Explaining a complex living system: dynamics, multi-scaling and emergence

Abstract

Complex living systems are difficult to understand. They obey the laws of physics and chemistry, but these basic laws do not explain their behaviour; each component part of a complex system participates in many different interactions and these interactions generate unforeseeable, emergent properties. For example, microscopic interactions between non-living molecules, at the macroscopic level, produce a living cell. Here we discuss how to explain such complexity in the format of a dynamic model that is mathematically precise, yet understandable. Precise, computer-aided modelling will make it easier to formulate novel experiments and attain understanding and control of key biological processes.

Figure 1

Life as a transformational system. In this scheme, the information encoded in the genome—the DNA—is transformed into the proteome—functional proteins—that, in turn, generate the organism and the species. The fitness of the organism and the species in the environment feed back to select better-adapted genomes and evolution results.

Figure 2

The living organism as a reactive system. According to this view, the cell, the organism and the species are not mere sequential transformations of information encoded in the genome—a DNA master program. Living cells, organisms and species emerge from a web of ongoing concurrent interactions of various entities and processes; DNA is only one of the many participating informational entities.

Figure 3

The emergence of objects. Objects emerge at higher scales from interactions at lower scales. Molecular interactions at one scale give rise to a cell at a higher scale: interactions between cells generate an organ; interactions between organs generate an organism; and interactions between organisms generate a society.

Figure 4

From a model of the lymph node [SCH06]. Snapshots of a Statechart simulation in Rhapsody, carried out under standard conditions, together with the animated outcomes presented in Flash. The left-hand statechart describes part of the behaviour of a B cell, which undergoes many changes as the organ evolves; the right-hand statechart describes four of the many cell receptors that play an important role in the immune response. Below the statecharts is a snapshot of the resulting animation in Flash showing the various elements in the various parts of the lymph node; see [SCH06].

Figure 5

Illustrating reactive animation in the lymph node model [SCH06]. In the top portion of the figure, the statechart transition from figure 4 that allows a B cell to differentiate to a plasma cell has been removed (top right) and as a result no plasma cells can be created. This can be seen in the animation snapshot (top left), which shows that B cells that were fated to become plasma cells (represented in the animation as yellow circles, secreting antibodies) stay undifferentiated (blue circles). In the bottom portion, the transition that allows receptor CXCR5 to be expressed has been removed (bottom right), thus preventing cells from expressing it. CXCR5 is necessary for cell migration as it responds to the chemokine signal BLC, which is secreted from the PF regions (primary follicles) and attracts cells to these regions. The animation snapshot shows that no cells are present in these areas (bottom left).