The Software Crisis of Synthetic Biology

Abstract

In fifteen years, Synthetic Biology (SB) has moved from proof-of-concept designs to several flagship achievements. Standardisation efforts are still under way, basic engineering concepts such as modularity and orthogonality are still controversial in biology, and making predictions from computer models is still unreliable. A deep characterization in the pattern of re-use of biological blocks in SB has not been attempted to date. We have compared the topological organisation of two different technological networks, one associated to a standard, large-scale software repository and the second provided by the Registry of Standard Biological Parts (RSBP). Our results strongly suggest that software engineering, and not industrial engineering, is the closest complex system to SB. In both cases, combining standard or quasi-standard components assembly with tinkering may not be at odds with success.

Synthetic microbiology as a source of new enterprises and job creation: a Mediterranean perspective

“…Both the potential and limitations of standardization in SB are exemplified by the international Genetically Engineered Machine (iGEM) competition, in which students worldwide present synthetic biology projects based on organisms engineered from a toolbox of BioBricks™. However, Biobricks™ has limitations as universal building blocks in SB (Vilanova and Porcar, ; Valverde et al ., ). Interestingly, these limitations have not been an obstacle for a dense network of synthetic biology enterprises to flourish in the US, while in Europe, the landscape of synthetic biology enterprises is sparse by comparison, even if the main efforts to overcome a paucity of standardization are totally or partially of European origin, such as the development of a Standard European Vector Architecture (SEVA; Silva‐Rocha et al ., ), or the standardized representation of SB designs known as the Synthetic Biology Open Language (SBOL; Galdzicki et al ., ).…”

DNA as Features

“…Ours is not the first analysis of the BioBricks repository. Valverde et al examined the relationships within the repository from a network perspective to gain an understanding of the software complexity (they too treat this as a software ecosystem) [37].…”

The Hidden Charm of Life

“…Intuitively, cells seem genomically and metabolically too entangled, flexible, interconnected, and adaptable to be considered mere Lego-like complicated (not to be confounded with complex) biostructures. Moreover, the compared analysis of the Biobrick repository, Lego, and software (Java) suggests that the closest comparative framework to biological complexity should be software rather than hardware [13]. It is, thus, somehow contradictory that the exaggerated goals and hype with which SB is often described are also associated with a reductionist view on biological complexity, which is thus seen as the unwanted trait to remove.…”