Mechanisms Versus Causes in Biology and Medicine - Mechanism and Causality in Biology and Economics - page 20

Mechanisms are entities and activities organized such that they are productive of regular
changes from start or set-up to finish or termination conditions. (MDC 2000 ,p.3)
The MDC characterization of mechanisms is not a definition giving necessary
and sufficient conditions for the term's usage in all cases. Instead it is a characteri-
zation to capture the way biologists use the term, as informed by our detailed
examination of cases from molecular biology and neurobiology and also informed
by philosophical reflection on requirements for productive changes.
An example of a biological mechanism is the mechanism of protein synthesis.
From the beginning of the field of molecular biology in the 1950s, one of the
phenomena puzzling biologists was how proteins are synthesized. By the 1970s,
molecular biologists and biochemists had discovered the key details of the mecha-
nism of protein synthesis (Darden and Craver 2002 ). The mechanism is often
represented by the abstract schema, called the “central dogma” of molecular
biology:

DNA RNA Protein

! !

It may also be represented by much more detail as in Fig. 2.1 , with structures of
entities, the organization of the mechanism components within a cell, and the
temporal stages and movements depicted by arrows. The mechanism begins in
the nucleus with the unwinding of the DNA double helix and the synthesis of
messenger RNA. The long ribbon of mRNA moves into the cytoplasm where it
attaches to the cell organelle, the ribosome. The ribosome is the site where transfer
RNAs, carrying their respective amino acids, attach to the messenger RNA (in a
specific order, determined by the genetic code). The growing chain of amino acids
will later leave the ribosome and fold into a three-dimensional protein (not shown in
Fig. 2.1 ).
This example illustrates many of the general features of biological mechanisms.
These are listed in Table 2.1 . The first feature is “phenomenon” because the first
step in the search for a mechanism is to identify and characterize a puzzling
phenomenon of interest. Next are componency features. The mechanism is com-
posed of entities and activities, sometimes further organized into functional
modules. Functional modules are groups of entities and activities that play a
given role in the mechanism and may recur in mechanisms of the same abstract
type, e.g., the module for translation in the mechanism of protein synthesis
(discussed below).
Note that the entities in the protein synthesis mechanism are not all at the same
size level. Working entities of the protein synthesis mechanism range from small
ions to larger macromolecules to cell organelles (composed of macromolecules).
Size level and mechanism level need not, and often do not, correspond (Craver
2007 , Ch. 5). Mechanisms have working components of a certain size, with
structure and with other properties that enable them to engage in the activities
that drive the mechanism.