Are Homologies (Selected Effect or Causal Role) Function Free?


Philosophy of Science, 76 ( July 2009) pp. 307–334. 0031-8248/2009/7603-0003$10.00
Copyright 2009 by the Philosophy of Science Association. All rights reserved.

307

Are Homologies (Selected Effect or
Causal Role) Function Free?*

Alex Rosenberg and Karen Neander†‡

This article argues that at least very many judgments of homology rest on prior at-
tributions of selected-effect (SE) function, and that many of the “parts” of biological
systems that are rightly classified as homologous are constituted by (are so classified
in virtue of) their consequence etiologies. We claim that SE functions are often used
in the prior identification of the parts deemed to be homologous and are often used
to differentiate more restricted homologous kinds within less restricted ones. In doing
so, we discuss recent criticism of this view that has been offered (especially that offered
by Paul Griffiths).

1. Introduction. Some philosophers have argued that all significant bio-
logical kinds—including homologies—are (implicitly or explicitly) to be
characterized in terms of selected-effect (SE) functions, that is, ones with
a “consequence etiology” (e.g., Neander 1991; Rosenberg 2006). Others
have argued that many important biological kinds—including many ho-
mologies—are characterized in this way (Neander 2002).

By contrast, some philosophers and biologists have argued that ho-
mologies (as opposed to analogies) are never characterized by their SE
functions. In particular, this claim has been made by those philosophers
of biology who endorse the “causal role” (CR) account of functions due
to Cummins, and by an overlapping group of philosophers of biology
who argue that most important biological predicates are defined by ho-
mology, and in addition that homologous classification has no need of,
or indeed no role for, SE functions. Among the most prominent of this

*Received July 2007; revised November 2008.

†To contact the authors, please write to: Department of Philosophy, 201 West Duke
Building, Box 90743, Durham, NC 27708; e-mail: alexrose@duke.edu or kneander@
duke.edu.

‡For comments on previous drafts we are grateful to Robert Brandon, Daniel McShea,
Paul Griffiths, Jason Clark, participants in the Triangle philosophy of biology semi-
nar—and most of all, to Michael Dickson.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


308 ALEX ROSENBERG AND KAREN NEANDER

overlapping group are Amundson and Lauder (1994) and Paul Griffiths
(1994, 2006).

Homology of biological traits or characters1 is standardly defined as
“sameness due to common descent,” and we use this definition here (as
did Amundson and Lauder [1994] and Griffiths [1994]).2 But as philos-
ophers will recognize, any definition that invokes vexed concepts such as
“sameness” and “due to”—that is, caused by—is likely itself to be prob-
lematic. In this article we review the way homology claims figure in the
classification of biological characters, and attempt to vindicate the im-
portance of SE function in biological kinds. We argue (primarily in the
first half of the article) that at least very many judgments of homology
do after all presuppose, imply, rest on, prior attributions of SE function,
and (primarily in the second half ) that many of the “parts” of biological
systems that are rightly classified as homologous are constituted by (i.e.,
are so classified in virtue of their) consequence etiologies.3

Some of our argument involves clarifying parts of Neander 2002 in
light of subsequent developments, especially as found in Griffiths 2006.
Two points are best mentioned immediately. According to Griffiths, Nean-
der rejects Functional Minimalism, which Griffiths defines as the view
that “disciplines like anatomy, physiology, molecular biology and devel-
opmental biology individuate character by homology” (Griffiths 2006, 3).
However, Neander defines Functional Minimalism as “the view that there
are no important functional categories in biology except perhaps for the
analogous categories” (Neander 2002, 395) and it is instead this view that
she rejects. This does not entail the position that Griffiths attributes to
her. Neander says, for instance, “some homologous categories might be
functional categories too” (398), so that “we can stress the importance
of homology all we like and yet still say nothing to any effect against
classification by function. . . . We can agree that homology is important
without concluding that function is thereby unimportant” (399). And, “I
agree that homology is important in the classification of traits. Where we
differ is on the role of function” (392). Nor do we, in this article, deny
the importance of homologous classification.

Griffiths further adds that, “Neander . . . thinks that all biological
categories are at least partly defined by selected function” (2006, 13; em-
phasis in original). However, Neander says, “I will argue that homologous
kinds are sometimes differentiated in terms of structure, sometimes in

1. We use “traits” and “characters” interchangeably.

2. This makes homology a historical concept. However, Griffiths (2006) distinguishes
between “historical” and “developmental” homologies, as further remarked toward
the end of the article.

3. On consequence-etiologies, see Wright 1976.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 309

terms of function, and sometimes, and often ideally, in terms of both”
(2002, 392). She also allows for some classification by functions in the
causal sense. Again, it is this pluralist claim on behalf of SE functions
that we aim to establish here. In our view, biologists must very often
reflect on SE functions in making judgments about homology and many
very important biological kinds—including homologous kinds—are, con-
stitutively, SE functional kinds. Ours is a pluralist position. In contrast,
Griffiths, for instance, argues that “if functional classifications are to be
of value to biology it must be because of their superior generality—the
fact that they unite disjunctions of cladistic homologues” (1994, 213–214).
In other words, he argues that SE functions have no role in biological
classification outside of the analogous categories.

Neander’s (2002) claim is that a notion of homology does not suffice
for classification, even if we ignore the analogous kinds. She argues that
many homologous kinds are also functional kinds (“functional homo-
logues”) because SE functions are often used in the prior identification
of the parts deemed to be homologous and because SE functions are often
used to differentiate more restricted homologous kinds within less re-
stricted ones. This is also one message of the present article. Another
important take home lesson from this dialectic between proponents of the
indispensability of SE functions and the exponents of SE-free homologies
is how theoretically intricate (not to say apparently circular, but in reality
“spiral”) even the most basic biological descriptions turn out to be. For
if we are correct, homology—similarity due to shared ancestry or common
descent—is a property of traits which are often individuated by their
functions in the SE sense, and selected effect traits are traits with a certain
type of ancestry, or that are in other words homologous.4 Both homology
and function, then, are notions shot through with Darwinian presuppo-
sitions about ancestry and adaptation. The difference between them is
that homologies don’t wear their adaptational pedigrees “on their sleeves,”
so to speak, while functions (SE functions) do.

Homologies are “sameness due to common descent” and we must ask
what the sameness consists in, for it cannot consist purely in common
descent. As Neander put it, “before two traits can be identified as ho-
mologous with respect to each other, we need some specification of the
traits in question” (2002, 402). The traits adjudged the same cannot, on
pain of circularity, be so judged on hypotheses of homology: their same-
ness or similarity can be explained by their common descent but it cannot
merely consist in their common descent. If all there were to membership
in a homologous kind were common descent, it would follow from Dar-

4. We assume rather than argue for the second part of the conjunction in this article,
but it is not in dispute and is discussed in Neander 2002, 403–404.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


310 ALEX ROSENBERG AND KAREN NEANDER

Figure 1. Variety of vertebrate forelimbs, all derived from a common ancestor and
showing homologous bone structures. Note that the bat and the bird forelimbs are not
homologous as wings.

win’s hypothesis of common descent that every organ type is the same
as every other, patently a reductio ad absurdum. If we are sensibly to
define homology it must be treated as a diagnostic/explanatory kind that
presupposes some prior categorization of traits. Therefore, the importance
of homology notwithstanding, much remains to be said about how traits
are classified.

Homology claims are hypotheses about common ancestors. SE function
ascriptions are hypotheses about common ancestors as well, to which is
added a hypothesis about selection. It is to be expected that, as we argue,
the evidence for each such hypothesis is intimately related, and it should
be unsurprising if, as we also argue, classifications based on homology
often involve classifications based on SE function.

