User:NKuldell/Q/A working page 4

09.29.06: Under construction: this is a re-organized set of Q/A intended for a broader audience. The reorg is intended to address some of the initial feedback from the Q/A v3 readers. These remain poorly formated wrt references and links, to be polished up into a single reference list and a uniform URL style once the text is refined. Feedback on the associated talk page will be welcome-NK

The following series of practical questions and factual answers grew out of a well-intentioned notion that we might use the Q/A format to frame some issues relevant to the emerging field of synthetic biology and its societal implications. Our imagined audience is an intelligent, busy person interested in both technology and its risk/rewards. We welcome all feedback and impressions of this ongoing effort since we intend to refine, revise and update this work regularly. Post your thoughts on the associated discussion page or email them to nkuldell AT mit DOT edu and lmccray AT mit DOT edu.

Q: What is synthetic biology?
Most broadly defined it is the application of engineering principles to enable the rational and predictable manipulation of biology. More specific is the definition offered by[| syntheticbiololgy.org] which describes synthetic biology as A) the design and construction of new biological parts, devices, and systems, and B) the re-design of existing, natural biological systems for useful purposes.

Q: Do engineering lessons really transfer to biology?
The engineering of biology is currently very hard to do, largely because engineers do not welcome uncertainty and unpredictable behavior but the biological world is full of these. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Existing descriptions of basic cellular activities and genetic codes do not allow biological activities to be predictably combined in novel and re-useable ways.The difficulties facing those who wish to engineer biology are concisely described by Endy Endy and Knight Knight-MSB-2005 . Read more

Q: How is synthetic biology different from existing, related fields like genetic engineering?
Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. What makes this effort novel? Breeding and genetic crosses have been used to modify genetic material throughout recorded history. The advent of recombinant DNA technology 30+ years ago allowed for more methodical combinations of DNA segments. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. Sequencing and synthesis enable cellular programs to be both read and written, thus enabling synthetic biologists to try to program the behaviour of living cells. Read more

Q: What questions or applications are being addressed by synthetic biology?
Some synthetic biologists are combining genomic information and synthesis technologies  to re-write the genetic code  from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 Chan-MSB-2005, two genomes in one cell Itaya-PNAS-2005 and characterization of a minimal E. coli genome Posfai-Science-2006. Other successful efforts in synthetic biology involve  metabolic engineering  of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria  or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast Ro-Nature-2006, an achievement that may allow cheap and clean production of this precursor for an antimalarial drug. Finally, synthetic biology can provide a framework for discovery-driven biologists who might like  to test their existing models by building them  from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains Giesecke-MSB-2006 and have applied this framework to determine dimerization specificity. More futuristic are related efforts to construct chemical systems capable of evolution to study the fundamental properties of life Chen-JACS-2005.

Q: Have primitive life forms or simple viruses been synthesized through synthetic biology?
Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful de novo synthesis of poliovirus Cello-Science-2002, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of de novo synthesis of viruses are the phiX174 bacteriophage reported in 2003 Smith-PNAS-2003 and human influenza in 2005 Tumpey-Science-2003. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature vanAken-Nature-2006.

Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 Johnston-Science-2001. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 Chen-JACS-2005, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

Q: How quickly is the field moving towards its goals?
Though not all dedicated to enabling synthetic biology efforts, a timeline of relevant events include:
 * Restriction enzymes, 1970 Werner Arber, Dan Nathans and Hamilton Smith
 * Dideoxy Sequencing, 1977 Frederick Sanger
 * PCR, 1983 Kary Mullis
 * First whole genome of free living organism sequenced, 1995
 * Repressilator paper, 2000 Michael Elowitz and Stanislas Leibler
 * Toggle paper, 2000 Timothy Gardner, Charles Cantor and James Collins
 * iGEM start date, summer 2004
 * Registry founding, 2004
 * SB1.0 and 2.0 meetings, 2004 and 2006 respectively
 * SynBERC founding, 2006

One oft cited paper by Carlson Carlson looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems. Related reference, not oft cited, is Zwick (2005) Technology: a genome sequencing center in every lab.

Q: Where can I read more?
Some recent reviews are listed here. More are in the pipeline. Reviews that focus on the technology itself are 
 * Sci Am Fab group
 * Pam's G&D paper (coming soon?)
 * Voigt's TIBS (?) paper (coming soon?)
 * Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7
 * Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"

Reviews in the lay press include 
 * The Economist, August 31st 2006
 * Tucker & Zilinskas, The New Atlantis, Spring 2006 link
 * Custom-Made Microbes, at Your Service by A Pollack NYT Science section January 17, 2006 link

Q: How is the synthetic biology community organized?
Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held (Synthetic Biology 1.0 at MIT and Synthetic Biology 2.0 at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.

