Synthetic biology

Synthetic biology

Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature.

A light programmable biofilm made by the UT Austin / UCSF team during the 2004 Synthetic Biology competition, displaying "Hello World"

Contents

History

The term "synthetic biology" has a history spanning the twentieth century.[1] The first use was in Stéphane Leducs’s publication of « Théorie physico-chimique de la vie et générations spontanées » (1910) [2] and « La Biologie Synthétique » (1912).[3] In 1974, the Polish geneticist Waclaw Szybalski used the term "synthetic biology",[4] writing:

Let me now comment on the question "what next". Up to now we are working on the descriptive phase of molecular biology. ... But the real challenge will start when we enter the synthetic biology phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes. This would be a field with the unlimited expansion potential and hardly any limitations to building "new better control circuits" and ..... finally other "synthetic" organisms, like a "new better mouse". ... I am not concerned that we will run out of exciting and novel ideas, ... in the synthetic biology, in general.

When in 1978 the Nobel Prize in Physiology or Medicine was awarded to Arber, Nathans and Smith for the discovery of restriction enzymes, Waclaw Szybalski wrote in an editorial comment in the journal Gene:

The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes, but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated.[5]

Perspectives

Biology

Biologists are interested in learning more about how natural living systems work. One simple, direct way to test our current understanding of a natural living system is to build an instance (or version) of the system in accordance with our current understanding of the system. Michael Elowitz's early work on the Repressilator[6] is one good example of such work. Elowitz had a model for how gene expression should work inside living cells. To test his model, he built a piece of DNA in accordance with his model, placed the DNA inside living cells, and watched what happened. Slight differences between observation and expectation highlight new science that may be well worth doing. Work of this sort often makes good use of mathematics to predict and study the dynamics of the biological system before experimentally constructing it. A wide variety of mathematical descriptions have been used with varying accuracy, including graph theory, Boolean networks, ordinary differential equations, stochastic differential equations, and Master equations (in order of increasing accuracy). Good examples include the work of Adam Arkin, Jim Collins and Alexander van Oudenaarden. See also the PBS Nova special on artificial life.

Chemistry

Biological systems are physical systems that are made up of chemicals. Around the turn of the 20th century, the science of chemistry went through a transition from studying natural chemicals to trying to design and build new chemicals. This transition led to the field of synthetic chemistry. In the same tradition, some aspects of synthetic biology can be viewed as an extension and application of synthetic chemistry to biology, and include work ranging from the creation of useful new biochemicals to studying the origins of life. Eric Kool's group at Stanford, the Foundation for Applied Molecular Evolution, Carlos Bustamante's group at Berkeley, Jack Szostak's group at Harvard, and David McMillen's group at University of Toronto are good examples of this tradition.[citation needed] Much of the improved economics and versatility of synthetic biology is driven by ongoing improvements in gene synthesis.[citation needed]

Engineering

Engineers view biology as a technology - the systems biotechnology or systems biological engineering[7] . Synthetic Biology includes the broad redefinition and expansion of biotechnology, with the ultimate goals of being able to design and build engineered biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health and our environment.[8] A good example of these technologies include the work of Chris Voigt, who redesigned the Type III secretion system used by Salmonella typhimurium to secrete spider silk proteins, a strong elastic biomaterial, instead of its own natural infectious proteins. One aspect of Synthetic Biology which distinguishes it from conventional genetic engineering is a heavy emphasis on developing foundational technologies that make the engineering of biology easier and more reliable. Good examples of engineering in synthetic biology include the pioneering work of Tim Gardner and Jim Collins on an engineered genetic toggle switch,[9] a riboregulator, the Registry of Standard Biological Parts, and the International Genetically Engineered Machine competition (iGEM).

