Can Synthetic Biology Produce Cheaper Biofuel? Should It?

News out of Washington at year-end included an announcement from the Department of Energy (DOE) concerning a breakthrough at the Joint BioEnergy Institute (JBEI) in which scientists have developed a methodology for creating “RNA machines” which can be used to enhance or express certain characteristics in a living organism.

This new capability is initially being used at JBEI to modify e-coli bacteria in such a way as to make them more efficient in their digestion of switchgrass, allowing them to convert released sugars into gasoline, diesel and jet fuel at lower cost.

This new RNA manipulation capability, which stems from an advanced type of computer-assisted design (CAD) for bio-molecules, can also be applied to a broad range of applications including medicines to more effectively treat diseases like diabetes and Parkinson’s.

A briefing from the DOE’s Energy Efficient and Renewable Energy (EERE) Lab says, “Specifically, researchers focused their design-driven approach on RNA sequences that can fold into complicated three-dimensional shapes called ribozymes and aptazymes. Using JBEI-developed computer-assisted models and simulations, researchers then created complex RNA-based control systems that are able to program a large number of genes. In microorganisms, "commands" sent into the cell will be processed by the RNA-based control systems, enabling them to help develop desired products.”

For anyone desiring the unadulterated version of these developments, the research was written up in last month’s Science.

An article in the newsletter of Lawrence Berkeley Lab (LBL), which is part of JBEI, describes the CAD tools being used in this effort as being similar to those used in the development of integrated circuits with millions of transistors. This new field is being called Synthetic Biology which is, “an emerging scientific field in which novel biological devices, such as molecules, genetic circuits or cells, are designed and constructed, or existing biological systems, such as microbes, are re-designed and engineered. A major goal is to produce valuable chemical products from simple, inexpensive and renewable starting materials in a sustainable manner.”

What the research produced was biochemical devices assembled from components that “were characterized in vitro, in vivo and in silico,” based on biophysical simulations, with which they achieved a 94% correlation with the predicted gene expression levels.

This type of genetic manipulation differs from transgenic genetic engineering normally associated with genetically modified organisms (GMO) in which genes from one organism is injected into another organism in an effort to express a desirable characteristic or trait in the target organism. Instead of the GMO paradigm, which could be likened to crossing a tomato with a fish, this type of manipulation can be viewed at one extreme as like giving drugs to a paramecium. At the other extreme however, it could entail creating entirely new life forms from scratch. This manipulation was done for the first time in May 2010 at the J. Craig Venter Institute, sparking quite a controversy about the safety of the practice at the time.

It would be nice to take comfort in knowing that the government is looking after our well-being here, but given their track record of aggressively promoting genetically modified foods in the absence of anything resembling scientific certainty of its safety, it is hard to take comfort in this.

Thus, the prospect of an enhanced version of e coli being produced is a bit unsettling, considering how that little critter has already caused more than its share of trouble among us humans in its un-enhanced form. Certain strains of the bacteria can cause an infection which can lead to kidney failure in older adults and young children.

Jay Keasling, Director of JBEI said that, “Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs.”

That same complexity is what gives one pause to consider what the consequences of this kind of manipulation might lead to. I’m not saying it shouldn’t be done, clearly there are tremendous potential benefits ranging from biofuels to synthetic plastics, to a possible cure for malaria. But I think it must be tested thoroughly and given a complete environmental impact review, from an integrated prospective that includes both human and ecosystem health, with the conditions under which it is made available in the balance.

[Image credit: Photo courtesy of Lawrence Berkeley National Lab]

RP Siegel, PE, is the President of Rain Mountain LLC. He is also the co-author of the eco-thriller Vapor Trails, the first in a series covering the human side of various sustainability issues including energy, food, and water.  Like airplanes, we all leave behind a vapor trail. And though we can easily see others’, we rarely see our own.

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