2. Homology Claims in Biology: The “Usual Suspects.” One of the classic
examples of a homologous structure is the vertebrate forelimb. One can
see why biologists might conclude that the bones of the vertebrate forelimb
(Figure 1) are homologous, that is, that their “similarity” is due to com-
mon descent. If one were to give the reasoning behind this conclusion it

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 311

would consist at least in three points: the similar material composition of
the bones of all these vertebrates, the similarity of complex topographic
relations among the bones in each species’ set of forelimb bones, and an
account of how the differences in their shapes and structure can be ex-
pected from the adaptational problems which the forelimb addresses for
each different species.

Homology claims are explanatory hypotheses. They presuppose causes
for similarities. Accordingly, the similarities among traits for which such
hypotheses are advanced are logically prior to homology hypotheses. As
remarked in the introduction, the similarity can be explained by common
descent but it cannot merely consist in common descent. Such circularity
is avoided in the case of the vertebrate forelimb by the considerations
adduced above: the similarity of the various forelimbs is pretty obvious,
the material composition and structure of the hard parts of the forelimbs—
the bones—are chemically very similar, and, more important, the topo-
graphic relations of the bones in each species are highly similar. In this
case, such morphological criteria could perhaps suffice for prior specifi-
cation of the similarities to be explained, and they are also highly sug-
gestive of homology.

However, even in this case, adaptational considerations are important
in an evidential sense. It is significant that the evident differences among
the forelimbs are to be expected given the different environments (aquatic,
avian, swamp, savannah, steppe, and forests) and the different tasks within
those environments (swimming, walking, running, tool manipulation, and
flight) to which they are adapted. Furthermore, these considerable dif-
ferences in the tasks for which and the environments in which selection
has shaped these forelimbs make a hypothesis of analogy or homoplasy
to explain the similarities implausible to say the least.

Similarity in material composition and topographic relations might suf-
fice for the identification of similarities to be explained in some cases, as
just explained. However, such considerations are not always sufficient to
ground a judgment of similarity that may be explained by hypotheses of
homology. Consider two of the bones which in the mammal make up
parts of the inner ear—the malleus and the incus (two tiny bones also
known as the hammer and anvil, respectively).5 These bones are homol-
ogous to two bones, the articular (homologous to the malleus) and the
quadrate (homologous to the incus), which in some fish and reptiles con-
stitute the jaw hinge. Both of these pairs of bones are homologous to

5. We expound this example, since it is employed by Griffiths as presumably favorable
to his view. The example’s prominence in the writing of the opponents of (SE) functional
individuation may be due to Steven J. Gould’s invocation of it. See the following
footnote.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


312 ALEX ROSENBERG AND KAREN NEANDER

Figure 2. Mammalian inner ear.

structures that, in other fish, constitute gill arches. Figures 2–4 provide
a comparison.6 Figure 2 shows the malleus and incus of the mammalian
inner ear. Figure 3 shows the articular and quadrate of a reptile jaw hinge
and the malleus and incus of the mammal in relation to its jaw. Figure
4 is a schematic drawing of a gill arch. This is the boney structure to
which the feathery gill rakes are attached. Fish have several such arches.
Early fish had no jawbones and a series of these gill arches behind their
mouths. In these early fish, which lacked bones, the gill arch was made
of cartilage.

The homology of these sets of bones and cartilage have been celebrated
among evolutionary biologists for a number of reasons, among them being
the way in which paleontological evidence about them has both vindicated
the fossil record’s support for the theory of natural selection and undercut
the confident claims of creationists that there are and could be no inter-
mediate forms between these three sets of bones and cartilage.7

6. Our thanks to Matt Chansky for help with the diagrams. Figure 2 is adapted from
Gilbert et al. 2006. Figure 3 is adapted from Vaughan et al. 2000.

7. See Gould 1993. In Gould (1994) 1997, 360–361, he writes: “The anatomical tran-
sition from reptiles to mammals is particularly well documented in the key anatomical
change of jaw articulation to hearing bones. Only one bone, called the dentary, builds
the mammalian jaw, while reptiles retain several small bones in the rear portion of the

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 313

Figure 3. Side views of an early reptile’s and mammal’s jaw and ear.

3. How the Usual Suspects Illustrate the Role of SE Functional Judgment
in Homology Claims. As Griffiths (2007, 2009) notes, three principle cri-
teria for judgments that distinct parts are homologous as opposed to
merely analogous are (a) identity or similarity in the relative position of
parts in the two organisms, to which may be added identity or similarity
in composition and topology if not topography;8 (b) the parts sharing
some trait which can play no SE or CR function in the economy of the
organism (this criterion was especially emphasized by Darwin); and (c),
where conditions a and b are not satisfied, the two parts can be subsumed
under a single homological kind via a chain of intermediary parts that
do satisfy criteria a and b.

These sets of body parts, the inner ear bones of mammals, the jawbone
connectors of some jawed fish and reptiles, and the gill-arch cartilage of
jawless fish do not obviously satisfy criteria a and b. While there are

jaw. We can trace, through a lovely sequence of intermediates, the reduction of these
small reptilian bones, and their eventual disappearance or exclusion from the jaw,
including the remarkable passage of the reptilian articulation bones into the mammalian
middle ear (where they became our malleus and incus, or hammer and anvil). We have
even found the transitional form that creationists often proclaim inconceivable in
theory—for how can jawbones become ear bones if intermediaries must live with an
unhinged jaw before the new joint forms? The transitional species maintains a double
jaw joint, with both the old articulation of reptiles (quadrate to articular bones) and
the new connection of mammals (squamosal to dentary) already in place! Thus, one
joint could be lost, with passage of its bones into the ear, while the other articulation
continued to guarantee a properly hinged jaw. Still, our creationist incubi, who would
never let facts spoil a favorite argument, refuse to yield, and continue to assert the
absence of all transitional forms by ignoring those that have been found, and continuing
to taunt us with admittedly frequent examples of absence.”

8. A topographic similarity is one of (rough) geometrical congruence. A topological
similarity is one that could result from any deformation that does not divide the part
into spatially separated regions. Plainly, topological similarity is rarely a sufficient basis
for the sort of similarities that homology explains. Indeed, homologies may obtain
between bones that are topologically continuous and ones that are not.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


314 ALEX ROSENBERG AND KAREN NEANDER

Figure 4. Gill structure.

significant similarities, there are also significant differences, one reason
why this has been such a celebrated case. For instance, mammals have
three inner ear bones, reptiles have only one; reptiles have two other
distinct jawbones besides the articular and the quadrate, while mammals
have just the one. The jaw hinge of reptiles is formed by the intersection
of the quadrate and articular, whereas the mammalian jaw hinge is formed
of different bones (the dentary and squamosal), and the malleus and incus
are in the ear. Nor are they compositionally the same, or even similar
enough (in their adult forms) to provide a sufficiently firm basis for any
judgment that they are the same type of body part, or similar to one
another in respects that require special explanation. Though all connective
tissue in vertebrates shares some similarities, these similarities are not
peculiar to the sets of body parts under discussion. Moreover, there are
many differences between bone and cartilage with respect to the abun-

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 315

dance and types of cells, the proportion of cells to extracellular matrix,
the ground substance of the matrix (whether it is mineralized), and so on.

Nor, if we ignore developmental considerations (to which we return in
a moment), do the homologous pairs share any special nonfunctional
morphological trait that clearly cries out for explanation in terms of
common descent. In fact, there is considerable structural, and topological
evidence against similarity on criteria a and b among these traits. Why
should physically diverse structures which came to function in hearing
and in biting be similar with ones that function to filter for food and
oxygen so that such an explanation of their similarity is motivated? Of
course, current dissimilarity of function is no basis for some sort of ex-
planation-demanding similarity.

