DIYbio/FAQ: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
m (change "file format" to "database". Makes more sense.)
(Update rev and add template to other locations for obvious navigation)
 
(251 intermediate revisions by 7 users not shown)
Line 1: Line 1:
'''DIYbio FAQ v1.1''': ''"The biohacker's FAQ"''
{{DIYbio:Top}}


: Please '''update this FAQ mercilessly with Q&A !'''


 
This Frequently Asked Questions document is for the [http://groups.google.com/group/diybio DIYBio mailing list].  ''This FAQ is now split into multiple topics for easier reading.''
 
This Frequently Asked Questions document is for the '''[http://groups.google.com/group/diybio DIYBio mailing list]'''.




Line 12: Line 9:
* 1.0 - copied on 4/7/2009 from [http://heybryan.org/mediawiki/index.php/DIYbio_FAQ heybryan.org...DIYbio_FAQ]
* 1.0 - copied on 4/7/2009 from [http://heybryan.org/mediawiki/index.php/DIYbio_FAQ heybryan.org...DIYbio_FAQ]
* 1.1 - some updates to clarify original version
* 1.1 - some updates to clarify original version
* 1.2 - new sections, add papar about agar DOI:10.1007/BF00152620 --'''[[User:Jonathan Cline|jcline@ieee.org]] 12:28, 16 September 2009 (EDT)'''
* 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]]'''
* 1.4 - 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? =
Line 18: Line 19:




DIYbio is a distributed community of amateur biologists (or bioengineers) and professional biologists (or bioengineers). Our activities range across a broad spectrum, from molecular naturalism (sequencing part of your own genome or bacterial populations) to biological engineering (RFP lactobacillus -> melanometer) to building low-cost, open-source alternative lab equipment (Gel Box 2.0).
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>
<html>
Line 27: Line 27:
</html>
</html>


* [http://diybio.org/blog blog]
* [http://diybio.org/blog DIYBio blog]
* [http://friendfeed.com/rooms/diybio friendfeed]
* [http://friendfeed.com/rooms/diybio DIYBio friendfeed]
* [http://twitter.com/DIYbio twitter feed]
* [http://twitter.com/DIYbio DIYBio twitter feed]




== What is DIYbio's mission? ==
== What is DIYbio's mission? ==
== Are we moving to a future where everyone performs a little genetic engineering? ==
== Who is a "biohacker"? ==
* [http://groups.google.com/group/diybio/browse_frm/thread/9faf557af36e1fd7/8e22f6f5133c0138?#8e22f6f5133c0138 What do people think of when they think of a typical biohacker?]
* probably in the sense of the [http://en.wikipedia.org/wiki/Hacker_(programmer_subculture) subculture] (more broadly, [http://en.wikipedia.org/wiki/Hacker_culture Hacker culture])
* combines the hacker ethic of biologists, programmers, DIY enthusiasts, etc.
* [http://en.wikipedia.org/wiki/Hacker_ethic Hacker ethic of the Homebrew Computer Club]
* [http://en.wikipedia.org/wiki/Free_software_movement Free software movement]
* people who enjoy "hacks".
** GNU is a hack: a recursive acronym for "GNU is Not Unix".
* might be somewhat related to [http://biopunk.org/ biopunk].


= How can I get involved? =
{{DIYbio:Top}}
Many ways! Here's a brief overview:
* [http://groups.google.com/group/diybio mailing list] (most activity) (note the [http://groups.google.com/group/diybio/browse_frm/thread/4c50d46c5d74b2eb discussion on the list's standards])
* IRC (#diybio on irc.freenode.net)
* local groups


So far, we mainly communicate through the [http://groups.google.com/group/diybio mailing list]. There is also a lower volume [http://groups.google.com/group/diybio-announce DIYbio announce] mailing list, which occassionally has announcements that the community might be interested in. Also, there are groups for:


*[http://groups.google.com/group/diybio-SF San Francisco]
""*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. ""
*[http://groups.google.com/group/diybio-chicago Chicago]
:: -- Len Sassaman, DIYbio google group
*[http://groups.google.com/group/diybio-nyc New York] (city)
*[http://groups.google.com/group/diybio-london London]
*[http://groups.google.com/group/diybio-boston Boston].
*The main list is (as mentioned above) [http://groups.google.com/group/diybio DIYBio mailing list]


You're welcome to subscribe to the mailing lists- in fact, we encourage it. Follow [http://www.netmeister.org/news/learn2quote.html conventional netiquette] rules. Historically, the main DIYbio mailing list hasn't really set its foot down regarding top versus bottom posting (or even side posting or diagonal posting). Please do be kind and trim your replies. Meredith also asks that users change the subject of their emails when they hijack a thread. Thanks.
== 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? ==


There are other forums:
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.''
*[http://biopunk.org/ biopunk.org]
*[http://diybioforum.org/ diybioforum.org]
*[http://www.sciencemadness.org/talk/ sciencemadness.org]
*[http://www.roguesci.org/theforum/index.php roguesci.org]
*''please expand this list''


= Is there a group in my area? =
Regarding whether genetic engineering is safe for hackers or for everyone, the group invites discussion.  There are the key points:
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 [http://diybio.org/local/ diybio.org/local].


<html>
* There are many unknowns in genetic engineering ("We don't know").
<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>.
* There are many more unknowns than we currently know are unknown ("We don't know what we don't know").
</html>


You may also be interested in other local science groups around the world:
* 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").
*[http://dorkbot.org/ dorkbot group] ("people doing strange things with electricity")
*[http://hackerspaces.org/wiki/List_of_Hacker_Spaces hackerspace].
*''please expand this list''


== Are there any videos from regional groups? ==
* There are unknown risks if genetic engineering experiments escape into the wild ("We don't know").
=== DIYbio-NYC: Shot glass DNA extraction ===
<youtube align="left">s2HPVs25HlY</youtube> <html><div style="clear:both;"></div></html>
=== DIYbio-SF: Tito's food coloring electrophoresis ===
<youtube align="left">wIzkiqCp4NQ</youtube> <html><div style="clear:both;"></div></html>
=== DIYbio-boston: diybio visits the fablab ===
<youtube align="left">oQ3BRKAsG0I</youtube> <html><div style="clear:both;"></div></html>


= Where can I see an archive of previous DIYbio discussions and questions? =
'''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.''
Right over [http://groups.google.com/group/diybio here].


