## 1. Introduction



Reduction (reductionism) encompasses several, related philosophical
themes. At least three types can be distinguished: ontological,
methodological, and epistemic (Sarkar 1992, cf. Nagel 1998). Even
though arguments for and against reductionism often include a
combination of positions related to all three, these distinctions are
significant because no straightforward entailment relations obtain
between the different types of reduction (although tacit commitments
about these relations are prevalent).



(*i*) *Ontological reduction* is the idea that each
particular biological system (e.g., an organism) is constituted by
nothing but molecules and their interactions. In metaphysics this idea
is often called
 physicalism
 (or materialism) and it assumes in a biological context that (a)
biological properties
 supervene
 on physical properties (i.e., no difference in a biological property
without a difference in some underlying physical property), and (b)
each particular biological process (or *token*) is
metaphysically identical to some particular physico-chemical process.
This latter tenet is sometimes called token-token reduction, in
contrast to the stronger tenet that each type of biological process is
identical to a type of physico-chemical process. Ontological reduction
in this weaker sense is a default stance nowadays among philosophers
and biologists though the philosophical details remain controversial
(e.g., are there genuinely
 emergent properties?)
 Different conceptions of physicalism may yield different implications
for ontological reduction in biology (Dowell 2006). The denial of
physicalism by vitalism, the view that biological systems are governed
by forces that are not physico-chemical, is largely of historical
interest. (Vitalism also admits of various conceptions, especially
with respect to how non-physico-chemical forces are understood; see
 Section 2.)
 Some authors have argued vigorously for the significance of
metaphysical concepts in discussions of reductionism in biology
(Rosenberg 1978, 1985, 1994, 2006).



(*ii*) *Methodological reduction* is the idea that
biological systems are most fruitfully investigated at the lowest
possible level, and that experimental studies should be aimed at
uncovering molecular and biochemical causes (Andersen 2017). A common
example of this type of strategy is the decomposition of a complex
system into parts (Bechtel and Richardson 1993); a biologist might
investigate the cellular parts of an organism in order to comprehend
its behavior, or investigate the biochemical components of a cell to
understand its features. Although methodological reductionism is often
motivated by a presumption of ontological reduction, this procedural
recommendation does not follow directly from it. In fact, unlike
token-token reduction, methodological reductionism can be quite
controversial. It has been argued that exclusively reductionist
research strategies exhibit systematic biases that overlook relevant
biological features, and that for certain questions a more fruitful
methodology consists in integrating the discovery of molecular causes
with the investigation of higher level features (Wimsatt 1980,
 2007).[1]



(*iii*) *Epistemic reduction* is the idea that the
knowledge about one scientific domain (typically about higher level
processes) can be reduced to another body of scientific knowledge
(typically concerning a lower or more fundamental level). While an
endorsement of some form of epistemic reduction can be motivated by
ontological reduction in combination with methodological reductionism
(e.g., the past success of reductionist research in biology), the
possibility of epistemic reduction does not follow directly from their
conjunction. Indeed, debates about reduction in the
 philosophy of biology
 have centered on this third type of reduction as the most
controversial issue (see
 Section 4),
 and therefore our discussion will focus primarily on issues related
to epistemic reduction. Prior to evaluating any reduction of one body
of knowledge to another, a conception of those bodies of knowledge and
what it would mean for them to be
 "reduced" must be explicated.
 A number of different models of reduction have been proposed. Thus,
the debate about reduction in biology has not only revolved around
whether epistemic reduction is possible, but also which notions of
epistemic reduction are operative in actual scientific reasoning. Two
basic categories can be distinguished: (a) models of *theory
reduction* maintain that one theory can be logically deduced from
another theory
 (Section 3.1);
 and, (b) models of *explanatory reduction* focus on whether
higher level features can be explained by lower level features
 (Section 3.2).



The philosophical study of reduction links up with several key issues
in the philosophy of science. As reduction involves relating (broadly
speaking) one "body of scientific knowledge" to another,
it presupposes an account of the relevant epistemic units to be
related (e.g.,
 theories,
 laws,
 models,
 mechanisms,
 concepts,
 or disciplines)--how should these be understood? Since the
reduction of one theory to another usually presumes that somehow the
reducing theory *explains* the principles of the reduced
theory, reduction is also related to the issue of
 scientific explanation.
 For example, if a more fundamental theory fully reduces another
theory or even reduces several theories,
 unification
 (of some sort) results. The situation where a historically earlier
theory is reduced to a later theory is an intuitive case in which
 scientific progress
 might occur. Arguments against the existence of this type of
historical reduction have maintained that terms occurring in both the
precursor and descendant theory have different meanings
 ("incommensurability").
 This indicates that questions about reduction also connect to the
meaning of scientific terms and conceptual change. Therefore, accounts
of reduction often involve commitments made about other notions and
their adequacy depends in many cases on these related philosophical
commitments. This has led some philosophers to pursue an account of
reduction in biology that is as uncommitted as possible regarding the
precise construal of general notions such as "law" and
"explanation" (Sarkar 1998, cf. Brigandt 2013a), or to
specifically highlight how a particular package of general notions
travels together and skews our perspective on the shape of epistemic
reduction in scientific practice (Godfrey-Smith 2008).



In philosophy of biology, reduction involves questions about how
different biological disciplines and theories are related, and how
biology is connected to physics and chemistry (e.g., is biology
autonomous, possessing its own theoretical principles, explanations,
and methods?). Over the past four decades, discussion has concentrated
primarily on the question of whether *classical genetics* can
be reduced to
 molecular genetics
 and biochemistry. This discussion was motivated by the increasing
significance of
 molecular biology
 within the life sciences (Morange 2020), and revolved around specific
accounts of reduction in science, such as Nagel's (1961) model.
A less central concern has been whether *evolutionary biology and
ecology* are autonomous disciplines or reducible to molecular
biology (Beatty 1990, Brandon 1996, Dupre 1993, Rosenberg
2006). For example, a notable issue in evolutionary contexts is the
relationship between functional explanation
 ("teleology")
 and causal-mechanistic explanation (Wouters 2005). The
 levels of selection
 debate includes questions about whether all evolutionary explanations
can be cast in terms of genes and whether selection operates primarily
or exclusively on the genetic level (Agren 2021, Okasha 2006).
The main debate about reduction in genetics has lost some intensity as
many philosophers developed a skeptical consensus regarding the
possibility of substantive theory reduction (but see Waters 1990).
This decline has been accompanied by increasing attention to models of
explanatory reduction (e.g., Kaiser 2015, Sarkar 1998, Weber 2005)
across a wider variety of domains in biology (e.g., development,
ecology, evolution, cell biology, and neuroscience). For example, the
question of whether *developmental biology* can be reduced to
developmental genetics and molecular biology has become salient due to
recent progress in developmental genetics and growing philosophical
interest in
 developmental biology
 (Love 2008b, Robert 2004, Rosenberg 1997, 2006, Weber 2022). Less
attention has been given to the question of whether biology can be
reduced to physics (but see Rosenberg 2006). This has been an issue of
concern to many biologists (e.g., Mayr 2004), both with respect to
methodology (e.g., the adequacy of analyzing a system by dissecting it
into component parts) and whether modes of explanation from physical
science are inherently inappropriate for biological science (Love and
Huttemann 2011).



Debates about reduction in biology have often been framed in terms of
"reductionism" vs. "anti-reductionism" (or,
more archaically, "mechanism" versus
"organicism" or "vitalism"). However, since
different models of reduction have been put forward, whether one takes
a reductionist or anti-reductionist stance about a particular
biological subdiscipline (e.g., classical genetics) depends on the
notion of "reduction" being utilized (Wimsatt 1976b, Hull
1979). Furthermore, this framing has tended to create a false
dichotomy between two extreme positions: reductionism as the idea that
molecular biology can in principle *fully explain* all
biological facts--making higher level biological theories
dispensable--and anti-reductionism as the idea that higher level
biological fields possess explanatory principles of their own and are
fully autonomous in the sense of *not benefiting* from
molecular biology. A variety of middle (and orthogonal) ground exists
between these extremes and has motivated the efforts seen in
alternative research programs in philosophy of science that address
questions about the nature and status of interdisciplinarity, such as
how data, standards, or explanations are integrated across biological
fields (see
 Section 5).
 Given that references to "reduction" in different areas
of biology pick out a variety of commitments in different contexts,
which makes pronouncements of both the success and failure of
"reduction" legitimate, the traditional assumption that
there is a unique and global notion in need of explication is
problematic (Huttemann and Love
 2011).[2]


## 2. Historical Background: Philosophical and Scientific



Undoubtedly, the growth and development of molecular biology over the
past half century has made reductionism in biology a central issue
(and DNA a household word). However, it would be wrong to assume that
different aspects of reductionism only gain traction in the wake of
the molecularization of biology juxtaposed with discussions of
reduction from a logical empiricist perspective (see
 Section 3.1).
 Besides a perennial concern with what makes
 life
 distinctive (Riskin 2018), we can distinguish at least two
reductionist themes throughout history relevant to the life sciences
and its philosophy: (1) the relation among different branches or
domains of knowledge and (2) the relation between
 parts and wholes
 (Grene and Depew 2004, Magner 1994). These two themes link up in a
complex fashion with both epistemic and ontological reduction.
(Questions about methodological reduction tend to coalesce around new
technologies that open up the possibility of pursuing reductionist
research methods, such as making observations at a lower level with
microscopy.) Additionally, these themes arise in the context of
specific domains of enduring interest: (a) the complex relations among
different animals and plants in natural environments, i.e.,
"ecology", (b) the integrated relations among the parts
and whole of an organism, i.e., "physiology/functional
anatomy", and (c) the dynamic relations among the homogeneous
components in the early stages of an embryo that eventually beget a
unified whole organism containing heterogeneous parts in appropriate
arrangement and connection, i.e.,
"development/reproduction".



Aristotle
 is the foundation for both philosophical themes pertaining to
reductionism. He addressed the relationship between domains of
scientific knowledge in his concepts of superordinate and subordinate
sciences (*Posterior Analytics* I). Each science has a
distinctive subject genus, first principles, and a set of predicates
that are commensurable with the subject genus (McKirahan 1978, 1992,
ch. 4-5). Though the relations among sciences are systematic,
they are not necessarily reductive because there is no most
fundamental science. These connections are relevant to relations
between parts and wholes because Aristotle utilized his science of
elements and their potentials (e.g., as seen in *On Generation and
Corruption* and *Meteorology*) to inform his description
and analysis of organism components in the *History of Animals*
and *Parts of Animals*. He treated three compositional
"levels": elements and their potentials; uniform parts
such as blood and bone; and, non-uniform parts that include multiple
uniform parts, such as the face or hands. The primary domain here is
physiology/functional anatomy but development/reproduction is always
in view and addressed directly in the *Generation of Animals*.
Claims about "potentials" are buttressed by an account of
their contributions to material properties composing uniform parts
(*Meteorology* IV; see Lennox 2001, ch. 8, Popa 2005). Complex
dispositions (e.g., the fleshy, sinuous elasticity of the esophagus)
are postulated from these material substrates that have relevance to,
but do not determine the nature of, these organismal parts because
functional strictures ultimately govern them (the fleshy, sinuous
elasticity of the esophagus is *for the sake of* repeated
dilation during food ingestion).



The
 teleological
 orientation of Aristotle's biology means that he is often
characterized as an ontological anti-reductionist (e.g., the elemental
potentials of lower levels of organization are for the sake of but do
not determine the uniform parts at higher levels of organization).
This blends with epistemic issues related to particular domains, such
as his rejection of Presocratic materialist (i.e., purely
"mechanistic") explanations for the origin of animal
morphology during development. (Empedocles apparently claimed that
vertebrae arise during ontogeny solely as a consequence of a unified
cylindrical column physically breaking into the observable iterated
units of the backbone; see *Parts of Animals* I.1
[640a].) Yet Aristotle was attentive to issues of material
composition and constraints arising from the nature of properties
exhibited by animal parts, which often mark commitments to types of
ontological and epistemic reduction. His concept of hypothetical
necessity (*Physics II*; see Cooper 1987) permitted the use of
one kind of material in many different organismal parts.
 Galen,
 among many others subsequent to Aristotle, also explored these
issues, whether from the perspective of how material complexes
generate higher level properties (*Mixtures*) or the relations
among parts and wholes in the context of development (*The
Construction of the Embryo*).