In some ways the synthetic biology is quite organized given that it is in its early stages. For instance,
 * 1) An NSF-funded effort called SynBERC was launched in August of 2006 . SynBERC (Synthetic Biology Engineering Research Center) initiates a multi-institutional, collaborative effort to lay the foundations for engineering with biological substrates.
 * 2) A community website exists that can be edited and revised by anyone in the field.
 * 3) The Registry of Standard Biological Parts enables people to contribute and obtain parts.
 * 4) There are community mailing lists on which open discussion of issues related to the field can occur.
 * 5) A public declaration is being discussed and prepared from Synthetic Biology 2.0 conference.
 * 6) UC Berkeley is archiving their synthetic biology seminar series online. Read more

Q: Who speaks for the community?
There is no single spokesperson.
 * Authors of recent review articles are key workers in synthetic biology.
 * 1) Andrianantoandro-MSB-2006 pmid=16738572
 * 2) Sprinzak-Nature-2005 pmid=16306982
 * 3) McDaniel-CurrOpin-2005 pmid=16019200
 * 4) Isaacs-NatBiotechnol-2006 pmid=16680139
 * 5) BioFABgroup-SciAm-2006 pmid=16711359
 * 6) Endy-Nature-2005 pmid=16306983
 * 7) Voigt-NatChemBiol-2005 pmid=16408063

Leaders can also be found on the speaker or organizer lists for SB1.0 and SB2.0. SB1.0: SB2.0:
 * Organizers
 * Speakers
 * Organizers: Berkeley Lab, MIT, UC Berkeley, and UCSF
 * Speakers

A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing.

Q: Is the synthetic biology community developing and operating awareness efforts?
Educational information and curriculum is being written by members of the synthetic biology community. These include:
 * the Synthetic Biology Engineering Research Center (SynBERC) has described an educational mission [|read about SynBERC's educational thrust here]
 * [| SyntheticBiology.org] is an open forum for collecting and discussing relevant topics in synthetic biology
 * a student competition in synthetic biology called iGEM], which stands for International Genetically Engineered Machines, attracts and educates new students in synthetic biology as well as populates [the Registry of Standard Biological Parts]
 * methodical and discipline-specific curriculum, for example [at UC Berkeley] and [at MIT], is being developed to train university students in synthetic biology

Q: Does the community include garage inventors?
Garage inventors themselves are not an organized community but synthetic biology may offer biohackers a new toolkit for the longstanding and common human drive to manipulate nature. Unnatural combinations of living matter are acheivable in many ways. Simple carpentry, i.e. grafting, of tree branches to heterologous trunks has allowed a backyard pear tree to grow two kinds of apples and a branch filled with quince [). More sophisticated methods are needed if the goal is to grow hybrids, for example a pear tree with apple-flavored, quince-shaped fruits. Such hybrid traits require methodical cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance . Alternatively, recombinant DNA technology can be used, generating products like the "Flavr Savr" tomato . The possibilities for genetic programs expand still further with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

Deliberately mischievous work is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have reagents and means to program cells for malevolent purposes. It's hoped that better responses will also emerge, through the rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts.

'' "read more" section might further explore "biohacking" as biological counterpart of a computer virus in the human environment. ''

Q: What groups are closely following synthetic biology and its implications?
Emerging technologies, including synthetic biology and its implications, are being followed and reported in the academic press. For example the European Molecular Biology Organization ("EMBO") published a special issue of EMBO Reports dedicated to science and security issues. The lay press has also taken an interest in this area, for example the recent issue of MAKE magazine (volume 7) dedicated to backyard biology and garage biotechnology. Finally, many social organizations, including "watchdog" groups seeking vigilant oversight of the work and inclusion in the regulatory dialog, are interested and following development of this field. See for example their open letter to the synthetic biology community:.

Q: Where can I read more?
BBF, SynBERC, Synthetic Society

Q: What are the perceived benefits of synthetic biology?
Given synthetic biology's wide scope for engineering biological systems, the potential application space of synthetic biology is similarly enormous. Novel medical applications, environmental remediation, energy production and biomaterials synthesis may all be approachable through synthetic biology. In the future, cells may be quickly and predictably programmed to meet these and other discrete engineering goals. Synthetic biology may also benefit traditional biologists in their efforts to understand the natural world since these investigators may more easily test existing models of natural systems by building them from the ground up. Additionally, synthetic biology presents opportunities for synthetic chemists since cells may be considered self-replicating bags of interesting chemicals. Thus synthetic biology may enable the synthesis of novel chemical species under environmentally-gentle conditions.

Q: Who is investing in this and what do they see as the pay-off?
The groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

Currently much of the investment in the field is from the venture capital community into startup companies (e.g. Codon Devices). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." Synthetic Genomics, Inc., another startup by J. Craig Venter, is founded on the idea that "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." 

The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. pdf The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit Bill and Melinda Gates Foundation has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin. Their motivation is to solve critical world health problems. .