Some of our favorites ("member picks") include discussions on ..
'''Readers are encouraged to watch the documentary, "The Future of Food" on Hulu: http://www.hulu.com/watch/67878/the-future-of-food '''
* [http://groups.google.com/group/diybio/browse_frm/thread/596dab589267bedf/67bdbb445ad435d9?#67bdbb445ad435d9 Public perception]
* your favorite thread here


* 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


= What are some educational resources? =
* 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. ""


There are many biology and science resources on the net, especially with universities providing "open course ware" for viewing or download. Here are a few university-sponsored educational resources which apply to biohacking.
* 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). ""


* MIT OpenCourseWare (also on iTunes)
* UC Berkeley educational webcasts: Biology, Chemistry, Chemical Engineering, etc.
* Many universities are hosting classes (such as Biology) on YouTube


Here are a few industry-sponsored or non-profit-sponsored educational resources which apply to biohacking.


* A SHORT COURSE ON SYNTHETIC GENOMICS, Edge Master Class 2009, George Church & J. Craig Venter.  http://www.edge.org/documents/archive/edge296.html
=== What are the social, ethical, legal/patent implications of DIY Bio or home genetic engineering? How might it be best to create more social, ethical, legal/patent discussion? ===


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


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


= What is synthetic biology and related technology? =
* 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>


: Synthetic Biology: A Definition <sup>[From Davidson College's Synthetic Biology Seminar in the Fall of 2007]</sup>
* '''Webcasts'''
:: [[Synthetic biology]] refers to the design and construction of novel biological systems. Applying an engineering approach to biology, this emerging field provides an opportunity to: 1) develop new organisms that are capable of performing useful functions and 2) test our understanding how complex biological systems work.
** 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'''
:: In 1978, the Nobel Prize in Medicine went to Werner Arber, Daniel Nathans, and Hamilton O. Smith for the discovery of restriction enzymes. This discovery marked the beginning of recombinant DNA technology and genetic engineering. Researchers now had the ability to modify the genomes of organisms by cutting and pasting segments of their DNA. For years, genetic engineers have made slight genome modifications in organisms, either by the insertion or deletion of one or two genes, in order to observe phenotypic changes. More recently, as our knowledge of biological systems has grown, the new field of synthetic biology has begun to steal the spotlight. This field builds on the principles of genetic engineering, but attempts to modify genomes on a much larger scale. Instead of inserting or deleting one or two genes, synthetic biologists use recombinant DNA technology and, increasingly, artificial DNA synthesis to introduce whole gene networks into organisms. Because of its complex nature, synthetic biology brings together many different disciplines such as biology, math, engineering and chemistry to try to engineer genomes using preexisting and new biological systems and components. Mathematical modeling enhances the design of synthetic systems before implementation in the wet lab. The possible areas of influence for such biological devices are seemingly infinite, ranging from the production of reusable biofuels to the treatment of some or all cancers. The ultimate goal of synthetic biology is to both build novel (new) biological systems and to create a better understanding of existing ones.  
** ''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.


: Also see http://syntheticbiology.org/FAQ.html


Other Papers:


== Drew Endy - Informal - Broad overview ==
* 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
<youtube align="left">XIuh7KDRzLk</youtube> <html><div style="clear:both;"></div></html>
* 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


Professor Drew Endy explains that Synthetic Biology techniques are built on top of the foundational technologies of [[genetic engineering]] ([[PCR]], oligonucleotides, and [[DNA sequencing]]) and are include abstraction, standardization (i.e., [http://biobricks.org/ biobricks]), and automated [[DNA synthesis]]. Insulation and Standard Measurement Units (i.e. signal carriers) in biological systems are also significant interests in current synthetic biology research. See also [http://syntheticbiology.org/ syntheticbiology.org].
* 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. ""


== What are biobricks? ==
* ""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


BioBricks can be described as Lego blocks for building biological systems.  However they are in "alpha" state and do not yet work for building arbitrary biological systems.  Research needs to be completed and this research will take at least another decade <sup>[1st hand quote from personal conversation with BioBricks founders -- jcline]</sup>.  As of 2009, less than five Biobrick parts have been characterized with reliable and quantifiable behavior.
=== Are there Historical Precedents or Prior Cases which have Demonstrated these Issues? ===


* http://biobricks.org/
==== U.S. ====
* http://partsregistry.org/


=== What is iGEM? ===
DIY/homebrew chemistry is already adversely affected by the War on Drugs via government regulations intended to limit manufacture of methamphetamine.
iGEM, the international genetically engineered machine competition, is the premiere undergraduate synthetic biology conference in the world using and developing Biobricks.  iGEM teams have been testing and realizing the principles of synthetic biology on a massive scale for the last 5 years, illustrating the viability of garage biotechnology.  Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells.  Check out [http://igem.org igem.org] or [http://wikipedia.org/en/wiki/iGEM wikipedia] for more info.


