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Design by Any Other Name

"Synthetic biology" is defined as applying engineering principles to biological parts. It is "an area of research focused on the design and construction of new biological parts and devices, or re-design of existing biological systems."

The genetic code of simple organisms, for example, can be constructed in the laboratory using techniques that sew together a strand of specific A's, T's, G's, and C's. Several potential applications have been touted, including creating organisms that are useful in cleaning up biofuels, drug delivery, and drug studies. A recent study involved creating E. coli that are addicted to caffeine, which could be helpful in purifying water and treating asthma.

While some interesting research has come out in this area, the practical applications have not yet caught up with the hype from several years ago when Craig Venter replicated the entire genome of a known bacterium and reinserted it in a cell (see our comments here). The lag is partly due to a couple of fundamental assumptions in synthetic biology that might pose problems in actual applications.

For one, synthetic biology assumes gene expression is the fundamental building block of organisms, which is a reductionistic view of how life works. Certainly, there are some cases where a particular gene codes for a particular disease or a particular function. One classic example is Huntington's disease, which has a very specific genetic marker. Those with the genetic marker will get the disease. However, as we have seen from the results of the ENCODE project, there are many factors that affect whether a gene is expressed, and how proteins function.

Second, according to Drew Endy, one of the authors of two papers on mass-producing synthetic biological components, many biologists have been trying to assemble the component parts of biological systems in a modular, piecemeal fashion (Nucl. Acid Res. published concurrently with Nature Methods). One reason for Endy's team's success is the way that they have approached biological systems. Rather than in terms of modular pieces, they took a more integrated approach. From an article in New Scientist:

The team found that bundling parts together according to their specific function gave more reliable results than considering them separately. This is how nature does it, says Endy, but the dogma had been that all parts should be clearly separated and assembled in a more modular way, which was the principle used to set up the BioBricks registry, an existing library of parts, in 2003. It was a case of "let's change our religion on how you assemble things", says Endy.
This view takes an engineering perspective on biological systems, which is counter to the typical neo-Darwinian style. Darwinism assumes that organisms are built from the bottom-up, where complexity comes from the incorporation of additional components via chance and selection pressure. An engineering perspective assumes that biological systems are built from the top-down.

In other words, the end function is already in mind when the biological system is constructed. Because of this, the system functions as a cohesive whole, rather than as modular components. Furthermore, and as Endy's group in particular points out, the parts of the biological systems are not interchangeable like Lego blocks. They have specific functions.

Evolutionary theory says that trial and error lead to the biological structures that we see today. But this same trial-and-error method does not work in the laboratory setting, so why should we assume that it worked in nature?

In synthetic biology, we have a field of science that applies engineering principles to biological systems. For practical purposes, it assumes that biological systems are engineered and that we can use design principles to re-construct these systems. Maybe that represents more than just a working assumption.