It is primarily criterion c the existence of a chain of intermediaries that
the biologist relies on to ground judgments of similarity to be explained
as homologies. As paleontologists note, in their glee to refute creationists,
a number of forms intermediate between the gill supports and the reptilian
jawbone and mammalian inner ear have been discovered. These inter-
mediaries provide greater similarity between the pairs in more closely
related species. But considerations used to establish this chain of inter-
mediaries—that is, that they are intermediaries—often concern SE func-
tions. Two kinds of considerations have been particularly important in
this case. One kind of consideration involves overlapping SE functions.
In some of these intermediaries, the bones have more than one function.
For example, in Morganucodon (small mammals of the Upper Triassic),
the quadrate and articular serve as ear bones and jawbones simultaneously
(Kermack, Mussett, and Rigney 1981). Modern reptilian quadrate and
articular jawbones also serve in a rudimentary way to transmit sound to
the stapes and the inner ear. Comparative anatomists describe the tran-
sition from jawbones to inner ear bones as one in which bones initially
located in the lower jaw are selected for hearing by variations that detach
them from the lower jaw and move them to the ear (Kardong et al. 2002).
A second kind of consideration involves functional “redundancy.” It is
because there are a series of gill supports in jawless fish that the first in
the series can evolve into the jawbones of jawed fish. And it is because
the jaws of the common ancestors of reptiles and mammals consisted of
four bones that it was possible for some of these bones to migrate to the
ear, without the necessity of passing through a period of evolution during
which the jaw was nonfunctional (as the creationists had maintained).
Thus apparently dissimilar traits can be identified as “the same” through
a chain of transformations that selection can explain, and this explanation
supports the hypothesis of homology.

A considerable part of the argument for homology here is SE functional.
It is because the different structures can be understood in terms of a

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


316 ALEX ROSENBERG AND KAREN NEANDER

process of adaptation, at times for overlapping roles, that the biologist
concludes that there is a basis for similarity or “sameness” despite large
differences in both form and function.

There is another important basis for the similarity judgments about the
incus/malleus pair and the quadrate/articular pair and the gill arches. In
embryological development, corresponding structures in fetuses give rise
to these pairs. So, they (along with other characters) share a developmental
source. But this shared source, this new similarity, raises another question:
on what basis does the fetal structure that is the source of the pair of
bones in mammals constitute the same trait-kind as the embryo structure
that is the source of the reptilian pair, or for that matter the same kind
of structure as the developmental source of the pair of jaw connectors of
boney fish and the pair of gill arches of cartilaginous fish? The similarities
between the developmental stages of the homologues are certainly sug-
gestive, but had they been compelling on their own, comparative embry-
ology would have been a lot easier, von Baer’s “laws” less a subject of
controversy,9 and the tree of life far more obvious a fact than it seems at
first blush to be. In any event, the importance of embryological evidence
concerning homology does not change the fact that reasoning about SE
functions is also important.

Nowadays these claims concerning sameness of developmental parts
are, in part, being cashed in for sufficient similarity in the types, numbers
and order of homeobox genes. Nonetheless, this does not negate the points
made above either. Judgment of homology still depend on understanding
many differences in terms of transformations in selected effects. Roughly,
in the case under discussion, the judgment is that the earliest structure
persists over time because it was selected for giving rise to gill arch car-
tilage, variation in this (“same structure”) was subsequently selected for
giving rise to jawbone hinges, and that (“same structure”) was in turn
selected for giving rise to inner ear bones in mammals. Evidence for
sameness in the line of descent is partaking in overlapping parts of a series
of consequence etiologies.

Of course, owing to Darwinian gradualism, in the long run and if
paleontologists are fortunate, a range of intermediate forms could be
found which makes gradualist “sense” out of structures radically different
in shape, location and topographic locations (differences great enough to
be paraded by creationists). Such a program of research eventuates in the

9. There are three “laws”: (1) The general characters of the larger group to which an
embryo belongs appear earlier in development than the more specific characters of the
smaller group; (2) the more specific the character, the later it appears in development;
and (3) the embryo does not pass through the forms of ancestral creatures, but rather
progressively separates itself from them.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 317

exhibition of developmental and adult gradients of form, such as those
elaborated by D’Arcy Thompson ([1917] 1992). But it proceeds on a prior
commitment to overlap of functions among developmental structures that
give rise to the diverse instances arranged in a gradient of changes in
form.

When can a judgment of biological similarity avoid making recourse
to selected effects altogether? There is no general recipe, but a consid-
eration of nucleotide and amino acid sequence structure shows how lim-
ited such cases might be. When a character can be unambiguously de-
scribed in nonbiological terms, similarities—indeed identities—can be
established free from functional hypotheses. In the simplest case, short
sequences of either nucleotides or amino acids may be molecule-for-mol-
ecule structurally identical (often without having any function—e.g.,
“noncoding multiple repeats”). However, considerations of SE function
still play an evidential role in establishing homology. The longer the linear
sequence of a pair of DNA strands or a pair of polypeptides (proteins)
are molecule-for-molecule identical, the greater is the likelihood that their
similarity is biologically significant, and calls for explanation (usually as
homologies, much more rarely as analogies). Even when the match is not
perfect, though, there may be similarity among such pairs of molecules
that is ground for seeking an explanation in terms of homology. When
two somewhat different DNA sequences produce the same protein or
similar ones with the same enzymatic role, there is also good reason to
conclude that they are homologous, especially when most of the differ-
ences in gene sequence do not make a difference to the structure of the
protein they code for. The regions of the two genes that are the same in
sequence are said to be “conserved” by selection, and the differences are
credited to neutral point-mutations. These judgments of homology are
thus made in the context of background judgments about the SE function
of the sequence as a whole, and such gene sequences are often charac-
terized in terms of their SE functions. Functional individuation will closely
approximate sequence identity when we exclude from consideration “neu-
tral” substitutions that do not change amino acid codings, or codon dif-
ferences that only change amino acid sequences far from the enzymatically
active or allosteric sites, and are therefore also selectively neutral.

In any event, almost immediately “above” the level of primary nucleic
acid and amino acid sequence, the multiple realizability of biological traits
grows so rapidly that compositional and topographic differences will often
make SE functions (of developmental and intermediate structures) indis-
pensable for character individuation, as in the case of the inner ear bones,
the jawbones and the gill arches of mammals and fishes.

One general conclusion to which these considerations drive us is epi-
stemic: in order to make a well-grounded judgment of homology—that

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


318 ALEX ROSENBERG AND KAREN NEANDER

is, to explain a biologically significant similarity, the biologist must ad-
vance a prior hypothesis of “sameness” or “similarity,” that will often be
as complex a theoretical judgment as any claim about SE functions, indeed
it will often be a claim about such functions.

There is also a more “metaphysical,” or at any rate constitutive, claim
to be made, one that is independent of the epistemic point but reinforces
it. This is about the nature of biological kinds and it is driven by the
adaptational program of Darwinian biology. Recall Gould and Lewontin’s
(1979) famous attack on the adaptationalist’s penchant for “atomizing”
the parts of the organism and attributing separate SE functions to each
of them. It is now recognized that common sense biological taxonomies
and observationally driven individuations do not map smoothly onto the
real kinds of biology and the adaptational scenarios that brought them
about. The role of constraints, Bauplane, drift and preadaptation now
qualify the adaptationalist program. Nevertheless, biologists hold that
these four sources play a supporting role to selection in the emergence of
biological parts, traits and characters from physical and chemical pro-
cesses. To the degree that this is so, the kinds of biology—not just the
species, but types of body parts, tissues, organs, cells, organelles, and so
on—must have been shaped by consequence etiologies, that is the com-
bination of their advantageous effects and their common descent working
together. On a more methodological note, only a thoroughly instrumental
science, or a thoroughly observational one, can avoid reflecting the causal
forces that shape its domain in its classification of that domain.

