SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions

合成生物学领域对人工（即人造）生物（子）系统的设计、构建和发展有着巨大的希望，从而为“转基因”生物、智能药物以及检测人工基因组和蛋白质组的模型系统提供了可行的新途径。对这种生物（子）系统的知情操纵可能对我们的社会产生巨大的积极影响，其影响遍及一系列活动，如提供医疗保健、环境保护和补救等。合成生物学的基本前提是，通常用于设计和构建非生物系统的方法，例如计算科学和工程学科中使用的方法，也可以用于模拟和编程新的合成生物系统。因此，合成生物学处于从生物学到化学、物理、计算机科学、数学和工程等各种学科的交叉点。该网络的总体目标将是通过支持一系列社区建设活动，在影响（并有助于）合成生物学的学科之间产生新的有力的互动。这些活动将以实现生物细胞和人造细胞之间可编程相互作用的具体技术目标为中心。通过专注于这一特定的技术挑战，我们希望有助于修补合成生物学社区中出现的裂痕，一些人认为合成生物学应该以自上而下的方式完成（即敲除或修改现有细胞的功能），另一些人认为它应该遵循自下而上的方法，从第一原则开始。我们相信这两种方法都很重要，并将在合成生物学的未来发挥作用，因此，要求自上而下的系统（修饰细胞）和自下而上的系统（细胞，原始细胞）之间相互作用的挑战为建立和维持一个新的研究社区提供了理想的背景。丽贝卡·莫雷尔的文章《在实验室创造生命》这篇文章出现在2007年10月19日的BBC新闻科学部分，不仅完美地说明了生物学中越来越严重的两极分化，即自上而下的人和自下而上的人，最后还引用了南安普顿大学的乔治·阿塔德的话，警告说，最大的挑战不一定是创造生命，但是知道你已经创造了生命——做了一个实验，这个实验明确地告诉你你已经拥有了生命……这是因为你将要看到的是一种“汤”，其中包含数百种，甚至数千种化学物质。你怎么知道你手里拿的不是一个化学废料瓶，而是有生命迹象的东西呢？”SynBioNT将通过促进所谓的“细胞模仿游戏”的研究来“精确地”关注这个问题，正如我们最近在《自然生物技术》（Nature Biotechnology）杂志上发表的开创性论文《模仿游戏/一种识别生命的计算化学方法》中所提出的那样。

The field of synthetic biology holds a great promise for the design, construction and development of artificial (i.e. man-made) biological (sub)systems thus offering viable new routes to 'genetically modified' organisms, smart drugs as well as model systems to examine artificial genomes and proteomes. The informed manipulation of such biological (sub)systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, environmental protection and remediation, etc. The basic premise of synthetic biology is that methods commonly used to design and construct non-biological systems, such as those employed in the computational sciences and the engineering disciplines, could also be used to model and program novel synthetic biosystems. Synthetic biology thus lies at the interface of a variety of disciplines ranging from biology through chemistry, physics, computer science, mathematics and engineering. The overarching aim of this network will be to generate new vigorous interactions between the disciplines that impinge (and contribute to) Synthetic Biology by supporting a range of community building activities. These activities will be centred on the specific technical goal of achieving programmable interactions between biological and artificial cells. By focusing on this specific technical challenge we hope to contribute to mending the rift that is appearing in the synthetic biology community between those who argue that synthetic biology should be done in a top-down fashion (i.e. knocking out or modifying functions of existing cells) and those that argue that it should follow a bottom-up approach that starts from first principles. We believe that both approaches are important and will have a role to play in the future of synthetic biology, hence a challenge that calls for the interaction between top-down systems (modified cells) and bottom-up systems (chells, protocells) provides the ideal background against which a new research community can be built and sustained. Rebecca Morell's article 'Creating Life in the Laboratory' that apeared in the BBC NEWS science section on the 19th of October 2007, not only illustrate *perfectly* the growing dichotomy in SB between those who approach it top down and those who do it bottom up but also ends up on a cautionary notice by citing George Attard from Southampton University as saying 'The biggest challenge is not necessarily creating life, but knowing that you have created life - doing the experiment that unambiguously tells you that you've got it..That's because you are going to be looking at a 'soup' that contains several hundred, possibly several thousand, chemical species. How on Earth can you tell that what you have isn't just a chemical waste bottle but something that is exhibiting the signs of life?' SynBioNT will focus *precisely* on shedding light into this question by fostering research on the so call 'cellular imitation game' as we have recently propose in our ground breaking paper 'The imitation game/a computational chemical approach to recognizing life' in Nature Biotechnology, 24:1203-1206, 2006.