In the early modern period, William Harvey adopted an Aristotelian
stance in the context of both physiology and development (Lennox 2006,
2017). The relation between parts and wholes in ontogeny, including
relevant material properties, is constantly in view (Harvey 1981
[1651]). Although Harvey used "mechanistic" analogies,
referring to the motion of the heart in terms of interlocking gears or
to the heart itself as a pump (Distelzweig 2016),
 Rene Descartes
 famously disputed Harvey's claims from the perspective of the
 "mechanical philosophy".
 Descartes sought to explain the movement of the heart not in terms of
function but rather by appeal only to the matter in motion composing
the circulating blood that is heated and thus expands akin to
fermentation (*Description of the Human Body*). He also
attempted to explain embryology in terms of matter and motion alone;
e.g., tissue and organ origination is accounted for via matter slowing
down and aggregating in different regions of the embryo (Des Chene
2001, ch. 2, Smith 2006, Part II).
 Robert Boyle
 defended teleological explanations in anatomy and physiology
(specifically, the integrated relations among the parts and whole of
an organism) by laying out how they were compatible with and supported
by mechanistic explanations (Lennox 1983). Thus, he offered a version
of epistemic reduction in line with his conception of mechanical
philosophy, which included a heterogeneous methodology (reductionist
and non-reductionist) and concomitant reservations about ontological
reduction.
 Baruch Spinoza
 famously used the image of a worm in a bloodstream to engage the
theme of part-whole relations and their complexity in a 1665 letter to
Henry
 Oldenburg.[3]
 More broadly, the emergence of distinctive scientific approaches to
living phenomena in the 18th century involved constant debate over
whether organisms were composed of "active" matter or
energized by an animating element, distinct from non-living entities,
such that their resistance to decay could be accounted for by a
"vital materialism" (Zammito 2018).



Immanuel Kant
 explicitly articulated a dialectic between a teleological outlook on
organismal functioning (including ecological relationships,
physiology, and development specifically) and a mechanistic
understanding of causation modeled on Newtonian mechanics
(*Critique of Judgment*, Part II; see Mensch 2013, Zuckert
2010). Kant's maintenance of this tension between the reciprocal
causal relations of parts in an organism ("teleology") and
the linear-mechanical causality justified within his critical
philosophy was a way of splitting apart epistemological and
metaphysical issues. It has elements of epistemic anti-reductionism
(organismal processes must be understood in terms of their reciprocal
contribution to a systemic goal--an epistemological subordination
of mechanism to teleology) and ontological reductionism (all causation
is ultimately linear-mechanical). But Kant also understood
linear-mechanical causation as a category by which the mind frames
experiences of the world. Thus, his understanding of metaphysics
differs from the realist one underlying most contemporary accounts of
ontological reduction. In addition to the theme of reductive relations
between parts and wholes, Kant also addressed relations among
different scientific domains in his discussion of sciences having
their own distinct concepts and subject matter (*Critique of
Judgment*, SS68, 79).



Kant's work was influential among those studying biological
phenomena, even if misinterpreted in various ways, and helped frame
the question of teleology versus mechanism in the early 19th century
(Lenoir 1982, Zammito 2012). His discussion stressed the significance
of methodological conclusions--it is necessary (a maxim or
regulative principle) to take organisms as natural purposes if we are
to investigate them scientifically. This encouraged speculations about
new forces, akin to those found in Newtonian mechanics, which would
explain biological phenomena "mechanistically" (e.g., the
formative force explaining embryonic development; see Look 2006,
Richards 2000). The Newtonian inspiration survived, with or without
Kantian traces, well into the 19th century and beyond. Comparative
anatomy (conceptualized broadly to include functional anatomy and
embryology) exploited methodological suggestions from successful
physical science. For example, Geoffroy St. Hilaire appealed to
Newton's musings that animals are governed by similar principles
or laws as those found in mechanics (Le Guyader 2004). More typical is
Richard Owen's discussion of matter and its properties within
living organisms, where he exhibits a clear anti-reductionist stance
and postulates something akin to emergent
 properties.[4]
 This perspective was shared by many comparative anatomists who used
an "analysis:synthesis" style of reasoning (Elwick 2007).
A related strand regarding reductionism winds its way through
physiological investigations of the 19th century. Here the Cartesian
mechanical-reductionist program is rejoined with an emphasis on the
animal machine (Canguilhem in Delaporte 1994, ch. 5, 8, 10, 12,
Coleman 1977, ch. 6). Despite clear metaphysical commitments to a form
of ontological reduction, methodological types of reductionism were
qualified because of their impact on experimental design (e.g.,
Bernard 1957 [1865]). Overall, there was a diversity of mechanist
("reductionist") and organicist
("non-reductionist") positions corresponding to
ontological, epistemic, and methodological types of reduction in the
19th century, similar to the philosophical diversity observable today
(see Sections
 3
 and
 5
 below).



In the late 19th and early 20th century, the topic of development
returned with a vengeance in the controversy over vitalism (sometimes
termed "organicism") (Normandin and Wolfe 2013). A general
movement towards more mechanistic or materialistic interpretations of
living systems was emerging at this time (e.g., Loeb 1912, cf. Allen
1975) and disagreements about explaining development loomed large
(Maienschein 1991). However, the famous example of vitalism in Hans
Driesch's interpretation of development and the autonomy of the
organism should be seen as an issue of epistemology as much as
metaphysics (Maienschein 2000). Instead of materialism versus vitalism
(i.e., ontological reduction questions), the explanatory conflict
involved the nature of differentiation in early ontogeny and to what
degree it is prespecified. The theme of order and organization in
living systems pervades many writings about methodological,
epistemological, and ontological types of reductionism at this time
(emphasizing both relations between physics and biology and between
parts and wholes) (Esposito 2014, Peterson 2016). Examples include
Joseph Needham's *Order and Life* (1936), Kurt
Goldstein's *The Organism* (1934/1963), E.S.
Russell's *The Interpretation of Development and
Heredity* (1930), D'Arcy Thompson's *On Growth and
Form* (1917), Ludwig von Bertalanffy's *Modern Theories
of Development* (1933), and J.H. Woodger's *Biological
Principles* (1929). Philosophers of science who have had less
influence on contemporary Anglo-American philosophy were keenly aware
of these discussions. For example,
 Ernst Cassirer
 (1950, Part II) explored reductionist themes related to causal
explanations of development, including the debates about mechanism and
vitalism surrounding Driesch, as well as the relations between
physical science and biology. These topics also appeared in the pages
of *Philosophy of Science* (e.g., Lillie 1934, 1942, 1948,
Singer 1934, 1946), although not necessarily utilizing the specific
terminology of reduction (Byron 2007).



Ernest Nagel's general treatment of reductionism in chapters 11
and 12 of *The Structure of Science* (1961) canvassed many
different aspects of these perennial debates (Sarkar 2015). Whereas
the sections concerning theory reduction have usually been in view
(connecting with the reductionist theme of relating domains of
knowledge), Nagel also interacted with biological literature
addressing claims about parts, wholes, and emergence, thereby
addressing the second reductionist theme that has been prominent since
Aristotle (see Nagel 1961, 366ff). He highlighted the polysemy of
"wholes", "parts", and "sums"
inherent in claims about success or failure in showing that the whole
is just the sum of its parts (pp. 380ff). Additionally Nagel treats
the question of evolutionary emergence, i.e., whether genuinely new
entities arise in the history of our universe and life on Earth (see
Goudge 1961). He dealt with the aforementioned theoretical biologists
(e.g., Bertalanffy, Russell, and Woodger) on the topic of hierarchical
organization and reduction in living systems, especially as seen in
ontogeny (Nagel 1961, pp. 432ff). Nagel's contemporaries
likewise treated reductionist themes, though their work has largely
been overlooked (e.g., Morton Beckner's discussion of
"organization" and "levels of analysis" as
methodological and explanatory aspects of reduction; Beckner 1959, ch.
9).



Despite Nagel's wide-ranging analysis, most subsequent
philosophical discussion has concentrated on his formal account of
theory reduction (see
 Section 3.1),
 and whether it serves as an adequate general characterization of
reductionism for all areas of scientific
 inquiry.[5]
 The biological case that has received the most scrutiny is the
relationship between classical and molecular genetics, in part because
the molecularization of genetics was palpable in this historical
period (Schaffner 1969). The manifold difficulties encountered in
applying Nagelian theory reduction to genetics (see
 Section 4)
 encouraged the growth of
 philosophy of biology
 as an independent disciplinary specialty, in part because these
difficulties seemed to fit a recurring pattern--misconstruing
biological reasoning with philosophical accounts of science forged on
physical science examples (Love and Huttemann 2011).
Philosophical issues in biology seemed to require distinct analyses
that are more sensitive to empirical research in biology (Brigandt
2011). Additionally, the rise of
 sociobiology
 and
 gene-centered
 evolutionary explanations provoked anti-reductionist stances among
biologists on the basis of social and political commitments (e.g.,
Levins and Lewontin 1985).



More recent attention to reductionism *in situ* within
different life science contexts has led many philosophers to revisit
the perennial aspects of reductionism, many of which were simply
tangential to controversies over theory reduction. A number of current
debates are unconscious returns to neglected issues, albeit in
different ways and in different contexts. That developmental biology
has returned to the center of discussions is not surprising because of
its enduring status as a biological topic inviting reflection on
reductionist themes. The same can be said for ecology and functional
anatomy, although they remain more peripheral for many philosophers.
Socially and politically tinged aspects of reductionist research in
biology, such as racial categorizations based on genetic profiles,
also continue to provoke philosophical analyses (see
 Section 5).


## 3. Models of (Epistemic) Reduction



Most discussion in contemporary philosophy of science has centered on
the issue of
 *epistemic reduction*
 (rather than ontological or methodological reduction; see
Hoyningen-Huene 1989). The basic idea that the knowledge (or other
epistemic units) pertaining to one scientific domain can be reduced to
another body of knowledge (or its epistemic units) has been spelled
out in different ways. It is useful to group different approaches to
reduction into two basic categories: (1) models of
 *theory reduction*,
 which maintain that a higher level theory can be logically deduced
from a lower level theory, and, (2) models of
 *explanatory reduction*,
 which focus on whether representations of higher level features can
be explained by representations of lower level features, typically by
decomposing a higher level system into parts (Sarkar 1992).
 Models of theory reduction
 were of primary interest in post-positivist philosophy of science
that emerged in the 1960s and have received the most sustained
attention (Schaffner 1993). More recently, accounts of explanatory
reduction have been developed to remedy the inadequacies of theory
focused accounts, so that theory reduction has been displaced as the
central issue by competing accounts of explanatory reduction (but see
Dizadji-Bahmani et al. 2010 and Sarkar 2015).


### 3.1 Theory Reduction



According to *theory reduction*, theory \(T\_A\) reduces \(T\_B\)
(e.g., \(A\)tomic physics reduces \(B\)iology) if \(T\_A\) logically
entails \(T\_B\). Assuming a deductive-nomological account of
 explanation
(Hempel and Oppenheim 1965 [1948]), theory reduction as deduction from
theoretical principles is an instance of explanation. In particular,
\(T\_A\) logically entails and explains the laws of \(T\_B\). Compare
this with the logically weaker notion of reduction put forward by
Kemeny and Oppenheim (1956), which includes instances of *theory
replacement*. The Kemeny-Oppenheim model concerns the situation
where the observable predictions made by \(T\_A\) include (at least)
all observable predictions of \(T\_B\). In this case \(T\_A\) can
explain everything that \(T\_B\) explains, but \(T\_A\) need not
encompass the theoretical principles of \(T\_B\) (as in genuine theory
reduction), which allows for the possibility that \(T\_B\) contains
inadequate theoretical notions and is replaced by \(T\_A\).