Any particular adaptational taxonomy is of course a hypothesis about
the past—immediate and distant. And testing it will certainly require the
employment of descriptive vocabulary that does not imply the truth of
the particular adaptational hypothesis under test. This methodological
demand may be mistaken for a much stronger, unreasonable requirement
that a given adaptation hypotheses be tested by data described indepen-
dently of any adaptational hypotheses. The functional anatomists’ deter-
mination of the shape and composition of a particular bone, and its
relationship to other bones—its form and (CR) function, can certainly
be free of any prior assumption about the specific adaptational scenario
that brought about its form and function. But even that it is a bone, as
opposed to a mere chunk of calcium carbonate, presupposes an adap-
tational hypothesis. More concretely, when paleontologists conclude that
an ancient skull is that of a hominin by quantitative comparison of its
shape and size, especially the bumps in it, to that of a known hominin,
they have already helped themselves to several adaptational hypotheses
behind the description of the items compared, as bones, skull part, brain
case, oxcipital lobe, and so on. (Thus the spiral nature of these concepts,
mentioned earlier.)

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 319

Amundson and Lauder have famously written,

In the functional anatomist’s vocabulary, [physical] form and [CR]
function were both observable, experimentally measurable attributes
of anatomical items (e.g., bones, muscles, ligaments). Neither form
nor function was inferred via evolutionary history. (1994, 449)

True enough as far as it goes. The particulars of form are observationally
determinable, at least in the case of individuals of extant species. But that
they are biological parts, and which parts they are, and what is homol-
ogous with what, is not a matter merely of observation and measurement.
A slightly more searching analysis of the vocabulary of the functional
anatomist will reveal that it is shot through with terms intelligible only
as names of parts with SE functions.

4. Griffiths, Amundsen, and Lauder on Homology. Griffiths argues that,
“if functional classifications are to be of value to biology it must be because
of their superior generality—the fact that they unite disjunctions of clad-
istic homologues” (1994, 213–214). Thus he argues that if functional clas-
sifications are to be of value to biology they must be analogous, rather
than homologous, classifications. Later, in “Function, Homology, and
Character Individuation,” he writes,

I defend the view that many biological categories are defined by
homology against a set of arguments designed to show that all bi-
ological categories are defined, at least in part, by selection function.
. . . I show that classification by selection function are logically de-
pendent on classifications by homology, but not vice versa. (Griffiths
2006, 1)

And later, “characters are homologies: . . . they are individuated by com-
mon ancestry or common developmental mechanisms,” and “homology
is a relation of biological sameness” (5). Amundsen and Lauder concur,
maintaining that

whatever the favored definition of homology, one feature of the con-
cept is crucial: the relation of homology does not derive from the
common function of homologous organs. Organs that are similar in
form not by virtue of phylogeny but because of common biological
role (or SE function) are said to be analogous rather than homolo-
gous—they have similar SE function and so evolved to have similar
gross structure. . . . The fact that anatomical or morphological terms
typically designate homologies shows that they are not functional cat-
egories. (1994, 455; emphasis added)

How to interpret the latter (italicized) claim is open to dispute, but we

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


320 ALEX ROSENBERG AND KAREN NEANDER

take them to mean, minimally, that SE functional kinds are not logically
prior to homologous kinds and that the latter do not logically depend on
the former.

Griffiths makes two claims. SE functions are logically dependent on
homology, but homology is not logically dependent on SE function. There
is no dispute over the first of his claims: SE functions arise when lineages
of traits are selected for certain of their dispositions and the notion of an
SE function is moreover defined in terms of what a lineage of traits was
selected for.10 Since the first of his claims is not in dispute, we therefore
focus on the second, which Amundson and Lauder also make.

We maintain that Griffiths’ and Amundson and Lauder’s understanding
of homology is at variance with the biology reported in Section 2 and
Section 3. As introduced above, homologies are invoked, and contrasted
with analogies, to explain and group together characters that have already
been individuated, an individuation that often involves thinking about
selection history and selected functions.

To articulate his own and Amundsen and Lauder’s account of the nature
of biological concepts, Griffiths erects a view which he calls “functional
revanchism,” which he attributes to Neander.

Functional Revanchism. The biological sciences are always at least
implicitly investigating function in the selected-function sense.

By contrast, he attributes to Amundson and Lauder and also endorses
the view that, “unless anatomy, physiology, molecular biology, develop-
mental biology, and so forth turn their attention to specifically evolu-
tionary questions, they investigate function in the causal sense” (Griffiths
2006, 3). This attributes to Neander (2002) a stronger and more sweeping
claim than she makes, and weakens the claim she was opposing, since the
biological sciences are turning their attention to specifically evolutionary
questions whether it is homology or analogy that they are considering.

Of course, we do not want to deny that biologists investigate “func-
tions,” in the causal sense, if all that this means is that, among other
things, they investigate what traits do, and do that is adaptive, and so
on. However, as long as we are not taken to be denying this, we agree
that “functional revanchism” captures one end of a spectrum towards
which we probably approach more closely than they do. We believe that
the biological sciences are very often, at least implicitly, investigating
function in the selected-function sense, even when they turn their attention

10. Neander (2002, 404) points out that, for this reason, not even in her earlier work
(1991) remarks to the effect that traits are always classified by (SE) function ought to
have been interpreted as a denial of the importance of homology.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 321

away from specifically evolutionary questions. However, we are not here
to discuss so very large a topic.

Our interest is in the more specific question of how homology is de-
termined and how homologous traits are classified. If “functional re-
vanchism,” is to name a position that the authors of this article share
and that is at issue, it names the claims that (i) one must often reflect on
SE functions in determining homology, and (ii) many very important
homologous kinds of traits are in part constituted by SE functions. The
first part of this article has established the first claim. We turn now to
the second. Griffiths’ view is that no important homologous kinds are in
part constituted by SE function. He sees a “stark contrast” between “the
view that biological categories of parts and processes are defined by their
selected function” and the assumption that “characters are homologies”
(Griffiths 2006, 4). We see no such stark contrast. We claim that the two
are complementary.

Against Neander’s ‘functional revanchism’, Griffiths (2006) seeks to
establish 3 theses about homology as a (SE) function-free basis of bio-
logical classification.

1. Homology defines a hierarchy of sets of characters—like taxa, ho-
mologous parts of organisms form groups within groups.

2. There are levels of homology: evolution can preserve a morpholog-
ical structure while transforming the molecular mechanism that pro-
duces it and conversely can redeploy an existing molecular mech-
anism to underpin development of a novelty.

3. There are two distinct homology-concepts: (a) taxic or Darwinian
homology (which in Griffiths 1994 were called “cladistic homolo-
gies”) and (b) developmental homology.