== See also ==
  There is a really interesting parallel between potential DIYbio
* [http://syntheticbiology.org Syntheticbiology.org] Join this mailing list (it's worth it).
  regulations and attempts to quash meth production in America. Biotech-
* [http://parts2.mit.edu/wiki/index.php/Main_Page Internationally Genetically Engineered Machines Competition] (see [[iGEM]])
  commentator Robert Carlson published an article in 2008 (
* [http://biobricks.org/ The BioBricks Foundation] (see [[biobricks]])
  http://www.springerlink.com/content/n211746672413507/ ) which confirms
* [http://parts.mit.edu/ Registry of Standard Biological Parts]
  the point you mention--mom and pop (drug-manufacturing) outfits changed into cartels across
* [http://arep.med.harvard.edu/SBP/ List of synthetic biology projects]
  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


= Videos =
See [[DIYbio/Videos]] for a collection of DIYbio, iGEM, and Synthetic Biology videos. For background history on the free software movement, GNU, Richard Stallman, Linus Torvalds, and others, consider watching the freely available video, "[http://video.google.com/videoplay?docid=7707585592627775409 Revolution OS]" ([http://www.revolution-os.com/ official site]). [http://en.wikipedia.org/wiki/Revolution_OS Wikipedia says]: "Directed by [http://en.wikipedia.org/wiki/J._T._S._Moore J. T. S. Moore], the film features interviews with prominent [http://en.wikipedia.org/wiki/hacker_(free_and_open_source_software) hackers] and [http://en.wikipedia.org/wiki/entrepreneurs entrepreneurs] including [http://en.wikipedia.org/wiki/Richard_Stallman Richard Stallman], [http://en.wikipedia.org/wiki/Michael_Tiemann Michael Tiemann], [http://en.wikipedia.org/wiki/Linus_Torvalds Linus Torvalds], [http://en.wikipedia.org/wiki/Larry_Augustin Larry Augustin], [http://en.wikipedia.org/wiki/Eric_S._Raymond Eric S. Raymond], [http://en.wikipedia.org/wiki/Bruce_Perens Bruce Perens], [http://en.wikipedia.org/wiki/Frank_Hecker Frank Hecker] and [http://en.wikipedia.org/wiki/Brian_Behlendorf Brian Behlendorf]."


= Do you recommend any feeds, blogs, wikis, instructables, .. ? =
==== Arizona, 2009 ====


= Safety documentation =
Recent example where a homebrew chemistry project runs into danger due to an accident, perhaps causing larger scrutiny for others in the future.
This section is for safety documentation from external bodies. DIYbio-related safety information should be found elsewhere.


* [http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/ Laboratory Biosafety Guidelines 2004]
  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


= Legal issues =
== Who is a "biohacker"? ==
Are gray. Email safety@diybio.org to get involved in the discussion.
* [http://groups.google.com/group/diybio/browse_frm/thread/9faf557af36e1fd7/8e22f6f5133c0138?#8e22f6f5133c0138 What do people think of when they think of a typical biohacker?]
* probably in the sense of the [http://en.wikipedia.org/wiki/Hacker_(programmer_subculture) subculture] (more broadly, [http://en.wikipedia.org/wiki/Hacker_culture Hacker culture])
* combines the hacker ethic of biologists, programmers, DIY enthusiasts, etc.
* [http://en.wikipedia.org/wiki/Hacker_ethic Hacker ethic of the Homebrew Computer Club]
* [http://en.wikipedia.org/wiki/Free_software_movement Free software movement]
* people who enjoy "hacks".
** GNU is a hack: a recursive acronym for "GNU is Not Unix".
* might be somewhat related to [http://biopunk.org/ biopunk].


* [http://groups.google.com/group/diybio/msg/0816447f7bd9c274 we need to understand and work on LICENSE COMPATIBILITY for software, hardware, and wetware objects and on a SOCIAL CONTRACT for our community that exhorts innovators to use the "OPEN" licenses.]
== How can I find out more and contribute? ==
Many ways! Here's a brief overview:
* [http://groups.google.com/group/diybio mailing list] (most activity) (note the [http://groups.google.com/group/diybio/browse_frm/thread/4c50d46c5d74b2eb discussion on the list's standards])
* IRC (#diybio on irc.freenode.net)
* local groups


== BioBricks (legal stuff) ==
So far, we mainly communicate through the [http://groups.google.com/group/diybio mailing list]. There is also a lower volume [http://groups.google.com/group/diybio-announce DIYbio announce] mailing list, which occassionally has announcements that the community might be interested in. Also, there are groups for:
* [http://biobricks.org/pipermail/legal_biobricks.org/2008-September/000019.html Drew Endy: update on legal matters, including hiring a legal firm]
* [http://biobricks.org/pipermail/legal_biobricks.org/2008-September/000021.html Bootstrapping an open parts collection]
* [http://www.youtube.com/profile?user=BioBricksFoundation&view=videos&query=legal Videos of the BioBrick Foundation talking about legal concerns]


<youtube align="left">l3q3T10GhxI</youtube> <html><div style="clear:both;"></div></html>
*[http://groups.google.com/group/diybio-SF San Francisco]
<youtube align="left">0ufAYS6v_6c</youtube> <html><div style="clear:both;"></div></html>
*[http://groups.google.com/group/diybio-chicago Chicago]
<youtube align="left">w6dG4G-e-l0</youtube> <html><div style="clear:both;"></div></html>
*[http://groups.google.com/group/diybio-nyc New York] (city)
*[http://groups.google.com/group/diybio-london London]
*[http://groups.google.com/group/diybio-boston Boston].
*The main list is (as mentioned above) [http://groups.google.com/group/diybio DIYBio mailing list]


= What's all this about "open", anyway? =
You're welcome to subscribe to the mailing lists- in fact, we encourage it.


This is the desire to continue to apply [http://sciencecommons.org/about/ open source concepts] to biology and related fields for great benefits.
There are other forums:
*[http://biopunk.org/ biopunk.org]
*[http://www.sciencemadness.org/talk/ sciencemadness.org]
*''please expand this list''


