Reply to ''Comment on 'Regularizing Capacity of Metabolic Networks' ''

TL;DR

This paper defends the original findings that real metabolic network topologies influence complex dynamics, countering recent criticism that used a different, more realistic dynamic model which fragmented the networks and obscured topological effects.

Contribution

The authors demonstrate that the criticism's dynamic model artificially fragments networks, and thus cannot invalidate the original conclusion about topology's role in metabolic dynamics.

Findings

Original topological effects on dynamics are preserved when using appropriate models.

Criticism's model causes network fragmentation, undermining its conclusions.

Metabolic network topology remains relevant for understanding steady states.

Abstract

In a recent paper [C. Marr, M. Mueller-Linow, and M.-T. Huett, Phys. Rev. E 75, 041917 (2007)] we discuss the pronounced potential of real metabolic network topologies, compared to randomized counterparts, to regularize complex binary dynamics. In their comment [P. Holme and M. Huss, arXiv:0705.4084v1], Holme and Huss criticize our approach and repeat our study with more realistic dynamics, where stylized reaction kinetics are implemented on sets of pairwise reactions. The authors find no dynamic difference between the reaction sets recreated from the metabolic networks and randomized counterparts. We reproduce the author's observation and find that their algorithm leads to a dynamical fragmentation and thus eliminates the topological information contained in the graphs. Hence, their approach cannot rule out a connection between the topology of metabolic networks and the ubiquity of steady states.