We find his use of 1 puzzling, for this is a point that Neander (2002)
was at pains to stress. Homologous groupings of traits do, to be sure,
form hierarchies. Larger, more inclusive groups of homologous characters
can be divided into more fine-grained, more closely related groups, in a
hierarchical fashion. Neander argued that we thus “have ways of distin-
guishing smaller homologous groupings within larger homologous group-
ings” (2006, 402),11 and therefore that the fact that classifications of char-

11. Griffiths interprets Neander’s comment that “homology is a relation of degree,
somewhat akin to the relation of resemblance or genetic relatedness” (Neander, 2002,
402) as appealing to Darwinian Gradualism. But her point was that traits can be more
or less closely homologous, and that just as we must specify the respects in which two
items resemble each other we must also specify the respects in which two items are
homologous. Her argument does not rely on Gradualism. Nor should she be read as
claiming, as Griffiths (2006, 12) suggests, that homology relations behave formally like
a measure of overall similarity, which is quite contrary to her view.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


322 ALEX ROSENBERG AND KAREN NEANDER

acters are homologous leaves open the question of what further
classificatory principles are involved. The earlier arguments that Griffiths
(1994) and Amundson and Lauder (1994) had offered against (SE) func-
tional categories had been arguments for the importance of homology,
seeming to imply that this by itself could show that (SE) functions were
unimportant. However, this is not so. Vertebrate forelimbs are a homol-
ogous classification, but certain less inclusive homologous kinds—of fins,
legs, arms, wings, flippers, and so on—are differentiated by their SE func-
tion.12 Robin wings are homologous to human arms in some respect or
respects (e.g., as vertebrate forelimbs). But robin wings are also homol-
ogous to the wings of a blackbird in some other respect or respects (e.g.,
as wings or, in other words, as limbs adapted for flight). Once we have
acknowledged the importance of homology, we are still left with the task
of explaining the further principles of classification.

Note that the hierarchy of homologies means that if SE functions are
required to establish similarity at lower levels of the hierarchy, as we
argued was the case in Section 3. Their roles in determining similarity
will continue to be carried by higher-level homologies even when they are
not easily visible at these higher level.

Perhaps another claim can also be made. If homology is similarity due
to descent then homology is an explanatory concept, for homologies will
explain the correctness of cladistic taxonomies in the way that atomic
theory explains the correctness of the Periodic Table of the Elements.
Griffiths wants to treat homologies in the way Mendeleev ([1869–1905]
2005) treated chemical reactivities, as diagnostic, not explanatory grounds
for classification in his period table of the elements. There is of course
no noncontroversial analytic/synthetic, or classificatory/explanatory dis-
tinction, but there is a difference and Griffiths does not accept that ho-
mology lies on the explanatory side of biology. He treats ‘homology’ as
the basement level classificatory scheme in biology.13

We also agree that 2 is a correct observation but again disagree that it
tells against our position. On the contrary, it reflects the degree to which
homology attributions are explanatory and rely on a great deal of bio-
logical theory. Thesis 2 makes it plain that judgments of developmental
homology cannot always rely on uncontroversial purely structural char-
acterizations of nucleotide or protein product molecular sequence. Rather,
they presuppose theoretical judgments of similarity that are likely to be
based on or qualified by SE functional analyses of gene action. How, after
all, can an underlying molecular developmental pathway be judged to

12. Of course, not all vertebrate wings are homologous as wings.

13. But cf. Griffiths 2007, in which he recognizes the explanatory role of homology.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 323

remain the same pathway to the same morphological structure, during a
substantial or even largely complete turnover of its nucleotide sequence
foundation? Shades of the ship of Theseus!

Amundson and Lauder (1994) allege that the (SE) function-free ho-
mologous kinds they advocate are “more observational” and “less infer-
ential” than those that rely on (SE) function, thus intimating that the
former are to be preferred. But as Neander (2002) argued, and as we
argue here, claims of homology are highly inferential, and 2 gives us
further reason to reject their allegation.14

This also has implications for 3’s distinction between what Griffiths
calls taxic or Darwinian homology claims and developmental homologies.
As in the case described in Section 3, when similarities among adult forms
are unobvious, taxic homology judgments will require developmental ho-
mology grounds. Indeed, there is good reason to hold that developmental
homology judgments will completely undermine taxic homology claims
when they conflict. If two topographically, structurally or topologically
similar traits can be shown to emerge developmentally from distinct path-
ways that begin at diverse genetic loci (not themselves homologous
through duplication events for example), it is hard to see what reason
there is for treating them as homologies instead of analogies.15 Griffiths
concludes:

What then is homology? It is a manifest fact that the same parts and
processes can be found in different organisms and in different places
in one organism, just as it is a manifest fact that organisms form
species. In the early nineteenth century, biologists started to develop
powerful operational methods for identifying these parts and pro-
cesses and that research tradition has ever since provided the basis
for the investigation of structure and (causal) function—‘the hier-
archical basis of comparative biology’ (Hall 1994). So homology, like
the existence of species, is a phenomenon that stands in need of
explanation. (2006, 11)

These are not obvious and anodyne observations. We dissent from them,
owing to a fundamentally different appreciation of the role of biological

14. Their claim that significant biological classifications were observational rather than
inferential lead Neander (2002, 409–410) to wonder if they saw no constitutive clas-
sificatory role even for homology, because the claim seems to presuppose nonhistorical
criteria. Historical criteria would seem to be inevitably “inferential.” Thus Neander
argued that the classifications were ‘essentially historical’.

15. Arguably, this evidential primacy of developmental homology reflects the special
role of the genome, including RNA and DNA, in carrying information about traits
(a claim which Griffiths has elsewhere rejected, in, e.g., Griffiths and Grey 1994).

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


324 ALEX ROSENBERG AND KAREN NEANDER

theory in classification. To begin with, it is not a manifest fact but an
inferred conclusion that the same part (and process) kinds or types can
be found in different organisms. For, as we have seen, sameness of part
is a theoretically tendentious conclusion, one that requires considerable
theoretical apparatus. Homology and its sister concept, analogy, do not
describe phenomena to be explained; they provide different explanations
for similarities which biologists’ operational measures have uncovered
since the nineteenth century.16

5. What Is Wrong with Functionalist Revanchism? Griffiths addresses sev-
eral arguments that he attributes to Neander 2002. “Functional revanch-
ism” begins with the observation made frequently so far in this article,
as Neander (2002, 402) expresses it, and Griffiths quotes it: “before two
traits can be identified as homologous with respect to each other, we need
some specification of the traits in question” (2006, 12). Neander (2002,
401–402) argued that cladistic divisions alone cannot serve to classify
traits, because clades do not allow us to draw the required biologically
significant distinctions among traits that are within clades.17 Consider the
clade that starts when gill arches appear and goes on to include fish and
reptiles with jawbones and mammals with inner ear bones. SE functional
characterizations, in contrast, distinguish inner ear bones from jawbones
and these in turn from gill arches. They thus provide the resources that
experimental or evolutionary biology requires to make obvious distinc-
tions between traits of mammals, reptiles, boney fish, and cartilaginous
ones. Whence the capacity of SE functions to carve nature’s joints more
finely.

Griffiths’ response is interesting and revealing for it turns on a coun-
terexample from molecular biology, where similarities and differences are
easier to establish chemically, without appeal to function, just as noted
in Section 3.

In cladistics, homologies are inferred from a set of measured simi-
larities between organisms, known as shared characteristics [not
‘characters’—a term Griffiths reserves for homologous traits]. Sup-

16. Richard Owen introduced the term “homology” in 1843, but it does not follow
that he had a merely developmental concept in mind. In his view, homologous char-
acters were from the same “plan,” an embodiment of the same “idea.”

17. Griffiths claimed that, “A homologous trait is a character that unites a clade”
(1994, 212). Griffiths says: “A clade is a taxon which contains an ancestral species and
all its descendant species and this was an attempt to capture the notion of taxic
homology, which I then referred (in 1994) to as ‘cladistic homology’. My [1994] defi-
nition is inadequate because it takes no account of the approaches to homology de-
scribed above (developmental and serial homology)” (2006, Section 3).

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 325

pose we want to construct a cladogram using sequence data from a
suitable molecule, such as 28S ribosomal RNA. The aligned se-
quences from any two species will be identical at some points and
different at others. When they are identical, this shared character
[sic] may be a homology or it may be a homoplasy. . . . When we
say that the character state of the first nucleotide in each sequence
is C[ytosine] we are giving a physical specification. (2006, 12)

Thus, Griffiths concludes, we can specify the “shared characteristics,”
which judgments of homology require, without invoking SE functions.
However, Neander (2002) does not maintain that there are no homologous
classifications that are defined in terms of structure, but agrees that some
are. Her claim is that there must be some specification of the trait, and
that this is sometimes in terms of SE function. Her position was (and our
position is) a pluralist one.