"Open" means sharing the biological protocols, the instructions for building the equipment and sources of the materials, the directions for using the equipment, the source code of the software used for the equipment, the raw data from the experiment, the results and any other aspects of the experimental process, in a digital format, on the internet.  All of this sharing occurs under typical information technology process (such as on a wiki, or source control, or open database) so that revisions of documents and data can be compared or copied to a new method (called "branching" in software terms).  The sharing can be performed under a variety of [http://creativecommons.org/about/licenses/ permissions such as open source licenses] which allow others to re-use, modify and distribute their own designs of the technology.  Benefits:
== Guidelines for Posting ==
* Patents. By using "Open" methods, [http://www6.miami.edu/ethics/jpsl/archives/papers/biotechPatent.html patent lockup (a big complaint in biotechnology)] is reduced. The hope is that "Open" will energize innovation in biology similarly to how "Open" has performed in computer/software engineering. 
* Collaboration.  Even nearing 2010, much of the raw data, working methods, or equipment improvements in biology are kept in hand-written lab notebooks in biology labs, so there are large gains to be made by moving towards "Open".  Access to scientific data can regain openness through open access publishing, as stated in the ''Public Library of Science FAQ'': [http://www.plos.org/about/principles.html Access to the vast majority of scientific and medical literature is currently restricted to those individuals and institutions that can afford to pay for subscriptions. Even though the vast majority of the research is publicly financed, access to research literature—the product of that research—is not freely and publicly available. Even institutions find it increasingly difficult to provide access to all the journals that their communities need. The Internet makes it possible to provide access to the literature to anyone in the world who has an Internet connection.]
* Re-use and cost.  As biology is inherently self-reproducing, it has the ability to make low-cost copies of itself for users.  The copies may also allow modification and re-design.


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


Background and References:  
Please:


* [http://www.synbioproject.org/events/archive/opensource/ Synthetic Biology: Feasibility of the Open Source Movement].
* Follow proper quoting rules:
* [http://onthecommons.org/content.php?id=436 A New Movement for Open Source Biology Is Launched. 16 Dec 2004].
<pre>
* [http://rsss.anu.edu.au/~janeth/OpenSourceBiotechnology27July2005.pdf J Hope, Open Source Biotechnology (PhD Thesis), The Australian National University, Canberra, 2004].
  One should reply using the standard technique:
::''Dramatic recent expansion of intellectual property protection in the field of biotechnology has led to concerns that ongoing innovation will be blocked unless actionis taken to preserve access to and freedom to operate with those tools that are important for further research and development.''
* [http://synthesis.cc/2007/03/thoughts-on-open-biology.html Thoughts on Open Biology, Rob Carlson, March 2, 2007]. [http://www.synthesis.cc/Biol_Tech_2050.pdf "Biological Technology in 2050", Robert Carlson, 2001].
:: ''A great deal of the innovation we need to see will not come from academia or existing corporations, but from people noodling around in their garages or in start-ups yet to be founded.''


-- *'''[[User:Jonathan Cline|jcline@ieee.org]] 13:40, 23 August 2009 (EDT)'''
    User C. wrote:
    > User B. wrote:
    > > User A. wrote:
    > > > blablabla
    > > blubberblubber
    > laberlaber


= What equipment do I need to perform DIYBio-related projects? =
    Your Thoughtful Reply Goes Here.
</pre>


* Basic biology equipment (see [http://adl.serveftp.org/skdb/doc/BOMs/pcr here] for PCR equipment, however much of the equipment isn't actually required)
For complete information on quoting, see [http://www.netmeister.org/news/learn2quote.html conventional netiquette].
** or generic tools used in other projects, just use it for biology (see MacGyverisms below)
* When quoting another author, keep the attribution line ("On such-and-such-date, Jonathan Cline wrote:").
* Basic computer equipment
** Delete portions of the paragraph which do not pertain to the new reply.  This is known as ''Trimming the post''. 
* Perhaps some open source software development tools
** 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.


== What equipment is in a basic biology lab ==
Please see the following Internet reference for complete information:
.. and how can I make it?
* http://www.faqs.org/rfcs/rfc1855.html


Would you like to contribute to an answer for this question? Run around a lab that you have access to and document all of the equipment that you see, or remember, etc. It's ok if some of the equipment is ridiculous (like 100k+ RPM centrifuges), because we can filter that out later and reduce the lists down to equipment in a basic biology lab.
== Where can I see an archive of previous DIYbio discussions and questions? ==


* [http://groups.google.com/group/diybio/browse_frm/thread/b014b25110c9922c/e9a22564708172df?#e9a22564708172df Using ebay to set up a molecular bio lab for less than $1k USD] (see also [http://www.boingboing.net/2009/04/09/howto-set-up-a-molec.html] and [http://scienceblogs.com/worldsfair/2009/04/using_ebay_to_set_up_a_molecul.php])
The [http://groups.google.com/group/diybio DIYbio google group mailing list] is hosted from Google Groups which allows reading prior discussions.


== MacGyverisms ==
Some of our favorites ("member picks") include discussions on ..
* [http://groups.google.com/group/diybio/msg/048ce958697fe6ba Cheap technology for biology]
* [http://groups.google.com/group/diybio/browse_frm/thread/596dab589267bedf/67bdbb445ad435d9?#67bdbb445ad435d9 Public perception]
* [http://groups.google.com/group/diybio/msg/a07ba5d01c61aa09 CO-2 rich environment in a ziplock baggie]
* your favorite thread here
* gel electrophoresis in a straw (keiki gels)
** [http://groups.google.com/group/diybio/msg/03a955483651a05c one of the original 'idea posts']
** [http://groups.google.com/group/diybio/browse_frm/thread/c77e9e5290e57383/4ab47e86c1eecc56?#4ab47e86c1eecc56 Keiki gels: Gel electrophoreis in a straw] (it works!)
*** [http://www.boingboing.net/2009/02/06/crowdsourced-science.html boingboing'd]
** [http://openwetware.org/wiki/DIYbio:Notebook/Keiki_Gels very basic protocol]
* inkjet, laser printer, wax, ice-lithography, sharpie, or other forms of diy microfluidics
* [http://www.instructables.com/id/5_minute_DNA_Extraction_in_a_Shot_Glass/ 5 minute DNA extraction in a shot glass]


== Where can I find auctions for biotech? ==


* [http://www.equipnet.com equipnet]
== Is there a group in my area? ==
* [http://ebay.com/ ebay]
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 [http://diybio.org/local/ diybio.org/local].
* [http://www.go-dove.com/ go-dove]
* [http://labx.com/ labx]
* ''please expand this list''


== How can I make a spectrophotometer? ==
<html>
* [http://openwetware.org/wiki/Citizen_Science/The_Urinomics_Project urinomics project] (the design might be a little broken at the moment)
<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 />


