called SOS repair. In very heavily damaged DNA containing large numbers of thymine dimers, a process called SOS repair is activated as kind of a last ditch effort to repair the DNA. In this process, a gene product of the SOS system binds to DNA polymerase allowing it to synthesize new DNA across the damaged DNA. However, this altered DNA polymerase loses its proofreading ability resulting in the synthesis of DNA that itself now contains many misincorporated bases. In other words, UV radiation causes mutation and can lead to faulty protein synthesis. With sufficient mutation, bacterial metabolism is blocked and the organism dies. Agents such as UV radiation that cause high rates of mutation are called mutagens.
 
The effect of this inproper base pairing may be reversed to some extent by exposing the bacteria to strong visible light immediately after exposure to the UV light. The visible light activates an enzyme that breaks the bond that joins the thymine bases, thus enabling correct complementary base pairing to again take place. This process is called photoreactivation.
 
UV lights are frequently used to reduce the microbial populations in hospital operating rooms and sinks, aseptic filling rooms of pharmaceutical companies, in microbiological hoods, and in the processing equipment used by the food and dairy industries.
 
An important consideration when using UV light is that it has very poor penetrating power. Only microorganisms on the surface of a material that are exposed directly to the radiation are susceptible to destruction. UV light can also damage the eyes, cause burns, and cause mutation in cells of the skin.
 
2. Ionizing Radiation
 
Ionizing radiation, such as X-rays and gamma rays, has much more energy and penetrating power than ultraviolet radiation. It ionizes water and other molecules to form radicals (molecular fragments with unpaired electrons) that can disrupt DNA molecules and proteins. It is often used to sterilize pharmaceuticals and disposable medical supplies such as syringes, surgical gloves, catheters, sutures, and petri plates. It can also be used to retard spoilage in seafoods, meats, poultry, and fruits.
 
 
== USING DISINFECTANTS ANTISEPTICS AND SANITIZERS TO CONTROL MICROORGANISMS ==
 
::This section is quoted from [http://student.ccbcmd.edu/courses/bio141/labmanua/lab20/lab20.html BIOL 230 MICROBIOLOGY LABORATORY MANUAL by Dr. G.E. Kaiser, Copyright © Gary E. Kaiser, Updated: March 4, 1999]
 
 
A. DISINFECTANTS, ANTISEPTICS, AND SANITIZERS
 
Disinfection is the elimination of microorganisms from inanimate objects or surfaces, whereas decontamination is the treatment of an object or inanimate surface to make it safe to handle.
 
a. The term disinfectant is used for an agent used to disinfect inanimate objects or surfaces but is generally to toxic to use on human tissues.
 
b. The term antiseptic refers to an agent that kills or inhibits growth of microbes but is safe to use on human tissue.
 
c. The term sanitizer describes an agent that reduces, but may not eliminate, microbial numbers to a safe level.
 
Because disinfectants and antiseptics often work slowly on some viruses - such as the hepatitis viruses, bacteria with an acid-fast cell wall such as Mycobacterium tuberculosis, and especially bacterial endospores, produced by the genus Bacillus and the genus Clostridium,  they are usually unreliable for sterilization - the destruction of all life forms.
 
There are a number of factors which influence the antimicrobial action of disinfectants and antiseptics, including:
 
1. The concentration of the chemical agent.
 
2. The temperature at which the agent is being used. Generally, the lower the temperature, the longer it takes to disinfect or decontaminate.
 
3. The kinds of microorganisms present. Endospore producers such as Bacillus species, Clostridium species, and acid-fast bacteria like Mycobacterium tuberculosis are harder to eliminate.
 
4. The number of microorganisms present. The more microorganisms present, the harder it is to disinfect or decontaminate.
 
5. The nature of the material bearing the microorganisms. Organic material such as dirt and excreta interferes with some agents.
 
The best results are generally obtained when the initial microbial numbers are low and when the surface to be disinfected is clean and free of possible interfering substances.
 
There are 2 common antimicrobial modes of action for disinfectants, antiseptics, and sanitizers:
 
1. They may damage the lipids and/or proteins of the semipermeable cytoplasmic membrane of microorganisms resulting in leakage of cellular materials needed to sustain life.
 
2. They may denature microbial enzymes and other proteins, usually by disrupting the hydrogen and disulfide bonds that give the protein its three-dimensional functional shape. This blocks metabolism.
 
A large number of such chemical agents are in common use. Some of the more common groups are listed below:
 
1. Phenol and phenol derivatives
 
Phenol (5-10%) was the first disinfectant commonly used. However, because of its toxicity and odor, phenol derivatives are now generally used. These include orthophenylphenol, hexachlorophene, triclosan, hexylresorcinol, and chlorhexidine. Orthophenylphenol is the agent in Lysol®, O-syl®, Staphene®, and Amphyl®. Hexachlorophene in a 3% solution is combined with detergent and is found in PhisoHex®. Triclosan is a chlorine-containing phenolic antiseptic very common in antimicrobial soaps and other products. Hexylresorcinol is in throat lozenges and ST-37. A 4% solution of chlorhexidine in isopropyl alcohol and combined with detergent (Hibiclens® and Hibitane®) is a common handwashing agent and surgical handscrub. These agents kill most bacteria, most fungi, and some viruses, but are usually ineffective against endospores. They alter membrane permeability and denature proteins.
 
2. Soaps and detergents
 
Soaps are only mildly microbicidal. Their use aids in the mechanical removal of microorganisms by breaking up the oily film on the skin (emulsification) and reducing the surface tension of water so it spreads and penetrates more readily. Some cosmetic soaps contain added antiseptics to increase antimicrobial activity.
 
