DIYbio/FAQ/Educational

This topic Educational Discussion & Resources is part of the DIYBio FAQ

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

There are many biology and science resources on the net, especially with universities providing "open course ware" for viewing or download. The sections below of the DIYbio FAQ list hobbyist, industry, and university-sponsored educational resources which apply to biohacking.

= Educational Videos =


 * Chris Seidel's 2008 "Biohacking - An Overview" talk at The Last HOPE. It's really, really good.
 * Video 1 of 6 http://www.youtube.com/watch?v=xMhLHCswYdI
 * Chris gets into the thick of things in video 4 - 6: http://www.youtube.com/watch?v=Q11A9JtFbVg


 * See DIYbio/Videos for a collection of 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, "Revolution OS" (official site). Wikipedia says: "Directed by J. T. S. Moore, the film features interviews with prominent hackers and entrepreneurs including Richard Stallman, Michael Tiemann, Linus Torvalds, Larry Augustin, Eric S. Raymond, Bruce Perens, Frank Hecker and Brian Behlendorf."


 * A thermal cycler heats and cools a PCR reaction, check out these videos:
 * http://www.youtube.com/watch?v=2KoLnIwoZKU&feature=related Polymerase Chain Reaction (PCR) DNALearningCenter
 * http://vcell.ndsu.edu/animations/ Virtual Cell Animation Collection

For university video and audio:


 * 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 genetic engineering.


 * A SHORT COURSE ON SYNTHETIC GENOMICS, Edge Master Class 2009, George Church & J. Craig Venter. http://www.edge.org/documents/archive/edge296.html

= Educational Textbooks =

Textbooks are by far one of the best ways to learn about the latest in Biology and Wetware.

Beginner textbooks:
 * Try the Manga version of Molecular Biology! (Yes, Really.)
 * http://nostarch.com/mg_mbiology.htm
 * http://www.amazon.com/Manga-Guide-Molecular-Biology/dp/1593272022
 * 36 Lectures in Biology, by Luria, is a very good starting point. -- Guido D. Núñez-Mujica on DIYbio google group
 * "Biotechnology Projects For Young Scientists" by Kenneth Rainis and George Nassis 1998
 * "Microbiology: 49 Science Fair Projects" by H. Steven Dashefsky 1994
 * "The Amateur Biologist" by Shawn Carlson 2002

More advanced textbooks:


 * Systems Biology and Synthetic Biology, http://books.google.com/books?id=kB8nA8b0TQMC&pg=PA411#v=onepage&q=&f=false
 * ""Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems.""


 * DNA Science: A First Course, http://books.google.com/books?id=l9Y9eJreVeEC&printsec=frontcover&source=gbs_v2_summary_r&cad=0#v=onepage&q=&f=false
 * ""As in the first edition of this book, the laboratory course is completely supported by quality-assured products from the Carolina Biological Supply Company, from bulk reagents, to useable reagent systems, to single-use kits, thus satisfying a broad range of teaching applications.""

Free textbooks


 * NCBI keeps a database of life science text books that you can access for free. You can't browse the texts but, if you know what you are looking for, you can type a search term in the query bar and click on a link to its location in the text.
 * http://www.ncbi.nlm.nih.gov/books
 * Molecular Biology of the Cell. http://www.ncbi.nlm.nih.gov/books/NBK21054/

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


 * http://labtutorials.org  Great microbiology tutorials with video


 * http://diybio4beginners.blogspot.com/ DIY BIO 4 Beginners. This Blog is for people with an interest in DIY BIO that have absolutely no knowledge in BIO Yet.


 * http://openwetware.org/wiki/Image:SB_Primer_100707.pdf Primer for Synthetic Biology


 * Add your favorite ones here.

= Is DNA, RNA really like Software? What does DNA, RNA look like? =

DNA is not really "like software." DNA is a physical structure, and much of biology operates on the physical (mechanical) fit of macro-molecules. Changing the sequence (the "software") can result in big changes in the physical structure, which changes the bio-properties of the macro-molecule.


 * Very good images of DNA and phages: http://www.biochem.wisc.edu/faculty/inman/empics/dna-prot.htm

= Safety documentation = This section is for safety documentation from external bodies. DIYbio-related safety information is found in the other FAQ sections (See 'DIYbio FAQ on Methods').


 * Laboratory Biosafety Guidelines 2004

= What is synthetic biology and related technology? Does DIYBio do Genetic Engineering? =


 * Synthetic Biology: A Definition [From Davidson College's Synthetic Biology Seminar in the Fall of 2007]
 * 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.
 * 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.


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

Drew Endy - Informal - Broad overview
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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., 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 syntheticbiology.org.

What are BioBricks?
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 [1st hand quote from personal conversation with BioBricks founders -- jcline]. As of 2009, less than five Biobrick parts have been characterized with reliable and quantifiable behavior.


 * http://biobricks.org/
 * http://partsregistry.org/

What is iGEM?
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 igem.org or wikipedia for more info.

More on Synthetic Biology Projects and Parts

 * Syntheticbiology.org - Synthetic Biology organization Mailing list
 * Internationally Genetically Engineered Machines Competition (see iGEM)
 * The BioBricks Foundation (see biobricks)
 * Registry of Standard Biological Parts
 * List of synthetic biology projects

= Legal Discussions =

Legal discussions include both patent issues and safety-regulatory issues. Email safety@diybio.org to get involved in the discussions of safety.


 * 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.

Legal Discussions from the BioBrick Foundation

 * Drew Endy: update on legal matters, including hiring a legal firm
 * Bootstrapping an open parts collection
 * Videos of the BioBrick Foundation talking about legal concerns

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What's all this about "open", anyway?
This is the desire to continue to apply open source concepts to biology and related fields for great benefits.

"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 permissions such as open source licenses which allow others to re-use, modify and distribute their own designs of the technology. Benefits:
 * Patents. By using "Open" methods, 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: 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.

Formal discussion of the BioBrick license is documented in BBF RFC 60:


 * BBF RFC 60: Open licensing of BioBrick(tm) parts
 * This document provides recommendations for licensing of community-created biological parts, especially in BioBrick standard. by Micha Lower, Anna Olchowik, Jaros³aw Pankowski, Milena Balekowa, Marta B³aszkiewicz, Dominik Cysewski, Kamil Koper, Joanna Leszczyñska, Cherry Moreno and Anna Puawska
 * DSpace, doi: 1721.1/60081 http://dspace.mit.edu/handle/1721.1/60081

Background and References:


 * Synthetic Biology: Feasibility of the Open Source Movement.
 * A New Movement for Open Source Biology Is Launched. 16 Dec 2004.
 * J Hope, Open Source Biotechnology (PhD Thesis), The Australian National University, Canberra, 2004.
 * 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.


 * Thoughts on Open Biology, Rob Carlson, March 2, 2007. "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.