Talk:Modularity (biology)

message: As a Computational Biology PhD student working with biological networks, I find the notion of "modularity" really ambiguous and troublesome - an opinion shared by other colleagues, even though the concept has been really successful, especially in the previous years. I suggest to assume a more critical perspective on the issue. For instance, the statement "Many organisms consist of modules" could be better formulated as "Modular parts can be recognized within organisms, at different organizational levels".
Specifically, I would like to point out that the example on the Citric Acid Cycle (a.k.a. Krebs Cycle, or TCA Cycle) is quite misleading. Refer to this resource for a diagramtic representation of the Krebs Cycle (human version):
http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00020
First of all, the Krebs Cycle is composed just by a few reactions (10 reactions and 10 metabolites, neglecting some intermediates); therefore it cannot really be termed "a complex network"; it is probably better to keep that word for larger networks (e.g. the entire metabolic network, the EGF signaling network). Second, it does not display a high degree of insulation from other metabolic pathways: besides the oxidation of NADH and FADH, out of 10 metabolites composing the cycle, 6 of them are connected to other metabolic pathways (e.g. aminoacid metabolism), thus displaying a high level of interconnection. I don't think it is appropriate to state that "[it] has only a few interfaces with other such modules". As a whole, I would rather regard the Krebs Cycle as an integrator of different afferent and efferent metabolic pathways, rather than as a stand-alone, insulated module. Therefore, I propose to remove the example on the Krebs Cycle. In the field of molecular biology, a more suitable example would be the ribosome; the ribosome was quoted as an example of modularity by one of the outstanding papers introducing the concept before the rise of Systems Biology:
"A functional module is, by definition, a discrete entity whose function is separable from those of other modules. This separation depends on chemical isolation, which can originate from spatial localization or from chemical specificity. A ribosome, the module that synthesizes proteins, concentrates the reactions involved in making a polypeptide into a single particle, thus spatially isolating its function. A signal transduction system, on the other hand, such as those that govern chemotaxis in bacteria or mating in yeast1, 2, 3, is an extended module that achieves its isolation through the specificity of the initial binding of the chemical signal (for example, chemoattractant or pheromone) to receptor proteins, and of the interactions between signalling proteins within the cell."
Hartwell LH, Hopfield JJ, Leibler S, Murray AW.
From molecular to modular cell biology.
Nature. 1999 Dec 2;402(6761 Suppl):C47-52.
.
Daniele.merico (talk) 21:14, 26 February 2008 (UTC)
thread_title:  A critical perspective on the notion of modularity 

message: Ok, so the following links are dead, and I am removing them. This is in accord with Wikipedia regulations. However, I googled some of these articles and found journal articles that had more or less the same names. I do not know whether the original poster meant these articles or not. Any person interested in this, can look at the old version and see for them selves.  — Preceding unsigned comment added by 88.114.154.216 (talk) 20:01, 23 September 2012 (UTC)
thread_title:  Links dead