Many models of theory reduction derive from the account of reduction
due to Ernest Nagel (1949, 1961). Working within the philosophical
framework of logical empiricism, Nagel construed reduction as a
logical relation between theories, where a theory is understood as a
system of statements, containing laws, formulated in a first-order
formal language (Sarkar 2015). The reduc*ing* theory \(T\_A\)
reduces the reduc*ed* theory \(T\_B\) if the laws of \(T\_B\) can
be logically derived from \(T\_A\), which Nagel called the
"condition of derivability". However, if \(T\_B\) contains
scientific terms that do not occur in the language of the reducing
theory \(T\_A\) ("organismal reproduction" is not an
expression of biochemistry), then derivability presupposes that the
primitive expressions of \(T\_B\) (in particular, its predicates) can
be logically related to the language of \(T\_A\). Nagel made this
explicit by a "condition of connectability": reduction
presupposes that there are statements (e.g., conditionals) that
contain expressions both from \(T\_A\) and \(T\_B\), such that \(T\_A\)
together with these statements entail the laws of \(T\_B\). These
connectability statements are often called *bridge principles*
(or correspondence rules, or reduction functions), and have been
interpreted diversely. Nagel rejected the idea that bridge principles
are analytic statements, but did not take a stand as to whether they
are factual or conventional. Some philosophers have required that
bridge principles are laws (rather than accidental generalizations),
whereas others have maintained that they should express metaphysical
identities between entities, properties, and processes (e.g.,
identifying cells with collections of molecules, in line with
ontological reduction). Nagel himself construed reduction as an
epistemic notion without ontological commitment; nor did he require
that bridge statements be biconditionals--mere conditionals when
conjoined with \(T\_A\) sometimes logically entail \(T\_B\). (The
Kemeny-Oppenheim notion of reduction / theory replacement is weaker
than Nagelian reduction as it does not require such bridge principles
connecting \(T\_A\) and \(T\_B\).)




 This account covers *interlevel theory reduction*. For
instance, Oppenheim and Putnam (1958) argued for a hierarchical or
layered model of scientific disciplines that assumes each layer or
level corresponds to a theory. Each discipline is reducible to the
theory on the next lower level, e.g., sociology to organismal biology,
organismal biology to molecular biology, molecular biology to
chemistry, and chemistry to microphysics (see also Brooks et al. 2021,
Walter and Eronen 2011). Another way to apply Nagel's general
model is *successional theory reduction*, where a historically
earlier theory is reduced to a later, more mature theory, so that
reduction can be an instance of theoretical progress (Nickles 1973).
In both cases, Nagel held that theories needed to be indexed to a
particular time: "The question whether a given science is
reducible to another cannot in the abstract be usefully raised without
reference to some particular stage of development of the two
disciplines" (1961, 361).
 Paul Feyerabend
 (1962, 1965a, 1965b) and
 Thomas Kuhn
 (1962) criticized successional theory reduction and especially
Nagel's connectability condition. Feyerabend argued that an
earlier and later theory might use the same theoretical term with a
different meaning (e.g., "mass" in classical and
relativistic mechanics). This
 incommensurability
 of meaning makes the connectability of these theories'
expressions, and thus the logical derivation of one theory from
another, impossible. Whether or not genuine incommensurability obtains
is controversial (see, e.g., Sankey 1994).



Nagel's model was revised and applied in a specifically
biological context--the reduction of classical genetics to
biochemistry--by Kenneth Schaffner (1967, 1969, 1976; see
Schaffner 1993 for his mature account). Schaffner's
"General Reduction Model" addresses a key drawback of
Nagel's account, first noted by Feyerabend: even though the
theory to be reduced may be approximately true, it might contain
empirically false statements, especially if it is a historical
precursor of the more mature reducing theory (e.g., the inheritance
"laws" of classical genetics have exceptions). If the
theory to be reduced \((T\_B)\) contains false statements, then it
cannot possibly be deduced from \(T\_A\). For this reason, Schaffner
considers instead \(T\_{B^\*}\), which is a *corrected* version
of the theory to be reduced in that \(T\_{B^\*}\) makes more adequate
predictions than \(T\_B\). On this model, reduction occurs if \(T\_A\)
and \(T\_{B^\*}\) can be related by reduction functions (bridge
principles) and \(T\_{B^\*}\) follows logically from \(T\_A\) enriched by
the reduction functions. (Whereas Nagel focused on the laws of
\(T\_B\) being deducible from \(T\_A\), Schaffner requires that all
statements of \(T\_B /T\_{B^\*}\) be deducible from \(T\_A\).)
Schaffner's central tenet about reduction in biology is that the
success of
 molecular biology
 shows that classical genetics and traditional fields of experimental
biology are in the process of being reduced to biochemistry. Although
this reduction has not been completed yet, a logical derivation of
traditional experimental biology from a (completed) theory of
biochemistry is *in principle* possible and will be achieved
eventually. Schaffner's account has an ontological aspect in
that he interprets the reduction functions as synthetic statements
expressing identities between the entities and processes of the two
domains related (in line with Sklar 1967 and Causey 1972a, 1972b),
though he does not argue that these identities are metaphysical
necessities. The Nagel-Schaffner approach to theory reduction assumes
a syntactic account of
 theory structure
 such that they are axiomatized systems formalizable in first order
predicate calculus. A variety of other models of theory reduction
exist, some of which use a semantic (i.e., theories as families of
 models)
 rather than a syntactic account of scientific theories (see Balzer
and Dawe 1986a,b, Hooker 1981, Suppes 1957, Woodger 1952).




 Schaffner's account provided the motivation and point of
departure for much of the reduction debate in philosophy of biology,
which was conducted primarily in the 1970s and 80s and revolved around
the issue of whether (and in which sense)
 classical genetics can be reduced to molecular genetics
 or biochemistry. Three criticisms pertaining specifically to the
Nagel-Schaffner model bear mentioning.
 (Section 4
 reviews the main objections to different models of reduction more
generally.)



(a) Michael Ruse (1971) and David Hull (1974) argued that the relation
between classical and molecular genetics is one of theory replacement,
not reduction in Schaffner's sense. Although Schaffner's
account permits a correction of the theory to be reduced \((T\_{B^\*}\)
instead of \(T\_B)\), it is not clear when a modified version
\(T\_{B^\*}\) (corrected "classical genetics") still counts
as being largely similar to \(T\_B\) (classical genetics). This leaves
an ambiguity of whether one should conclude that \(T\_B\) was reduced
because \(T\_{B^\*}\) is similar enough or that \(T\_B\) has been
replaced by another theory because the two are so dissimilar (Hull
1976, Ruse 1976). Schaffner only requires that \(T\_B\) and \(T\_{B^\*}\)
are "strongly analogous" (1993, 429), without offering a
specification of how much similarity is required for reduction rather
than replacement (Winther 2009). William Wimsatt (1976b) emphasizes
that while interlevel, compositional reductions are transitive,
successional reductions through history are intransitive, so that a
continuum between genuine successional reduction and replacement
obtains. Any sequence of successive reductions can be expected to
evolve into an instance of replacement given enough time.



(b) Nagel and Schaffner relied on a
 syntactic construal of theories,
 which assumes that a theory is a set of statements in a formal
language, including laws (Kitcher 1984). Yet it has been argued that
molecular biology as the reducing theory does not consist of a small
body of laws, so that a covering-law model of explanation and
reduction is not applicable (Culp and Kitcher 1989, Kitcher 1984,
Sarkar 1998). If molecular biology or other biological fields are
inadequately represented as consisting of a clearly delineated theory,
reconstructed as a set of statements in a formal language, then an
account of reduction that presupposes this construal of scientific
theories is problematic.



(c) Hull (1976), Wimsatt (1976a, 1976b), and Sahotra Sarkar (1992,
1998) have objected that Schaffner focuses too much on formal
considerations about reduction, rather than substantive issues. His
account construes reduction as a logical relation that is "in
principle" possible even though it is not occurring in practice.
If reduction in this sense is not occurring in biology, then there are
significant questions about whether it best fits biological knowledge
and practice. Nagel claimed that premature attempts at reduction could
retard scientific progress, thus implicitly decoupling methodological
demands from epistemological ones (Nagel 1961, 362-3). Schaffner
(1974, 1993) acknowledges that reductionism in his sense has been
peripheral to the practice of molecular biology, but maintains that
his formal model of reduction captures the reduction relation between
theories. Wimsatt (1979) suggests that Nagel's and
Schaffner's focus on in-principle considerations and the context
of justification, to the exclusion of in-practice considerations and
the context of discovery, leads to misunderstandings about the nature
of reductionism debates, including historical and current controversy
among scientists (see
 Section 2).
 Reduction may obtain between classical and molecular genetics, but
not in the sense of Nagel's or Schaffner's logical
empiricist approach (Hull 1974).


### 3.2 Explanatory Reduction



A variety of explanatory reasoning patterns used by life scientists
are now under scrutiny in philosophy of biology and theory reduction
is no longer the primary focus. Various models of *explanatory
reduction* focus on reductive explanation and differ from theory
reduction (which is also a kind of explanation on the
deductive-nomological notion of explanation) in two important
ways:



(a) Whereas theory reduction assumes that reduction is a relation
between theories, models of explanatory reduction permit other
features as the relata of a reductive explanation, such as fragments
of a theory, generalizations of varying scope, mechanisms, and even
individual facts. One approach pursued along these lines is due to
Kenneth Waters (1990, 1994, 2000). Instead of construing theory
relations in terms of the Nagel-Schaffner model, he identifies a key
principle of inference operating in classical genetics and molecular
genetics: the "difference making principle" (gene
differences cause differences in phenotypes). This principle can be
ascribed to
 genes
 in both classical and molecular genetics. An explanatory reduction is
achieved between them because their causal roles correspond. Waters
(2008) extends this account by emphasizing how the investigative
practices of classical genetics were "retooled" by
developments in molecular genetics, which accounts for the success of
the corresponding explanations.



Another example of explanatory reduction is due to Marcel Weber
(2005). In line with models of theory reduction, Weber maintains that
biochemical ("physico-chemical") laws carry the
explanatory force, but that a fact or basic generality about
biological mechanisms (rather than a genuine law or a whole theory),
such as the mechanism of action potentials in neurotransmission, is
what is explained. By permitting reference to higher level structures
in the *explanans*, such as axons, he does not require that a
reductive explanation contain exclusively biochemical expressions.



(b) A characteristic difference between theory reduction and
explanatory reduction stems from the fact that the
former--focusing on the epistemic notion of logical
deduction--does not incorporate the historically ubiquitous
ontological idea that a reduction explains the whole in terms of its
parts (see, e.g., Winther 2011). Models of explanatory reduction
typically assume that reductive explanation is
 causal explanation,
 where a higher level feature is explained by the interaction of
constituent parts. Stuart Kauffman (1971) gave an early expression of
the idea that the search for explanations in experimental biology
proceeds by decomposing an overall system into interacting parts.
Wimsatt (1976b) also recognized that this mapped more naturally onto
the language of biologists, especially the practice of discovering and
elucidating mechanisms (see also Bechtel and Richardson 1993).
Mechanism approaches have now developed into a robust alternative to
theory reduction (see
 Section 5).
 Since many philosophers of biology and neuroscience conceive of
explanation as the description of
 mechanisms,
 accounts of explanatory reduction can rely on the notion of a
mechanistic explanation (e.g., Delehanty 2005).



