distinction between intrinsic and extrinsic properties. Without
going too much into metaphysical details, we define a property
Fofxas an intrinsic property ifxhasFonly in virtue of whatxis.
For example, having a specific mass is an intrinsic property, while
weight does not seem so. Having a certain weight is an extrinsic
property, i.e. it is a property we have because of the way we interact
with the world. Relations might be considered properties [13], and
in particular extrinsic properties (though this is not necessarily the
case, such as in the case of biological derivation; genealogy is
fundamental to the predicate of other intrinsic and extrinsic proper-
ties). But since the distinction between intrinsic and extrinsic prop-
erties does not always reflect the idea of intrinsic versus relational,
we just restrict our focus to the distinction between properties that
objects have in virtue of what they are (which we callintrinsic) and
properties that entities have because of the way they interact with
other entities (which we callrelational). A relational ontology will
be an ontology emphasizing the fact that even properties that seem
to beinternalare actually relational. A relational ontology in
biology will be the recognition that the understanding and the
conceptualization of biological entities relies upon the recognition
and causal relevance of some relationship (genealogical, ecological,
functional, etc.).
Take for instance the notion of gene [14]. A specific gene may
be defined in terms of properties that seem to beinternal(i.e., the
genexis a specific sequence of nucleotides), while in other contexts
such as in networks biology a specific gene is defined as a node
within a network [15], i.e., a genexis a node within a network of
interactions, defined by certain value about its connectivity (e.g.,
degree, clustering coefficient, etc.). However, the fact that a gene
has a specific sequence, and the fact that this sequence has a certain
causal role(i.e., being transcribed as a blueprint for a specific
protein) strictly depend on the context where the gene happens
to be. Therefore, even properties that seem prominently internal
are somehow relational, i.e., they depend on the context.
At this point, it should be noticed that the importance of the
organic and functional context—and hence of the related relational
properties that any biological entity possesses—are implicitly
emphasized also by traditional molecular biology. For instance,
the fact that in order to study the action of a gene an in vivo
validation is taken as the gold standard means that, in order to
observe the real behavior of a certain biological entity, we need to
re-create a context that is similar to thewild-type. Therefore, even
old-fashioned molecular biology implicitly thought that the specific
web of relations that a biological entity has in a specific context is
actually very important in defining what this biological entity
is. The epistemic move of molecular biologists is to put in brackets
the characterization of the context, and then to identify the explan-
atory relevance of certain entities over time and across a number of
Conceptual Challenges in Systems Biology 5