== How can I make an atomic force microscope (AFM)? ==
<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>.
* [http://groups.google.com/group/diybio/browse_thread/thread/e3ea9182fe618a71 How to use plastic printed parts to do a DIY AFM]
</html>
* AFM != STM


== How can I make a sterile environment? ==
You may also be interested in other local science groups around the world:
*[http://dorkbot.org/ dorkbot group] ("people doing strange things with electricity")
*[http://hackerspaces.org/wiki/List_of_Hacker_Spaces hackerspace].
*''please expand this list''


=== Using Ultraviolet (UV) for sterilization ===
== 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/


Here is a [http://www.uvp.com/pdf/ab-115.pdf table of how much UV exposure it takes to kill various organisms and bacteria]. Note units are in microwatt-seconds per cm2. Specs for UV lamps usually give emission as microwatts per cm2 measured at a distance of 1 m from the lamp.
=== DIYbio-NYC: Shot glass DNA extraction ===
<youtube align="left">s2HPVs25HlY</youtube> <html><div style="clear:both;"></div></html>
=== DIYbio-SF: Tito's food coloring electrophoresis ===
<youtube align="left">wIzkiqCp4NQ</youtube> <html><div style="clear:both;"></div></html>
=== DIYbio-boston: diybio visits the fablab ===
<youtube align="left">oQ3BRKAsG0I</youtube> <html><div style="clear:both;"></div></html>


Do not leave UV lamps on for long periods of time because the bulbs "wear out".  Specifically, the amount of UV produced will decrease over time (see manufacturer spec sheets).  With extended use, it may seem that the bulb is creating a sterile environment when actually it is not producing enough UV.
---


Warning:  UV spectrum of sterilization bulbs are bad for you.  Do not expose yourself to the UV.  If you build a UV "hood", add a switch which always turns the light off when the door is opened.
=== Bio-Artist Multimedia ===




== Chemicals and Reagents are expensive. How can I make my own?  What can I substitute? ==
: '''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


=== Substitutes for Expensive Agarose ===
== What does a Garage Lab look like? ==


==== Using Agar instead of Agarose ====
http://farm3.static.flickr.com/2478/4044058001_71291f7196_m.jpg


:"We have recently attempted to find an inexpensive alternative to agarose  for analytical purposes. We observed that agar is an adequate support medium for gel electrophoresis (Fig 1).  [...] These included Difco Bacto-Agar (Detroit, U.S.A.), Merck Agar-Agar (Darmstadt, Germany), Oxoid agar (London, UK.), Biolab Agar (Halfway House, R.S.A.), Bitek Agar (Detroit, U.S.A.) and bulk agar obtained from New Zealand. All these agar formulations gave good separation of our DNA ... Conclusion: ... agar can be used as a gel matrix in place of agarose in many instances. We do not recommend using agar if the DNA is to be purified from a gel. We have attempted experiments involving the southern blotting technique using agar as our gel matrix. Our results were, however, unsatisfactory. We therefore recommend that agar gels can be used as a cheap altelnative to agarose to check the purity, size and amount of DNA in a sample."
:'''Post pictures of your own home laboratory setup, and view some: http://www.flickr.com/groups/diylabs/ '''
:: From: AGAR, AN ALTERNATIVE TO AGAROSE IN ANALYTICAL GEL ELECTROPHORESIS, BIOTECHNOLOGY TECH, CD. Viljoen, B.D. Wingfield* and M.J. Wingfield Volume 7 No.10 (October 1993) pp723-726. DOI:10.1007/BF00152620
::-- From Raymond McCauley, DIYbio google group


:"The other option is to wash with two changes of EDTA (think it was 25mM) to remove divalent metals and sulfonated (non-gelling) agar. There is also a process based on alcohol washes - but can't find my reference to it." -- Abizar on DIYBio google group


=== Using Other Substitutes for Agarose ===
== Has DIYbio been in the news? ==
Yes.  Frequently!  '''See [[DIYbio/FAQ/News|In The News]] for a significant list of articles.'''


:Table lists starches & flours:
= What are some educational resources for DIYBio and Biology? What are all these terms and technologies DIYBio keeps discussing? =
:: [http://heybryan.org/books/papers/graph1_alternate_agar_formula.png Table: Alternate to Agar]


:"Silica gel is another possible solidifying agent. Likely totally inert, and stable at high temperatures for thermophiles. "  -- Tom Knight, diybio google group
See [http://openwetware.org/wiki/DIYbio/FAQ/Educational DIYBio FAQ: Education & Resources]


:"None of those (in the 'starches & flours' table) work (well).  Agar is clear and indigestable by bacteria, none of those replacements have those properties. Guar gum is the only substitue worth trying, but from what I understand it's a LOT harder to work with.  For the price of food grade agar it just isn't worth trying to save money.  Food grade works great for everything I've tried and you can get it pretty dang cheap online." -- Jake, diybio google group
== How can I grow and engineer yeast? How can I grow and engineer bacteria? ==


=== How do you purify agar? ===
See [http://openwetware.org/wiki/DIYbio/FAQ/Projects DIYBio FAQ: Projects]


:"here is a good washed agar protocol, cleans up contaminants. It involves acetone, easy to find at home depot, but dont be smoking. Also the washed agar will gel at a lower concentration, 1% instead of 1.5% or 2%. As store bought stuff is less pure than Difco, it would certainly benefit more from cleaning. I have only done the second protocol."  http://www.fgsc.net/neurosporaprotocols/How%20to%20wash%20agar.pdf -- Tom on the diybio google group
= What equipment do I need to perform DIYBio-related projects? =
 
