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#What is synthetic biology?
===What is synthetic biology?===
#*Synthetic biology refers to both (a) the design and fabrication of biological components and systems that do not already exist in the natural world and (b) the re-design and fabrication of existing biological systems.
*Synthetic biology refers to both:
#What is the difference between synthetic biology and systems biology?
**the design and fabrication of biological components and systems that do not already exist in the natural world
#*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.  
**the re-design and fabrication of existing biological systems.
#*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.
===What is the difference between synthetic biology and systems biology?===
#Why bother?  
*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.  
#*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.
*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.
#What is your approach towards synthetic biology?
===Why bother? ===
#*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.
*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.
#Why are you working to redesign bacterium?
===What is your approach towards synthetic biology?===
#*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.
*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.
#Life isn't digital. Why are you trying to implement digital logic in cells?
===Why are you working to redesign bacterium?===
#*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.
*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.
#Is what you're doing dangerous?
===Life isn't digital. Why are you trying to implement digital logic in cells?===
#*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.
*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.
#What about ethical or moral issues?
===Is what you're doing dangerous?===
#*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.
*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.
#What technologies would benefit synthetic biology?
===What about ethical or moral issues?===
#*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.
*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.
#I want to study synthetic biology, where should I go?
===What technologies would benefit synthetic biology?===
#*The field's relatively new and so there aren't any critical mass programs in place as yet. In terms of programs where such work is happening, here is a short list: MIT Electrical Engineering and Computer Science ([[Tom Knight]]); MIT Biological Engineering ([[Drew Endy]]); MIT Computational and Systems and Biology Initiative ([[Drew Endy]] and [[Tom Knight]]); UC Berkeley Bioengineering ([http://www.lbl.gov/pbd/about/people/keasling.htm Jay Keasling], [http://www.lbl.gov/pbd/about/people/arkin.htm Adam Arkin] and others); Caltech Bioengineering, Biology, Engineering and Applied Science ([http://www.aph.caltech.edu/people/elowitz_m.html Michael Elowitz] and [http://www.che.caltech.edu/groups/fha/ Frances Arnold]); Princeton Electrical Engineering ([http://www.princeton.edu/~rweiss/ Ron Weiss]) and Boston University Biomedical Engineering ([http://www.bu.edu/dbin/bme/faculty/?prof=jcollins Jim Collins] and [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Tim Gardner])
*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.
#I'm interested in donating time, money, and/or moral support. What do I do?
===I want to study synthetic biology, where should I go?===
#*Donations of any sort are always welcome. Contact us.
*The field's relatively new and so there aren't any critical mass programs in place as yet. In terms of programs where such work is happening, here is a short list: MIT Electrical Engineering and Computer Science ([[Tom Knight]]); MIT Biological Engineering ([[Drew Endy]]); MIT Computational and Systems and Biology Initiative ([[Drew Endy]] and [[Tom Knight]]); UC Berkeley Bioengineering ([http://www.lbl.gov/pbd/about/people/keasling.htm Jay Keasling], [http://www.lbl.gov/pbd/about/people/arkin.htm Adam Arkin] and others); Caltech Bioengineering, Biology, Engineering and Applied Science ([http://www.aph.caltech.edu/people/elowitz_m.html Michael Elowitz] and [http://www.che.caltech.edu/groups/fha/ Frances Arnold]); Princeton Electrical Engineering ([http://www.princeton.edu/~rweiss/ Ron Weiss]) and Boston University Biomedical Engineering ([http://www.bu.edu/dbin/bme/faculty/?prof=jcollins Jim Collins] and [http://www.bu.edu/dbin/bme/faculty/?prof=tgardner Tim Gardner])
#Why isn't my question listed here?
===I'm interested in donating time, money, and/or moral support. What do I do?===
#*Because you haven't [http://web.mit.edu/synbio/www/comments.html asked us].
*Donations of any sort are always welcome. Contact us.
===Why isn't my question listed here?===
*Because you haven't [http://web.mit.edu/synbio/www/comments.html asked us].

Revision as of 11:14, 16 June 2005

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.

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.

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.

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

  • The field's relatively new and so there aren't any critical mass programs in place as yet. In terms of programs where such work is happening, here is a short list: MIT Electrical Engineering and Computer Science (Tom Knight); MIT Biological Engineering (Drew Endy); MIT Computational and Systems and Biology Initiative (Drew Endy and Tom Knight); UC Berkeley Bioengineering (Jay Keasling, Adam Arkin and others); Caltech Bioengineering, Biology, Engineering and Applied Science (Michael Elowitz and Frances Arnold); Princeton Electrical Engineering (Ron Weiss) and Boston University Biomedical Engineering (Jim Collins and Tim Gardner)

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

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

Why isn't my question listed here?

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