entities. A relational ontology is not a trivial alternative to other
ontologies, in fact it does not dismiss the existence of systems,
parts, and wholes; rather—and very importantly—it dynamizes
them, as, for example, parts can be lost, generated, acquired, and
wholes can emerge, disappear, be displaced. Something very pecu-
liar can be said for the biological realm (or, when the questions are
biological), as here the very properties of objects, parts, wholes,
systems—even those that classical ontology defines as “intrinsic”—
are themselves relational.
The structure of the chapter is as follows. In Subheading2,we
introduce the dominant view in molecular biology, in order to
understand—by contrast—the issues that should be emphasized
in a relational ontology. In Subheading3, we introduce some
abstract notions forming a relational ontology. In Subheading4,
we show how evidence from the biological sciences needs to be
interpreted in light of the general categories of a relational
ontology.2 Mechanisms and Biological Atomism
A good way to introduce a “relational ontology” is to start with a
very different thesis. The success of molecular biology in the second
half of the twentieth century [1–3] is associated with a cognitive
approach toward biological systems. This cognitive approach,
explicitly advocated by several prominent molecular biologists,
has been emphasized by so-called mechanical philosophers
[4, 5]. In order to understand biological systems, we should
decompose them in discrete entities, analyze each part in isolation,
and then compute the contribution of each part in order to obtain
the behavior of the whole system; to understand the whole, we
need tosee it asthe sum of its parts. What once was a methodologi-
cal attitude, became later—at least in molecular biology—a meta-
physical thesis, namely that the wholeisthe sum of its parts. The
ontological assumption behind this view is that biological entities
(genes, proteins, etc.) behave in the specific way we observe because
of some intrinsic properties they possess, meaning that an object is
itself because of properties that pertain to itself only, and neither
because of something wholly distinct from it, nor because of some
operation performed by the scientist through a specific technology.
Accordingly, some biological entities will be fundamental because
their contributions are necessary to make sense of bigger systems.
In philosophy of biology the latter assumption is sometimes called
biological atomism,i.e., the thesis that there are elementary units
the sum of which can in principle explain life [6]. Therefore, the
process of (material) abstraction—namely studying in vitro the
behavior of specific entities, out of their context—is not just a
compromise we have to accept to discover something out of2 Marta Bertolaso and Emanuele Ratti