Synthetic Biology:FAQ

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Go to [http://syntheticbiology.org/ http://syntheticbiology.org/]
 
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'''<big>Synthetic Biology</big> is '''<br>
 
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'''A) the design and construction of new biological parts, devices, and systems, and'''<br>
 
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'''B) the re-design of existing, natural biological systems for useful purposes.'''
 
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<div>[[Image:Cells-to-gears-big.png|750px|Synthetic Biology Logo]]</div>
 
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===What is synthetic biology?===
===What is synthetic biology?===
*Synthetic biology refers to both:  
*Synthetic biology refers to both:  
**the design and fabrication of biological components and systems that do not already exist in the natural world
**the design and fabrication of biological components and systems that do not already exist in the natural world
**the re-design and fabrication of existing biological systems.
**the re-design and fabrication of existing biological systems.
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There are two types of synthetic biologists. The first group uses unnatural molecules to mimic natural molecules with the goal of creating artificial life. The second group uses natural molecules and assembles them into a system that acts unnaturally. In general, the goal is to solve problems that are not easily understood through analysis and observation alone and it is only achieved by the manifestation of new models. So far, synthetic biology has produced diagnostic tools for diseases such as HIV and hepatitis viruses as well as devices from biomolecular parts with interesting functions. The term “synthetic biology” was first used on genetically engineered bacteria that were created with recombinant DNA technology which was synonymous with bioengineering. Later the term “synthetic biology” was used as a mean to redesign life which is an extension of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules such as enzymes. Synthetic biologists are trying to assemble unnatural components to support Darwinian evolution. Recently, the engineering community is seeking to extract components from the biological systems to test and confirm them as building units to be reassembled in a way that can mimic the living nature. In the engineering aspect of synthetic biology, the suitable parts are the ones that can contribute independently to the whole system so that the behavior of an assembly can be predicted. DNA consists of double-stranded anti-parallel strands each having four various nucleotides assembled from bases, sugars and phosphates which are made of carbon, nitrogen, oxygen, hydrogen and phosphorus atoms. In the Watson-Crick model, A pairs with T and G pairs with C although occasionally some diversity exists. This simplification doesn’t exist in proteins. With analysis and observation alone, scientists convince themselves that the paradigms are the truth and if the data contradicts the theory, the data normally is discarded as an error, where synthesis encourages scientists to cross into the new land and define new theories. The same synthesis has long been used in chemistry such as chromatography. The combination of chemistry, biology and engineering can therefore create artificial Darwinian systems.
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===What is the difference between synthetic biology and systems biology?===
===What is the difference between synthetic biology and systems biology?===
*Systems biology studies complex biological systems as integrated wholes, using tools of modeling, simulation, and comparison to experiment. The focus tends to be on natural systems, often with some (at least long term) medical significance.  
*Systems biology studies complex biological systems as integrated wholes, using tools of modeling, simulation, and comparison to experiment. The focus tends to be on natural systems, often with some (at least long term) medical significance.  
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*Many members of the community are in the process of developing classes or courses in synthetic biology.  There are several sites that might be helpful in this endeavor.  The [http://parts.mit.edu/wiki/index.php/Main_Page international Genetically Engineered Machines competition] is an international competition in which teams of students design and build an engineered biological system from [http://parts.mit.edu BioBricks] during the summer.  iGEM maintains a list of [http://parts.mit.edu/wiki/index.php/Resources teaching materials] in synthetic biology.  A list of some existing synthetic biology courses is maintained on the [[Synthetic Biology|synthetic biology main page]].
*Many members of the community are in the process of developing classes or courses in synthetic biology.  There are several sites that might be helpful in this endeavor.  The [http://parts.mit.edu/wiki/index.php/Main_Page international Genetically Engineered Machines competition] is an international competition in which teams of students design and build an engineered biological system from [http://parts.mit.edu BioBricks] during the summer.  iGEM maintains a list of [http://parts.mit.edu/wiki/index.php/Resources teaching materials] in synthetic biology.  A list of some existing synthetic biology courses is maintained on the [[Synthetic Biology|synthetic biology main page]].
===Why isn't my question listed here?===
===Why isn't my question listed here?===
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*Because you haven't asked us yet - add it [[Talk:Synthetic Biology:FAQ|here]] or email synbio-admin AT openwetware DOT org.
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*Because you haven't asked us yet - add it [[Talk:Synthetic Biology:FAQ|here]] or email discuss AT syntheticbiology DOT org.
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Current revision

