288 CATALYZING INQUIRY
and neutralization, biomaterials synthesis, or any task that can be done by biochemistry. This is essen-
tially a form of nanotechnology, in which the already existing mechanisms of biology are employed to
operate on structures at the molecular scale.
However, all of these goals will require a different set of approaches and techniques than traditional
biology or any natural science provides. While synthetic biology employs many of the same techniques
and tools as systems biology—simulation, computer models of genetic networks, gene sequencing and
identification, massively parallel experiments—it is more of an engineering discipline than a purely
natural science.
8.4.2.1 An Engineering Approach to Building Living Systems
Although as a viewpoint it is not shared by all synthetic biology researchers, a common desire is to
invent an engineering discipline wherein biological systems are both the raw materials and the desired
end products. Engineering—particularly, electronics design—is an appropriate discipline to draw on,
because no other design field has experience with constructing systems composed of millions or even
billions of components. The engineering design approaches of abstraction, modularity, protocols, and
standards are necessary to manage the complexity of the biomolecular reality.
One important piece of establishing an engineering discipline of building living systems is to create
a library of well-defined, well-understood parts that can serve as components in larger designs. A team
led by Tom Knight and Drew Endy at the Massachusetts Institute of Technology (MIT) have created the
MIT Registry of Standard Biological Parts, also known as BioBricks, to meet this need.^121 An entry in the
registry is a sequence of DNA that will code for a piece of genetic or metabolic mechanism. Each entry
has a set of inputs (given concentrations or transcription rates of certain molecules) and a similar set of
outputs.
The goal of such a library is to provide a set of components for would-be synthetic biology design-
ers, where the parts are interchangeable, components can be composed into larger assemblies and easily
be shared between separate researchers, and work can build on previous success by incorporating
existing components. Taken together, these attributes allow the designers to design in ignorance of the
underlying biological complexity.
These BioBricks contain DNA sequences at either end that are recognized by specific restriction
enzymes (i.e., enzymes that will cut DNA at a target sequence); thus, by adding the appropriate en-
zymes, a selected DNA section can be spliced. When two or more BioBricks sequences are ligated
together, the same restriction sequences will flank the ends of the DNA sequence, allowing the re-
searcher to treat the composite as a single component. BioBricks are in the early stages of research still,
and the final product will likely be substantially different in construction.
8.4.2.2 Cellular Logic Gates
Of particular interest to synthetic biologists are modifications to cellular machinery that simulate
the operations of classical electronic logic gates, such as AND, NOT, XOR, and so forth. These are
valuable for many reasons, including the fact that that their availability in biological systems would
mean that researchers could draw on a wide range of existing design experience from electronic circuits.
Such logic gates are especially powerful because they increase the ability of designers to build more
sophisticated control and reactivity into engineered biological systems. Finally, it is the hope of some
researchers that, just as modern electronic computers are composed of many millions of logical gates, a
new generation of biological computers could be composed of logic gates embedded in cells.
(^121) T. Knight, “Idempotent Vector Design for Standard Assembly of Biobricks,” available at http://docs.syntheticbiology.org/
biobricks.pdf.