Biology Reference
In-Depth Information
example, we encountered a pre-existing wiring diagram of connected neu-
rons, in addition to pre-existing compartments characterizing the neurons.
See Kitano (2001) for the importance of taking structural information into
account in systems biology.
(6) Biological prototypes may be most useful when they display dynamical
or behavioral features, in addition to structural organization, whether these
dynamical/behavioral aspects are presented as temporal-causal sequences
or as a dynamics that can be captured mathematically and in simulations,
as in the H and H and F and L exemplars discussed in this paper. The
importance behavior and dynamics for systems biology is also stressed by
Kitano (2001).
(7) In the case where the systems are characterized quantitatively, as in the
H and H and F and L exemplars, simulations can be constructed fairly
easily, and these can be valuable both in testing a prototype and in possibly
extending it, by allowing for variation of parameters in a precise manner and
their application to experimental systems. These simulations, however, need
to be controlled both by specific data and by general biological principles,
and not be purely speculative exercises in mathematical model building, as
in much of von Bertalanffy's (1968) writings.
(8) The two exemplars discussed above go some way toward identifying some
potentially useful philosophical issues in systems biology, but they need to
be supplemented with other exemplars, to provide a more comprehensive
picture. One such additional area might involve gene-based systems together
with high-throughput data. A valuable proof of a principal paper along these
lines is the Ideker et al.'s (2001) galactose metabolism model for yeast, one
that points toward additional features, such as gene-protein and protein-
protein interactions, that are likely to be important in a philosophy of systems
biology.
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