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

生物学将是21世纪许多技术的核心，以可持续地应对社会面临的众多挑战，如废物、能源、水、医疗保健、新化学品和材料以及农业。这一雄心勃勃的项目寻求开发一套通用原则和模型，用于开放生物系统的可扩展模拟，从而使自然或合成生物(主要是微型生物)提供的新功能得以工程设计，以造福人类。我们生活在一个城市化和人口日益增长的世界，这给全球及其自然资源带来了许多压力。最大的挑战之一是以一种既不损害需要这些好处的社会也不损害地球自然资源的方式维持全球健康、繁荣和福祉。在过去的两个世纪里，工程在提供基础设施和资源方面发挥了核心作用，这些基础设施和资源对这些社会收益负有责任。21世纪的工程挑战是继续以更可持续的方式为更多的人提供这些新的供应。土木工程师学会首任主席托马斯·特雷德戈尔德将工程学定义为“引导大自然中巨大的能源为人类服务和造福的艺术”。工程学已经扩大，因为它在自然界中寻找和利用新的能源来源，以及可以操纵这些来源的新概念和工具。许多人认为生物学是下一个动力来源，工程生物学将是我们产生一套新的本质上可持续的技术的目标的核心。然而，在工程生物学应用的许多描述中，花言巧语和现实之间存在着巨大的差距。只有我们对局限性极其诚实，敏锐地分析瓶颈，并有效地创新以避免这些瓶颈，我们才会开辟这一前沿。虽然这是当代的挑战，但这是工程师们一直在做的事情，他们使用数学模型和科学原理将白日梦从令人敬畏但可以实现的东西中筛选出来(Rankine，1855)。生物学中最大的限制之一是，在试管中取得可能的东西，并在反应堆或环境中实现它；使用相对廉价的资源，以及面对大量和高度多样化的自然微生物种群。在这个项目中，我们试图使用最好的科学原理和理论来开发一套通用的原理和模型，用于开放生物系统的可扩展模拟。这些模型将允许对天然或合成有机体为人类造福的一系列技术提供的新功能进行工程设计，以应对一系列不同的挑战。

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.