User:NKuldell/Q/A working page 3

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<font color=red>NOTE: still under construction....stay tuned...</font color>
<font color=red>NOTE: still under construction....stay tuned...</font color>
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Introduction: 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. We welcome your feedback on this ongoing effort that we intend to refine, revise and update regularly.  Post your thoughts on the associated discussion page or email them to nkuldellATmitDOTedu and lmccrayATmitDOTedu.  
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Introduction: 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. We welcome your feedback and impressions of this ongoing effort that we intend to refine, revise and update regularly.  Post your thoughts on the associated discussion page or email them to nkuldellATmitDOTedu and lmccrayATmitDOTedu.  
==Part 1: Defining the field and its capabilities==
==Part 1: Defining the field and its capabilities==
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Reviews that focus on the technology itself are <br>  
Reviews that focus on the technology itself are <br>  
*Sci Am Fab group
*Sci Am Fab group
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*Pam's G&D paper
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*Pam's G&D paper (coming soon?)
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*Voigt's TIBS paper
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*Voigt's TIBS (?) paper (coming soon?)
*Voigt,Keasling  Nat Chem Biol. 2005 Nov;1(6):304-7
*Voigt,Keasling  Nat Chem Biol. 2005 Nov;1(6):304-7
*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"
*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"
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Relevant events that might be placed on a timeline:<i> dates, landmarks still needed</i>  
Relevant events that might be placed on a timeline:<i> dates, landmarks still needed</i>  
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*Restriction enzymes
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*Restriction enzymes, 1970 Werner Arber, Dan Nathans and Hamilton Smith
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*Sequencing
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*Dideoxy Sequencing, 1977 Frederick Sanger
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*PCR
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*PCR, 1983 Kary Mullis
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*Elowitz paper
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*Repressilator paper, 2000 Michael Elowitz and Stanislas Leibler
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*Toggle paper
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*Toggle paper, 2000  Timothy Gardner, Charles Cantor and James Collins
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*iGEM start date
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*iGEM start date, summer 2004
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*Registry founding
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*Registry founding, 2004
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*SB1.0 and 2.0 meetings  
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*SB1.0 and 2.0 meetings, 2004 and 2006 respectively
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*SynBERC founding, 2006
One oft cited paper by Carlson <cite>Carlson</cite> 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.  
One oft cited paper by Carlson <cite>Carlson</cite> 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.  

Revision as of 21:39, 29 August 2006

NOTE: still under construction....stay tuned...

Introduction: 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. We welcome your feedback and impressions of this ongoing effort that we intend to refine, revise and update regularly. Post your thoughts on the associated discussion page or email them to nkuldellATmitDOTedu and lmccrayATmitDOTedu.

Contents

Part 1: Defining the field and its capabilities

Q1: How is synthetic biology different from existing, related fields like genetic engineering and metabolic engineering?

In some ways, it's no different. People have been modifying genetic material for much of recorded history via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology. Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. An illustrative example is that of improved insulin production through genetically engineering bacterial cells to express the human gene for that protein. 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. Metabolic engineering can be thought of as a specialization of synthetic biology for the purpose of retooling cellular metabolism for human purposes. Synthetic biology also has applications in other areas like materials fabrication, energy production, information processing and more.Read more

Q2: Is there an expert review of the nature and potential benefits and risks of synthetic biology?

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"

[1]

Reviews that focus on 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
  • 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.

Reviews in the lay press include

  • Tucker & Zilinskas, The New Atlantis, Spring 2006 link
  • Custom-Made Microbes, at Your Service by A Pollack NYT Science section January 17, 2006 link

Q3: What questions or applications are being addressed by synthetic biology that aren't being explored or built using other technologies?

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 [1], two genomes in one cell [2] and characterization of a minimal E. coli genome [3]. 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 [2] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast [4], 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 [5] and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life [6].

Q4: Why is biology so hard to engineer now?

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.Read more

The difficulties facing those who wish to engineer biology are concisely described by Endy [7] and Knight [8].

  1. Endy D. . pmid:16306983. PubMed HubMed [Endy]
  2. Knight TF. . pmid:16729055. PubMed HubMed [Knight-MSB-2005]
All Medline abstracts: PubMed HubMed

Q5: Some people may foresee a day when synthetic biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?

Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful de novo synthesis of poliovirus [9], 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 [10] and human influenza in 2005[11]. 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 [12].

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 [13]. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 [6], 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)

Q6: How quickly is the field moving towards its goals?

Relevant events that might be placed on a timeline: dates, landmarks still needed

  • Restriction enzymes, 1970 Werner Arber, Dan Nathans and Hamilton Smith
  • Dideoxy Sequencing, 1977 Frederick Sanger
  • PCR, 1983 Kary Mullis
  • 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 [14] 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.

Part 2: Defining the community

Q1: What is the nature of the synthetic biology community?

Like most emerging research fields, the synthetic biology community is loosely defined with no single unified voice. 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.

Yet 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 [3]. 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

Q2: Who speaks for the field?

There is no single spokesperson.