:"Soak agar shreds or granules in "several changes" of distilled water (DI).  Make a 4% gel, slice, dialyze or electrodialyze it, then use that to make a more dilute gel (no specified dilution) through reheating. Alternatively- dry and dissolve flakes later as needed.  Dissolve agar "in the solvent to be employed," and hot-filter through several layers of "lintless gauze, coarse filter paper, shredded paper or diatomaceous earth, or centrifuge at high speed (eg, 5000 g) for 10 mins in a rotor pre-heated to 80 C" (small volume technique: pull into 10 mL pipette with loose cotton plug. Remove plug and deliver to plate or slide).  Make agar gel from this, then chil, freeze, and thaw it to disrupt gel and "express the water and dissolved impurities." The reader is referred to Crowle 1961 (first edition of Immunodiffusion) for more detailed explanations."
::From Crowe's "Immunodiffusion," 2nd ed., 1973
:::-- AJ, diybio google group
 
:Preparation of agarose with cetylpyridinium chloride "or other tertiary ammonium compounds."
::From Clausen in "Laboratory Techniques in Biochemistry and Molecular Biology" (volume 1, part 3, edited by Burdon and Knippenberg)
:::-- AJ, diybio google group
 
:"There was another text- it mostly consisted of making slabs of gel that are then allowed to sit in distilled water, which is changed every day for a week or more."
:: Maybe from "Handbook of Immunoprecipitation-in-Gel Techniques," edited by Axelson (1983).
:::-- AJ, diybio google group
 
 
 
* Much of the above is distilled from the thread: [http://groups.google.com/group/diybio/browse_thread/thread/3d7e7d6424e0d2a6/bbab3ffcb5b7913e agar purification recipes]


=== How to Make Taq ===
See [http://openwetware.org/wiki/DIYbio/FAQ/Equipment  DIYBio FAQ: Equipment]




:*'''[[User:Jonathan Cline|jcline@ieee.org]] 10:38, 14 July 2009 (EDT)''': From the list:
::Taq is super easy to purify, you don't need a column.  If you want Taq to use in PCR, you can just grow the plasmid with the DeltaTaq insert (available from ATCC), and heat the crude lysate. If you want to clean it up a bit more, for example for an enzymatic study, try this protocol: ''Rapid purification of high-activity Taq DNA polymerase Pluthero Nucl. Acids Res..1993; 21: 4850-4851'' -Stacy


= Are there any plans for a DIYbio-friendly, open source database system for biology protocols, how-tos and hardware/equipment construction? =
== What is open source hardware? ==
Yes, absolutely. You should consider contacting [http://heybryan.org/ Bryan Bishop] about this. There is also a lot of reading material distributed throughout the web on this topic.


* [http://adl.serveftp.org/lab/presentations/updates-from-austin.pdf Updates from Austin, TX] related to diybio packaging standards (2009-08-13).
* [http://heybryan.org/om.html An index of threads related to open manufacturing] and standardized packaging of open source hardware projects
* [http://groups.google.com/group/openmanufacturing/msg/1fc4fbbfd4a6fb23 Recipe representation]
* [http://groups.google.com/group/diybio/browse_frm/thread/ada2289ebbc00fe0/6081750dd0eb5de1?lnk=gst&q=pcr.xml#6081750dd0eb5de1 Recipe representation as it concerns DIYbio]
* [http://groups.google.com/group/diybio/msg/de9db7503c48c5c2 More on recipe representation] (especially re: an [[Open Thermocycler|open thermocycler project]])
* [http://groups.google.com/group/diybio/msg/ed52133e3c681100?dmode=source More on protocols and hardware packaging formats] (2009-04-15) (see also [http://groups.google.com/group/diybio/msg/4a7c4208682b9dfe?dmode=source Meredith's notes])
* ''please expand this list''


= What is open source hardware? =
http://p2pfoundation.net/Open_source_hardware
http://p2pfoundation.net/Open_source_hardware


Line 319: Line 343:
* [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]


= Has DIYbio been in the news? =
=== Open Source Ecology ===
Yes.
 
* 2009-08-01: [http://www.the-scientist.com/2009/08/1/17/1/ Am I a biohazard?] (The Scientist)
* June 2009 issue of [http://hplusmagazine.com/ hplusmagazine]
* 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
 


= Keiki gels (gels-in-a-straw) MiniFAQ =
Open source hardware includes large systems.
* [http://groups.google.com/group/diybio/msg/03a955483651a05c one of the original 'idea posts']
* [http://groups.google.com/group/diybio/browse_frm/thread/c77e9e5290e57383/4ab47e86c1eecc56?#4ab47e86c1eecc56 Keiki gels: Gel electrophoreis in a straw] (it works!)
** [http://www.boingboing.net/2009/02/06/crowdsourced-science.html boingboing'd]
* [http://openwetware.org/wiki/DIYbio:Notebook/Keiki_Gels very basic protocol]


== Do all of the straws run at the same rate? ==
  This is Chris Fornof with Open Source Ecology, http://opensourceecology.org
"I think the key there will be making sure that all the straws are exactly the same length -- each straw behaves like a resistor, so just like any other resistive material, a greater amount of material will mean a higher resistance (and thus lower current at constant voltage)." -- [http://groups.google.com/group/diybio/msg/09e4bcf12548501a Meredith]
  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


== How do you strain for DNA in a straw? ==
= Projects =
"Easiest way to do that would be to use a stain that you add to the warm agarose before pouring, such as SYBR Safe or GR Safe (or ethidium bromide, but the cool kids don't use that anymore). I suppose you could slit the straw open with a razor blade if you wanted to use methylene blue, but that sounds like a huge pain in the ass." -- [http://groups.google.com/group/diybio/msg/09e4bcf12548501a Meredith]


= What equipment do I need to perform experiment XYZ? =
== 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? ==
Just run it through the handy "checktools" program. ((Note: the idea here is that once the pcr.xml file makes a few friends with other protocols, software can then be written to extract a list of tools from the standardized protocol format. But this doesn't exist yet, since we only have "pcr.xml".))