Models of explanatory reduction avoid several problems facing theory
reduction (see
 Section 3.1).
 Since explanatory reduction is not committed to the relata of an
explanation being theories involving laws, it can defend the
possibility of reduction without formally reconstructing a clearly
delineated theory of molecular biology or classical genetics. Its
focus on reduction as explanation of a whole in terms of its parts
captures a feature of actual molecular explanations. Whereas accounts
of theory reduction have to acknowledge that reduction (in this sense)
has not yet been achieved and must appeal to its "in
principle" possibility, accounts of explanatory reduction
comport well with the piecemeal nature of actual scientific research.
Experimental and molecular biology can offer reductive explanations
even if many facts remain unexplained and existing explanations still
require more details to be filled in. Current biology effectively
explains individual facts and generalities of smaller scope, and the
*explanans* can be a mere fragment of a theory (see, e.g.,
Schaffner 2006 on "patchy and fragmentary" reductions).
Finally, given that mechanistic explanations in experimental biology
are preceded by and closely tied to the discovery of mechanisms
(Craver and Darden 2013), explanatory reduction provides an account of
reduction that can be related to scientific discovery, while
approaches of theory reduction have to separate the context of
justification (reduction and explanation) from the context of
discovery.



An early model of explanatory reduction due to William Wimsatt (1976b)
assumes that reduction is the causal explanation of an *individual
event* (rather than a generality), involving a
"compositional redescription" of a higher level state of
affairs into some of its component features. This model is related to
Wesley Salmon's (1971) account of statistical explanation, which
uses the notion of
 screening off
 to explicate the idea of one property being statistically more
relevant (and thus more explanatory) than another one. Wimsatt
replaces Salmon's statistical relevance with the idea of causal
relevance (as explanatory reduction in biology involves the search for
causally relevant factors), and he develops the notion of
"effective screening off". Compositional redescription and
explanation in terms of lower level properties can have a greater
"cost" of explanation (e.g., by being more complicated)
than the description in terms of the higher level property that is
effectively screened off. A consequence of the epistemic
"cost" requirement is that an explanatory reduction that
effectively screens off a described higher level feature does not make
it irrelevant and thus eliminable (as in Salmon's account)
because it can be retained for pragmatic purposes.



 Sahotra
 Sarkar's (1998) detailed discussion of reductionism and
genetics offers several relevant conceptual clarifications. Focusing
on substantive issues about reduction in genetics (especially
*representation*, see
 Section 4.3),
 rather than formal considerations in a theory of reduction, Sarkar
develops a view of explanatory reduction that is not committed to a
particular account of explanation. Two such basic types of reduction
are "abstract hierarchical reduction" and "strong
reduction" (or spatial hierarchical reduction), where the
latter--unlike abstract hierarchical reduction--requires
that entities of a lower hierarchical level are physical parts of
higher level entities. (Each type of reduction can come in stronger
and weaker forms as different kinds of approximations are involved in
different explanations.) Sarkar argues that explanations in
*classical genetics*, which explain phenotypic patterns in
terms of classical genes, are abstract hierarchical reductions. The
entities involved in this case are alleles, loci, linkage groups,
genotypes, and phenotypes, which stand in hierarchical relations
(e.g., alleles \(A\) and \(a\) form genotype \(Aa)\), with individual
alleles occupying the lowest level. However, this is an abstract
rather than a spatial hierarchy; the assumption that \(A\) and \(a\)
map to \(Aa\) at the next higher level does not require \(Aa\) to be a
physical entity that has \(A\) and \(a\) as its spatial
parts. Furthermore, the genotypic entities in this hierarchy are
governed by various transformations and regularities (principles of
inheritance), such as segregation, linkage, and mutation, which help
to explain phenotypic patterns of inheritance. Although this abstract
hierarchy can be interpreted as a spatial hierarchy by viewing
classical genes as being parts of chromosomes, Sarkar's point is
that the various practices in classical genetics, such as segregation
and linkage analysis, did not require a physical interpretation of
genetic maps, and that explanations in terms of an abstract hierarchy
can be genuine reductions since they invoke a lower and thus more
fundamental hierarchical level.



Regarding spatial hierarchical reduction, Sarkar argues that this
regularly occurs in *molecular biology*, where certain cellular
features are explained by macromolecular physics. The various
components of cells form nested part-whole relations, resulting in a
spatial hierarchy. Many mechanisms of classical genetics can be
reductively explained by the physical principles governing the
behavior of macromolecules (though approximations are still
necessary). Explanatorily relevant principles for the physics of
macromolecules include weak interactions, hydrogen bonding,
hydrophobic bonding, allosteric transformations, lock-key fit, and the
idea that structure determines function. Sarkar's central tenet
is that the elucidation of the molecular mechanisms of replication,
recombination, and cell division provide reductive explanations of the
principles of classical genetics. Even though classical genetics
offered an account of gene transmission and could rely on cytological
explanations, these accounts did not yield a complete explanation of
how and why recombination occurs. Molecular biology filled in this gap
and corrected classical genetics.



Other models of explanatory reduction have been put forward by
philosophers, many with an explicit eye to capturing how reduction
occurs in scientific practice (e.g., Bickle 2003, 2006, 2008). In some
ways the most unique defense of explanatory reduction is found in the
work of Alex Rosenberg (2006), which departs from his earlier critical
focus on theory reduction (1978, 1985, 1994). First, according to his
position, strict laws (universal, exceptionless, spatio-temporally
unrestricted) are required for explanation and the only candidate law
in biology is the principle of natural selection (PNS). Second,
why-necessary explanations are better than how-possible explanations
in historical sciences such as biology, but why-necessary explanations
are only available at the molecular level because structure becomes
decoupled from function above this level. Therefore, all how-possible
explanations in "functional biology" (i.e., non-molecular
biology), even those invoking the PNS, and any descriptions from
functional biology involving higher levels of organization get
explained (why-necessarily) by the PNS operating on the molecular
level (often occurring at some relatively distant point in
evolutionary
 history).[6]



Marie Kaiser (2011, 2015) has offered a thorough analysis of reductive
explanation, including a systematic treatment of metaphilosophical
issues that underlie different approaches (see 2015, Chapter 2).
Instead of arguing for or against reduction, she both articulates the
advantages of an explanation being reductive and indicates that many
biological phenomena cannot be explained in this way. On
Kaiser's account, an explanation is reductive if it has three
characteristics: (1) lower-level, (2) internal, and (3)
parts-in-isolation. "Lower-level" means that the
explanation relies only on features that are at a lower level than the
phenomenon being explained. Similar to Sarkar's hierarchical
account, a reduction does not have to be a molecular or lowest-level
explanation because Kaiser wants to capture reductive explanations
throughout biology, including ecology. Explanations with this
characteristic provide an epistemically important unidirectional
"flow" of explanation from the lower to the higher level,
even if some of the relevant lower-level entities are not spatial
parts of the *explanandum* phenomenon. However, Kaiser also
requires that reductive explanations appeal only to physical parts
("internal") of the *explanandum* phenomenon or
system. Additionally, to fully qualify as reductive, an explanation
must represent each part it invokes in isolation--not in
isolation from any context, but rather in isolation from a
part's original complex context. This
"parts-in-isolation" characteristic is associated with a
system being near-decomposable; upon decomposition, the actual
functioning of a part can be understood in isolation. The whole
system's operation then can be recomposed from the parts
interacting in a largely sequential and linear fashion (Bechtel and
Richardson 1993, Bechtel and Abrahamsen 2009). Using these three
characteristics, one can classify different explanations and
distinguish a reductive explanation from a mechanistic explanation or
from a part-whole explanation (Kaiser 2015, ch. 6).


## 4. Problems with Reductionism



Different accounts of theory reduction and explanatory reduction face
several potential problems. Some critiques of (epistemic) reductionism
emphasize that the effects of molecular processes strongly depend on
the context in which they occur, so that *one* molecular kind
can correspond to *many* higher level kinds
 (Section 4.1).
 Another significant challenge to reductionism stems from the fact
that higher level biological structures and processes can be (and
typically are) realized by different kinds of molecular processes, so
that *many* molecular kinds can correspond to *one*
higher level kind
 (Section 4.2).
 Finally, because biological processes must be represented before they
can be explained (Sarkar 1998), two further features become salient as
issues for explanatory reduction: temporality and intrinsicality
 (Section 4.3).


### 4.1 Context-Dependence of Molecular Features (one-many)



One key challenge for reduction stems from the fact that the effect of
a molecular entity or mechanism may depend strongly on the
*context* in which it occurs (Hull 1972, 1974, 1976; see also
Wimsatt 1979, Gilbert and Sarkar 2000, Laubichler and Wagner 2001).
Classical geneticists were fully aware of the fact that a phenotype is
brought about by the interaction of several (many) classical
genes--the same allele may lead to two different phenotypes if
occurring in two individuals with a different overall genotype (Waters
2004). Although one-many phenomena have been known for some time, it
is now a robust empirical generalization that a molecular pathway may
have different effects in different cellular contexts; the same
pathway can be involved in different functions in different species or
in different parts of an individual (Gilbert and Sarkar 2000,
Laubichler and Wagner 2001, Burian
 2004).[7]
 These different contexts include developmental and physiological
history, which condition the behavior of molecular pathways (Brigandt
2006, Kirschner 2005). Even the amino acid sequence produced by a
molecular gene may depend on both DNA elements outside of the gene and
non-genetic factors, which means the same gene can code for distinct
products in different cells or different states of a cell (Griffiths
and Stotz 2013, Stotz 2006a,b). Thus, there are one-many relations
between molecular kinds and higher level kinds: a molecular mechanism
can causally lead to or be part of different higher level states
depending on the
 context.[8]



A common conclusion drawn from these one-many relations is that the
parts and molecular components of an
 organism
 have to be understood in terms of the organized whole in which they
occur (recall Kant's regulative principle;
 Section 2).
 Although biologists view the decomposition of a system into
lower-level parts as reductionist (an instance of methodological
reduction, see
 Section 1),
 they often construe the attempt to understand how the parts are
organized to bring about the system-level properties as a synthetic,
non-reductionist endeavor (Bechtel 2010, 2013). Paying attention to
context and organismal organization is a valid *methodological*
recommendation; however, it is less clear why this is an argument
against *epistemic* reduction. For example, proponents of
theory reduction, such as Nagel (1961) and Schaffner (1976), have
replied that a molecular reduction can take the relations of parts and
the context of molecular processes into account. For example, one can
specify the relevant context as initial conditions in the molecular
premises from which the higher level state is to be deduced
(Frost-Arnold 2004).



Context-dependence is primarily a problem for models of theory
reduction; some models of explanatory reduction take the organismal
context for granted without being committed to reducing it molecularly
(as seen in explanations offered in developmental biology). Sciences
can avail themselves of
 causes as difference makers
 relative to a given causal context (Waters 2007, Woodward 2003). Both
experimental investigation and explanation can focus on one among many
causes, relegating everything else to the context or background (which
is often held fixed in experimental studies). For example, if the loss
in function of a particular gene leads to an abnormal phenotype in a
knock-out experiment, this gene is *one* causal factor
implicated in the development of the normal phenotype. Explanations
appealing to this gene--as a salient causal factor relative to a
context--are genuinely explanatory even if other genes involved
in the phenotype are unknown and the cellular context for the gene is
not yet understood (Waters 1994, 2007). If molecular biologists
discover that the same mechanism produces different effects in
distinct contexts and only one of these effects is the target of
inquiry, a part of the mechanism's context becomes epistemically
relevant and can be included in the explanation (Delehanty 2005).



