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Hartwell et al. (1999): From Molecular to Modular Cell Biology
In the introduction, the authors define functional modules a "critical level of biological organization" that is "made up of many species of interacting molecules" which carry out "cellular functions, such as signal transmission". To understand how modules work, "phenomenological analysis" has to be combined with "molecular studies". The authors further explain:
[A] discrete biological function can only rarely be attributed to an individual molecule, in the sense that the main purpose of haemoglobin is to transport gas molecules in the bloodstream. In contrast, most biological functions arise from interactions among many components. [...] To describe biological functions, we need a vocabulary that contains concepts such as amplification, adaptation, robustness, insulation, error correction and coincidence detection.
To make it even more clear what a functional module is, the authors define:
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. [...] Modules can be insulated from or connected to each other. Insulation allows the cell to carry out many diverse reactions without cross-talk that would harm the cell, whereas connectivity allows one function to influence another. [...] Functional modules need not be rigid, fixed structures; a given component may belong to different modules at different times. The function of a module can be quantitatively regulated, or switched between qualitatively different functions, by chemical signals from other modules. Higher-level functions can be built by connecting modules together.
The authors further explain why "[c]omplete understanding of a biological module has depended on the ability of phenomenological and molecular analyses to constrain each other":
Phenomenological models have fewer variables than molecular descriptions, making them easier to constrain with experimental data, whereas identifying the molecules involved makes it possible to perturb and analyse modules in much greater detail.
Modules may be related by descent, by shared design or by functional principles.
Finally, the authors write about the transition from molecular cell biology to modular biology:
A major challenge for science in the twenty-first century is to develop an integrated understanding of how cells and organisms survive and reproduce. Cell biology is in transition from a science that was preoccupied with assigning functions to individual proteins or genes, to one that is now trying to cope with the complex sets of molecules that interact to form functional modules. There are several questions that we want to answer. What are the parts of modules, how does their interaction produce a given function, and which of their properties are robust and which are evolvable? How are modules constructed during evolution and how can their functions change under selective pressure? How do connections between modules change during evolution to alter the behaviour of cells and organisms? [...]
Another approach to discerning module function is that of ‘synthetic biology’. Just as chemists have tested their understanding of synthetic pathways by making molecules, biologists can test their ideas about modules by attempting to reconstitute or build functional modules. This approach has already been used to construct and analyse artificial chromosomes made by assembling defined DNA elements, and cellular oscillators made from networks of transcriptional regulatory proteins. Seeing how well the behaviour of such modules matches our expectations is a critical test of how well we understand biological design principles.
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