Modularity (biology)
Encyclopedia
Many organisms consist of modules, both anatomically and in their metabolism
. Anatomical modules are usually segments or organs. When we look at illustrations of metabolic reactions, we find that they, too, are modular: we can clearly identify, for instance, the citric acid cycle
as a complex network that has only a few interfaces with other such modules. This principle holds true at various scales: we can identify smaller modules within such larger networks that are similarly self-contained. We say that metabolic modularity is scale-free.
In addition to showing scalefree and small world properties, biological networks appear to exhibit modularity in topological structure. In the field of network biology, the definition of nodes and edges in a given network depends on the type of network examined. For example, in a protein interaction network, nodes correspond with individual proteins and edges represent the interactions between them (either through direct physical interaction, or compound-mediated). Metabolic network
s, on the other hand, contain metabolite
nodes and edges that represent the specific enzymes that connect them (in catalyzing biochemical reactions). As with any type of network, modularity in biological networks allows sub-groups of nodes and edges to function in a semi-autonomous fashion.
The concept of modularity resurfaces at the scale of organs and developmental units. Why are there distinct cell types organised into spatial aggregations (organs), and what are the benefits of having a segmented
body plan, containing different modules (for instance, thoracic and abdominal segments in an arthropod) and where one of the possible differences between species is in the number of each type of module they possess?
Interestingly, this property has led researchers to suggest that modularity imparts a certain degree of evolvability
to a system by allowing specific features (i.e. network sub-groups) to undergo changes without substantially altering the functionality of the entire system. Essentially, each module is free to evolve within, so long as the interfaces between modules remain consistent. This would suggest that the metabolic pathways at the edges between modules are more constrained. It is thought that there exists an optimal
degree of modularity for each given organism.
Metabolism
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...
. Anatomical modules are usually segments or organs. When we look at illustrations of metabolic reactions, we find that they, too, are modular: we can clearly identify, for instance, the citric acid cycle
Citric acid cycle
The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...
as a complex network that has only a few interfaces with other such modules. This principle holds true at various scales: we can identify smaller modules within such larger networks that are similarly self-contained. We say that metabolic modularity is scale-free.
In addition to showing scalefree and small world properties, biological networks appear to exhibit modularity in topological structure. In the field of network biology, the definition of nodes and edges in a given network depends on the type of network examined. For example, in a protein interaction network, nodes correspond with individual proteins and edges represent the interactions between them (either through direct physical interaction, or compound-mediated). Metabolic network
Metabolic network
A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell...
s, on the other hand, contain metabolite
Metabolite
Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. Alcohol is an example of a primary metabolite produced in large-scale by industrial...
nodes and edges that represent the specific enzymes that connect them (in catalyzing biochemical reactions). As with any type of network, modularity in biological networks allows sub-groups of nodes and edges to function in a semi-autonomous fashion.
The concept of modularity resurfaces at the scale of organs and developmental units. Why are there distinct cell types organised into spatial aggregations (organs), and what are the benefits of having a segmented
Segmentation (biology)
Segmentation in biology refers to either a type of gastrointestinal motility or the division of some animal and plant body plans into a series of repetitive segments. This article will focus on the segmentation of animal body plans, specifically using the examples of the phyla Arthropoda,...
body plan, containing different modules (for instance, thoracic and abdominal segments in an arthropod) and where one of the possible differences between species is in the number of each type of module they possess?
Interestingly, this property has led researchers to suggest that modularity imparts a certain degree of evolvability
Evolvability
Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.In order for a biological organism...
to a system by allowing specific features (i.e. network sub-groups) to undergo changes without substantially altering the functionality of the entire system. Essentially, each module is free to evolve within, so long as the interfaces between modules remain consistent. This would suggest that the metabolic pathways at the edges between modules are more constrained. It is thought that there exists an optimal
Optimality theory
Optimality theory is a linguistic model proposing that the observed forms of language arise from the interaction between conflicting constraints. OT models grammars as systems that provide mappings from inputs to outputs; typically, the inputs are conceived of as underlying representations, and...
degree of modularity for each given organism.