= DIY Genetic engineering =
See [http://openwetware.org/wiki/DIYbio/FAQ/Projects DIYBio FAQ: Projects].
* [http://groups.google.com/group/diybio/browse_frm/thread/0bc28b8116eb254c# Basic questions on genetic engineering]
* [http://groups.google.com/group/diybio/msg/284f254d52930b4c Notes on gene vectors and miRNAs (gene silencing)]
* [http://groups.google.com/group/diybio/msg/35e5dce66a713308 Gene naming, homologous sequence similarity]
* [http://groups.google.com/group/diybio/msg/7088d103c90e59c5 Genetic engineering (in general)]


== Discussion of Organisms for DIY Genetic Engineering ==
::''Please add your own project info to the [http://openwetware.org/wiki/DIYbio/FAQ/Projects DIYBio FAQ: Projects] topic!''


See the group discussions and the [http://groups.google.com/group/diybio/web/diybio-model-organisms diybio model organisms] list.
Candidates are:
*Psychomitrella patens (a moss that is naturally competent)
*Halobacterium  NRC1 (grows in very salty media)
*Acinetobacter baylyi ADP1
=== ADP1 ===
ADP1 has been considered a good candidate for DIY Genetic Engineering
because it is naturally competent.
From the list:
: ''I developed ADP1 as a model organism for simple genetic engineering
while at Scripps. The paper appears under my name in Nucleic Acids
Research (5780–5790 Nucleic Acids Research, 2004, Vol. 32, No. 19
doi:10.1093/nar/gkh881). When I did the work, ADP1 was considered A.
calcoaceticus, and was given a clean bill of health (biosafetly level
1). Later, to my dismay, it was collapsed into A. baylyi, grouping it
with nasty pathogens and making it thereby less accessible. My
interpretation: they probably are all the same species, technically,
but Acinetobacter's predisposition for collecting genes from outside
sources (which is exactly what makes it so useful - read the paper),
led some strains to collect a bunch of virulence factors and become
superbugs, like the ones that plague hospitals. If you can get some
ADP1, I would consider it as safe as Ec K-12, but be very careful with
less well-characterized strains of this species, because it can and
will pick up genes that offer an adaptive advantage in it's
environment, so you never know what a wild-type Acinetobacter might be
capable of.''  - dmetzgar 
= DNA synthesis MiniFAQ =
* [http://groups.google.com/group/diybio/msg/f2d636339a6e9c4d DIY DNA synthesis and bibliography]
* [http://groups.google.com/group/diybio/msg/5f77c7fab381e5ed DLP projector based gene synthesizer proposal]
* [http://groups.google.com/group/diybio/msg/6676a7ec80d37ef9 Some ranting notes on schemes for microfluidic DNA synthesizers]
* [http://groups.google.com/group/diybio/msg/52b93a96a4927e45 Sequencing and synthesis predictions for 2010 from 2003]
* [http://groups.google.com/group/diybio/msg/912e485da761b3c6 Synthesis of unnatural nucleic acids (like GNA)]
* [http://groups.google.com/group/diybio/msg/70bea2b53b7716af Short bibliography of DIY-friendly DNA synthesis techniques]
* [http://groups.google.com/group/diybio/msg/6feeeb29e4d5bc3a Notes towards DIY DNA synthesis and the synthesis of photolabile protecting groups from kitchen household products]
* [http://heybryan.org/books/papers/phosphoramidites/origin_of_oligonucleotide_impurities_and_errors.txt Origins of oligonucleotide impurities and errors]
== Can I order DNA over the internet? ==
mrgene, e-oligos, geneoracle, etc.
== What are oligonucleotides? ==
[http://en.wikipedia.org/wiki/Oligonucleotides Wikipedia sez]: "An oligonucleotide is a short nucleic acid polymer, typically with twenty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of the oligonucleotide is usually denoted by "mer" (from Greek meros, "part"). For example, a fragment of 25 bases would be called a 25-mer. Because oligonucleotides readily bind to their respective complementary nucleotide, they are often used as probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. Oligonucleotides composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction, a procedure that can greatly amplify almost any small piece of DNA. There, the oligonucleotide is referred to as a primer, allowing DNA polymerase to extend the oligonucleotide and replicate the complementary strand."
== How are oligonucleotides synthesized? ==
Oligonucleotide synthesis is done via a cycle of four chemical reactions that are repeated until all desired bases have been added:
*Step 1 - De-blocking (detritylation): The DMT is removed with an acid, such as [http://en.wikipedia.org/wiki/Trichloroacetic_acid TCA] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/SIAL/T4885 get it at Sigma-Aldrich]), and washed out, resulting in a free 5' hydroxyl group on the first base.
*Step 2 - Base condensation (coupling): A '''phosphoramidite nucleotide (or a mix)''' ([http://www.csun.edu/~hcbio027/biotechnology/lec3/pitt8.html struct], [http://www.bhk-lab.com/publications/2003/69.pdf synthesis of phosphoramidite building blocks] [pdf]) is activated by [http://en.wikipedia.org/wiki/Tetrazole tetrazole] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/FLUKA/88185 get]) which removes the iPr2N group on the phosphate group. After addition, the deprotected 5' OH of the first base and the phosphate of the second base react to join the two bases together in a [http://en.wikipedia.org/wiki/Phosphite phosphite] linkage. These reactions are not done in water but in [http://en.wikipedia.org/wiki/Tetrahydrofuran tetrahydrofuran] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/ALDRICH/494461 get]) or in [http://en.wikipedia.org/wiki/Dimethyl_sulfoxide DMSO] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/SIGMA/D2438 get]). Unbound base and by-products are washed out.
*Step 3 - Capping: About 1% of the 5' OH groups do not react with the new base and need to be blocked from further reaction to prevent the synthesis of oligonucleotides with an internal base deletion. This is done by adding a protective group in the form of [http://en.wikipedia.org/wiki/Acetic_anhydride acetic anhydride] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/SIAL/539996 get]) and [http://en.wikipedia.org/wiki/1-methylimidazole 1-methylimidazole] ([http://www.sigmaaldrich.com/catalog/search/ProductDetail/ALDRICH/336092 get])which react with the free 5' OH groups via [http://en.wikipedia.org/wiki/Acetylation acetylation]. Excess reagents are washed out.
*Step 4 - Oxidation: The phosphite linkage between the first and second base needs to be stabilized by making the phosphate group pentavalent. This is achieved by adding iodine (go to local store) and water which leads to the [http://en.wikipedia.org/wiki/Oxidation oxidation] of the phosphite into [http://en.wikipedia.org/wiki/Phosphate phosphate]. This step can be substituted with a [http://en.wikipedia.org/wiki/Sulphorylation sulphorylation] step for [http://en.wikipedia.org/wiki/Thiophosphate_nucleotide thiophosphate nucleotides].
(Note: [http://biosupport.licor.com/docs/whatsnew/DNASynth800Phos.pdf this] might be a good document to see how phosphoramidites can be ordered from suppliers.) Here are some [http://www.protocol-online.org/prot/Molecular_Biology/Oligonucleotide/ oligo synth protocols in molecbio]. [http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=2932 Quantifying oligos from phosphoramadite synth]. Note that you may not have to actually purchase phosphoramadites to start off with, but instead begin with a purified solution of nucleic acid??
== What are the origins of oligonucleotide impurities and errors? ==
See [http://heybryan.org/mediawiki/index.php/DNA_synthesis#Origin_of_oligonucleotide_impurities_and_errors here].
= Microfluidics MiniFAQ =
== What are microfluidics? ==
[http://en.wikipedia.org/wiki/Microfluidics Wikipedia sez]: Microfluidics deals with the behavior, precise control and manipulation of fluids that are geometrically constrained to a small, typically sub-millimeter, scale. Typically, micro means one of the following features: small volumes(nl, pl, fl); small size; low energy consumption; effects of the micro domain (i.e., [http://en.wikipedia.org/wiki/Laminar_flow laminar flows], [http://en.wikipedia.org/wiki/Surface_tension surface tension], [http://en.wikipedia.org/wiki/Diffusion diffusion], Marangoli forces, capillary forces, ...).
=== Even more on 'what are microfluidics' ===
See also:
* [http://heybryan.org/mediawiki/index.php/Microfluidcs Microfluidics]
* [http://groups.google.com/group/diybio/msg/1197606e3c3dc439 the original sharpie microfluidics post to diybio]
* [http://groups.google.com/group/diybio/browse_frm/thread/b3bb2d8b8a654fd4/1197606e3c3dc439?#1197606e3c3dc439 the rest of the thread].
* [http://groups.google.com/group/diybio/msg/0e6ec2484dde6ea7 DIY microfluidics for continuous liquid flow using toner transfer (How To)]
== An example of microfluidics ==
The following is a run of the example microfluidics T-junction simulation in elmer, an open source CFD/FEM/FEA package. What you see here is the progression of an analyte due to electro-osmotic flow. There are two electric fields, three boundary conditions and a lot of wasted hours playing around with ElmerGUI and ElmerFront.
<youtube align="left">sPY84NelFO4</youtube> <html><div style="clear:both;"></div></html>
== What is a lab on a chip (LOC)? ==
A '''lab-on-a-chip (LOC)''' is a device that integrates one or several laboratory functions on a single chip of only millimeters to a few square centimeters in size. LOCs deal with the handling of extremely small fluid volumes down to less than pico liters. Lab-on-a-chip devices are a subset of MEMS devices and often indicated by "'''Micro Total Analysis Systems'''" ('''µTAS''') as well. Microfluidics is a broader term that describes also mechanical flow control devices like pumps and valves or sensors like flowmeters and viscometers. However, strictly regarded "Lab-on-a-Chip" indicates '''generally the scaling of single or multiple lab processes down to chip-format''', whereas "µTAS" is dedicated to the integration of the total sequence of lab processes to perform chemical analysis. The term "Lab-on-a-Chip" was introduced later on when it turned out that µTAS technologies were more widely applicable than only for analysis purposes.
Ultimately the idea is to have all of the typical components, procedures and processes of a laboratory available on a "chip", on a single perhaps disposable device, rather than having to build or purchase bulky equipment that sometimes tends to be hard to acquire or learn about.