Q: How can synthetic biology contribute to human health?
A recent achievement in the field of synthetic biology for the purposes of human health is the recent report by Jay Keasling and colleagues at UC Berkeley and Amyris Biotechnologies regarding the microbial production of the antimalarial drug precursor artemisinic acid. This breakthrough is key to reducing the cost of this highly effective drug against malaria to a point where it is affordable to the 100 million people that die each year from malaria ( Ro-Nature-2006, Amyris Biotechnologies press release). Thus, synthetic biology offers the promise of synthesizing drugs cheaply and in an environmentally-friendly manner.

A longer term goal of synthetic biology is to potentially develop new kinds of therapeutics. For instance, Chris Voigt and colleagues at UCSF report the controlled invasion of cancer cells by engineered bacteria. These engineered bacteria are designed to sense environmental conditions associated with tumors and invade those cancer cells. One can imagine that such bacteria can eventually be engineered to selectively deliver drugs to and destroy the tumor itself. Such programmable behavior in living cells is a hallmark of synthetic biology.

Q: What other classes of benefits are foreseen?
In addition to building on its early success in metabolic engineering of therapeutically relevant compounds, synthetic biology holds promise in other application areas. These still futuristic visions include:
 * alternative energy production. Retooling microbes to yield clean, usable fuels.
 * biodefense. Rapidly engineered organisms that might respond to harmful agents.
 * biofabrication.  Programmed unicellular organisms capable of organizing and synthesizing materials (e.g. nanowires).
 * clean chemistry.  Facile biosynthesis of compounds that now require harsh conditions for fabrication.
 * information processing.  Not bacteria as supercomputers, but rather implementing computing power where none currently exists.

 ideally will have link to "Read more" for each item on list 

Q: where can I read more?
SynBERC, SB2.0, Nature issue from Nov 2005, others?

Q: Does synthetic biology bring with it new risks not associated with existing, related fields?
The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses.

Understanding that synthetic biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly. A full day of relevant discussion was programmed into the UC Berkeley hosted conference, Synthetic Biology 2.0, day 3. Consequently, the Goldman School of Public Policy report PDF link and a draft declaration from the conference pdf article have been prepared. Additionally, some researchers within the community have self-organized to form a "synthetic society working group", allowing scientists and engineers to engage with scholars expert in considering societal issues associated with emerging technologies, community leaders, and interested individuals. Finally, a report is anticipated from an ongoing project, sponsored by the Department of Energy and bio-era, that considers the impact of the genome synthesis and design.

Q: What federal program[s] has responsibility for synthetic biology safety assurance?
Synthetic biology is regulated by the safety and oversight programs that regulate more traditional recombinant and microbial research.

At the federal level, safety assurance is guided by Additional regulations restrict import of biological materials and the use of "select agents" (agents with potential use in terrorism).
 * the  National Institutes of Health. The NIH has established guidelines for recombinant DNA . While they're called "guidelines", they're mandatory for any institution that receives funding from NIH.
 * the  Center for Disease Control. The CDC has described "biosafety levels,"  which establishes good lab practices for microbial agents. The Biosafety levels classify agents on a scale of one to four based on the risk the agents pose to human health, with correspondingly greater containment procedures considered good laboratory practice.
 * the Occupational Safety and Health Administration.  OSHA has set standards for working with potentially infectious human materials.

Safe laboratory practices are further defined and enforced at the state and local level. For example, waste disposal is regulated at the state level and individual research institutions are responsible for training its laboratory personel.

 thanks to Rhonda O'Keefe at MIT's EHS office for the links and descriptions  '' would a "read more" section useful to summarize regulatory framework from these sources: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution, how do these regulations differ for research in an industry setting. ''

Q: What's to keep someone from using synthetic biology to harm others?
"DNA on demand" technology significantly lowers barriers to potentially dangerous substances in the hands of miscreants. Most companies check sequence requests to look for ones that might encode dangerous substances. Companies can and have refused to synthesize such DNA. It is unclear, however, if the synthesis orders were placed by miscreants or by researchers with legitimate scientific interests. Thus, synthesis technology seems ripe for abuse but there is no evidence supporting or denying the misappropriation of the technology. ''Still to add to answer: the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Thus part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start ''

Q: Where can I read more?
Reviews that focus on security and societal implications of the technology are 
 * Synthetic Biologists face up to security risks Nature 436, 894-895 (18 Aug 2005) News [[Image:Presentation material-synthbiolrisks Nat05.pdf| pdf]]
 * From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology, Stephen M. Maurer, Keith V. Lucas & Starr Terrell, Goldman School of Public Policy, University of California at Berkeley PDF link
 * Draft Declaration of the Second International Meeting on Synthetic Biology, Attendees of SB2.0, University of California at Berkeley, May 2006. pdf article
 * (AJ) Bhutkar's article in The Journal of Biolaw & Business analyzing patentability, ethical and regulatory challenges in Synthetic Biology.
 * National Academy Study related to security issues?