Fossil fuels are running out
Since the mid nineteenth century, humans have progressively mastered the discovery, extraction, and combustion of fossil fuels. Fossil fuels are the remains of organisms, mostly thick growths of plants from more than 500 million years ago, that were buried under heavy layers of sediment and slowly heated and compressed, under conditions without oxygen, into carbon-rich deposits. These are now used as the energy source for almost all modern transportation and electricity generation systems.
There are many reasons why this is now believed to be unsustainable. Fossil-based fuels are just the remains of photosynthetic activity that once took place on the earth’s surface over hundreds of millions of years — when plants converted solar energy and carbon dioxide into biomass. However, by burning all this carbon very rapidly, we are returning carbon dioxide, sulfur and nitrous oxides to the atmosphere in very high concentrations and rates that cannot be balanced by the planet’s natural cycles. Hence, we are beginning to observe several adverse affects of this build up including global warming and increased incidences of asthma and pulmonary disorders.
It is obvious that, since we are burning fuels at a pace far exceeding that of their creation, we will eventually exhaust them. By most estimates we have 50-100 years’ worth of oil and gas left under the earth’s surface. The search for renewable fuels is thus well motivated.
The challenge of renewable fuels
Solar energy is the most abundant renewable resource available, and photosynthesis is a great template for how this energy can be converted into chemical energy (which is the energy stored in the chemical bonds connecting atoms together in matter). The ability to transform sunlight into fuel is, after all, what has always powered human societies, starting from the use of firewood as our primary fuel, to the use of coal, oil and gas. It is therefore natural that, when looking for sustainability, we turn back to the sun and photosynthesis to transform its energy into biofuels.
The total solar energy falling on the earth exceeds the energy humans consume globally by several thousand fold . However, the two main challenges of harvesting this energy are its diffuse nature and the low efficiencies in capturing and storing it. Sunlight is diffuse in two ways – it is distributed across a wide range of wavelengths (a property of light manifested through the different colors of light, which carry different amounts of energy), and is also spread across the surface of the earth.
One way to capture this solar energy is biofuels. Biofuels are fuels, which are chemically similar to gasoline and diesel, but are produced by processing crops, algae or microbial culture. The carbon in biofuels comes from carbon dioxide that plants convert to their biomass through photosynthesis. Hence, burning them for energy doesn’t add any net carbon dioxide to the atmosphere, making them ‘carbon neutral’. However, by some estimates, we would need to use an area as large as a quarter of the total land used for agriculture in the US today to generate enough biofuels to meet American transportation fuel use . It is thus easy to see that, to avoid biofuel production from competing with food production and other land-use, there is a need for much more efficient biological conversion of sunlight into chemicals. Synthetic biology may be part of the answer.
What is Synthetic Biology?
In its earliest days, biology was a largely observational endeavor, looking at how whole organisms act and survive. But in the last 6-7 decades biology has undergone a revolutionary transformation with an understanding of the molecular processes underlying how cells and organisms work. Synthetic biology is a new field of biological engineering that aims to use and build upon our vast leaps in the molecular understanding of biological systems to make it easier and more systematic to redesign microorganisms, plants, animals and algae by tinkering with their genetic materials.
Molecular biology has revealed that there are many common and basic genetic motifs that combine in innumerable ways to create the brilliant diversity of life on earth. Now that we know some of these basic parts, engineers are beginning to try building new biological functions by rearranging these parts in new patterns. Synthetic biology methods can, for instance, help make plants more resistant to drought and pests by artificially enhancing genes responsible for those tasks. An example is DroughtGard Hybrid corn, a drought tolerant variety engineered by Monsanto  to produce a protein (cspB) that helps bacteria deal with heat, cold and dryness stresses. In a similar vein, engineers can now create yeast and bacteria that can convert substantial amounts of plant husk into ethanol or oils that can then be used as fuel . Synthetic biology has the potential to be breeders’ dreams come true. What traditional plant breeders would rarely achieve after generations of mixing plant varieties and selecting for different traits, synthetic biology offers the ability to quickly engineer in a lab simply by directly giving organisms the genes to produce the wanted traits.
