Paradigms in Synthetic Biology Part II: Semiotics and Economics

In the first post in this series (See PartI: Analog to Digital), I point out how synthetic biology will require researchers and engineers to remain flexible with regards to the conceptual framework they use. Indeed, entirely new concepts may be necessary for this field, which is the intersection of engineering and molecular biology (which is not as fully understood as other sciences which have been grappled by engineers). Treating a genetic network or transcription circuit as components that follow digital logic has it's advantages, but also it's limitations (mostly due to the real physical nature of transcription and molecular biology occurring in the cell). Other paradigms, such as analog computing, can also be applied and sometimes inform more powerful designs in synthetic biology.

Beyond different types of computing, it may be helpful to borrow concepts and framework from a wide variety of fields. Below, I discuss several other fields and concepts which may find use in synthetic biology. One prism through which molecular biology can be viewed is that of semiotics; the study of information and signs. Even the field of economics may have concepts which biologists can find useful. After all, economists need to model complex studies, which many different actors / agents, with a great deal of uncertainty.

How do you see Synthetic Biology? Is there a certain paradigm or field that you think Synthetic Biologists can borrow useful concepts from? Does all of this dense, abstract blather simply amount to hot air? Feel free to share by leaving a comment below.

I recently attended the iGEM 2013 world championship jamboree. Stay tuned for a future post reflecting on my experience!

Synthetic Biology Paradigms, Part I

Is any one conceptual framework is sufficient for advancing the field of Synthetic Biology? Will a new paradigm be needed eventually? We can apply a diverse set of paradigms to think about how biology works: Analog devices (clocks, gears, etc) or digital circuits (processor), biochemical pathways where the flow of substrates can resemble the flow of fluids through a complex network of pipes, or even complex mathematical constructs (like those developed by Wolfram) can all be used to represent or draw parallels with different aspects of molecular biology.

Synthetic Biology is sometimes described as molecular biology with an engineering perspective. Indeed, many leading researchers in the field have backgrounds in electrical engineering or some related discipline. Much of the earlier work done by pioneering synthetic biologists has been to formulate biological phenomenon in more familiar engineering terms. These efforts has enabled engineers to leverage their expertise during the design of complex artificial genetic networks and cell behaviors. Are the promises of synthetic biology within our grasp, limited only by a need for the import of more engineering knowledge?

Despite the success of an engineering paradigm in synthetic biology, I believe that harnessing the full potential of this field will require new concepts and perspective. Synthetic Biology can and should grow from conceptual frameworks borrowed from engineering disciplines, but also must not be constrained by them. 

Incorporating ideas and concepts from fields other than the digital logic of electrical engineering can only serve to strengthen the efforts of a synthetic biologist. In this series of articles, I will detail how perspectives from Molecular Biologists, as well as Economists and other Engineers (particularly those that deal with Analog systems) may prove to be an invaluable part of the synthetic biologist's conceptual toolkit. The remainder of this article (which you can view by selecting 'Read More') details a recent advance in synthetic biology: the design of an analog genetic circuit by the Sarpeshkar Laboratory Group. I also discuss how Synthetic Biology can mimic and learn from nature, and why keeping an open mind and a flexible vocabulary may be important.