The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors
The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors
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DOI：
10.1016/j.shpsc.2013.05.013
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发表时间：
2013-12-01
期刊：
影响因子：
--
通讯作者：
Pigliucci, Massimo
中科院分区：
文献类型：
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作者：
Boudry, Maarten;Pigliucci, Massimo
对生物体的科学研究充满了机器和设计隐喻。基因被认为是生物体的“蓝图”，生物体被“逆向工程”以发现其功能，活细胞被比作生化工厂，配有装配线、运输系统、信使电路等。尽管设计的概念对于考虑适应性是必不可少的，并且工程类比具有相当大的启发价值（例如，最优性假设），但我们认为它们在几个重要方面受到限制。特别是，当我们深入到分子生物学和遗传学的水平时，与人造机器的类比就站不住脚了。生物体比人造机器更加混乱和不透明。众所周知，进化是一个机会主义的修补匠，盲目地绊倒任何明智的工程师都不会想出的“设计”。尽管技术创新令人印象深刻，但事实证明，从头开始人工设计新生命形式的前景比“编程”正确的“软件”所暗示的表面类比更加困难。将简单的工程方法应用于生命系统及其基因组的想法——分离功能组件，从头开始设计新部件，将它们重新组合并组装成新的生命形式——将与人类人工制品的类比推向了极限。在基因型和表型之间缺乏一一对应的情况下，没有直接的方法来实现新的生物功能和设计新的生命形式。基因表达的发育复杂性以及基因与环境的多种相互作用都是“工程”特定表型的严重障碍。除了最简单的表型之外，将所需表型逆向工程到其遗传“指令”的问题可能是棘手的。生物工程和合成生物学领域的最新发展反映了这些局限性。研究人员并没有像机器/工程隐喻所承诺的那样从头开始基因改造所需的性状，而是通过利用自然选择来“搜索”合适的基因型，或者通过借用和重组现有生命形式的遗传物质来取得更大的进步。 (C) 2013 Elsevier Ltd. 保留所有权利。
The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the "blueprint" of an organism, organisms are "reverse engineered" to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on "designs" that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with "programming" the right "software" would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes-isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms-pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for "engineering" a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic "instructions" is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to "search" for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (C) 2013 Elsevier Ltd. All rights reserved.