Functional Synthetic Biology

Abstract

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.

Standardized Representation of Parts and Assembly for Build Planning

“…The resulting build terminology, illustrated in Figure and detailed below, is centered on three main concepts: part , backbone , and assembly . The terminology also originally included a definition for a device as a functional mechanism in some biological context, but that definition proved unnecessary for the discussion of build planning and has since been more fully developed in a compatible fashion within the framework of “functional synthetic biology” . We therefore use the term “device” only as an informal or intuitive notion in this presentation and refer the reader to the other article if a more formal or precise definition is desired.…”

Synthetic Biology and Its Potential in U.S. Medical Therapeutics: A Comprehensive Review: Exploring the Cutting-Edge Intersections of Biology and Engineering in Drug Development and Treatments

“…The review underscores synthetic biology's role in bringing new capabilities to medical and pharmaceutical research (Yan et al, 2023). Aldulijan et al (2022) explore the concept of Functional Synthetic Biology, focusing on designing biological systems based on function rather than sequence. This approach decouples the engineering of biological devices from their specific applications, allowing more flexibility and predictability in design.…”

“…Functional Synthetic Biology aims to overcome current limitations in synthetic biology by emphasizing conceptual and organizational change, supported by software tooling. This reorientation towards function-based design represents a significant advancement in the field, enhancing the engineering of biological systems (Aldulijan et al, 2022). Buecherl and Myers (2022) highlight advancements in genetic design automation (GDA) tools and standards for synthetic biology.…”

Engineering is evolution: a perspective on design processes to engineer biology

“…A common trend across the field has been to apply classical engineering principles such as standardisation 7 – 11 , decoupling 12 – 17 and abstraction 18 , 19 in an attempt to tame biological complexity. However, there has been a conspicuous lack of consideration as to how these principles should be applied and whether the fact that biology is an evolved and evolving substrate warrants a different approach.…”