In contrast, theory reduction (such as the Nagel-Schaffner approach)
is committed to deducing a description of the higher level phenomenon
from purely molecular premises. In order to deduce even a single
higher level statement (*a fortiori* a total higher level
theory on Schaffner's account), the premises must contain (in
addition to the lower level laws) a specification of the total lower
level context--*every* feature that has *some*
causal impact. This includes features internal to an organism and some
parts of its environment. While explanatory reduction can appeal to
particular causes relative to a background that is not molecularly
specified, a logical deduction (as required by theory reduction) can
go through only if the total causal context is contained in the
 premises.[9]
 A molecular characterization of the total context is *in principle
possible* due to ontological reduction: for any higher level state
there is always a total molecular configuration that determines this
higher level phenomenon. However, this entails a retreat to the
"in principle" possibility of a molecular derivation; not
only is a molecular specification of the total context currently
unavailable but it may not be forthcoming in the future (Hull 1972,
1974,
 1976).[10]
 In this respect, accounts of explanatory reduction have a clear
advantage over models of theory reduction because the former are
committed neither to formal derivation nor the assumption that the
*explanans* of the reductive explanation involves only
molecularly characterized notions.



Although context-dependence is not a problem for many models of
explanatory reduction, issues can arise for some models of mechanistic
explanation. A mechanistic approach decomposes a system into
components and scrutinizes the functioning of each component in
isolation (where possible). However, a mechanistic explanation must
also epistemically "recompose" the mechanism behavior (the
*explanandum*) from these component functions (Bechtel 2010,
Bechtel and Abrahamsen 2009). There are molecular systems consisting
of highly interconnected and functionally integrated networks whose
complex organization does not permit a recomposition of the system
behavior from the component functions studied in isolation (Green et
al. 2018, Kaiser 2015). The functioning of individual components is
transformed by the many influences of the other components. This
empirical situation also is important because it stands behind many
instances where molecular biologists claim a limit of
"reduction"--these complex system interactions lead
to emergence (in some sense). This highlights that biologists
frequently attempt to account for mechanism functioning or system
dynamics and not just mereological or structural constitution (e.g.,
reducing the Mendelian kind "gene" to biochemical
kinds).



Jason Robert's (2004) treatment of explanation and methodology
in
 developmental biology
 describes what is probably the main valid point stemming from the
context-dependence of molecular features. While acknowledging the
legitimacy of reductionist research strategies that isolate molecular
causes relative to a background held fixed for experimental purposes,
Robert emphasizes that this methodology does not license an inference
to an exclusively reductionist position where all explanatorily
relevant causes are molecular. That developmental genetics uncovers
various differences between individuals that are due to differences in
gene expression does not entail that genes are the only factors
relevant in ontogeny. Since genetic research holds other cellular and
organismal factors fixed, the causal influence of these non-genetic
resources is simply not assessed by *this* research method. It
begs the question against those who maintain that some explanations of
development must invoke higher level features to assert that the
organismal context can always be described molecularly. For example,
an appeal to developmental genetics research success alone is
inadequate for reducing cellular context to molecular causes because
the discovery of genetic causes occurs against a fixed organismal
background (Robert 2004). The dependence of molecular features on
cellular and organismal contexts poses problems for theory reduction
approaches maintaining that higher level phenomena can be deduced from
purely molecular premises. (It is also a problem for claims that the
embryo can be computed from a purely molecular specification of the
fertilized egg, as endorsed by Rosenberg 1997; see Keller 2002, ch.
9.) Thus, there are limitations on the kinds of inferences that can be
drawn from reductionist research strategies. What remains missing from
many philosophical discussions critical of reduction is an explicit
account of methodological strategies and epistemological frameworks
that both capture actual scientific reasoning and offer an alternative
to reductionism (Love 2008a; see
 Section 5).


### 4.2 Multiple Realization of Higher Level Features (Many-One)



In addition to the one-many relation between molecular and higher
level kinds, Hull (1972, 1974, 1976) also pointed to the existence of
many-one relations as a challenge for reductionism. The same higher
level phenomenon (e.g., a Mendelian trait such as coat color) can be
produced by several different molecular mechanisms or a higher level
phenomenon is realized by different kinds of molecular configurations
 (multiple realization).
 This is a potential problem for both theory reduction and explanatory
reduction (though to differing degrees). In defense of his model of
theory reduction, Schaffner (1976) replies that it is sufficient to
specify one such molecular situation. Then the higher level situation,
which is determined by the molecular constellation, can be derived
logically from this molecular specification of the higher level
situation. However, one has to be clear about the nature of the
*explanandum* in a reductive explanation (i.e., what is the
consequent of a reductive deduction). Is it a *type* of higher
level phenomenon (described by higher level predicates) or merely a
*token* phenomenon (an instance of a higher level phenomenon)?
Theory reduction is the idea that a whole theory (such as classical
genetics) can be reduced, or at least that its laws can be reduced.
For example, the Mendelian principle of segregation is a law
describing a phenomenon occurring in all sexually reproducing
organisms, not just a token phenomenon, so this general
principle--covering various lower level realizations--would
have to be explained/deduced molecularly.



Consider the example that Schaffner (1993) offers in support of the
possibility of reduction: the Mendelian concept of
"dominance". On his account, given classical genes \(a\)
and \(b\), the property "allele \(a\) is dominant (relative to
allele \(b)\)" can be expressed in molecular terms as
follows. Assume that genotype \(aa\) yields phenotype \(A\) and
genotype \(bb\) corresponds to phenotype \(B\), while \(ab\) yields
\(A\) (because of dominance). We ascertain that gene \(a\) consists of
DNA sequence \(\alpha\) and gene \(b\) consists of DNA sequence
\(\beta\), and that phenotype \(A\) is brought about by protein
 while phenotype \(B\) is brought about by protein
b. This yields the following supposed reduction:



> 
> Allele \(a\) is dominant (relative to \(b)\) iff the
> presence of two copies of DNA sequence \(\alpha\) molecularly produces
> protein  [thus phenotype \(A\)], the presence of two
> copies of sequence \(\beta\) produces protein b [phenotype
> \(B\)], and the presence of one copy of \(\alpha\) and one copy of
> \(\beta\) produces  [phenotype \(A\)]. (Schaffner 1993, 442)
> 



Although Schaffner explicitly claims to have shown that the
*predicate* (or concept of) "dominance" can be
reduced to the language of biochemistry, his evidence actually shows
how a single *instance* of dominance (allele \(a\) is
dominant to allele \(b)\) could be brought about by states on the
molecular level. But epistemic reduction requires reducing higher
level concepts and, since Mendelian dominance can be brought about by
different *kinds* of molecular situations, this higher level
*predicate* corresponds to many molecular *predicates*,
which makes any reductive translation of higher level concepts very
complex. (In addition to translating such concepts into molecular
terms, theory reduction also requires deducing higher level
generalizations involving such concepts.) A similar issue can apply to
explanatory reduction. Biology attempts to explain *kinds* of
phenomena occurring in different contexts and organisms: reductive
explanations must molecularly explain *kinds* of phenomena in
addition to single instances.



Subsequent discussion based on ideas in metaphysics and
 philosophy of mind
 has clarified how one conception of the many-one relation between
molecular and higher level kinds can bear on epistemic reduction. In
his general treatment of reduction in psychology and social science,
Jerry Fodor (1974, 1975, 1997) distinguishes between *token-token
reduction* and *type-type reduction* (or between token
physicalism and type physicalism). Token-token reduction is the idea
that each *token* higher level property or process is
metaphysically identical to a token physico-chemical property or
process (the weak sense of ontological reduction that is
uncontroversial: see
 Section 1).
 The dispute centers on how much more than token-token reduction is
possible. A substantially stronger idea is that each *type* of
higher level phenomenon corresponds to one *type* of lower
level phenomenon. Type-type reduction yields a bold version of
*epistemic* reductionism where higher level concepts and
knowledge about higher level phenomena could be immediately reduced to
molecular notions. Yet Fodor argues that type-type reduction
(regarding mental and social kinds in particular) is empirically
false. Consider a simple law or causal principle of a higher-level
science relating two kinds, \(S\) and \(T\), such that \(\forall x(Sx
\rightarrow Tx)\), which can be read as "all \(S\)s are
\(T\)s" or "all events of type \(S\) bring about events of
type \(T\)". (Some laws or principles might be of a more complex
logical form.) As a matter of fact, a higher level kind is often
realized by several different kinds on the physical level; different
instances of the higher level kind are of a different type on the
molecular level. If kind \(S\) is realized by the lower level kinds
\(M\_1, M\_2 , \ldots ,M\_i\), the bridge principle (reduction function)
is of a disjunctive form:



\[
\forall x (Sx \leftrightarrow (M\_1 x \vee M\_2 x \vee \ldots \vee M\_i x))
\]


\(T\) is likewise multiply realized, say by the molecular kinds \(N\_1,
N\_2 , \ldots ,N\_j\). Fodor's point is that the lower level basis
of the higher level law \(\forall x(Sx \rightarrow Tx)\) consists in
several laws that reduce different higher level instances, such
as:



\[ 
\forall x(M\_1 x \rightarrow N\_3 x), \forall x(M\_2 x \rightarrow N\_1
x), \forall x(( M\_3 x \vee M\_4 x) \rightarrow N\_2 x),\ldots
\]


Thus, while on the higher level there is one *unified* law
\(\forall x (Sx \rightarrow Tx)\),
its translation into molecular terms is a *disjunctive*
statement:



\[
\forall x ((M\_1 x \vee M\_2 x \vee \ldots \vee M\_i x) \rightarrow (N\_1
x \vee N\_2 x \vee \ldots \vee N\_j x))
\]


This disjunctive statement has the appearance of being a gerrymandered
combination rather than a genuine law. Therefore, the higher level law
cannot be reduced to a *unified* lower level law. Token-token
reduction obtains, but since the natural kinds (to which laws apply)
of the higher level science cross-cut the kinds of the lower level
science, type-type reduction fails and the law-based explanation from
the higher level cannot be replaced by a unified law-based explanation
on the lower level. Steven Kimbrough (1978) argues that this situation
also applies to the relation between classical and molecular genetics:
ontological (token-token) reduction is possible, but not epistemic
(type-type)
 reduction.[11]



The multiple realizability of higher level kinds is typically viewed
as an obstacle to reduction (e.g., Kincaid 1997), and many have
interpreted the many-one relation between molecular and higher level
phenomena in a similar way. Rosenberg's earlier discussions that
criticized theory reduction in light of multiple realization (1978,
1985, 1994) used the notion of
 supervenience,
 which is another way to spell out an idea of ontological without
epistemic reduction
 (non-reductive physicalism).[12]
 Higher level facts supervene on physical facts if any difference
between two higher level situations implies a difference in the
physical basis. Yet this is consistent with two distinct physical
situations corresponding to the same higher level state (many-one).
Since biological properties such as fitness supervene on physical
properties, fitness can be nothing more than a combination of physical
properties, even though no such property complex is necessary for
having a particular fitness value. Higher level theories abstract away
from irrelevant variation in lower level features and thereby arrive
at generalizations that are explanatory precisely because they do not
include features irrelevant to explaining the phenomenon (Putnam 1975,
Strevens 2008). From this perspective, theory reduction of classical
to
 molecular genetics
 is impossible as the many-many relations between classical and
molecular kinds make any reductive account radically disjunctive. At
the same time, the notion of supervenience implies that classical and
molecular genetics are not incommensurable, and that molecular
genetics can shed light on the exceptions of classical genetics.



A related critique of reductionism in genetics is due to Philip
Kitcher (1984). It is not that the complexities of any reduction due
to many-one relations between molecular and higher level kinds exceed
our *cognitive* capacities. Rather, the reductive, molecular
account does not adequately explain because it does not involve the
natural kinds that underlie the appropriate causal relations.
Principles of classical genetics (e.g., segregation) are explained by
cellular processes (e.g., the behavior of chromosomes in meiosis)
because the higher level kinds picked out by cytology are causally
relevant. Rephrasing these cellular processes in molecular terms leads
to an account that mentions various disjunctive combinations of
molecular kinds, while failing to exhibit the unified kinds that are
the causes of the cellular process. A key aspect of Kitcher's
argument is that an epistemic account of reduction fails for
ontological reasons: it does not capture the natural kind structure of
chromosomal phenomena studied by classical genetics.