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What is synthetic biology?

  • Synthetic biology refers to both:
    • the design and fabrication of biological components and systems that do not already exist in the natural world
    • the re-design and fabrication of existing biological systems.

There are two types of synthetic biologists. The first group uses unnatural molecules to mimic natural molecules with the goal of creating artificial life. The second group uses natural molecules and assembles them into a system that acts unnaturally. In general, the goal is to solve problems that are not easily understood through analysis and observation alone and it is only achieved by the manifestation of new models. So far, synthetic biology has produced diagnostic tools for diseases such as HIV and hepatitis viruses as well as devices from biomolecular parts with interesting functions. The term “synthetic biology” was first used on genetically engineered bacteria that were created with recombinant DNA technology which was synonymous with bioengineering. Later the term “synthetic biology” was used as a mean to redesign life which is an extension of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules such as enzymes. Synthetic biologists are trying to assemble unnatural components to support Darwinian evolution. Recently, the engineering community is seeking to extract components from the biological systems to test and confirm them as building units to be reassembled in a way that can mimic the living nature. In the engineering aspect of synthetic biology, the suitable parts are the ones that can contribute independently to the whole system so that the behavior of an assembly can be predicted. DNA consists of double-stranded anti-parallel strands each having four various nucleotides assembled from bases, sugars and phosphates which are made of carbon, nitrogen, oxygen, hydrogen and phosphorus atoms. In the Watson-Crick model, A pairs with T and G pairs with C although occasionally some diversity exists. This simplification doesn’t exist in proteins. With analysis and observation alone, scientists convince themselves that the paradigms are the truth and if the data contradicts the theory, the data normally is discarded as an error, where synthesis encourages scientists to cross into the new land and define new theories. The same synthesis has long been used in chemistry such as chromatography. The combination of chemistry, biology and engineering can therefore create artificial Darwinian systems.

What is the difference between synthetic biology and systems biology?

  • Systems biology studies complex biological systems as integrated wholes, using tools of modeling, simulation, and comparison to experiment. The focus tends to be on natural systems, often with some (at least long term) medical significance.
  • Synthetic biology studies how to build artificial biological systems for engineering applications, using many of the same tools and experimental techniques. But the work is fundamentally an engineering application of biological science, rather than an attempt to do more science. The focus is often on ways of taking parts of natural biological systems, characterizing and simplifying them, and using them as a component of a highly unnatural, engineered, biological system.

Why bother?

  • Biologists are interested in synthetic biology because it provides a complementary perspective from which to consider, analyze, and ultimately understand the living world. Being able to design and build a system is also one very practical measure of understanding. Physicists, chemists and others are interested in synthetic biology as an approach with which to probe the behavior of molecules and their activity inside living cells. For example, differences between how a synthetic system is designed to behave and how it actually behaves can serve to highlight relevant intracellular physics. Engineers are interested in synthetic biology because the living world provides a seemingly rich yet largely unexplored medium for controlling and processing information, materials, and energy. Learning how to effectively harness the power of the living world will be a major engineering undertaking.

What is your approach towards synthetic biology?

  • We are working to help create a general scientific and technical infrastructure that supports the design and synthesis of biological systems. Specifically we are working to (a) specify and populate a set of standard parts that have well-defined performance characteristics and can be used (and re-used) to build biological systems, (b) develop and incorporate design methods and tools into a integrated engineering environment, (c) reverse engineer and re-design pre-existing biological parts and devices in order to expand the set of functions that we can access and program (d) reverse engineer and re-design a 'simple' natural bacterium.

