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              <p>Unlike inert objects, organisms and their cells have the ability to initiate activity by themselves,and thus change their properties or states even in the absence of an external cause. This crucialdifference led us to search for principles suitable for the study organisms. We propose that cellsfollow the default state of proliferation with variation and motility, a principle of biologicalinertia. This means that in the presence of sufficient nutrients, cells will express their defaultstate. We also propose a principle of variation that addresses two central features of organisms,variation and historicity. To address interdependence between parts, we use a third principle, theprinciple of organization: more specifically, the notion of the closure of constraints. Within thistheoretical framework, constraints are specific theoretical entities defined by their relativestability with respect to the processes they constrain. Constraints are mutually dependent in anorganized system and act on the default state.Here we discuss the application and articulation of these principles for mathematical modeling ofmorphogenesis in a specific case, that of mammary ductal morphogenesis, with an emphasis onthe default state. Our model has both a biological component, the cells, and a physicalcomponent, the matrix that contains collagen fibers. Cells are agents that move and proliferateunless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on othercells. As fibers are organized, they constrain the cells’ ability to move and to proliferate. Thismodel exhibits a circularity that can be interpreted in terms of the closure of constraints.Implementing our mathematical model shows that constraints to the default state are sufficient toexplain the formation of mammary epithelial structures. Finally, the success of this modelingeffort suggests a step-wise approach whereby additional constraints imposed by the tissue andthe organism can be examined in silico and rigorously tested by in vitro and in vivo experiments,in accordance with the organicist perspective we embrace.</p>
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