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and for systems biology in particular, by virtue of the fact that such emergence
cannot exist in the absence of vital forces or 'intelligent design'. There is no
consistent evidence for such vital forces or design.
However, the ultimate resolution of these paradoxes may reside not so much in
the definition of emergence but in the definition of what constitutes a mechanistic
explanation. As also discussed by Westerhoff and Hofmeyr (2005), truly new
properties do not emerge in any odd calculation of systems behavior. They
arise only when that calculation is nonlinear in the sense that it accommodates
that the properties of a component are codetermined by the properties of other
components. The crux is that the definition of component properties is ambiguous
in dynamic systems. The properties of components can be defined exclusive or
inclusive of the effect of system reverberation. An example is the usual case
where the control by an enzyme on the flux through itself is smaller than 1.
This implies that if the enzyme 'decides' to become 10% more active, one may
say that the component property of the enzyme is that its activity is 110%.
However, its flux does not increase by 10% but by a percentage that is usually
smaller and codetermined by the response of the other dynamic components
in the system. If that percentage were only 3, then the second meaning of
component property would be an activity of 103%. The actual percentage can be
calculated from the interactive properties and network topology of the system,
through metabolic control analysis. Now there would be a way to calculate the
system properties without taking into account this mollification of the properties
of the components by the dynamics of the system, i.e., assuming an activity
of 110%. Such a calculation would not deliver the emergent properties and
would not be consistent with a stable steady state. We surmise that emergent
properties should be defined as properties that are not explainable/calculable
through the latter, 'linear' (110%) method, which keeps component properties
the same as those of the properties in isolation, i.e., does not calculate how the
components properties change when the components are active in the system. It
is here that the methodological and philosophical foundations of systems biology
must be recognized and have strong implications in the context of emergence of
unexpected properties.
7. THEORIES AND LAWS IN SYSTEMS BIOLOGY
Traditionally, in physics theories were considered to be coherent networks of
natural laws. Laws were supposed to be universal, general, and necessary. How-
ever, even for physics, this picture of laws as being applicable throughout the
universe, without exceptions and with effects that were deducible from causes,
has been challenged (cf. Cartwright, 1983). In biology, many philosophers have
raised their doubts about the existence of laws in the physical sense. Biological