Why are you working to redesign bacterium?

  • Bacteria are the simplest known objects from the natural world that are capable of replicating when provided with only simpler components (e.g., broth). Still, bacteria are far from simple. Bacteria also provide the basic environment in which synthetic biological systems exist and act (i.e., they are like the power supply and chassis of a computer). By re-designing/refactoring a simple living system we hope to learn how to better couple (and decouple) our designed systems from their host environment.

Life isn't digital. Why are you trying to implement digital logic in cells?

  • As engineers we are much better at thinking and designing digital systems. One reason we are better at digital system design is that such systems create an 'abstraction barrier' between the detailed device physics level and the system design and operation levels.

Is what you're doing dangerous?

  • Many technologies have the potential to be dangerous either through their direct application or through society's (inappropriate) reliance on their continued successful operation. Imaginable hazards associated with synthetic biology include (a) the accidental release of an unintentionally harmful organism or system, (b) the purposeful design and release of an intentionally harmful organism or system, (c) a future over-reliance on our ability to design and maintain engineered biological systems in an otherwise natural world. In response to these concerns we are (a) working only with Biosafety Level 1 organisms and components in approved research facilities, (b) working to educate and train a responsible generation of biological engineers and scientists, (c) learning what is possible (at what cost) using simple test systems. All told, we believe that the understanding and abilities to be gained from synthetic biology justifies its responsible exploration and development.
  • More recently, MIT, the J. Craig Venter Institute in Rockville, Md., and the Center for Strategic and International Studies in Washington, D.C. have announced a new study of the societal implications of synthetic genomics. Press releases: MIT, CSIS and Venter Institute. More information also available at Synthetic Genomics Study.

What about ethical or moral issues?

  • Do we inherit and passively pass along the living world or do we have a responsibility to interact rationally with it? If we are going to interact with the living world should we ground this interaction at a level of resolution (i.e., molecular) that allows for the precise description of our actions and their consequences? We don't presume to know all the answers to these questions (and others) but we hope to participate in a thoughtful discussion of such issues.

What technologies would benefit synthetic biology?

  • Fast and cheap DNA sequencing and synthesis would allow for rapid design, fabrication, and testing of systems. Software tools that enable system design and simulation are also needed. Still-better measurement technologies that allow for observation of biological system state (i.e., the equivalent of a biological debugger) are also needed.

What is the current commercial availability for de-novo gene synthesis? Has this technology become competitive with standard gene cloning in terms of cost per base and time?

  • Current synthesis costs are about $1 per base pair. Current synthesis times for a 1,500 bp gene are of order 4 weeks. So, we need a ~3-fold reduction in cost and a ~10-fold reduction in turn-around time, from where we are today for commercial DNA synthesis to be competitive with standard gene cloning. Such a cost reduction could play out within the next two years; however, changes in turn-around time are much harder to predict.

I want to study synthetic biology, where should I go?

  • The field's relatively new and so there are few critical mass programs in place as yet. A list of schools and labs that support graduate study in synthetic biology is available on the Graduate Programs page. Please add to it if you know of others. To date, there are not any undergraduate curriculums in synthetic biology but some universities are beginning to offer courses in the subject.

I'm interested in donating time, money, and/or moral support. What do I do?

  • Donations of any sort are always welcome. Contact us.

Will there be another synthetic biology conference?

  • We are maintaining a list of conferences relevant to the synthetic biology community. Please check there for the latest information.

How can I learn more?

  • Explore this site. Also, you can join the synthetic biology community mailing lists.

I'm interested in teaching a class on synthetic biology. Can you help?

Why isn't my question listed here?

  • Because you haven't asked us yet - add it here or email discuss AT syntheticbiology DOT org.

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