Schaffner's reply to the multiple realization objection (1993,
463-6) emphasizes that the same DNA sequence can be present in
many individuals, which means that molecular biology studies more than
*token* phenomena; molecular generalizations apply to
restricted *types*. This is true but fails to address the core
issue. Critics of reductionism do not argue that each higher level
type corresponds to several lower level *tokens* (which is
trivially true) or that molecular biology can study token phenomena
only. Rather, the point is that a higher level type corresponds to
several lower level *types*, and for each of these lower level
kinds a distinct molecular account obtains. Thus, a unified (as
opposed to disjunctive) causal explanation of the higher level
phenomenon appears impossible.



Waters (1990) challenges the commitment to unification that implies
there is explanatory loss in appealing to the multiply realized
"gory details" of molecular biology. In some cases,
disjunctive explanations at a lower level seem to explain better than
unified explanations at higher levels. Elliott Sober (1999) extends
this line of argument: an explanation in terms of higher level kinds
can be more unified or general by encompassing heterogeneous lower
level kinds, but this same heterogeneity exhibits important
differences in scientifically interesting properties. Only the lower
level science can account for such differences and therefore, in this
sense, offers a deeper explanation than the higher level science.
Explanations are not better or worse along a one-dimensional scale.
There are several epistemic virtues an explanation can possess, such
as generality, depth, or specificity. Sometimes a lower level
explanation is better relative to one epistemic virtue, while a higher
level explanation is preferable relative to another, such as
unification. And unification itself can be explicated differently in
terms of functional or structural features of biological systems (see,
e.g., Weiskopf
 2011).[13]



Many contemporary accounts of explanatory reduction focus on
 mechanisms
 and the study of
 model organisms.
 One reply to the multiple realization objection from this perspective
argues explicitly for token-token reduction, discussing how the causal
description of a token mechanism explains (Delehanty 2005). Weber
(2005) acknowledges that higher level features are multiply realizable
but notes that this does not hamper the reducibility of token systems
or individual organisms: "the fact that chemotactic behavior is
multiply realizable does not affect the reductionistic explanation of
*this* organism's behavioral biology" (48).
However, this stratagem ignores the key point of contention because
token-token reduction is uncontroversial. The focus on token phenomena
or individual organisms fails to address an important epistemological
feature of scientific knowledge: explanations often cover
*types* of phenomena. In many biological contexts, such as
 developmental biology,
 the *intellectual aim* is to explain phenomena instantiated in
many organisms and the use of model organisms is predicated on this
 aim.[14]
 Any version of epistemic reductionism has to address this feature of
scientific explanation to be adequate. Explaining development--as
understood by many developmental biologists--means to have an
account of ontogeny exhibited by individual organisms belonging to a
larger group (e.g., understanding the developmental principles that
govern *vertebrate* or *amphibian* development). As the
same morphological structure may develop in different species by means
of different processes and based on the action of different genes,
multiple realization obtains and is relevant for such explanations
(Laubichler and Wagner 2001).



Moreover, even if the aim is to explain a feature of a single
organism, it does not follow that an explanation should appeal
exclusively to factors on the lowest level. An explanation should only
include factors that are explanatorily relevant; an irrelevant factor
is one whose omission from (or modification in) the explanation does
not prevent the *explanandum* from following (Strevens 2008).
This also holds for mechanistic explanation, which should cite those
features as components of a mechanism whose modification would make a
causal difference to the *explanandum* phenomenon (Craver
2007). For instance, chromosomes are relevant parts of the mechanisms
("working entities") needed to explain Mendelian patterns
of inheritance (Darden 2005), but this particular explanation will
apply regardless of the lower level, molecular composition of the
chromosomes (e.g., whether or not the various genes have similar or
very different DNA sequences).



In the context of developmental biology, even during the development
of a single organism, a structure may be present across time and have
a stable developmental-functional role, but its underlying molecular
and cellular basis may change (Brigandt 2006, Kirschner 2005).
Entities above the molecular level can be more robust so that when
some molecular processes change or break down these higher level
entities are not modified or removed. Knocking out a gene need not
have any impact on ontogeny due to genetic redundancy, while
eliminating a particular cell or group of cells may dramatically
interfere with normal development (Brigandt 2013a, 2015, Mitchell
2009). A higher level causal connection can be more salient in that
the regular operation of the mechanism strongly depends on the
presence of this kind of causal relation. Such a higher level causal
relation is realized by molecular entities and their interactions
(i.e., supervenience obtains), but if relevant higher level processes
are less sensitive to disturbance or intervention than certain
molecular causes, the more powerful mechanistic explanation can be the
one that appeals to more robust, higher level causal connections. This
is one reason why some biological sciences preferentially invoke
higher level entities and processes in the face of multiple
realization, explaining in terms of higher level natural kinds and
causes.



In summary, the level(s) of organization a successful explanation
addresses often depends on the particular *explanandum*. If the
aim is to explain a type of phenomenon, multiple realization issues
(many-one relations) are likely pertinent. In the explanation of a
token phenomenon, the explanation should include lower level factors
only to the extent that they are explanatorily relevant for that
particular *explanandum*.


### 4.3 Representation, Temporality, and Intrinsicality



Sarkar's (1998) account of explanatory reduction draws attention
to the requirement of representation: natural phenomena must be
symbolized, embodied, pictured, or designated through media such as
equations, scale miniatures, or abstract diagrams (Abrahamsen et al.
2018, Bechtel et al. 2018, Potochnik 2017, Sheredos and Bechtel 2020).
Every reductive explanation in science involves representations of the
systems or features to be related by reduction. (Note that this is not
the question of how theory structure is represented; see, e.g.,
Schaffner 1996.) Almost all of the discussion surrounding one-many
 (Section 4.1)
 and many-one problems
 (Section 4.2)
 for theory and explanatory reduction assume or presume particular
representations that directly impact the arguments offered (e.g., they
involve approximations of different kinds). Sarkar distinguishes three
representational criteria for a reductive explanation: (i)
fundamentalism: the explanation of the phenomenon relies entirely on
features that pertain to a more fundamental realm; (ii) abstract
hierarchy: the system is represented as a hierarchy, where the lower
levels are regarded as more fundamental; and, (iii) spatial hierarchy:
the abstract hierarchy is rendered physical by the requirement that
the entities on the lower level are (spatial) parts of the entities at
higher levels (see
 Section 3.2).
 Whether or not there are one-many or many-one relations between
different hierarchical levels turns on the nature of the hierarchy
invoked and how it is characterized. The decomposition of a system is
not a univocal enterprise and, depending on the principles utilized,
can generate both competing and complementary sets of part
representations from the same system (Craver 2009, Kauffman 1971,
Wimsatt 1974, Winther 2011). Certain governing principles are often
visible, such as functional versus structural decompositions (Bechtel
and Richardson 1993, Winther 2006). Therefore, prior to determinations
of whether reductive explanations succeed or fail, questions of
representational choice and adequacy need to be addressed
explicitly.



These representational issues are not idle with respect to differing
explanations, both past and present, because the same line of argument
about the non-independence of organismal parts constituted reasons for
treating the organism from a non-reductionist standpoint (Aristotle,
*Parts of Animals* II.3, Owen, Hunterian Lectures [1837] in
Sloan 1992, 213-4). Individuation of parts and their explanatory
relationship to wholes is critically dependent on the principles
utilized in representing them (Love 2012). Wimsatt (1974, 1986, 1997,
2007) has claimed that reduction and emergence are compatible within
the context of explaining organizational complexity in living systems,
going so far as to argue that reductionist methodology can identify
emergence when specific conditions of aggregativity are delineated.
Different failures of aggregativity result when different conditions
are not met, which yields a subtle taxonomy of compositional
relations, as well as highlighting that different decompositions
produce distinct fulfillments and/or violations of those conditions
that can be methodologically exploited by scientists for the purpose
of causal discovery.



In addition to individuation, two other issues related to
representation are germane: temporality and intrinsicality
(Huttemann and Love 2011). In most discussions of epistemic
reduction, both theoretical and explanatory, no explicit distinction
has been drawn between constitutional or spatial relations
(arrangements) and causal or temporal relations (dynamics; but see
Mitchell 2009, 2012). One source of the focus on spatial relations is
the objection to reductionism from structural organization (Polanyi
1968, cf. Delehanty 2005, Frost-Arnold 2004, Schaffner 1993, ch. 9.2),
which is related to the "context" objection
 (Section 4.1).
 Moreover, physical science models that serve as templates for
thinking about reduction emphasize spatial composition questions
rather than causal relations (Love and Huttemann 2011). As
Schaffner has remarked: "Biological theories are usually given
in the form of a series of temporal (and frequently causal) models. In
physics, time is usually eliminated by making it implicit in
differential equations, whereas in biology a temporal process ...
is the rule" (1993, 83-4, cf. Kellert 1993, 93). Nagel
presciently recognized differences between spatial and temporal
organization in his discussion of teleological explanation (in part
because he was reading the literature on explaining ontogeny by
theoretical biologists; see
 Section 2).



> 
> The contrast between structure and function is evidently a contrast
> between the *spatial* organization of anatomically
> distinguishable parts of an organ and the *temporal* (or
> spatiotemporal) organization of changes in those parts. What is
> investigated under each term of the contrasting pair is a mode of
> organization or a type of order. In the one case the organization is
> primarily if not exclusively a spatial one, and the object of the
> investigation is to ascertain the spatial distribution of organic
> parts and the modes of their linkage. In the other case the
> organization has a temporal dimension, and the aim of the inquiry is
> to discover sequential and simultaneous orders of change in the
> spatially ordered and linked parts of organic bodies. (Nagel 1961,
> 426)
> 



Kitcher also glimpsed the potential significance of temporality for
reductive explanation in the context of embryology: "Because
developmental processes are complex and because changes in the timing
of embryological events may produce a cascade of effects at several
different levels, one sometimes uses descriptions at higher levels to
explain what goes on [later] at a more fundamental level" (1984,
371).



A very different distinction utilizing time, which is agreed upon by
diverse participants, distinguishes between the historical succession
of theories via reduction ("diachronic reduction") and
current attempts to relate parts to wholes, such as in explanatory
reduction or interlevel theory reduction ("synchronic
reduction"; see
 Section 3.1).



> 
> Synchronic reduction is mereological explanation, in which the
> behavior of more composite items described in reduced theories is
> explained by derivation from the behavior of their components by the
> reducing theory. Thus, reduction is a form of explanation. Diachronic
> reduction usually involves the succession of more general theories
> which reduce less general ones, by showing them to be special cases
> which neglect some variables, fail to measure coefficients, or set
> parameters at restricted values. As the history of science proceeds
> from the less general theory to the more general, the mechanism of
> progress is the reduction of theories. (Rosenberg 2006, 28)
> 



> 
> The first distinction to note is that between synchronic and
> diachronic conceptions of reductionism. The term *reduction* is
> often used to refer to the relation between a theory and its
> historical successor. ... This is ... what I mean by
> diachronic reductionism. My concern, on the other hand, is solely with
> synchronic reductionism, that is to say, with the relations between
> coexisting theories addressed to different levels of organization.
> (Dupre 1993, 94-5)
> 



What this distinction misses is the possibility of diachronic aspects
of part-whole or interlevel relations. Scientific explanations
commonly invoke dynamic (causal) processes involving entities on
several levels of organization (Craver and Bechtel 2007). This is one
of the core reasons why development is a persisting biological topic
for reductionism. During ontogeny there are causal interactions over
time among parts and activities (both homogeneous and heterogeneous)
to bring about new parts and activities (both homogeneous and
heterogeneous), eventually generating an integrated adult (whole)
organism.



