DRS2012 Bangkok Proceedings Vol 4 - Design Research Society

A Critique of Design Methods in Synthetic Biological Design
inventing new spaces for representation and abstraction is also key for composing,
structuring, and designing biological systems that differ from what is already observed in
nature.
Abstraction and Units of Design
At the heart of synthetic biological design lies an inherent desire for abstraction and
functionalism. The study of the most essential units of living systems—from the molecular
composition of cells to the transportation of the information of hereditary characteristics—
informs the units of design that can be used to build or rebuild the living (Jacob 1974).
For example, while in transgenic design the goal is to abstract the units of the living—
genes—from their current organisms to be able to mobilize them in new biological
contexts, Synthetic Biology intends to build new units—bricks—that can encapsulate both
nature-born or human-made biological functions into standardized components that can
then be used to compose complex biological systems.
Design paradigms from computer science and engineering immediately find parallels in
modern biological design. Biological products are designed as abstract chemical or fluidic
automata; biological functions are grouped in modules and assembled like electronic
circuits or networks of signaling pathways; and the kinetics of living systems are modeled
with differential equations and controlled by numerical methods (Purnick and Weiss
2009).
Synthetic Biology intends to build the biological equivalent of electronic parts—such as
transistors, oscillators, logic gates, and chips that can be assembled together to build
complex biological machinery, as noted in Mead and Conway’s oft-cited book,
“Introduction to VLSI Design.” Published in 1979, the book is a cornerstone in electrical
engineering that bridged the gap between the design and fabrication of very large
integrated hardware systems (1979). The premise of VLSI design is quite simple: it allows
system designers to compose circuits without knowing the inner-workings of the
components or their fabrication methods. The design method is based on the ability to
“black box” the function of unknown parts, as each part is expected to operate like a
module within predictable margin of error.
Synthetic Biology embraces the VLSI logic to abstract the biological design process from
unitary and modular design to computation-driven synthesis techniques. The level of
abstraction follows the same logic: sequences of DNA molecules are ‘packed’ as discrete
parts; parts with different functions can then be combined with each other to build
devices; and devices are eventually ordered based on computational logic for the design
of biological circuitry.
Biological Functionalism
Both the analytic drive of Natural Sciences—breaking up the living into understandable
components—and the synthetic drive inherited from Synthetic Chemistry or
Engineering—building up new design from standardized parts—are inherently tied to the
desire to ascribe function to various units. Analytical functionalism is highly debated in
Biology, as assigning retrospective functions to systems that have not evolved in such
manner can be highly misleading and often attributed to a mechanistic view of life (Krohs
& Kroes 2009). On the other hand, synthesizing or building with components is the
primary means of practice in design and engineering. Since the industrial revolution, from
cars, to buildings, computers, and airplanes, almost all complex systems are conceived
and manufactured with this mindset.
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