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The Role of Theory in Advancing 21st-Century Biology: Catalyzing Transformative Research
matters are the cell membrane and interface components such as receptors, transporters, and junctions (Bonnefont et al., 2005). The internal dynamics of a module and the interaction of its parts could be both cooperative and antagonistic and both optimized and random; the parts could also be ephemeral, experiencing constant turnover. In fact the degradation or death of individual modules, while the overall function is maintained, is another universal theme of biological organization. The critical point is that modules should show external coherence, independent of internal complexities. In addition to an invariant external interface, the interfaces should be finite in kind—similar to the finite number of interfaces on a computer such as the USB interface. Sharing a uniform or finite interface (e.g., the phospho-diester bond in nucleotides), especially across functionally distinct modules such as the mitochondrion and the Golgi, allows exchangeability of the modules (Del Sol et al., 2007; Pereira-Leal et al., 2007). The ability to exchange modules creates the possibility of generating combinatorial complexity. For example, during development, gene regulatory feedback loops that have the property of driving cells into a new developmental stage can, through evolution, be linked to other developmental modules to implement major phenotypic changes. In Box 6-1 an example is given of a regulatory loop preserved in star fish and sea urchins but which in sea urchins has evolved to link to another module that drives the development of a skeletal system.
A module as described here is made up of interacting parts, which together interface with the external environment. Variations of the questions “How are such interacting ensembles constructed?” and “How are they maintained?” are found in all subfields of biology. Enumerating the composition and interaction of parts in a cell, in an organ, in a population, and in a community are classic research programs. What varieties of RNA are in a cell and how do they interact with the DNA genome? What are the different types of neurons constituting a hippocampus? How many different species of bacteria make up a gut community? Such inquiries might be considered an essential part of the classic reductive research paradigm, the goal of which is to use the enumeration to build a constructive understanding of emergent properties from the bottom up. Attempts at a constructive understanding of the combined action of the parts lead to the next level functional or interrelational questions: Are all the entities essential? Do the entities segregate into functional groups? What types of interactions are present and, at an abstract level, what is the network topology of their interactions? What are the forces that maintain the ensemble through dynamic changes? Although the research program of characterization and assembly of parts is classically reductive, from a modular perspective, these questions or approaches clearly apply throughout the scales of modular hierarchy—from molecular parts to ecosystems. To put it broadly,