In any case, Griffiths needs, at a minimum, a counterexample from a
level of organization where there is no scope for recourse to physics and
chemistry to establish uncontroversial identity or similarity. If homologies
were called upon to explain only similarities in molecular sequence, we
could more easily dispense with (SE) functions. But Griffiths is perhaps
the last philosopher to make this concession. He not only rejects the claim
that genes can be individuated by their molecular sequences,18 and rejects
the centrality of the gene in determining biological traits—characters—
but, as his elaboration of Thesis 2 above notes, cladistic or taxic homology
will sometimes remain the same under changes in underlying molecular
mechanisms. Further, since Griffiths makes the remarkably strong claim
that SE function is never involved in trait classification, outside of the
analogous categories, it is incumbent on him to show that this stability
of homologous kinds never rests on the stability in (SE) functions. To
repeat, our position is a pluralist position; it is not incumbent on us to
show that it always is.

So, how do we draw distinctions between biologically important char-
acters, such as inner ears, jaw hinges, and gill-rake supporters within
individual clades? Neander’s suggestion is that “one main way in which
this is done is by drawing conceptual lines at those places where there is
significant change in what there was selection for” (2002, 403). She also
points out that there is selection for dispositions (the SE, as it were) and
selection of the structures and mechanisms that are responsible for them,
and argues that these are but two sides of the same coin and can each
have complementary classificatory roles. Selection for supporting gill rakes
creates the gill arch, selection for biting changes the gill arch into the jaw

18. See, e.g., Griffiths 2009.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


326 ALEX ROSENBERG AND KAREN NEANDER

hinge, and selection for hearing moves bones that used to hinge the jaw
away from the jaw so they can play a role in hearing. In our view, the
different stages of this selection history provide a particularly fruitful basis
for differentiating among the traits involved.

What is wrong with this claim, according to Grififths? First, that the
three pairs of bone and cartilage are not defined in terms of their selected
function “is evident from the usual theories about their evolution” (2006).
It is unclear what he has in mind by this, but keep in mind that “functional
revanchism,” if it be something we support, is not the view that (SE)
functions are the sole basis of classification, only that they are an im-
portant one. He continues with what might be a second or a supporting
point: in some reptiles one pair of bones sometimes discharges both func-
tions of jaw hinge and hearing. But this does not tell against our view.
Classifications can involve more than one SE function. Moreover, the
consideration adduced by Griffiths is one of the most powerful arguments
for the claim that reasoning to homologies rests on attributions of SE
function. After all, the topographic and compositional differences between
inner ear bones, jaw hinges and gill-arch cartilage are so great as to have
made SE functional considerations indispensable to judgments that they
also constitute instances of a single, more inclusive kind, and require a
homology explanation.

Griffiths’ third argument might almost seem to be a strong consider-
ation in favor of “functional revanchism,” in the light of our discussion
in Section 3.

The transformation of the quadrate into the incus may have been
driven by increased selection for hearing in early, nocturnal mammals,
but what creates an obvious break at this point in the series is not
a change of function but traditional morphological criteria—the quad-
rate bone in all other osteichtyans (boney fish) have no obvious re-
semblance to the incus that we see in mammals. The realization that
the incus is a modified quadrate was the result of the comparative
anatomists looking for a way to bring their descriptions of different
vertebrate skeletons under a single, general account of the structure
of the vertebrate skeleton. (Griffiths 2006, 15; emphasis added)

As Griffiths indicates, the quadrate bone of fish has little resemblance
to the contemporary mammalian incus, other than that both are derived
from a single type of structure. In making their apparently counterintuitive
claim that the incus is a modified quadrate so as to make Darwinian sense
out of the very different vertebrate skeletons (it was not anything like as
easy as the vertebrate forelimb), the comparative anatomists relied on the
fact that differentiation of function could drive a single structure into two
different ones. Thus the judgment as to their sameness of kind depends

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 327

on understanding the differentiation in their SE function. However, Grif-
fiths’ point here seems to be that we can classify the mammalian incus
and the quadrate of fish into distinct kinds on the basis of morphological
criteria alone. He suggests that there is, in this respect, “an obvious break
. . . in the series” (2009) and hence that the different SE functions are
not needed for their classification into two distinct kinds. Our “functional
revanchism” has a place for morphological criteria, as noted above, but
Griffiths’ argument is anyway overly hasty. That one can easily tell apart
instances that are distant from transitional forms does not show that there
is an “obvious break” in the series. Nor does an ability to tell them apart
by virtue of their morphology demonstrate that functional criteria are not
involved. (Consider that we can easily tell a cup from a saucer on the
basis of their shapes, and yet it does not at all follow that functional
considerations are irrelevant to the one being a cup and the other a saucer.)

Another argument for “functional revanchism” that Griffiths attributes
to Neander and seeks to rebut relates to her allusion to the manifestly
evident fact that many experimental biologists, for example physiologists
studying muscle fibers, persistently employ functional vocabulary and
their research programs are guided by functional attributions. “The prob-
lem with this appeal to practice is that it equivocates on two sense of the
word ‘function’: actual causal roles (Cummins functions) and selected
effects,” says Griffiths (2006, 16–17). The former, he insists plays an im-
portant role in classification. Griffiths continues, “There is a sense in which
this reply is unfair to Neander, since she believes that all references to
function (and indeed structure) are implicitly references to adaptive func-
tion.” And a moment later, “not marking this distinction causes her to
misunderstand Amundson and Lauder” (17).

However, neither Amundson and Lauder (1994) nor Griffiths (1994)
had seemed (at least to Neander) to concede any classificatory role to
functions of either kind outside of the analogous categories. Though
Amundson and Lauder (1994) speak of biological investigation into causal-
role functions, one can search their paper in vain for any description of
their role in classification. And Griffiths writes (as quoted before) that,
“if functional classifications are to be of value to biology it must be because
of their superior generality—the fact that they unite disjunctions of clad-
istic homologues” (i.e., it must be because they form analogous kinds)
(1994, 213–214). Griffiths (2006) has since clarified that he intended here
only to refer to SE functions, and it is worth emphasizing the importance
of this clarification given the recent tendency amongst a variety of authors
toward the view that functions (unqualified) are not required for trait
classification. But, in any case, Neander (2002, 393) marks the distinction
between SE functions and CR functions and explicitly prefaced her whole
paper on what she took to be a shared assumption: that if functions were

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


328 ALEX ROSENBERG AND KAREN NEANDER

implicated in abnormality inclusive categories (categories that include mal-
functioning instances) then they were SE functions. Though this assump-
tion is now revealed as not at all shared, there remain two points that
can be made: (a) that functions of some kind are involved and (b) that
specifically SE functions are. The discussion of muscle fibers addressed
a.19 We fine-tune the argument for b as distinct from a in the light of
recent clarifications below.

Before we do this, it is worth noting that if we reach back for a moment
to even earlier discussions of this issue, the dialectical ground shifts again.
At one point, proponents of the classificatory importance of SE functions
were defending their view against the idea that Cummins-style causal-role
functions could suffice as an ahistorical alternative, and one that many
(particularly in philosophy of mind, but also in philosophy of biology)
thought preferable on those grounds.

At least Griffiths (2006) and, according to him, also Amundson and
Lauder (1994) agree with “functional revanchists” on this: that functional
considerations of some kind are important in the classification of traits,
and not only in the case of the analogous ones, and that at least some
homologous classifications are historical. So much of what we have been
defending all along is therefore either restored or was never really withheld
by these authors: that is, many trait classifications are both functional
and historical.

