Mechanisms Versus Causes in Biology and Medicine - Mechanism and Causality in Biology and Economics - page 22

The mechanism's components have spatial and temporal organization. Spatial
organization includes location, internal structure, orientation, and connectivity
(both among component parts within the mechanism and to other mechanisms
before the start condition and after the termination condition). Sometimes a molec-
ular mechanism is compartmentalized, e.g., occurring in one part of the cell and
surrounded by a membrane that protects its parts from dissipation and attack or
from attacking other parts of the cell. (Lysosomes, e.g., contain caustic enzymes
that break down waste materials; their enzymes are enclosed in that cell organelle
and thus do not attack other cellular components.) Also, the stages of the mecha-
nism occur in a particular order and they take certain amounts of time (duration).
Some stages occur at a certain rate or repeat with a given frequency. In addition to
the componency, spatial, and temporal features of a mechanism, the mechanism
may be situated in wider contexts—in a hierarchy of mechanism levels (Craver
2007 , Ch. 5) and in a temporal series of mechanisms (Darden 2005 ). These features
of mechanisms can play roles in the search for mechanisms, and then they become
parts of an adequate description of a mechanism. What counts as an adequate
description (i.e., how much detail needs to be specified) depends on the context
in which an explanation of the puzzling phenomenon is sought and the purposes for
which the description is to be used.
One use is to make predictions. When the mechanism is in place and the start
conditions obtain, then the orderly operation of each stage of the mechanism results
in the production of the phenomenon. Hence one can predict what the outcome will
be. However, if a portion of the mechanism is broken, then one can predict that the
earlier stages operated and an intermediate product accumulates (or perhaps no
product at all is produced). Knowing about the intermediate stages allows more
fine-grained predictions about what is the output of each stage and what will happen
when a stage breaks. A scientist may be able to run a mental simulation of the
mechanism and thereby predict what phenomenon it will produce or to predict what
will happen if a part of the mechanism is broken. (On mental simulations of
mechanisms operating, see Bechtel and Abrahamsen 2005 .) However, sometimes
the complexity of the mechanism makes mental simulations difficult. Computa-
tional simulation models of the mechanism are more useful, especially for quanti-
tative predictions about, e.g., concentrations of products (e.g., Eisenhaber 2006 )or
for predicting complex spatial interactions as in molecular dynamic simulations
(e.g., Watanabe et al. 2010 ).
A mechanism schema is a truncated abstract description of a mechanism that we
know how to fill with more specific descriptions of component entities and
activities, such as the schema for the central dogma, discussed above. In contrast,
a mechanism sketch cannot (yet) be instantiated. Components are (as yet) unknown.
Sketches may have black boxes for missing components that are sought as the
search for the mechanism proceeds. An adequate description of a mechanism (in the
context of a given puzzling phenomenon) is an account with all the black boxes
filled, with the overall organization specified (e.g., linear or cyclic), and with the
features of Table 2.1 noted.