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.
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.