Studies in synthetic biology can be subdivided into broad classifications according to the approach they take to the problem at hand: photocell design, biomolecular engineering, genome engineering, and biomolecular-design. The photocell approach includes projects to make self-replicating systems from entirely synthetic components. Biomolecular engineering includes approaches which aim to create a toolkit of functional units that can be introduced to present new orthogonal functions in living cells. Genome engineering includes approaches to construct synthetic chromosomes for whole or minimal organisms. Biomolecular-design approach refers to the general idea of the de novo design and combination of biomolecular components. The task of each of these approaches is similar: To create a more synthetic entry at a higher level of complexity by manipulating a part of the proceeding level.[10]

Re-writing

Re-writers are Synthetic Biologists who are interested in testing the idea that since natural biological systems are so complicated, we would be better off re-building the natural systems that we care about, from the ground up, in order to provide engineered surrogates that are easier to understand and interact with. Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software. Drew Endy and his group have done some preliminary work on re-writing (e.g., Refactoring Bacteriophage T7). Oligonucleotides harvested from a photolithographic or inkjet manufactured DNA chip combined with DNA mismatch error-correction allows inexpensive large-scale changes of codons in genetic systems to improve gene expression or incorporate novel amino-acids (see George Church's and Anthony Forster's synthetic cell projects.[11] As in the T7 example above, this favors a synthesis-from-scratch approach.

Key enabling technologies

There are several key enabling technologies that are critical to the growth of synthetic biology. The key concepts include standardization of biological parts and hierarchical abstraction to permit using those parts in increasingly complex synthetic systems.[12] Achieving this is greatly aided by basic technologies of reading and writing of DNA (sequencing and fabrication), which are improving in price/performance exponentially (Kurzweil 2001). Measurements under a variety of conditions are needed for accurate modeling and computer-aided-design (CAD).

DNA sequencing

DNA sequencing is determining the order of the nucleotide bases in a molecule of DNA. 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.[citation needed]

Fabrication

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 a process commonly referred to as gene synthesis.

In 2000, researchers at Washington University, mentioned synthesis of the 9.6 kbp Hepatitis C virus genome from chemically synthesized 60 to 80-mers.[13] In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the second synthetic genome. This took about two years of painstaking work.[14] In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks.[15] 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.[16][17]

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.[18] By September 2009, the price had dropped to less than $0.50 per base pair with some improvement in turn around time. Not only is the price judged lower than the cost of conventional cDNA cloning, the economics make it practical for researchers to design and purchase multiple variants of the same sequence to identify genes or proteins with optimized performance.

In 2010, Venter's group announced they had been able to assemble a complete genome of millions of base pairs, insert it into a cell, and cause that cell to start replicating.[19]

Modeling

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.[20]

Measurement

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.

Examples

Molecular cloning is a method used frequently by geneticists to obtain large quantities of a particular strand of DNA. It involves shaping a selected piece of DNA and inserting it into the DNA of a bacterium called a plasmid. Once the alien DNA is inserted the bacteria is allowed to replicate thus replicating the DNA that it contains. After replication is completed the copies of foreign DNA are separated from the plasmid. In this sense the bacteria becomes a cyborg because a foreign element is introduced and interacts with the bacteria.

The Sleeping Beauty transposon system is an example of an engineered enzyme for inserting precise DNA sequences into genomes of vertebrate animals. The SB transposon is a synthetic sequence that was created based on deriving a consensus sequence of extinct Tc1/mariner-type transposons that are found as evolutionary relics in the genomes of most, if not all, vertebrates. This enzyme took about a year to engineer[21] and since its creation has been used for gene transfer, gene discovery, and gene therapy applications[22][23][24]

Biosensor technology is another example of cyborg bacteria. One such sensor created in Oak Ridge National Laboratory and named “critter on a chip” used a coating of bioluminescent bacteria on a light sensitive computer chip to detect certain petroleum pollutants. When the bacteria sense the pollutant, it lights up and is then processed or amplified.[25] In Australia, biosensors have been created to detect viruses, bacteria, hormones, drugs, and DNA sequences. In the future scientists hope to create chips that can sense toxins such as environmental estrogens and warfare agents. Even more recently chemists at the University of Nebraska created a humidity gauge by using gold plated bacteria on a silicon chip. With a decrease in humidity there was an increase in the circuit flow. One unique feature that separates the chip from the bioluminescent ones is that that after it has been assimilated the bacteria no longer needs to be kept alive for the humidity gauge to work.[26]

