change of the subsystems as well (e.g., genetic instability). From
this point of view cancer can be considered a disease of the
on-going systemic organization of an organism, of its natural dyna-
mism. Parts lose their integrated functional properties and become
more rigid falling into apparently functional states that mainly
require a lower level of energy to be maintained.
On the one hand, the mechanistic approach has been proven
useful, and it will be extremely useful in the future as well to
understand how some biological processes are realized: we do not
have to throw the baby out with the bathwater. On the other hand,
the ontological assumptions are problematic, especially if we take
them to be an ontological thesis rather than just an epistemic
approach to the study of complexity [10]. The mechanistic
approach actually works for some specific scientific questions
related to linear pathways and interactions, or punctual events and
molecular changes. But scientific shortcomings and anomalies, as
well as philosophical reasons, point toward paying more attention
to the causal relevance of long-range interactions between entities.
For these reasons, we now introduce a different picture, which
is the picture of Systems Biology [11]. We try to be as explicit as
possible in depicting the fundamentals of this view, since it is not
rare to appeal to buzzword such as “systems,” “holism” with no
explicit definitions. We further specify that we are interested in
“system-level understanding,” as opposed to “system-centered
view,” because the former is the right term combined with a proper
relational ontology, while the latter is tightly related to an ontology
of systems.
The starting point of Systems Biology is based on the idea that
there are no biological entities with their respective properties if not
as parts of specific systems. Accordingly, trying to define what
biological entities can or cannot do on the basis of their internal
properties is rather hopeless. In other words, the process of abstrac-
tion of entities from their contexts in order to identify their funda-
mental properties can be problematic because entities could not
have the properties that they have if they were not placed in a
specific context. Such context dependency has been addressed and
discussed in terms of “system level understanding.” The idea is that
a biological entity shows certain properties only if part of a specific
context suggests the turn from a mechanistic ontology to a systemic
one. A relational ontology incorporates such an assumption
[12]. But what exactly does this mean? Which are the fundamental
concepts of relational ontologyin abstracto?
Appealing to a relational ontology means that the understand-
ing of the biological realm should be characterized as a cognitive
process where relations are somehow prior to entities in both
explanatory and conceptual terms. Byentitieswe mean a specific
class of “things” (specific in the sense of “biological”), where things
are subjects of the predication of properties. Here comes the4 Marta Bertolaso and Emanuele Ratti