This blog is for assorted documentation of synthetic biology, systems biology, genetically engineering organisms, bioinformatics related to modeling synthetic lifeforms, and design of biobricks-style compatible DNA parts.
I stem from an electrical engineering / computer engineering / software engineering background (not biology or life science) so my perspective may differ from the typical biologist’s. In particular, I’m not afraid of math. ;-D After many years developing low-level hardware and embedded software for consumer and telecommunications products, working at my own company, at small startups, and at large companies, I find the challenges of biology quite refreshing.
Interesting people may contact me as follows.
Jonathan Cline jcline at no spam email, thanks ieee.org Mobile: +1-805-617-0223 skype: d2_jcline
A neat quote describes the state of synthetic biology; from a recently published editorial in Molecular Systems Biology 3:158, 18 December 2007, by Luis Serrano, from EMBL-CRG Systems Biology Unit, Centro de Regulación Genomica CRG, Barcelona, Spain. doi:10.1038/msb4100202
According to this vision, Synthetic Biology should be able to rely on a list of standardized parts (amino acids, bases, proteins, genes, circuits, cells, etc…) whose properties have been characterized quantitatively and on software modeling tools that would help putting parts together to create a new biological function. In this respect, it is encouraging to observe how fast the number of parts and circuits is growing at the MIT ‘Registry of Standard Biological Parts’ (http://parts.mit.edu), encompassing terms that will make any engineer happy (invertors, noise suppressors etc…).
However, life is not that simple. Although clearly a repository of well-characterized parts is a great idea, we should not forget about the daunting complexity of living systems, especially eukaryotes compared with prokaryotes. Thus, aside from the challenging task of having a repository of parts for different organisms (there is no guarantee that a part that works in Escherichia coli will work in Bacillus subtilis), we can never rule out the possibility that new emergent unexpected properties pop up when putting together parts that have been characterized in isolation or in a different context. Moreover, if we want to redesign a car, we already know the specifications of all its components, how they work together and how the car will behave under different conditions. This is obviously not the case for living systems, where even for the simplest of them we know very little (i.e., phage simplification by Chan et al, 2005). Tom Knight, a strong advocate of Synthetic Biology, argues that many problems regarding complexity can be overcome if we keep to key notions: the principles of hierarchical abstraction, modularity, standardization and flexibility, and define appropriate levels of abstraction in the description and design of biological systems. But the complexity of life continues to surprise us and even concepts like the central dogma—one gene, one RNA, one protein—is becoming more and more eroded, with new discoveries in epigenetics, splicing, transcript analysis etc…, increasingly challenging our classical simplified view of gene regulation.
Thus, the engineers still have a lot of work to do.
If you’d like a simpler overview of this merging technology of biology & engineering, a good introduction is this video from MIT: