Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules

Background
It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein networks are one particular network type of special importance, because proteins form the functional base units of every biological cell. On a mesoscopic level of protein networks, modules are of significant importance because these building blocks may be the next elementary functional level above individual proteins allowing to gain insight into fundamental organizational principles of biological cells.
Results
In this paper, we provide a comparative analysis of five popular and four novel module detection algorithms. We study these module prediction methods for simulated benchmark networks as well as 10 biological protein interaction networks (PINs). A particular focus of our analysis is placed on the biological meaning of the predicted modules by utilizing the Gene Ontology (GO) database as gold standard for the definition of biological processes. Furthermore, we investigate the robustness of the results by perturbing the PINs simulating in this way our incomplete knowledge of protein networks.
Conclusions
Overall, our study reveals that there is a large heterogeneity among the different module prediction algorithms if one zooms-in the biological level of biological processes in the form of GO terms and all methods are severely affected by a slight perturbation of the networks. However, we also find pathways that are enriched in multiple modules, which could provide important information about the hierarchical organization of the system

Feasibility, normative heuristics and the proper place of historical responsibility – a reply to Ohndorf et al.

In this comment, we pick up three points raised by Ohndorf et al. (2015) in their reply to our ethical assessment of the German Advisory Council’s Budget Approach (WBGUBA). First, we discuss and clarify the relationship between ethics and political feasibility, highlighting that the way Ohndorf et el. use feasibility creates an unwarranted status quo bias. Second, we explain the proper place historical responsibility should have within the WBGUBA, stressing the fact that the reasons why we choose one policy proposal over another matter. Third, we analyze the limited extent to which a normative heuristic should motivate an ethically ambitious policy proposal like the WBGUBA.