3.

2 Explanation
Traditionally, philosophers of science took successful scientific explanations to result from
derivation from laws of nature (see the entries on laws of nature and scientific explanation).
On this deductive-nomological account (Hempel and Oppenheim 1948), an explanation of
particular observation statements was analyzed as subsumption under universal (applying
throughout the universe), general (exceptionless), necessary (not contingent) laws of nature
plus the initial conditions of the particular case. Philosophers of biology have criticized this
traditional analysis as inapplicable to biology, and especially molecular biology.
Since the 1960s, philosophers of biology have questioned the existence of biological laws of
nature. J. J. C. Smart (1963) emphasized the earth-boundedness of the biological sciences (in
conflict with the universality of natural laws). No purported “law” in biology has been found
to be exceptionless, even for life on earth (in conflict with the generality of laws). And John
Beatty (1995) argued that the purported “laws” of, for example, Mendelian genetics, were
contingent on evolution (in conflict with the necessity of natural laws). (For further
discussion, see Brandon 1997; Lange 2000; Mitchell 1997; Sober 1997; Waters 1998; Weber
2005.) Hence, philosophers’ search for biological laws of nature, characterized as universal,
necessary generalizations, has ceased.
Without traditional laws of nature from which to derive explanations, philosophers of
biology have been forced to rethink the nature of scientific explanation in biology and, in
particular, molecular biology. Two accounts of explanation emerged: the unificationist and
the causal-mechanical. Philip Kitcher (1989, 1993) developed a unificationist account of
explanation, and he and Sylvia Culp explicitly applied it to molecular biology (Culp and
Kitcher 1989). Among the premises of the “Watson-Crick” argument schema were
“transcription, post-transcriptional modification and translation for the alleles in question”,
along with details of cell biology and embryology for the organisms in question (Kitcher
1989). An explanation of a particular pattern of distribution of progeny phenotypes in a
genetic cross resulted from instantiating the appropriate deductive argument schema: the
variables were filled with the details from the particular case and the conclusion derived
from the premises.
Working in the causal-mechanical tradition pioneered by Wesley Salmon (1984, 1998), other
philosophers turned to understanding mechanism elucidation as the avenue to scientific
explanation in biology (Bechtel and Abrahamsen 2005; Bechtel and Richardson 1993;
Craver 2007; Darden 2006a; Glennan 2002; Machamer, Darden, and Craver 2000; Sarkar
1998; Schaffner 1993; Woodward 2002, 2010). There are differences between the various
accounts of a mechanism, but they hold in common the basic idea that a scientist provides a
successful explanation of a phenomenon by identifying and manipulating variables in the
mechanisms thereby determining how those variables are situated in and make a difference
in the mechanism; the ultimate explanation amounts to the elucidation of how those
mechanism components act and interact to produce the phenomenon under investigation. As
mentioned above (see Section 2.1, see also entry on mechanisms in science), an elucidated
mechanism allows for the explanatory features of understanding, prediction, and control.
There are several virtues of the causal-mechanical approach to understanding scientific
explanation in molecular biology. For one, it is truest to molecular biologists’ own language
when engaging in biological explanation. Molecular biologists rarely describe their practice
and achievements as the development of new theories; rather, they describe their practice and
achievements as the elucidation of molecular mechanisms (Baetu 2017; Craver 2001;
Machamer, Darden, Craver 2000). Another virtue of the causal-mechanical approach is that
it captures biological explanations of both regularity and variation. Unlike in physics, where
a scientist assumes that an electron is an electron is an electron, a biologist is often interested
in precisely what makes one individual different from another, one population different from
another, or one species different from another. Philosophers have extended the causal-
mechanical account of explanation to cover biological explanations of variation, be it across
evolutionary time (Calcott 2009) or across individuals in a population (Tabery 2009, 2014).
Tabery (2009, 2014) characterized biological explanations of variation across individuals in
a population as the elucidation of “difference mechanisms”. Difference mechanisms are
regular casual mechanisms made up of difference-making variables, one or more of which
are actual difference makers (see Section 2.3 for the discussion of Waters’ (2007) concept of
an actual difference maker). There is regularity in difference mechanisms; interventions
made on variables in the mechanisms that change the values of the variables lead to different
outcomes in the phenomena under investigation. There is also variation in difference
mechanisms; interventions need not be taken to find differences in outcomes because, with
difference mechanisms, some variables are actual difference makers which already take
different values in the natural world, resulting in natural variation in the outcomes.
But philosophers have also raised challenges to the causal-mechanical approach. One
complaint has been that mechanistic explanations don’t work well in systems biology, a field
distinct from molecular biology but that nonetheless draws on the work of molecular
biologists. While some argue that systems biology is best explained using mechanisms (cf.
Boogerd et al. 2007; Matthiessen 2017; Richardson and Stephan 2007; Bechtel 2011; Bechtel
and Abrahamsen 2013), others argue that it requires non-mechanistic explanation (cf.
Braillard 2010; Kuhlmann 2011; Silberstein and Chemero 2013).
Another complaint has been that mechanistic explanations fail to provide a satisfactory
account of the complexity of living systems because they fail to devote serious attention to
the “thoroughly processual character of living systems” (Dupre 2012: 19). Those who prefer
a “process-oriented” ontology (Bapteste and Dupre 2013; Bickhard 2011; Campbell 2015;
Dupre 2012; Jaeger and Monk 2015; Jaeger et al. 2012; Meincke 2018; Nicholson and Dupre
2018) argue that mechanistic accounts mistakenly assume that parts composing a mechanism
can be identified independently of the activities or processes in which they are involved.
Instead, as Anne Sophie Maincke explains, if there are parts or substances, they must be
“reconceptualised as stabilized higher-order processes that persist as long as stabilization can
be maintained” (2018). Processes are ontologically primary. Recent literature in molecular
biology on molecular pathways (cf. Boniolo and Campaner 2018; Brigandt 2018; Ioannides
and Psillos 2017; Ross 2018) seems to be another instantiation of this shift from mechanistic
to processual explanations. But Christopher Austin (2016) has recently challenged the idea
that processual explanations can be sufficiently grounded “without the metaphysical
underpinning of the very mechanisms which processes purport to replace” (639).