The remaining issue would then seem to be whether SE functions are
needed, or if only causal-role functions combined with homology are. The
gap between opposing views will have shrunk, and will now need to be
more delicately defined than before.

Now, an SE function depends on there being a lineage of traits which
has undergone selection for a Cummins’ style causal-role function, give
or take a few niceties (e.g., Cummins’ causal-role functions are essentially
interest-relative, a feature that we do not endorse, but which we can ignore
here given that it has played no role in the arguments offered on either
side). It is clear that Griffiths agrees that ‘causal functions’ are important,
and that he is willing to combine them with history, in the form of his-
torical homology. But two further questions of clarification arise: Does
he also agree that selection is important in classifying (historical) ho-
mologous traits? And does he also agree that selection history (i.e., what
there was selection for, and not only what is apt for future selection) is?
If he concedes all of this, the gap disappears. So we will assume that he

19. In fact, of the muscle fiber case, Neander asks just this, “which kinds of criteria—
the functional or the structural—will become constitutive in this case?” She answers,
“But this sets up a false dichotomy. The two are intimately interwoven and are more
or less two aspects of the same thing” (2002, 408).

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 329

does not concede at least the last, on pain of collapsing the distinction
between the two views, and turning the dispute that remains into a merely
terminological one.20

What is at issue in that case is the very role of selection history in trait
classification. We maintain that many homologous types of traits are,
constitutively, types of adaptations, whereas Griffiths is obliged to deny
it.

Note, in making the claim that adaptation is important in homologous
trait classification; we are not denying the importance of other things. In
contrast, the proponents of the opposite view have denied that adaptation
has any role in trait classification, outside of the analogous categories.
Why take this extraordinary view? Why would biologists, who are after
all so very concerned with adaptation and adaptations, among other
things, not want a taxonomy of adaptations? We are not aware that any
argument has been offered to persuade us that selection history is not
present and operative in constituting categories of homologous traits.
(Unless it is the contention that SE function is too inferential and non-
observational.) The arguments that were originally offered, when the first
sallies among the present parties were sent forth by Griffiths (1994) and
Amundson and Lauder (1994), were merely arguments to the effect that
most interesting biological classifications were homologous, as if this pre-
cluded their being functional, or at least SE functional. But their status
as homologies leaves the role of selection history undecided, as we have
argued. In contrast, we have offered a number of arguments for the clas-
sificatory indispensibility of selection history.

One powerful consideration is that the dispositions for which there has
been selection, and the structures and mechanisms that are responsible
for them, are of great biological significance. Dobzhansky’s dictum—that
nothing in biology makes sense except in the light of evolution, and more
specifically in the light of Darwinian natural selection—might be an ex-
aggeration but (without debating that) it holds more than enough truth
for our present claim. If classifications are sensitive to the kinds of sim-
ilarities and differences among traits that mattered in selection, they will
thereby be sensitive to many of the kinds of similarities and differences
that are important to biological theory, whether these be evolutionary,
ecological, morphological, physiological or psychological. The task of
classification is to carve nature at its most theoretically important joints,
not just at any old joints; there are vastly too many of them for that,
especially in the biological sciences. One main way that biologists do this,
we claim, is by doing so directly, by carving at those places where—and

20. Confirmation of this attribution comes in a later paper, Griffiths 2007.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


330 ALEX ROSENBERG AND KAREN NEANDER

because those places are where—there is a significant change in what there
has been selection for.

A second consideration is less obvious and so we have taken some pains
in this article to further articulate it. Not only does homology require
prior specification of the trait in question, an inference to homology also
often requires prior reasoning about adaptive pathways. It is often because
a certain sequence in a proposed lineage makes adaptive sense that an
inference to homology is justified. This speaks most directly to how we
investigate the truth of homology claims, and less directly to the consti-
tutive conditions for classification, which is the more immediate concern
at this moment. However, it supports our contention that homology claims
and SE function claims are both highly inferential, and interdependent,
and so it undermines the counterclaim, which we take to be quite false,
that homology is “manifest.” There is no such reason to prefer an alter-
native approach that avoids the carving of nature at those places where—
and because those places are where—there are significant changes in what
there has been selection for.

A third consideration still turns on the significance of what Neander
(2002) calls “abnormality inclusive categories.” Since the dialectical ground
has (at least as she sees it) shifted, the argument needs some recalibration.
We have argued that similarity judgments, or at least specifications of the
traits or characters judged to be homologous, are prior to homology
claims. A resemblance in two separate species is regarded as homologous
if it is derived from a common ancestor. But, as we know, traits or char-
acters are not homologous simpliciter. Something is said to be homologous
to something else as a forelimb, or as a wing, or as a flipper. Now let’s
consider how these specifications tell us in which respect two things are
being said to be homologous. Suppose that two traits or characters in
two separate species are homologous as wings. Is there, then, some re-
semblance that they share in virtue of being wings? Or suppose that two
traits are homologous as flippers. Is there some resemblance that they
share in virtue of being flippers? We do not assume that there must be a
neat set of necessary and sufficient conditions, but there had better be
something to say about it. We must then ask, What is a forelimb? What
is a wing? What is a flipper? But this is, no less, and as we said above,
a question about how traits are classified. We are now asking how traits
are classified as forelimbs, and as wings, and as flippers. Our answer is,
to say the least, very tempting here, at least for many biological classi-
fications. Whether something is a wing or a flipper is, in part at least, a
matter of its SE function.21

21. What of vestigial wings? It is constitutive of being a vestigial wing that the lineage

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 331

But now suppose that someone tells us that there is no need for SE
functions in classifying these traits as homologous, because causal-role
function suffices (i.e., we can ignore selection history). It is hard to know
what is being proposed precisely. Causal-role functions on their own do
not suffice to classify wings as wings, and flippers as flippers, and esoph-
ageal valves as esophageal valves, and for well-worn reasons—because
these classifications are abnormality inclusive. CR functions are actual
causal dispositions, and some wings, flippers, esophageal valves, and so
on, are abnormal and have abnormal causal roles. Some wings can and
some cannot help a sparrow fly. Some flippers can and some cannot help
a penguin swim. And some esophageal valves can and some cannot help
us to move food through to and remain in the gut. Yet a sparrow’s wing
is homologous to a robin’s as a wing even if it is broken.

One might attempt to give a prior specification of the traits in question
in terms of their structural features, and we do not wish to rule this out
as one strategy among others. However, just as some wings, flippers, and
esophageal valves have abnormal causal roles, they can also have ab-
normal structures. The motivation for historical classifications of traits
is akin to the motivation for having historical classifications of taxa, such
as species. There are few purely ahistorical essences in biology.

We believe that, when we speak of two similar traits or characters in
two separate species being homologous, we are ordinarily implicitly speak-
ing of normal structural features and capacities. We are not merely speak-
ing of actual structures or capacities (CR functions). Of course, congenital
impairments can be inherited. And so there are lineages of such character
traits as, e.g., hemophilia, which plagued the royal families of Europe for
a few hundred years. Perhaps someone might want to say that the he-
mophilia of one royal male was homologous to the hemophilia of another.
We see no great conceptual impropriety in speaking this way, but it is not
typical homology-speak. Nor, to repeat, do we claim that typical ho-
mology-speak always refers to adaptations. We do not deny, for instance,
that some “spandrels” are homologous to others. We repeat: ours is a
pluralist position. We nonetheless maintain that many homologous types
of traits are, constitutively, adaptations.

