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This tension between the justification of the 'unbiased' strategy and the status
of the result of the procedure needs to be resolved. This could be done in different
ways. First, there is the aforementioned secondary ascription of functions to the
'unbiased' modules. This is a reasonable strategy, which, from an epistemologi-
cal point of view, does not differ much from any other ascription of functions to
known sub-structures of an organism in other physiological disciplines, includ-
ing molecular biology. On this account, the unbiased modularization helps to
identify, by top-down analysis, the physiological subunits of a network, which
cannot be identified bottom-up merely from knowledge of its components with-
out bias. As soon as functions can be ascribed to these modules with respect to
an organismic capacity, 'meaning' is bestowed on the modules with respect to
the organism as a whole. A second way of reading 'meaning' from top-down
models could refer to capacities of the network itself rather than of the organism.
The network has, e.g., (self-)regulatory properties that may be regarded as its
capacities. These may be analyzed functionally, without requiring reference to
capacities of the organism. On this account, both the organism and the network
itself must be considered as ontological wholes because functional decomposi-
tion cannot be applied satisfactorily to incomplete entities (otherwise one would
end up with ascriptions like the function of the wound of a severely injured
animal to be squirting blood and the like). The strategy of relating biological
function and hence 'meaning' to 'omic' biological systems as wholes, however,
required to explicate the concept of wholeness with respect to networks, a topic
to which we turn next.
8.2. The 'holism' of systems biology
Systems biology shifts the focus of physiological inquiry from the analysis of
(molecular) subsystems that contribute to certain capacities to 'whole system'
accounts. What systems biology lacks, however, is a clear ontology of systems: It
is neither clear how systems are to be individuated nor what it means for a whole
system, in contrast to an incomplete one, to be under consideration (Mesarovic
et al., 2004; O'Malley & Dupré, 2005; Krohs, 2006a). In systems biology,
'holism' is often used as a mere buzzword to oppose 'reductionism', which is
often pejoratively connotated. 17 Thus, e.g., when Mendes (2002) diagnoses the
“trend away from extreme reductionism to systems descriptions and analyses”
17 To complicate matters, reduction(ism) is also often opposed to emergence (emergentism), which invites the
further question how holism and emergentism are to be related (see, e.g., Williams, 2002 and Boogerd et al.,
2005 on emergent properties at the molecular and cellular levels, and Thalos, 2006 on emergent physical
processes). These issues cannot be pursued in this chapter. Let us only note that on at least some authoritative
current accounts, (certain kinds of) emergence, rather than implying the failure of reduction, presupposes
reducibility; see, e.g., Stephan, 2002; Boogerd et al., 2005: Wimsatt, in press.
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