Nanotechnology also has made advances by using cyborgs.. Researchers at the École polytechnique de Montréal in Canada have attached a microscopic bead to swimming bacteria. Using a magnetic resonance imaging machine (MRI) the researchers have been able to use the magnetic properties of the bacteria to direct it to certain locations. The bead has no purpose at the moment but researchers hope store drugs or other viral fighting agents inside so that it may be released at the directed location.[27]

Challenges

Opposition to Synthetic Biology

Opposition by civil society groups to Synthetic Biology has been led by the ETC Group who have called for a global moratorium on developments in the field and for no synthetic organisms to be released from the lab. In 2006 38 civil society organizations authored an open letter opposing voluntary regulation of the field and in 2008 ETC Group released the first critical report on the societal impacts of synthetic biology which they dubbed "Extreme Genetic Engineering".[28]

Safety and Security

In addition to numerous scientific and technical challenges, synthetic biology raises questions for ethics, biosecurity, biosafety, involvement of stakeholders and intellectual property.[29][30] To date, key stakeholders (especially in the US) have focused primarily on the biosecurity issues, especially 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.[31] Proposals for licensing and monitoring the various phases of gene and genome synthesis began to appear in 2004. A 2007 study compared several policy options for governing the security 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 synthetic biology 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.[32]

An initiative for self-regulation has been proposed by the International Association Synthetic Biology[33] that suggests some specific measures to be implemented by the synthetic biology industry, especially DNA synthesis companies. Some scientists, however, argue for a more radical and forward looking approaches to improve safety and security issues. They suggest to use not only physical containment as safety measures, but also trophic and semantic containment. Trophic containment includes for example the design of new and more robust forms of auxotrophy, while semantic containment means the design and construction of completely novel orthogonal life-forms.[34]

Social and Ethical

Online discussion of “societal issues” took place at the SYNBIOSAFE forum on issues regarding ethics, safety, security, IPR, governance, and public perception (summary paper). On July 9–10, 2009, the National Academies' Committee of Science, Technology & Law convened a symposium on "Opportunities and Challenges in the Emerging Field of Synthetic Biology" (transcripts, audio, and presentations available).

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,[35] and critics worry about uncritical complicity.[28]

An example of efforts to develop ongoing collaboration is the "Human Practices" component of the Synthetic Biology Engineering Research Center in the US and the SYNBIOSAFE project in Europe, coordinated by IDC,[36] that investigated the biosafety, biosecurity and ethical aspects of synthetic biology. A report from the Woodrow Wilson Center and the Hastings Center, a prestigious bioethics research institute, found that ethical concerns in synthetic biology have received scant attention.[37]

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.[38] Public perception and communication of synthetic biology is the main focus of COSY: Communicating Synthetic Biology, that showed that in the general public synthetic biology is not seen as too different from 'traditional' genetic engineering.[39][40] To better communicate synthetic biology and its societal ramifications to a broader public, COSY and SYNBIOSAFE published a 38 min. documentary film in October 2009 [1].

After a series of meetings in the fall of 2010, the Presidential Commission for the study of Bioethical Issues released a report, on December 16, to the President calling for enhanced Federal oversight in the emerging field of synthetic biology. The panel that facilitated the production of the report, composed of 13 scientists, ethicists, and public policy experts, said that the very newness of the science, which involves the design and construction of laboratory-made biological parts, gives regulators, ethicists and others time to identify problems early on and craft solutions that can harness the technology for the public good.

“We comprehensively reviewed the developing field of synthetic biology to understand both its potential rewards and risks,” said Dr. Amy Gutmann, the Commission Chair and President of the University of Pennsylvania. “We considered an array of approaches to regulation—from allowing unfettered freedom with minimal oversight and another to prohibiting experiments until they can be ruled completely safe beyond a reasonable doubt. We chose a middle course to maximize public benefits while also safeguarding against risks.”[citation needed]

Dr. Gutmann said the Commission’s approach recognizes the great potential of synthetic biology, including life saving medicines, and the generally distant risks posed by the field’s current capacity. “Prudent vigilance suggests that federal oversight is needed and can be exercised in a way that is consistent with scientific progress,” she said.[41]

See also

References

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