  • Authors of recent review articles are key workers in synthetic biology.
  1. Andrianantoandro E, Basu S, Karig DK, and Weiss R. . pmid:16738572. PubMed HubMed [Andrianantoandro-MSB-2006]
  2. Sprinzak D and Elowitz MB. . pmid:16306982. PubMed HubMed [Sprinzak-Nature-2005]
  3. McDaniel R and Weiss R. . pmid:16019200. PubMed HubMed [McDaniel-CurrOpin-2005]
  4. Isaacs FJ, Dwyer DJ, and Collins JJ. . pmid:16680139. PubMed HubMed [Isaacs-NatBiotechnol-2006]
  5. Bio FAB Group, Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, and Weiss R. . pmid:16711359. PubMed HubMed [BioFABgroup-SciAm-2006]
  6. Endy D. . pmid:16306983. PubMed HubMed [Endy-Nature-2005]
  7. Voigt CA and Keasling JD. . pmid:16408063. PubMed HubMed [Voigt-NatChemBiol-2005]
All Medline abstracts: PubMed HubMed

Leaders can also be found on the speaker or organizer lists for SB1.0 and SB2.0.

SB1.0:

SB2.0:

  • 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 (see Part 2, Question 1).

Part 3: Possible future benefits of synthetic biology

Q1: 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.

Q2: 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." [4] Synthetic Genomics, Inc., another startup by J. Craig Venter, believes "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." [5]

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. [6].

Q3: 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 ([4], 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.

Q4: What other classes of benefits are foreseen?

alternative energy sources
materials synthesis
clean chemistry


Part 4: Possible future risks and safeguards for synthetic biology

Q1: 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. If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something with biological materials. 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.

Q2: What federal program[s] has responsibility for synthetic biology safety assurance?

Synthetic biology has safety/oversight methods no different from those that regulate more traditional recombinant research.

  • Info from Rhonda O'Keefe at MIT's EHS office:

The NIH Guidelines for Recombinant DNA Research deal with rDNA. See this address: [7] While they're called "guidelines", they're mandatory for any institution that receives funding from NIH. Another reference (not a regulation, but considered good practice) is called BMBL; it's published by the CDC and it spells out the biosafety levels. See this site: [8] . Also relevant is the OSHA Bloodborne Pathogen Standard for work with potentially infectious human materials; see this site: [9] . There are import regulations via the CDC [10] as well as regulations on use of "select agents" [11](agents with potential use in terrorism). Waste disposal is generally regulated on the state level.


coming soon: summary of 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.

Q3: What are the existing barriers to the risk of potentially harmful synthetic biology products?

answer should included mention of barriers in place to regulate research labs and commercial fabricators. Could also bring in surveillance ideas to monitor SB biohackers and any means of restricting products from overtly malicious agents (if there is evidence for this). As a correlary (or maybe as the lead line) can describe how community of openess and dialog (i.e. the “ethos” of current researchers) acts to anticipate and root out potential risk.

Q4: Is there evidence of interest in synthetic biology capabilities in the part of terrorists?

Facile DNA synthesis is a key enabling technology for synthetic biology, but DNA on demand significantly lowers barriers to potentially dangerous substances in the hands of miscreants. DNA synthesis companies have a record of synthesis orders but it’s not clear how or if that information would be shared. 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

Q5: Is biohacking possible?

Existing approaches to answering this question include the idea that SB is sometimes presented as a special form of information processing technology…a program written for assembly of organisms or parts of organisms. This leads to the question: is it significantly more difficult for “biohackers” to cause mischief that those who wish for whatever reason to set loose the biological counterpart of a computer virus into the human environment? Another part of this answer has been that right now SB is incredibly hard. Very little works as predicted and there are only a few interchangeable parts to play with. But with time and success both these statements will be false and then hackers will have plenty to use for mischief. It might be best understood by thinking about computer operating systems and computer viruses. No computer viruses were written until lots of folks had their own computers and there were programs to attack and damage to be done.

Part 5: Social implications and public attitudes

Q1: Is synthetic biology distinct from genetic engineering in the minds of the public, administrators, and other relevant groups?

all are questions trying to calibrate public confidence by asking if misgivings or trust can be infered from those surrounding genetic engineering.

The answer to this question varies depending of the section of the public in question-

  • For the average person in society with little or no formal training in Biology, given a 5min description of synthetic biology without specifically differentiating it from other fields, I believe it would be seen as indistinguishable from genetic engineering.
  • For the average biologist, given a 5min description of synthetic biology, I believe a distinction between the approach of the two fields would be seen, albeit a subtle one.
  • For the average funding agency or administrator, given the fact that the risks, benefits and applications are qualitatively similar for SB and GE, I believe they would be treated as one field.

As indicated in the lack of public controversy over the implementation of genetically engineering safeguards and the open release of GMO products, the public has some level of confidence in those who are doing that work. Is the SB community effectively part of the same community?

Q2: What groups are closely following synthetic biology and its implications?

Question is looking for an SB "watchdog," and there is none (at least none dedicated to SB). Public perceptions are sometimes affected by the knowledge that entities exist that focus on palpable risks, playing a “watchdog” role. If there are no public or private groups that appear to be applying vigilance against or address events involving man-made organisms, are there other assurances to offer?

Q3: Is the synthetic biology community devoloping and operating awareness efforts?

this question was originally posed to probe public awareness efforts. Premise is: for some potentially risky technologies, professional organizations themselves develop and operate awareness efforts and training aids to reduce public and worker risk and asks if the SB community already doing this. This answer might offer nice place to talk about curriculum/education efforts underway.

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