Temporality can be added as a fourth criterion on representations for
reductive explanations: (iv) temporal hierarchy: for an abstract
hierarchy embedded in an explanation, the entities and their behaviors
on the lower level are temporally prior to the entities and their
behaviors at the higher levels (Huttemann and Love 2011).
Although temporal or process hierarchies have not received the same
attention as spatial hierarchies (such as in Wimsatt's
aggregativity criteria), their importance is seen in explanations that
invoke higher level features (e.g., tissue interactions during
ontogeny) at an earlier time to causally explain lower level features
at a later time (e.g., gene expression patterns). For example, a study
of the developmental origin of aortic arch asymmetry involves a
mixture of reductionist and non-reductionist representations according
to the criterion of temporality (Yashiro et al. 2007; see also Love
2017). The explanation depicts several events in a sequential process.
First, fundamental level properties (gene expression) change
non-fundamental level properties (arterial structure), which alters
blood flow dynamics (thereby fulfilling the temporality condition).
These new dynamics induce a subsequent change in gene expression
(thereby violating the temporality condition). This altered gene
expression then produces the non-fundamental property of interest,
aortic arch asymmetry (thereby fulfilling the temporality condition).
Thus, depending on how time is represented and which temporal
partitions are utilized, an explanation may be reductive,
non-reductive, or both. This is a good example of how ontological and
epistemic reduction can yield strikingly different answers. A
biologist using a higher level feature at an earlier time to explain a
lower level feature at a later time (a non-reductionist explanation by
the criterion of temporality) is not denying that this higher level
feature is composed of lower level features (e.g., cells and
molecules), nor the possibility that the higher level feature was
caused by a different set of lower level features at some more distal
point in time.



Another example is found in protein folding within molecular biology
(Huttemann and Love 2011). Functional proteins are folded
structures composed of amino acid components linked together into a
linear chain. If we ask whether the folded protein is mereologically
composed of its amino acid parts given current representations in
molecular biology, then the affirmative answer seems to favor
explanatory reduction with respect to the spatial hierarchy. But if we
ask whether the linear amino acid chain folds into a functional
protein (a causal process with a temporal dimension) purely as a
consequence of its linked amino acid parts, then the answer is less
clear. Empirical studies have discerned a necessary role for *other
folded* proteins to assist in the proper folding of newly
generated linear amino acid chains (Frydman 2001). That the linked
amino acid components alone are insufficient causally, even if they
are sufficient constitutionally, allows for a more explicit
appreciation of the significance of temporality and dynamics (Mitchell
2009), especially because the relations of interest concern only
molecular biological phenomena (as opposed to higher levels of
organization, such as cells or anatomy).



A final representational feature is intrinsicality, whereby what is
"internal" and "external" are explicitly or
implicitly distinguished in reductive explanations. Wimsatt (1980)
drew attention to the fact that every investigation must divide a
system from its environment and that methodological reductionism
favors attributions of causal responsibility to internal parts of a
system rather than those deemed external (see also Wilson 2004). In
the protein folding case, it appears that the failure of temporally
indexed explanatory reduction involves the causal powers of something
*extrinsic* to (an instance of) the process under scrutiny
(i.e., the folding of a single amino acid chain). The presumption of
atemporal, compositional relationships has encouraged a neglect of
this distinction because nested part-whole relations are predicated on
a prior individuation of a system from its environment (Huttemann
and Love 2011). Kaiser's (2015) idea that a reductive
explanation must (among other things) represent each lower-level part
of the explanation "in isolation" from other parts is one
explicit attempt to engage representational questions related to
intrinsicality
 (Section 3.2).
 Overall, this line of thought relates to the context-dependency
objection
 (Section 4.1),
 but emphasizes the importance of functional dependency relations
uncovered by attending to temporality in addition to structural
organization.



Recognizing temporal aspects of reductive explanations found in
biology alongside other representational issues like intrinsicality,
both of which are not captured by a focus on mereology alone,
strengthens the argument in favor of talking about different
*kinds* of reductionism rather a unified account of reduction
or overarching dichotomies of "reductionism" versus
"anti-reductionism" (or "holism"). Once we
incorporate distinctions about different types of reduction
(ontological, epistemic, and methodological), the different
interpretations of these types (e.g., theoretical versus explanatory
epistemic reductions), the different representational features
involved (spatial, temporal, etc.), and the distinct biological topics
to which philosophers have applied them (e.g., development or
functional anatomy), then any single conception of reduction appears
inadequate to do justice to the diversity of phenomena and reasoning
practices in the life sciences. The multiplicity and heterogeneity of
biological subdisciplines only reinforce this argument and suggest to
some that we should move beyond reductionism entirely.


## 5. "Alternatives" to Reductionism: Moving Beyond Dichotomies



Much of the past discussion about reduction presupposes a unitary view
of the scientific enterprise that involves a close relation between
natural kinds, laws, counterfactual dependence, explanation, and
confirmation (Godfrey-Smith 2008). One of the ubiquitous features of
modern biology that is *prima facie* incompatible with many
methodological and epistemological reductionist theses is the
proliferation and flourishing of diverse biological subdisciplines,
molecular and otherwise. Despite the purported "hegemony of
molecular biology" (Kitcher 1999a), biological subdisciplines
focused on higher levels of organization have not disappeared:
"Special sciences: still autonomous after all these years"
(Fodor 1997). For some time this feature of biological research, along
with many of the problems associated with theoretical reduction
(especially its inapplicability to scientific practice, but also the
difficulties in identifying clear-cut and distinct
"levels" to relate reductively; Brooks 2014, 2021, Brooks
et al. 2021, McGill and Potochnik 2012, Potochnik 2021), has prompted
philosophers to reject "reduction" as the appropriate (or
only) relation among concepts and explanations from different
 domains.[15]
 Instead, relations of coordination driven by a commitment to
unifying, integrating, or synthesizing aspects of scientific knowledge
have been offered (Bechtel and Hamilton 2007, Brigandt 2013b, Love
2017, Potochnik 2011).



Lindley Darden and Nancy Maull were at the forefront of this
discussion with the concept of an
 inter-field theory
 (Darden and Maull 1977, Maull 1977). For example, the advent of the
chromosome theory of inheritance in the 1910s bridged the previously
unrelated fields of Mendelian genetics (which studied phenotypic
patterns of inheritance across generations) and cytology (which dealt
with the material contents of cells). This interfield theory effected
a kind of unification, but Mendelian genetics and cytology were not
reduced to each other, nor did the interfield theory reduce both
fields. More recent work has articulated interfield relations without
relying on the notion of a theory (Ankeny and Leonelli 2016, Bechtel
1986, Burian 1993, Grantham 2004a, 2004b, Leonelli 2013, Mitchell
2002). This parallels the trend in models of explanatory reduction of
moving away from theories as the only epistemic units of interest
 (Section 3.2),
 but the emphasis is on such relations as coordination, integration,
synthesis, or reciprocal interaction (Bechtel 2013, Green 2013,
Hochstein 2016, Love 2017, Nathan 2017, Plutynski 2013). A rationale
for these complex relations emerges from the demand for
multidisciplinary research (O'Rourke et al. 2016); the
explanatory task involves coordinating diverse epistemic resources
(Ankeny and Leonelli 2016), which amounts to an implicit rejection of
the "fundamentality" of one particular discipline
producing the most empirically adequate explanations.



In this context, Alan Love (2008a, 2014) uses the notion of a problem
agenda to argue that some scientific problems not only motivate
interdisciplinary research but also provide structure for the
requisite intellectual coordination (see also Brigandt 2010, 2012,
Brigandt and Love 2012, Villegas et al. 2023). Problem agendas consist
of numerous component questions that stand in systematic relations and
are tied to associated standards of explanatory adequacy. These
standards imply what epistemic resources and different disciplines are
needed to address the problem. The relations among component questions
of the problem agenda (i.e., its internal structure) foreshadow how
various contributions can be coordinated to generate an adequate
explanatory framework. Building on this perspective, Ingo Brigandt
(2010) suggests that there is no single, linear hierarchy among
scientific fields (e.g., Oppenheim and Putnam 1958), but that the
relationships among theories and disciplinary approaches are
determined by and vary with the scientific problem being addressed.
These philosophical accounts align with general research on
interdisciplinarity, which has identified the presence and
articulation of a complex question as a prerequisite (Repko 2008,
Szostak 2002, 2009). Thus, instead of unification being a regulative
ideal with biologists seeking as much unity as possible in their
explanations of the complex natural world (e.g., Kitcher 1999b), an
erotetic perspective suggests that particular problems determine the
need for and degree of any integration (Brigandt 2010). William
Bechtel's (1993, 2006) studies of cell biology document how the
formation of new subdisciplines generates both integration among
approaches and some disintegration due to new specializations.
Bechtel's attention to the institutional underpinnings of
biology also meshes with sociological analyses of disciplinary
organization (Gerson 1998, 2013).



Recently, accounts of explanation revolving around
 "mechanisms"
 have been widely discussed (e.g., Baetu 2015, Bechtel 2006, 2008,
Bechtel and Abrahamsen 2005, Craver 2006, 2007, Darden 2006, Glennan
1996, 2017, Machamer et al. 2000). Many philosophers view experimental
biology as fundamentally concerned with the discovery of mechanisms
(Craver and Darden 2013, Darden and Craver 2002, Tabery 2004), where
mechanisms are understood as akin (though not equivalent) to machines
with interconnected, organized parts operating to produce regular or
expected outcomes. Conceiving of biological explanation in terms of
mechanisms provides a philosophical framework that closely tracks
biological practice and does not rely on the notion of a theory.
Besides providing new models for explanatory reduction
 (Section 3.2),
 mechanisms also have been used to demonstrate integration among
different fields. Darden (2005) argues that both reduction and
replacement fail to capture the relations between classical and
 molecular genetics.
 Both fields deal with different mechanisms that occur at different
periods of the cell cycle and involve different working entities:
classical genetics focuses on meiosis and involves chromosomal
behavior; molecular genetics focuses on gene expression and involves
various molecular entities such as nucleotide sequences. Relations
between the two fields are manifested as differential attention to
distinct aspects of a larger, temporally extended mechanism.



The mechanisms framework has proved particularly fruitful in capturing
explanations that appeal to entities at several levels of organization
(Darden 2016, Tabery 2014). An instructive example is Carl
Craver's (2005, 2007) discussion of multilevel and multifield
explanation in the context of neuroscientific studies of learning.
While the cellular-molecular process of long-term potentiation is
critical for memory formation, it is not merely a molecular
counterpart of memory. Long-term potentiation is a lower-level
component of an overall, multilevel mechanism. Reductionist accounts
have neglected the phenomenon of disciplinary integration at the same
level of structural organization and invested too heavily in finished
reductive explanations, ignoring the dynamic changes in research
strategy that precede them (Craver 2005). In addition to searching for
molecular correlates of higher-level phenomena
("downward-looking" episodes), there also have been
attempts to understand the role of molecular mechanisms in complex
higher-level phenomena ("upward-looking" periods of
research). Sometimes progress has been achieved independently of or by
abandoning reduction as an explanatory goal. This need to change
strategies depending on the research context is ubiquitous in
mechanistic research (Bechtel 2010), which serves as another reminder
for philosophers to attend to actual scientific practice. Even though
a mechanism is temporally extended, philosophical analyses of
mechanisms may not capture all aspects of temporality (see
 Section 4.3).
 While discussions have focused on the representation of time relative
to a mechanism (e.g., Bechtel 2006, Machamer et al. 2000), not all
aspects of the dynamics of biological systems are well represented as
mechanisms involving entities and activities. Some might be better
modeled using equations (Bechtel 2012, Bechtel and Abrahamsen 2010,
2011, Brigandt 2015, Weber 2008), and in other cases time might be
represented independently of the mechanisms being
 investigated.[16]



Complexity also has been a source for articulating non-reductionist
epistemological accounts of biological reasoning (Wimsatt 1974, Hooker
2011). Sandra Mitchell (2003, 2009) has argued that different forms of
biological complexity block standard reductionist perspectives.
Multiple (idealized) causal models must be integrated from different
disciplinary approaches to adequately represent this complexity,
including our uncertainty in predicting its behavior, which has
implications for any social policy derived from these models (see also
Mitchell 2008, 2020, Mitchell and Gronenborn 2017). She specifically
draws attention to the phenomenon of self-organization, which refers
to how system behaviors or patterns emerge from non-specific
interactions among lower-level components (Camazine et al. 2001,
Kauffman 1993), such as the collective behavior of social insects.
(Self-organizing phenomena are also relevant to reductionism in
physical science; see, e.g., Goldenfeld and Kadanoff 1999, Whitesides
and Ismagilov 1999.) Although decomposing a system into parts is
important for claims about self-organization, there is no localization
of causal responsibility to individual components (Bechtel and
Richardson 1993, ch. 9). Instead, the system behavior is a function of
generic patterns of component interaction, which foregrounds how
complexity emerges from dynamics rather than constitution (see
 Section 4.3).
 For example, gene networks and human social networks may exhibit
isomorphic patterns of self-organization due to their interactive
structure, which is unrelated to whether genes or humans are the
components. Thus, self-organizing phenomena occupy an odd place in the
reductionism discussion because even though components are used to
explain the behavior of the system, it is the nature of their
interactions (not their specific characteristics) that generate
patterns of behavior. These patterns are often referred to as
 emergent properties
 of the system (see also Bishop et al. 2022, Grantham 2007, Mitchell
2012).