Making fuels faster and cheaper
Biofuel production involves a few interesting design choices for synthetic biologists. These include picking organism(s) to engineer and choosing the elements of their genetic make up to tinker with. Microbes are a favorite for many researchers since they are relatively easy and cheap to grow in labs. The workflow for most engineers involves repeats of a “Design-Build-Test” cycle, which can be performed more quickly and cheaply in microbes than in larger plants. However, working with plants does have the advantage that they are more compatible with current agricultural setups. Photosynthetic microbes like algae and cyanobacteria often need special reactors designed for them, which involve pumping large amounts of water and have high maintenance.
Once the choice of organism is made, the actual engineering is done on two main fronts. Efforts are being made to increase the efficiency of sunlight and carbon dioxide capture so that organisms can grow faster and, secondly to change the chemical composition that these organisms grow into. While plants or microbes typically convert sunlight and carbon dioxide into their biomass (mostly in the form to of substances like sugars and proteins), scientists are trying to engineer them produce and secrete oily substances, fatty acids, alcohols etc. These are chemicals that carry much more energy per pound and are much better suited for use as fuels than cellular biomass.
Many synthetic biologists are also attempting to get heterotrophic microbes (ones that can’t make their own food with photosynthesis but instead need to be fed with organic compounds) to convert the biomass from plants into usable fuels. Creating biofuels this way would then involve a two-step approach in producing the fuel, where plants are first engineered to grow as quickly as possible and then are ground up and fed to E. coli, yeast, etc., that would convert that biomass into ethanol and other fuels. The efforts to produce corn ethanol with engineered yeast have become popular recently, and can be considered an extension of what beer and malt brewers have been doing for centuries. Synthetic biology aims to make this process many fold more efficient and better suited for fuels, like octane, that can be used to run existing gasoline engines much more efficiently than ethanol can, which is crucial in making the transition from a fossil fuel to a biofuel-based society as easily as possible.
Concerns, prospects and a look towards the future
Synthetic biology, with its promise of being a means to design desired features into organisms, is understandably faced with controversy. Criticisms range from concerns about the environmental effects of creating ‘super-bugs’ in labs, to ethical questions about humans’ efforts to play intelligent re-designers of natural beings. Safety and environmental impact are very important considerations that scientists are actively trying to address already by making these organisms unable to grow outside of controlled laboratory, farm or bioreactor conditions. In terms of the ethical question, it might be argued that most engineers aren’t necessarily creating new “unnatural” entities – they are just using the repertoire of very powerful biological functions created by nature and rearranging them, much in the same way as a gardener selects for desirable traits when breeding flowers. As synthetic biology is just in its early stages of development, it will be important to involve all stakeholders in a reasoned consideration of all possible concerns, and an open and democratic deliberation on the pace and extent that we as a society will pursue synthetic biology. With these issues properly addressed, synthetic biology may yet fulfill its promise as a way forward in our quest for clean, sustainable fuel.
Gairik Sachdeva is a PhD student in Bioengineering at the Harvard School of Engineering and Applied Sciences.
 Savage, DF, Way, J, Silver, PA. (2008) Defossiling Fuel: How Synthetic Biology Can Transform Biofuel Production. ACS Chemical BiologyDavid F. Savage, Jeffrey Way and Pamela A. Silver. ACS Chemical Biology 3(1):12-16.
 Stecker, T, and ClimateWire. “Drought-Tolerant Corn Efforts Show Positive Early Results”, Scientific American (July 27,2012) http://www.scientificamerican.com/article.cfm?id=drought-tolerant-corn-trials-show-positive-early-results
 “Bioenergy Introduction”, Joint Bioenergy Institute, Berkeley http://www.jbei.org/bioenergy.html
 Hutson, J. “Synthetic biology explained”, techNyouvids (August 9, 2011) http://www.youtube.com/watch?v=rD5uNAMbDaQ
 Synthetic Biology Engineering Research Center (Synberc) http://www.synberc.org/
 Joint Bioenergy Institute, Berkeley http://www.jbei.org/bioenergy.html