Synthetic Biology | Definition and delimitation
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2
Definition and delimitation of
synthetic biology
2.1
“Synthetic biology” and “Synthetic genomics”
The origin and, as a consequence, the definition of synthetic biology are not well established (Stephanopoulos
2012). A consensus has yet to be reached on a precise definition of synthetic biology (Cameron et al. 2014).
Although there is general assent to differentiate synthetic biology from biotechnology, metabolic engineering
and systems biology, it is still difficult to distinguish it from more traditional engineering goals, and implies,
e.g., a higher rate of sophistication as compared to metabolic engineering (Porcar and Pereto 2012). One
characteristic, however, is the use of molecular biology tools and techniques to forward-engineer cellular
behaviour; to reach this, a set of common engineering approaches and laboratory practices have developed.
The principal idea was to follow a bottom-up approach based on molecular “parts” that should be used to
forward-engineer regulatory networks. The first genetic circuits were created using
Escherichia coli, and were
described using simple mathematical models (model-based design approach). The desired behaviour,
however, was only reached after replacing parts.
Porcar and Pereto (2012) proposed to restrict the term “synthetic biology” to four research fields:
Model-inspired research following strict engineering principles
applied to biotechnology
Top-down approaches significantly simplifying cell complexity and aiming to implement semi-synthetic
cells that are easier to manipulate further (in a broad sense, a chassis)
Bottom-up, empirical explorations aiming at
de novo construction of increasingly complex proto-cells,
displaying a link between genotype (informational substance) and phenotype/behaviour
Xenobiology research
They also suggest “exclusion criteria”, like lack of design, use of assay/error tuning strategies, lack of
orthogonality and/or modularity, and in addition propose that ad-hoc strategies and standard-free approaches
are incompatible with the concept.
According to Stephanopoulos (2012) it is important to distinguish synthetic biology from other areas to avoid
the replication of existing fields under a different name.
There is no official or formal definition of “synthetic biology” or “synthetic genomics”.
One frequently cited (and modified) definition of “synthetic biology” is that on
http://syntheticbiology.org/
:
Synthetic biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the
re-design of existing, natural biological systems for useful purposes.
More papers include a definition of “synthetic biology” compared to “synthetic genomics”. Following analysis
of the two terms, they appear to be interchangeable; no clear difference between them could be found in
various publications.
König et al. (2013) tried to differentiate between “synthetic biology” and “synthetic genomics”:
Synthetic biology is the design and construction of biological components, functions and organisms (that do
not exist in nature) and the redesign of existing biological systems (to perform new functions)
Synthetic genomics encompasses technologies for the generation of chemically synthesised genomes to allow
for simultaneous multiple changes to the genetic material of organisms.
The following main elements of synthetic biology (genomics) are identified in the definitions:
Synthetic Biology | Definition and delimitation
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Engineering principles are applied and include metabolic engineering as the simplest form of synthetic
biology up to the engineering of complex biological entities (regulatory networks, systems, organisms,
ecosystems). In this context the term “construction” is frequently used to describe the construction of
biological parts but also systems.
Synthetic biology is clearly defined as inter- or transdisciplinary field. It includes the use of state-of-
the-art molecular technologies (“omics”-approaches).
Novelty: concepts and design, and the used elements like biological parts, devices, and systems are
novel. New functions and unique functionality are created.
The basis encompasses naturally existing elements from biological blueprints that are engineered to
improve their function. By this, a toolbox of biological building blocks (“BioBricks™”) is created.
Systems are designed from simple, predictable and powerful modules. The ultimate aim is to be
independent from standard biological “bricks”.
Minimal genomes are constituted in order to render the outcome predictable and efficient. These
genomes contain only the essential parts.
Self-replication is an important feature of the resulting living organisms.
Knowledge on the behaviour of biological systems is the basic prerequisite for the concept.
In conclusion and based on the published definitions, for the purpose of this project we propose to define
synthetic biology/genomics as
The design and construction of novel organisms with the capability to self-replicate, based on the
concept of minimal genomes and by using well-defined biological building blocks.
Note: In September 2014 an “Opinion on Synthetic Biology I Definition” was published addressing a mandate
on synthetic biology from Directorates Health and Consumers (SANCO), Research and Innovation (RTD),
Enterprise and Environment to the three Scientific Committees Health and Environmental Risks (SCHER),
Emerging and Newly Identified Health Risks (SCENIHR), and Consumer Safety (SCCS). The Opinion includes an
operational definition for synthetic biology (SCENIHR et al. 2014):
SynBio is the application of science, technology and engineering to facilitate and accelerate the design, manufacture
and/or modification of genetic materials in living organisms.
2.2
Synthetic biology, systems biology, metabolic engineering and the need to
differentiate between the fields
There is general assent that synthetic biology is a well-defined field different from systems biology, metabolic
engineering and biotechnology (Porcar and Pereto 2012).
On the other hand, there is
a close coupling between
synthetic biology, systems biology and metabolic engineering (Nielsen and Keasling 2011). The techniques and
methodology developed in synthetic biology are also important to promote the development of systems
biology (Kitney and Freemont 2012).
In the course of our literature research we identified the need to distinguish between synthetic biology and
metabolic engineering. However, it has also been found to be difficult if not impossible to distinguish some
aims of synthetic biology from more traditional engineering goals (Porcar and Pereto 2012), and that to date
there is no consent concerning the boundaries between synthetic biology and metabolic engineering (CBD
2014).