292 CATALYZING INQUIRY
Aside from the technical challenges of achieving the desired results of synthetic biology projects,
there are significant concerns about the misuse or unintended consequences of even successful work. Of
major concern is the potential negative effect on the environment or the human population if modified
or created organisms became unmanaged, through escape from a laboratory, mutation, or any other
vector. This is especially a concern for organisms, such as those intended to detect or treat pollutants,
that are designed to work in the open environment. Such a release could occur as a result of an accident,
in which case the organism would have been intended to be safe but may enter an environment in
which it could pose a threat. More worrisome, an organism could be engineered using the techniques of
synthetic biology, but with malicious intent, and then released into the environment. The answer to
such concerns must include elements of government regulation, public health policy, public safety, and
security. Some researchers have suggested that synthetic biology needs an “Asilomar” conference, by
analogy to the conference in 1975 that established the ground rules for genetic engineering.^132
Some technical approaches to answer these concerns are possible, however. These include “bar-
coding” engineered organisms, that is, including a defined marker sequence of DNA in their genome
(or in every inserted sequence) that uniquely identifies the modification or organism. More ambitiously,
modified organisms could be designed to use molecules incompatible with natural metabolic pathways,
such as right-handed amino acids or left-handed sugars.^133
8.4.3 Nanofabrication and DNA Self-Assembly^134
Nanofabrication draws from many fields, including computer science, biology, materials science,
mathematics, chemistry, bioengineering, biochemistry, and biophysics. Nanofabrication seeks to apply
modern biotechnological methodologies to produce new materials, analytic devices, self-assembling
structures, and computational components from both naturally occurring and artificially synthesized
biological molecules such as DNA, RNA, peptide nucleic acids (PNAs), proteins, and enzymes. Ex-
amples include the creation of sensors from DNA-binding proteins for the detection of trace amounts of
arsenic and lead in ground waters, the development of nonsocial DNA cascade switches that can be
used to identify single molecular events, and the fabrication of novel materials with unique optical,
electronic, rheological, and selective transport properties.
8.4.3.1 Rationale
Scientists and engineers wish to be able to controllably generate complex two- and three-dimen-
sional structures at scales from 10–6 to 10–9 meters; the resulting structures could have applications in
extremely high-density electronic circuit components, information storage, biomedical devices, or
nanoscale machines. Although some techniques exist today for constructing structures at such tiny
scales, such as optical lithography or individual atomic placement, in general they have drawbacks of
cost, time, or limited feature size.
Biotechnology offers many advantages over such techniques; in particular, the molecular precision
and specificity of the enzymatic biochemical pathways employed in biotechnology can often surpass
what can be accomplished by other chemical or physical methods. This is especially true in the area of
nanoscale self-assembly. Consider the following quote from M.J. Frechet, a chemistry professor at the
(^132) D. Ferber, “Synthetic Biology: Microbes Made to Order,” Science 303(5655):158-161, 2004.
(^133) O. Morton, “Life, Reinvented,” Wired 13.01, 2005.
(^134) Section 8.4.3 draws heavily from T.H. LaBean, “Introduction to Self-Assembling DNA Nanostructures for Computation and
Nanofabrication,” World Scientific, CBGI, 2001; E. Winfree, “Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D
Assembly Experiments,” Journal of Biomolecular Structure and Dynamics 11(2):263-270, 2000; J.H. Reif, T.H. LaBean, and N.C.
Seeman, “Challenges and Applications for Self-Assembled DNA Nanostructures,” pp. 173-198 in Proceedings of the Sixth Interna-
tional Workshop on DNA-Based Computers, A. Condon and G. Rozenberg, eds., DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, Springer-Verlag, Berlin, 2001.