The philosophical import of biological complexity is underscored by
recent trends in systems biology (Boogerd et al. 2007, Green 2015,
2017, Green et al. 2015, Mazzocchi 2012, Noble 2006, O'Malley
and Soyer 2012). In addition to the mathematical modeling of
system-wide behavior, systems biology has a wealth of data about
various molecular components of cells stemming from functional
genomics, transcriptomics, proteomics, and metabolomics methods.
Downward looking strategies in systems biology attempt to analyze
systemic dynamics into different components, whereas upward looking
strategies aim to synthesize how the quantitative interactions among
individual molecules result in higher-level behavior (Green et al.
2018, Krohs and Callebaut 2007). Despite the focus on molecular
components and their interactions, non-reductionist themes tied to
complexity are motivated by non-linear interactions and feedback loops
that generate emergent behaviors, distributed control, and system
robustness (Brigandt 2015, Bruggeman et al. 2002, Westerhoff and Kell
2007).



Another distinct strand of discussion about reductionism is found in
critical analyses of methodology and explanation from the perspective
of
 feminist philosophy of science
 and studies of the
 social aspects of science
 (e.g., Fehr 2004, Longino 1990, 1996).
 Feminist philosophy of biology
 has related reductionism and pluralism to other philosophical,
scientific, and social issues. One core idea in these discussions is
that forms of reductionism are involved in mutually reinforcing
feedback loops with other factors, such as socioeconomic status or
expectations about gender (Keller and Longino 1996, Levins and
Lewontin 1985). Thus, reductionism, whether ontological, epistemic, or
methodological, can be understood as the manifestation of more diverse
commitments (e.g., political ideology) than much of the philosophy of
biology literature on reductionism would suggest--the history of
biology points in this direction as well (see, e.g., Allchin 2008).
This line of criticism also suggests that the interrelations between
reductionism in biology and the social sciences should be treated more
explicitly. Elisabeth Lloyd (2002) has argued that medical research
should not be restricted simply to molecular biological investigation
because higher levels of social organization that are culturally
sanctioned have unrecognized causal effects on health. As the social
sciences and medicine attempt to apply different life science
reasoning strategies, similar philosophical issues predictably
transfer, but with the potential for more socially damaging
consequences (see, e.g., Richardson 2013, 2021).



A shared feature of many alternatives to reductionism is an emphasis
on pluralist dimensions of epistemology in biology that situate
methodological or explanatory reduction as only one among many
components (Dupre 1993, Kellert et al. 2006, Longino 2000,
2002, 2013, Mitchell 2003, Muszynski and Malaterre 2021,
O'Malley 2013). In different ways, these positions stress how
the scientific investigation of biological phenomena demands diverse
epistemic tools without a requirement to tie it all together into
fundamental physics, macromolecular chemistry, or even
 molecular biology.
 Thus, ontological reduction becomes more or less unhinged from
epistemological reduction because there is no need to demonstrate how
each and every domain of scientific inquiry is anchored in physical
stuff. Scientists are epistemologically profligate, even if they are
largely metaphysically frugal (see Dupre 1993 and van Fraassen
2002 for differing perspectives on science and metaphysics). The
plurality of biological research motivates a philosophical
 pluralism
 about biology, both in terms of the many meanings available for
different methodological and epistemological types of reduction, and
the need to have multiple dimensions of reductionism in order to
secure empirical adequacy with respect to modeling biological
phenomena (Grantham 1999, Kellert et al. 2006, Looren de Jong 2006,
Morange 2006, Sullivan 2009, van der Steen 1999, Wylie 1999).



It is clear that these different kinds of "alternatives"
to reductionism successfully capture a number of features left
untreated or ignored by theory reduction. However, it is an open
question whether they supplant discussions of reduction or bear some
complex relation to them (Craver 2005). Reasons in favor of the latter
position include the continued use of "reductionist"
language (for and against) in biological research, as well as the fact
that a near universal reason for rejecting reduction and choosing an
alternative is the problematic nature of *theory* reduction,
which only represents a small space of the philosophical
possibilities. One interpretation of some alternatives to reduction is
that they are responding to the complexity of reduction that has
become more apparent over the past two decades (e.g., seeing
explanations as inherently interlevel), and the fact that
biologists' use of the term "reductionism" refers to
different specific commitments in different cases and research
contexts. Thus, for example, mechanisms approaches are another way to
treat the heterogeneity of explanation (including reductive and
non-reductive aspects), which was largely ignored in the literature on
theory reduction, which assumed that a few select examples from
biological research were representative. This heterogeneity is a
pervasive feature of the history of biology; philosophical
alternatives to reduction are responding in part to long-standing
controversies among life science investigators about the legitimacy of
reductionist research strategies and modes of explanation (see
 Section 2).
 The compatibility or conflict among these various alternatives and
different accounts of explanation in biology is still being probed
(e.g., Bechtel 2006, 40-44), but the traditional philosophical
project of articulating a single notion of reduction to capture most
essential aspects of theory structure and explanation across biology
is unlikely to succeed.


## 6. Future Prospects



Arguably, discussions of reductionism in biology are becoming more
rather than less philosophically interesting. This is a consequence of
recognizing the diverse conceptual landscape carved out over past
decades, one that is much larger than that conceived of when only
Nagelian theory reduction was in view. Biological science is now more
specialized than ever, but disciplinary proliferation brings with it
issues relevant to any analysis of reduction: using the same terms
differently, disparate methodologies, distinct explanatory norms, and
divergent interests in "levels" of biological organization
(Brooks 2021, Potochnik 2021). It also includes an acknowledgment that
certain enduring biological topics like development still engender
difficult questions about reductionism and new fields of inquiry
reinvigorate these discussions (e.g., synthetic biology's appeal
to molecular components as Lego-like building blocks in the
 Registry of Standard Biological Parts).
 Philosophers need to recognize that a criterion of adequacy on
accounts of reductionism in biology involves interpreting why
scientists make pronouncements about the failure of reductionism in
different areas of life science (see, e.g., De Backer et al.
 2010).[17]



There also is increasing contact between neuroscience and
psychologically oriented investigations (Barwich 2020, Bechtel 2008,
Boogerd et al. 2002, Craver 2007, Sullivan 2016, 2017, Tabb 2019). A
potential prospect related to the contact between molecular
neurobiology and psychology is the injection of *epistemic*
considerations into philosophy of mind discussions (Godfrey-Smith
2008). More attention to issues of representation, decomposition, and
temporality could alter the nature of these debates. At the same time,
a more explicit evaluation of *metaphysical* components
imported from philosophy of mind into philosophy of biology is
warranted. Discussions of the status of downward causation and
realization in biological systems are relevant for a better
understanding of the intersection between epistemological and
metaphysical components of reduction (Craver and Bechtel 2007, Green
2021, Love 2012, Robinson 2005, Wilson and Craver 2007, Woodward
2021). For example, an interest in the context sensitivity of
realization in philosophy of mind (Wilson 2004, ch. 6) invokes issues
pertaining to the context objection, individuation, temporality
(especially causation versus constitution), and intrinsicality. These
analyses can then be imported into biological contexts to argue for or
against particular aspects of reductionism (see, e.g., Wilson
2005).



More work is needed in how to relate different kinds of hierarchies to
questions of reductionism. Biological hierarchies are diverse (Grene
1987, Korn 2002, 2005) and subject to evolutionary change (Baedke
2021, DiFrisco, 2021, Temkin 2021), and some areas of biological
research, such as paleontology and systematics (Valentine and May
1996; see also Grantham 1999, 2004a, 2004b, 2007), have been ignored
when reductionism comes into view. Paying attention to temporality
encourages the exploration of functional or control hierarchies in
more detail (Love 2021, Salthe 1985, 1993, Wimsatt 2002). The
limitations of representing biological systems in terms of hierarchies
should be explored in more depth as well (Bechtel 2022, Brooks 2014,
O'Malley et al. 2014, Potochnik 2021, Potochnik and McGill
2012).



All of these possibilities suggest more scrutiny of disciplinary
heterogeneity in biological investigation relevant to reductionism.
Although ecology has received some treatment (Dupre 1993, ch.
5, Mikkelson 2004), issues of decomposition and representation have
not yet received wide attention. Other topics connected to explanatory
reduction and mechanisms in experimental research are cancer
(Bertolaso 2013, 2016, Bizzarri et al. 2008, Green 2021, Moss 2002,
Plutynski 2013, Soto and Sonnenschein 2005, 2006) and stem cells
(Fagan 2013, Laplane 2016, Laplane and Solary 2019). Because of the
diversity of explanations found in these different disciplines, the
nature of scientific explanation returns with a vengeance (Schaffner
2006). Although only a few reductionists demand that explanation be
strictly nomological (Rosenberg 2006, Weber 2005), the subtle
interplay between explanation and reduction must be treated when
ranging over diverse biological subdisciplines. Additionally, as more
attention is given to the diversity of investigative reasoning (or
"scientific practice") in and among these disciplinary
contexts, the interplay between different aspects of methodological
and epistemic reduction will become more salient. To achieve an
understanding of the intricacy and diversity of scientific practice,
it has become more common for philosophers of science to interact or
collaborate with scientists from various fields ("engaged
philosophy of science"), where some of the engagement with
practicing scientists and stakeholders affected by science and
technology also aims at influencing the methodological approaches
adopted in such research (Brister and Frodeman 2020, Kaiser and
Meunier 2014, Plaisance and Elliott 2021, Tuana 2010, 2013).



A final prospect concerns whether discussions of reduction in
different sciences will interact fruitfully. Although questions about
reduction in philosophy of physics have largely diverged from those in
philosophy of biology, some connections have been drawn (Batterman
2021, Green and Batterman 2017). For example, Sarkar has approached
quantum mechanics using his account of reductionism that was forged in
a biological context (Jaeger and Sarkar 2003). A potential
intersection between these discussions arises around the relations
between parts and wholes or temporality, which have come under
scrutiny from philosophers focused on the physical sciences
(Huttemann 2004, Love and Huttemann 2011, Rueger 2000,
Rueger and McGivern 2010). Another area worthy of more attention is
reductive explanation in chemistry, which has been ignored in large
part by philosophers of biology (see, e.g., Bishop 2010, LePoidevin
2005, Ramsey 1997, Scerri 1994, 2000).



In all these cases it seems clear that debates about reductionism in
biology have not reached a denouement but rather portend vigorous
philosophical discussion as the heterogeneity of issues related to its
ontological, epistemological, and methodological types are brought to
bear on perennial biological topics. The task of philosophers focused
on reductionism in biology will be to analyze these promiscuities of
reasoning and seek to develop different accounts of reduction that
capture what scientists actually do and contribute to more general
perspectives on biological knowledge and scientific inquiry.