Gus Woltmann » Synthetic biology

Measurement

admin — Mon, 21 Sep 2009 13:17:40 +0000

Precise and accurate quantitative measurements of biological systems are crucial to improving understanding of biology. Such measurements often help to elucidate how biological systems work and provide the basis for model construction and validation. Differences between predicted and measured system behavior can identify gaps in understanding and explain why synthetic systems don’t always behave as intended. Technologies which allow many parallel and time-dependent measurements will be especially useful in synthetic biology. Microscopy and flow cytometry are examples of useful measurement technologies.

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Modeling

admin — Mon, 21 Sep 2009 13:14:59 +0000

Models inform the design of engineered biological systems by allowing synthetic biologists to better predict system behavior prior to fabrication. Synthetic biology will benefit from better models of how biological molecules bind substrates and catalyze reactions, how DNA encodes the information needed to specify the cell and how multi-component integrated systems behave. Recently, multiscale models of gene regulatory networks have been developed that focus on synthetic biology applications. Simulations have been used that model all biomolecular interactions in transcription, translation, regulation, and induction of gene regulatory networks, guiding the design of synthetic systems.

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Fabrication

admin — Mon, 21 Sep 2009 13:12:33 +0000

A critical limitation in synthetic biology today is the time and effort expended during fabrication of engineered genetic sequences. To speed up the cycle of design, fabrication, testing and redesign, synthetic biology requires more rapid and reliable de novo DNA synthesis and assembly of fragments of DNA.

In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the first synthetic organism. This took about two years of painstaking work. In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks. In 2006, the same team, at the J. Craig Venter Institute, has constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and is working on getting it functioning in a living cell.

In 2007 it was reported that several companies were offering the synthesis of genetic sequences up to 2000 bp long, for a price of about $1 per base pair and a turnaround time of less than two weeks.

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Sequencing

admin — Mon, 21 Sep 2009 13:08:41 +0000

Synthetic biologists make use of DNA sequencing in their work in several ways. First, large-scale genome sequencing efforts continue to provide a wealth of information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, synthetic biologists use sequencing to verify that they fabricated their engineered system as intended. Third, fast, cheap and reliable sequencing can also facilitate rapid detection and identification of synthetic systems and organisms.

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Social and Ethical

admin — Mon, 21 Sep 2009 13:05:08 +0000

Online discussion of so-called “societal issues” online at OpenWetWare, at the SYNBIOSAFE forum on issues regarding ethics, safety, security, IPR, governance, and public perception (background document).

Some efforts have been made to engage social issues “upstream” focus on the integral and mutually formative relations among scientific and other human practices. These approaches attempt to invent ongoing and regular forms of collaboration among synthetic biologists, ethicists, political analysts, funders, human scientists and civil society activists. These collaborations have consisted either of intensive, short term meetings, aimed at producing guidelines or regulations, or standing committees whose purpose is limited to protocol review or rule enforcement. Such work has proven valuable in identifying the ways in which synthetic biology intensifies already-known challenges in rDNA technologies. However, these forms are not suited to identifying new challenges as they emerge, and critics worry about uncritical complicity. An example of efforts to develop ongoing collaboration is the “human practices” component of the Synthetic Biology Engineering Research Center (SynBERC), an NSF funded collaboration among a number of leading research universities. In Europe, the multi-partner project SYNBIOSAFE, coordinated by IDC, is investigating the biosafety, biosecurity and ethical aspects of synthetic biology. The International Consortium for Polynucleotide Synthesis was formed in 2006 to encourage sharing of ideas and resources for pro-actively monitoring synthetic gene orders and enforcing safe practices, (ICPS). The recently formed Industry Association Synthetic Biology (IASB) has also started to tackle open biosecurity problems for biotech companies doing gene synthesis.

A report from the Hastings Center and Woodrow Wilson Center found that non-physical moral concerns in synthetic biology have received scant attention. Distributive justice and our relationship with nature are two such concerns. The authors suggest that what is needed most is a better understanding of precisely what values are considered at play in the context of synthetic biology.

In January 2009, the Alfred P. Sloan Foundation funded the Woodrow Wilson Center, the Hastings Center, and the J. Craig Venter Institute to examine the public perception, ethics, and policy implications of synthetic biology.

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Safety and Security

admin — Mon, 21 Sep 2009 13:02:01 +0000

In addition to numerous scientific and technical challenges, synthetic biology raises questions for ethics, biosecurity, biosafety, health, energy and intellectual property. To date, key stakeholders have focused primarily on the so-called dual-use challenge. For example, while the study of synthetic biology may lead to more efficient ways to produce medical treatments (e.g. against malaria), it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox) by malicious actors.[citation needed]. Proposals for licensing and monitoring the various phases of gene and genome synthesis began to appear in 2004. A 2007 study by the J. Craig Venter Institute, MIT, and CSIS compared several policy options for governing the safety risks associated with synthetic biology. Other initiatives, such as OpenWetWare, diybio, biopunk, biohack, and possibly others, have attempted to integrate self-regulation in their proliferation of open source synbio projects. However the distributed and diffuse nature of open-source biotechnology may make it more difficult to track, regulate, or mitigate potential biosafety and biosecurity concerns. An initiative for self-regulation has been proposed by the International Association Synthetic Biology, which held a workshop on technical solutions for biosecurity in synthetic biology. The report emerging from the workshop proposes a set of measures to be implemented by the synthetic biology industry for improved biosecurity and biosafety. Deliberate misuse aside, harm to human health or the environment could potentially result from error (e.g. failure to follow standard laboratory containment protocols).

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Ethical, Legal, Social, and Policy Challenges

admin — Sat, 19 Sep 2009 06:19:19 +0000

Key enabling technologies

admin — Sat, 19 Sep 2009 06:09:04 +0000

Re-writing

admin — Sat, 19 Sep 2009 06:05:06 +0000

Engineering

admin — Sat, 19 Sep 2009 06:03:11 +0000

Chemistry

admin — Sat, 19 Sep 2009 06:02:14 +0000

Biology

admin — Sat, 19 Sep 2009 06:01:28 +0000

History of the term

admin — Sat, 19 Sep 2009 06:00:40 +0000

Synthetic biology

admin — Sat, 19 Sep 2009 05:59:49 +0000