In those cases, the similarity judgments and the intraspecies trait clas-
sifications that are prior to homology claims will have to bring together
both normal, properly working, and abnormal, defective and diseased in-
stances of structures that vary along many topographic, morphological
and compositional dimensions. As Darwin recognized, variation is the
rule and not the exception, it has many sources and most variations are

has had and then lost the SE function of flight, so SE function is still constitutively
involved.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


332 ALEX ROSENBERG AND KAREN NEANDER

deleterious. Such deleterious effects have causal-role consequences. What
they retain, in the face of their abnormal causal roles and abnormal
morphology, and sometimes in the face of their abnormal development,
is a shared selection history. The role of a natural selection etiology in
drawing the normal/abnormal distinction needed for correct judgments
of similarity makes such judgments “essentially historical,” in Neander’s
terms.

To classify something as either biologically normal or abnormal—by
the by, a mode of classification in itself—requires that there be a standard
of biological normality, and this is given, not by a statistical distribution,
but by the solution to the design problem that created selection pressure
on the lineage within which it figures.22 Biologists, including and, perhaps,
especially those concerned with questions of physiology, have a great many
classifications of traits that more or less explicitly appeal to this distinc-
tion.

Griffiths grants the importance of abnormality inclusive categories.
However, he counters, first, that “even if abnormality inclusive categories
have to be ‘essentially historical’ this is no argument against their being
defined by homology” (2006, 18). However, this misses the point since we
do not deny that they are defined by homology. The question is what else
is involved, because homology alone cannot suffice.

But there is a much more consequential oversight, according to Grif-
fiths’ second response to the claim that abnormality inclusive categories
are “essentially historical.” To show this he invokes the notion of devel-
opmental homology:

The developmental approach to homology yields abnormality inclu-
sive categories which are not essentially historical. This should come
as no surprise. It would be puzzling if an approach designed to iden-
tify characters across evolutionary transformations could not identify
them across perturbing causes such as diseases process. . . . Nean-
der’s ‘master argument’ fails, and the need for abnormality inclusive
categories can be met using homology. (Griffiths 2006, 18)

The question of whether there is a legitimate ahistorical (i.e., non-
evolutionary) notion of homology cannot be treated in this article. How-
ever, Griffiths’ appeal to developmental homology cannot show that ho-
mology is abnormality inclusive without presupposing selected effects,
unless developmental homologies themselves are innocent of any selective
effect presupposition. That they do often have such presuppositions is we
think apparent in the role of developmental homology in grounding the

22. We take it that this is not in dispute by Griffiths, though it is disputed by some
people.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


ARE HOMOLOGIES (SE OR CR) FUNCTION FREE? 333

taxic homologies of inner ear, jawbone joint and gill arch expounded in
Section 3. Recall, the crucial point there is that, as with taxic homologies,
before a claim of homology can be made for a type of developmental
structure, we need criteria of similarity to bring together a diverse set of
topographies, compositions, and structures, as its instances. And that the
kind in question is often constituted by the developmental structures’ (SE)
function—giving rise to diverse adapted characters.

6. Conclusion. Biology encompasses many different fields of specializa-
tion and there will be no one-size-fits-all formula for taxonomizing bio-
logical traits. We have therefore exercised some caution when it comes to
making sweeping generalizations about how trait classifications are con-
stituted. Though Dobzhansky’s dictum—that nothing in biology makes
sense except in the light of evolution, and more specifically in the light
of Darwinian natural selection—is perhaps an exaggeration, it holds much
truth. Natural selection, we all agree, sheds abundant light on how traits
evolved. We maintain that it also sheds light on how traits are classified
in theoretically interesting and useful ways. We conclude –still—that very
many types of traits are types of adaptations, classified at least in part
on the basis of their SE functions.

Objections to this view have taken different forms over the past several
decades. In this article we defend it against those who argue that a com-
bination of homology, morphology, and CR function can achieve the goals
of biological classification, in the absence of considerations of past selec-
tion history. In closing, let us add that even if this claim were true, it
would not show that our view was false, in so far as we claim that very
many types of traits are, constitutively, types of adaptations, whether or
not biology could or could not do without them. It would at most only
show that they did not need to be used, in which case the parties to the
debate about the nature of such classifications could call it a draw, at
least for this round. However, we do not agree that a combination of
homology and CR function, when divorced from considerations of past
selection history, can achieve all of the same classificatory goals. The
judgment that the same trait or two similar traits in two separate species
is or are homologous often requires considering a chain of adaptation.
And the claim that the same trait or two similar traits in two separate
species is or are homologous always requires prior specification of the
traits in question, a specification that cannot—for the abnormality inclu-
sive categories—be done in terms of mere causal roles, for reasons we
have explained.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp


334 ALEX ROSENBERG AND KAREN NEANDER

REFERENCES

Amundson, Ron, and G. V. Lauder (1994), “Function without Purpose: The Uses of Causal
Role Function in Evolutionary Biology”, Biology and Philosophy 9: 443–469.

Gilbert, S. F., et al. (2006), Developmental Biology. Sunderland, MA: Sinauer.
Gould, Stephen Jay (1993), “An Earful of Jaw”, in his Eight Little Piggies. New York:

Norton, 95–108.
——— ([1994] 1997), “Hooking Leviathan by Its Past”, in his Dinosaur in a Haystack:

Reflections in Natural History. New York: Three Rivers, 359–377.
Gould, Stephen Jay, and Richard C. Lewontin (1979), “The Spandrels of San Marco and

the Panglossian Paradigm: A Critiquie of the Adaptationist Programme”, Proceedings
of the Royal Society of London B 205: 581–598.

Griffiths, Paul E. (1994), “Cladistic Classification and Functional Explanation”, Philosophy
of Science 61: 206–227.

——— (2006), “Function, Homology, and Character Individuation”, Philosophy of Science
73: 1–25.

——— (2007), “The Phenomenon of Homology”, Biology and Philosophy 22: 643–658.
——— (2009), “In What Sense Does ‘Nothing Make Sense Except in the Light of Evolu-

tion’?”, Acta Biotheoretica 57: 11–32.
Griffiths, Paul, and Russell D. Grey (1994), “Developmental Systems and Evolutionary

Explanation”, Journal of Philosophy 91: 277–304.
Hall, B. (1994), Homology: The Hierarchical Basis of Comparative Biology. New York:

Academic Press.
Kardong, K. V., et al. (2002), Vertebrates: Comparative Anatomy, Function, Evolution. 3rd

ed. New York: McGraw-Hill.
Kermack, K. A., F. Mussett, and H. W. Rigney (1981), “The Skull of Morganucodon”,

Zoological Journal of the Linnean Society 71: 1–158.
Mendeleev, N. ([1869–1905] 2005), Mendeleev on the Periodic Law: Selected Writings, 1869–

1905. Selected and edited by William B. Jensen. New York: Dover.
Neander, Karen (1991), “Functions as Selected Effects: The Conceptual Analysts Defense”,

Philosophy of Science 58: 168–184.
——— (2002), “Types of Traits: The Importance of Functional Homologues”, in Andre

Ariew, Robert Cummins, and Mark Perlman (eds.), Functions: New Essays in the Phi-
losophy of Psychology and Biology. Oxford: Oxford University Press, 390–415.

Rosenberg, Alex (2006), Darwinian Reductionism; or, How to Stop Worrying and Love Mo-
lecular Biology. Chicago: University of Chicago Press.

Thompson, D’Arcy ([1917] 1992), On Growth and Form. Reprint. Edited by John Tyler
Bonner. New York: Dover.

Vaughan, T. A., et al. (2000), Mammalogy. 4th ed. Forth Worth, TX: Saunders.
Wright, Larry (1976), Teleological Explanations. Los Angeles: University of California Press.

This content downloaded from 131.104.62.10 on Thu, 17 Oct 2013 23:07:24 PM
All use subject to JSTOR Terms and Conditions

http://www.jstor.org/page/info/about/policies/terms.jsp