Gatherer Derek, Galpin Vashti
MRC-University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, UK.
BMC Syst Biol. 2013 Nov 17;7:128. doi: 10.1186/1752-0509-7-128.
Robert Rosen's Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has been claimed to be non-reducible to its components and algorithmically non-computable, in the sense of not being evaluable as a function by a Turing machine. If (M,R)-like structures are present in real biological networks, this suggests that many biological networks will be non-computable, with implications for those branches of systems biology that rely on in silico modelling for predictive purposes.
We instantiate (M,R) using the process algebra Bio-PEPA, and discuss the extent to which our model represents a true realization of (M,R). We observe that under some starting conditions and parameter values, stable states can be achieved. Although formal demonstration of algorithmic computability remains elusive for (M,R), we discuss the extent to which our Bio-PEPA representation of (M,R) allows us to sidestep Rosen's fundamental objections to computational systems biology.
We argue that the behaviour of (M,R) in Bio-PEPA shows life-like properties.
罗伯特·罗森的代谢替代，即（M，R）系统，可以表示为一种紧凑的网络结构，有一个单一的源以及由该源通过三个连续反应产生的三种产物。有人声称（M，R）不可简化为其组成部分，并且在图灵机无法将其作为函数进行求值的意义上，算法上不可计算。如果真实生物网络中存在类似（M，R）的结构，这表明许多生物网络将不可计算，这对系统生物学中那些依赖计算机模拟进行预测的分支具有影响。
我们使用进程代数Bio-PEPA实例化（M，R），并讨论我们的模型在多大程度上代表了（M，R）的真实实现。我们观察到在某些起始条件和参数值下，可以实现稳定状态。尽管（M，R）的算法可计算性的形式证明仍然难以捉摸，但我们讨论了我们对（M，R）的Bio-PEPA表示在多大程度上使我们能够避开罗森对计算系统生物学的基本反对意见。
我们认为Bio-PEPA中（M，R）的行为表现出类似生命的特性。
