Biology Reference
In-Depth Information
to explain phenomena. It is only satisfactory for a description of the system's
parts and their properties; it yields only a parts list, an inventory of the parts. To
explain behaviour, the parts have to be considered in their natural context, i.e. as
components in the functioning system, and at the same time, the system has to
be studied as a whole. Often the kind of explanation sought for is a mechanistic
explanation which tries to make intelligible how the joint behaviours of the parts,
while embedded in the system, bring about the behaviour of the system that is
to be explained. Mechanistic explanation, therefore, is an interlevel activity that
does not cherish the system more than the parts or vice versa; that is to say,
it is neither holistic nor reductionistic. In the end, a mechanistic explanation of
a cellular behaviour amounts to a quantitative, mechanistic model that captures
those molecular phenomena in the cell responsible for the cellular behaviour
that is be explained.
The search for and articulation of mechanisms also has methodological impli-
cations. Various experimental strategies can be followed to go from 'possible' to
'plausible' to 'actual' mechanisms (Darden & Tabery, 2005). Such strategies have
three basic elements: (i) an experimental set-up inwhich themechanism is running,
(ii) an intervention (perturbation) technique and (iii) a detection technique (Craver,
2002). Basically, intervention strategies may involve activating the normal work-
ing of the mechanisms or modifying the working of the mechanism, and in both
cases, detecting some downstream effect. Systems biology stresses the idea that
besides the qualitative aspects of mechanisms, represented by cartoons of mech-
anism, quantification of the behaviour of mechanisms is of utmost importance. It
is noted that many scientists do not pay much attention to experimental quantifi-
cation as a means to find plausible and actual mechanisms On average, molecular
biology has a tendency to articulate mechanisms only in qualitative terms. It is
stressed here that combined experimental-theoretical approaches as carried out in
systems biology allow for such a quantitative analysis of the systemic behaviour
upon perturbations made to the system (e.g. Jensen et al., 1993; Bakker et al., 1997;
Hoefnagel et al, 2002; Snoep et al., 2002; Hornberg et al., 2005; Bruggeman et al.,
2005). Also, most philosophers of science do not engage in discussions about quan-
titative, computational aspects of mechanisms. They almost invariably refer to
mechanisms in qualitative terms. Systems biology, however, strongly focuses on
this quantitative aspect and is therefore also fundamentally different frommolecu-
lar biology in this respect. The underlying reason is that in nonlinear systems (i) the
actual operation of a mechanism depends on the precise state the system is in and
(ii) more than one mechanismmay operate at the same time.
4.5. Systems biology and models
Living organisms are complex systems. Cellular behaviour arises though
the action and interaction of thousands of molecules and macromolecules.