Detergents may be anionic or cationic. Anionic (negatively charged) detergents, such as laundry powders, mechanically remove microorganisms and other materials but are not very microbicidal. Cationic (positively charged) detergents alter membrane permeability and denature proteins. They are effective against many vegetative bacteria, some fungi, and some viruses. However, bacterial endospores and certain bacteria such as Mycobacterium tuberculosis and Pseudomonas species are usually resistant. They are also inactivated by soaps and organic materials like excreta. Cationic detergents include the quaternary ammonium compounds such as benzalkonium chloride, zephiran, diaprene, roccal, ceepryn, and phemerol.
 
3. Alcohols
 
70% solutions of ethyl or isopropyl alcohol are effective in killing vegetative bacteria, enveloped viruses, and fungi. However, they are usually ineffective against endospores and non-enveloped viruses. Once they evaporate, their cidal activity will cease. Alcohols denature membranes and are often combined with other disinfectants, such as iodine, mercurials, and cationic detergents for increased effectiveness.
 
4. Acids and alkalies
 
Acids and alkalies alter membrane permeability and denature proteins and other molecules. Salts of organic acids, such as calcium propionate, potassium sorbate, and methylparaben, are commonly used as food preservatives. Undecylenic acid (Desenex®) is used for dermatophyte infections of the skin. An example of an alkali is lye (sodium hydroxide).
 
5. Heavy metals
 
Heavy metals, such as mercury, silver, and copper, denature proteins. Mercury compounds (mercurochrome, metaphen, merthiolate) are only bacteriostatic and are not effective against endospores. Silver nitrate (1%) is sometimes put in the eyes of newborns to prevent gonococcal ophthalmia. Copper sulfate is used to combat fungal diseases of plants and is also a common algicide. Selinium sulfide kills fungi and their spores.
 
6. Chlorine
 
Chlorine gas reacts with water to form hypochlorite ions, which in turn denature microbial enzymes. Chlorine is used in the chlorination of drinking water, swimming pools, and sewage. Sodium hypochlorite is the active agent in household bleach. Calcium hypochlorite, sodium hypochlorite, and chloramines (chlorine plus ammonia) are used to sanitize glassware, eating utensils, dairy and food processing equipment, hemodialysis systems, and treating water supplies.
 
7. Iodine and iodophores
 
Iodine also denatures microbial proteins. Iodine tincture contasns a 2% solution of iodine and sodium iodide in 70% alcohole. Aqueous iodine solutions containing 2% iodine and 2.4% sodium iodide are commonly used as a topical antiseptic. Iodophores are a combination of iodine and an inert polymers such as polyvinylpyrrolidone that reduces surface tension and slowly releases the iodine. Iodophores are less irritating than iodine and do not stain. They are generally effective against vegetative bacteria, Mycobacterium tuberculosis, fungi, some viruses, and some endospores. Examples include Wescodyne®, Ioprep®, Ioclide®, Betadine®, and Isodine®.
 
8. Aldehydes Aldehydes, such as formaldehyde and glutaraldehyde, denature microbial proteins. Formalin (37% aqueous solution of formaldehyde gas) is extremely active and kills most forms of microbial life. It is used in embalming, preserving biological specimens, and in preparing vaccines. Alkaline glutaraldehyde (Cidex®), acid glutaraldehyde (Sonacide®), and glutaraldehyde phenate solutions (Sporocidin®) kill vegetative bacteria in 10-30 minutes and endospores in about 4 hours. A 10 hour exposure to a 2% glutaraldehyde solution can be used for cold sterilization of materials.
 
9. Ethylene oxide gas
 
Ethylene oxide is one of the very few chemicals that can be relied upon for sterilization (after 4-12 hours exposure). Since it is explosive, it is usually mixed with inert gases such as freon or carbon dioxide. Gaseous chemosterilizers, using ethylene oxide, are commonly used to sterilize heat-sensitive items such as plastic syringes, petri plates, textiles, sutures, artificial heart valves, heart-lung machines, and mattresses. Ethylene oxide has very high penetrating power and denatures microbial proteins. Vapors are toxic to the skin, eyes, and mucous membranes and are also carcinogenic. Another gas that is used as a sterilant is chlorine dioxide which denatures proteins in vegetative bacteria, bacterial endospores, viruses, and fungi.
 
 
 
B. EVALUATION OF DISINFECTANTS, ANTISEPTICS, AND SANITIZERS
 
It is possible to evaluate disinfectants, antiseptics, and sanitizers using either in vitro or in vivo tests. An in vitro test is one done under artificial, controlled laboratory conditions. An in vivo test is one done under the actual conditions of normal use.
 
 
C. EFFECTIVENESS OF HAND WASHING


There are 2 categories of microorganisms, or flora, normally found on the hands. Resident flora are the normal flora of the skin. Transient flora are the microorganisms you pick up from what you have been handling. It is routine practice to wash the hands prior to and after examining a patient and to do a complete regimented surgical scrub prior to going into the operating room. This is done in order to remove the potentially harmful transient flora, reduce the number of resident flora, and disinfect the skin.


Actual sterilization of the hands is not possible since microorganisms live not only on the surface of the skin but also in deeper skin layers, in ducts of sweat glands, and around hair follicles. These normal flora are mainly nonpathogenic staphylococci (Lab 15) and diphtheroid bacilli.
{{DIYbio:Top}}

Latest revision as of 21:20, 5 September 2012

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
  • 1.5 - Add 'News' section, move news articles there. jcline@ieee.org 23:40, 23 May 2011 (EDT)
  • 1.6 - Multiple updates to project section jcline@ieee.org 00:20, 6 September 2012 (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.

<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?

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.


""*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 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

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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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---

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

How can I grow and engineer yeast? How can I grow and engineer bacteria?

See DIYBio FAQ: Projects

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 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

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.


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.
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