404 9.3  Synthetic Biology, Biomimicry, and Bionanotechnology

polarization effects, and a far broader spectral diversity which pigment-​based systems cannot

achieve including color tuneability.

There are myriad other examples of biomimicry which have emerged over the past decade,

methods of developing highly advanced structured light (which refers to the engineering of

optical fields both spatially and temporally in all of their degrees of freedom) from biological

photonics crystal structures, smart syringes which cause significantly less pain by adapting

structures inspired from the mouth parts of mosquitos, synthetic proteins motivated by

silk produced from spiders and silk worms designed to help wound healing, natural photo­

synthetic machinery being adapted to develop devices to reduce global warming by cap­

turing carbon from the atmosphere, and even faster trains conceived by using the core fluid

dynamics concepts derived from the shape of the beak of the kingfisher bird (for a super and

fun suite of more examples from the animal kingdom at least, check out the inspired podcasts

by Patrick Aryee, 2021-​22).

9.3.1  COMMON PRINCIPLES: TEMPLATES, MODULARITY, HIERARCHY, AND

SELF-​ASSEMBLY

There are four key principles that are largely common to synthetic biology: the use of

scaffolds or templates, modularity of components of devices (and of the subunits that com­

prise the components), the hierarchical length scales of components used, and the process

of self-​assembly. Nature uses templates or scaffolds that direct the fabrication of biological

structures. For example, DNA replication uses a scaffold of an existing DNA strand to make

another one.

Synthetic biology components are implicitly modular in nature. Components can be

transposed from one context to another, for example, to generate a modified device from

different modules. A key feature here is one of interchangeable parts. Namely, that different

modules, or parts of modules, can be interchanged to generate a different output or function.

This sort of snap-​fit modularity implies a natural hierarchy of length scales, such that the

complexity of the device scales with the number of modules used and thus with the effective

length scale of the system, though this scaling is often far from linear and more likely to be

exponential in nature. This hierarchical effect is not to say that these are simply materials out

of which larger objects can be built, but rather that they are complete and complex systems.

Modularity also features commonly at the level of molecular machines, which often comprise

parts of synthetic biology devices. For example, molecular machines often contain specific

protein subunits in multiple copies.

Self-​assembly is perhaps the most important feature of synthetic biology. A key advan­

tage with synthetic biology components is that many of them will assemble spontaneously

from solution. For example, even a ribosome or a virus, which are examples of very complex

established bionanotechnologies, can assemble correctly in solution if all key components

are present in roughly the correct relative stoichiometries.

9.3.2  SYNTHESIZING BIOLOGICAL CIRCUITS

Many molecular regulation systems (e.g., see Chapter 7) can be treated as a distinct biological

circuit. Some, as exemplified by bacterial chemotaxis, are pure protein circuits. A circuit

level description of bacterial chemotaxis relevant to E. coli bacteria is given in Figure 9.2a.

However, the majority of natural biological circuits involve ultimately gene regulation and

are described as gene circuits. In other words, a genetic module has inputs (transcription

factors [TFs]) and outputs (expressed proteins or peptides), and many of which can function

autonomously in the sense of performing these functions when inserted at different loci in

the genome. Several artificial genetic systems have now been developed, some of which have

clear diagnostic potential for understanding and potentially treating human diseases. These

are engineered cellular regulatory circuits in the genomes of living organisms, designed in

much the same way as engineers fabricate microscale electronics technology. Examples