= Appendix 1 - list of Synthetic Biology Companies =
= Appendix 1 - list of Synthetic Biology Companies =
Line 456: Line 365:
*[http://www.atg-biosynthetics.com/ ATG:biosynthetics]
*[http://www.atg-biosynthetics.com/ ATG:biosynthetics]
*[http://www.blueheronbio.com/ Blue Heron Biotechnology, Inc.]
*[http://www.blueheronbio.com/ Blue Heron Biotechnology, Inc.]
*[http://www.codagenomics.com/ CODA Genomics]
*[http://www.dna20.com/ DNA2.0]
*[http://codondevices.com/ Codon Devices, Inc.]
*[http://www.dna20.com/ DNA 2.0]
*[http://www.febit-synbio.com/ febit synbio gmbh]
*[http://www.febit-synbio.com/ febit synbio gmbh]
*[http://www.geneart.com/ GENEART]
*[http://www.geneart.com/ GENEART]
Line 466: Line 373:
*[http://www.syntheticgenomics.com Synthetic Genomics, Inc.]
*[http://www.syntheticgenomics.com Synthetic Genomics, Inc.]
*[http://mrgene.com Mr.Gene GmbH]
*[http://mrgene.com Mr.Gene GmbH]
= Appendix 2 - List of Equipment Suppliers =
See [http://openwetware.org/wiki/DIYbio/FAQ/Equipment DIYBio FAQ: Equipment] for new/used/refurbished equipment suppliers.
= Appendix 3 - Laboratory Basics =
See [http://openwetware.org/wiki/DIYbio/FAQ/Methods DIYBio FAQ: Methods] for basic lab technique, including sterilization, using animals, etc.
{{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

<html><div style="clear:both;"></div></html>

DIYbio-SF: Tito's food coloring electrophoresis

<html><div style="clear:both;"></div></html>

DIYbio-boston: diybio visits the fablab

<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?

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.
Retrieved from "https://openwetware.org/mediawiki/index.php?title=DIYbio/FAQ&oldid=623964"