Abstraction

Abstraction is also an integral part of the methods underlying synthetic biology. In synthetic biology, we use an abstraction hierarchy to help us organize our projects. I have devised a hypothetical synthetic biology project that aims to produce a biosensor in E. coli that causes cells to glow green in the presence of lead. Such a system could be used to test soil, drinking water, or paint samples for toxic levels of lead. The figure at right summarizes the description that follow.

Since synthetic biology programs living systems using DNA, we have to begin by ensuring we have all of the physical DNA required to build our sensor. This takes us to the first level of abstraction: DNA sequences. For example, our biosensor requires the DNA that encodes the GFP gene (atgcgtaaagga . . . taa) somewhere in the DNA programming to allow the cells to glow green. Once we have all of the DNA, we no longer have to deal with individual DNA sequences. Instead we can give each functional unit of DNA a part name (such as GFP) and number (E0040). The part level of abstraction is the step above DNA sequences on the hierarchy.

We can move to the third level of abstraction by combining parts into devices. A device is composed of several parts connected together in a meaningful way. When dealing with devices we only have to know their overall behavior, or their inputs and outputs. Their component parts are unnecessary details. For our biosensor, we can imagine two devices working in concert. The first device is a sensor that produces the lac repressor in the presence of lead ions (Pb²⁺). This device would utilize a lead-sensitive promoter part and the lacI gene part. The second device uses the lac repressor produced by the first device as an input and produces GFP as its output. Such a device would utilize an inverter part, which changes a repressor input into a positive output, and the GFP part.

Combining these two devices brings us to the fourth level of abstraction: systems. Our lead biosensor system uses the presence of lead as an input, and its output is making the E. coli cells glow green. Anyone who uses this biosensor would only need to know the connection between toxic levels of lead and the cultures of E. coli glowing green. They would not need to concern themselves with the devices, parts, and DNA sequences used to build the system.

Synthetic biology makes full use of this convenience. It is easier, and often more meaningful, to speak about a project at the part, device, or system level (we rarely rattle off DNA sequences!). And this practice is something that we are all familiar with. The electronic devices we use every day-computers, cell phones, and watches-can be understood without knowing anything about their component parts. If you wanted to know a bit more about your computer, you could look up which processors, chips, and drives it contains without concerning yourself with how the resistors, transistors, capacitors, etc. are hooked together.

Image Credit: Adapted from PDB file 1EMA; Benjah-bmm27 (via Wikimedia); personal images

References and Further Reading:

Campbell, A.M. What is Synthetic Biology? (2009).

Endy, D. Foundations for Engineering Biology. Nature 438(24), 449-53 (2005).