An New Frontier in Design: The Simulation of Open Engineered Biological Systems

Biology will lie at the heart of many 21st century technologies to sustainably address the numerous challenges facing societies such as waste, energy, water, healthcare, new chemicals and materials, and agriculture. This ambitious project seeks to develop a suite of universal principles and models for the scalable simulation of open biological systems thereby allowing the engineering of new functionalities offered by natural or synthetic, mainly micro-, organisms for the benefit of mankind.

We live in a world that is increasingly urbanising and populated putting many pressures on the globe and its natural resources. One of the biggest challenges is sustaining global health, prosperity and well-being in a way that does not harm societies requiring these benefits nor the earth's natural resources. In the last two centuries, engineering has been central in providing the infrastructure and resources responsible for these societal gains. The engineering challenge in the 21st century is to continue to make these, and new, provisions for more people in a more sustainable way.

Thomas Tredgold, the first President of the Institute of Civil Engineers, defined engineering as "the art of directing the great sources of Power in Nature for the use and benefit of mankind". Engineering has expanded as it has sought and exploited new sources of Power in Nature and new concepts and tools by which said sources can be manipulated. Many believe that Biology is the next source of Power and that Engineering Biology it will be central to our goal of generating a new suite of intrinsically sustainable technologies. However, there is a substantial gap between rhetoric and reality in many accounts of the application of engineering biology. We will only open up this frontier if we are a brutally honest about the limitations, astute in our analysis of the bottlenecks and effective in innovations to obviate them. Though this is a contemporary challenge, it is something engineers have always done, using mathematical models and scientific principles to winnow the pipe dreams from the awesome but achievable (Rankine, 1855).

One of the greatest limitations in biology is taking what is possible in the test-tube and making it a reality in the reactor or environment; using relatively cheap resources and in the face of a large and highly diverse natural microbial population. In this project, we seek to use the best scientific principles and theories to develop a suite of universal principles and models for the scalable simulation of open biological systems. These models will allow the engineering design of new functionalities offered by natural or synthetic organisms for the benefit of mankind for a range of technologies addressing a range of different challenges.

The potential impact of this research is as broad and ubiquitous as microbial communities themselves. We hope to transform our ability to predict and engineering naturally occurring microbial communities where ever they are found. The water industry is hopefully but a launching pad for our approach. But here transformative biological technologies could change the treatment of wastes in temperate climate from a net energy consumer to a net energy generator. We might, at the same time, find ways to rationally engineer low energy attached growth systems to remove micropollutants. This will benefit the industry and their customers by lowering costs and insulating consumers from the effect of higher energy costs. At a totally different scale, in a totally different industry, we could design personal care products in simulated hair follicles, reducing the cost and time of getting an idea to market and widening the range of biota friendly products. In the oil industry corrosion is thought to cost between 10 and 100 billion dollars a year: valid multiscale model of may allow us to ameliorate or avoid this cost by conceiving of corrosion resistant pipe surface geometries or by using ecological principles to discourage the bacteria responsible for corrosion. The impact of paints used in the shipping industry to reduce drag could be tested in silico before ever being applied to a ship. The wealth of microbial resource in the natural world could be harnessed more predictably and more quickly with benefits that we have not yet conceived. This would allow engineers to use microbes in areas where, for cultural or technical reasons, synthetic biology may not be an option. And where synthetic biology does have a role to play in an open microbial system, the "synbio" solutions will be found faster and more cheaply. If these ideas are even half right, we could enter a generation of engineering biology with broad applications opening up new lines of business for start-ups and established enterprises alike.