Biology Reference
In-Depth Information
5. MODELS AND THE NONEQUILIBRIUM ORGANIZATION
OF LIVING SYSTEMS
Of necessity, living systems are open and displaced from equilibrium. Self-
organization, once thought to be dominant, appears to have a limited role,
perhaps because biology needs to be robust and heritable. The expression of a
robust genome appears to direct dissipative processes that may reinforce them-
selves through self-organization, such as through positive feedback loops. Mosaic
nonequilibrium thermodynamics, kinetics, and metabolic control analysis are
systems biology methods that are perhaps the natural successors (Westerhoff
& Palsson, 2004) to the nonequilibrium thermodynamics that emphasized just
self-organization (Glansdorff & Prigogine, 1971).
Two other topics that are highly relevant for systems biology and concern
the organization of living systems have been addressed more at length in this
topic. Wolkenhauer and Ullah analyzed whether the types of models that are
constructed at present can indeed capture all phenomena associated with living
systems. They concluded that this is unlikely and that alternative approaches
should also be considered. Indeed, systems biology is in need of new modeling
methodologies. A second issue was addressed by Hofmeyr. He analyzed how
the organization of cells may bring about self-replicating systems.
The related notion of complexity was also addressed by various authors. Some
are of the opinion that cells are too complex to fully catch their behavior and that
models serve the purpose of reducing the complexity (Wolkenhauer & Ullah),
while others stress that it is not just complexity that matters for biology but
organized forms of complexity (Keller) or functional organization in the light of
context (Hofmeyr).
6. EMERGENT PROPERTIES
The concepts of mechanism and emergence have long been considered to be
mutually exclusive. As soon as a mechanistic explanation could be given for
some behavior, that behavior was not considered emergent, as it was to be
expected, already implied by what was known. Conversely, it was thought that
emergent properties could not be explained mechanistically. For some philoso-
phers, this was a matter of definition: emergence was defined as the appearance
of phenomena that could not be explained mechanistically (Kim, 1999). In this
topic, two different notions of emergence have surfaced. In their contribution,
Westerhoff and Kell consider a weaker notion of emergence, taken by many
scientists working with nonlinear systems, and note that it is relevant for science
that in some systems properties appear that would not appear should the compo-
nents have been isolated from each other. Such properties can differ qualitatively
