Biology Reference
In-Depth Information
as a positive outcome of the emerging 'omic' disciplines, 'reductionism' for him
simply means a focus on specific organismal components, which he contrasts
with 'whole-organism measurement'. Since it is blatantly unclear how one is to
'measure' a whole organism, we assume that the point is that parameters of a
certain kind (related to, e.g., genes, proteins, or metabolic processes) are collected
on an organismic or cellular scale in an attempt at completeness (cf. Butcher
et al., 2004 on integrating 'reductionist data'). Wholeness in this sense can
be regarded as completeness of data of a certain kind with respect to a given
compartment, which may be an organelle, a cell, an organ, an organism, or even
an ecosystem.
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Though it initially seemed plausible, using compartmentalization as an indi-
cator for the delineation of a whole system needed justification for the different
kinds of 'omic' systems that may be subjected to systems biological investiga-
tion. 'Whole' cannot mean 'closed', since any biological system that interacts
with its environment by exchange of mass and energy is an open system.
A reasonable criterion would therefore be the strength of internal and external
interactions. Wholeness should not be ascribed to a system whose components
interact with the environment as strongly as with each other. On this account,
a whole system can be individuated in very much the same way as unbiased
modules from a network by its partial autonomy with respect to its environment.
This, of course, is not yet an applicable criterion but a meta-requirement that any
criterion should meet. The compartmentalization criterion, on the other hand,
could probably be used as a substitute in the case of cellular genomes, but even
in this case one should discuss whether in eukaryotes the whole system includes
only nuclear or also extranuclear DNA, whether the DNA of an organelle is
really a whole system in itself, and whether it would be consistent to regard
nuclear DNA as a systemic whole but not mitochondrial and plastidal DNA. It
would seem to be even more questionable whether the borders of proteomes,
metabolomes, and interactomes coincide with the borders of compartments. If
not - and there is strong evidence that '-omes' should be conceived as span-
ning different levels and compartments (Finkelstein et al., 2004; Thiele et al.,
2005) - a top-down systems biological model that relies on 'omic' data for a
certain compartment represents an incomplete system. 'Omic' data on whole
organisms, on the other hand, distort the picture of network dynamics as there
are in fact different processes going on in different compartments. An ontology
of systems and an epistemology of systems-as-wholes is required if top-down
systems biology is to find criteria for structuring its models adequately.
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In systems biological parlance, a compartment is a container of finite size for substances. A substance
requires a unique compartment to contain it. Compartments need not correspond to actual structures in- or
outside of, say, a cell. For a discussion of the problems arising with species that can cross compartment
boundaries see Hattne (2004).
