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ZACHARY ERNST
ABSTRACT. The gene concept has fallen on hard times in the philosophy of biology. Although
we are confronted on a regular basis with reports that the gene for such-and-such has been
discovered, the received viewin the philosophy of biology is that current work in genomics shows
that there is no such thing as the gene. In this paper, I argue that such a skeptical conclusion is
unwarranted. In fact, contemporary work in genomics not only shows us that the gene does
exist, but it points the way toward a precise characterization of the gene concept. In the course
of making this argument, I provide an overview of one contemporary approach to gene discovery
and genome annotation that makes crucial use of techniques from computer science.
1. INTRODUCTION
If there is a philosophical consensus on the status of the gene, it would be that current re-
search into molecular biology shows us that the gene is an outmoded concept. John Dupr put
the point succinctly when he said that such modern research was the beginning of the end of
the traditional concept of the Mendelian gene. This argument owes much to the work of David
Hull [8, 9], whose classic skeptical stance on the reality of the gene has become somewhat of a
received view.
But the received view is mistaken; we have good reason to hold onto a suitably revised gene
concept. In this paper, I will argue that doubts about the gene concept are rooted in a faulty
theory of reference for theoretical terms. When we critically examine how the theory of refer-
ence should be applied to terms such as gene, then we see that we must attend to the details of
contemporary genomics research if we are to determine whether genes exist. Accordingly, this
paper provides an overview of one approach to comparative genomics research. This research
strongly suggests a revised, but recognizable gene concept. This concept crucially makes re-
course to the evolution of modularity. Thus, while I propose a positive solution to the problem
of characterizing the gene concept, it also turns out that genomics research focuses our atten-
tion on another (and perhaps more important) problem. This is the problem of understanding
why natural selection sometimes seems to favor the evolution of highly modular structures.
Date: April 10, 2008.
Many thanks to Ross Overbeek for his instruction at Argonne National Laboratory, and to Alexander Rosenberg for
saving me from a couple of awful howlers in this paper.
1
2. THE LOGIC OF SKEPTICAL ARGUMENTS
In order to motivate the central argument of this paper, I shall summarize and critique com-
mon arguments that aim to establish that the gene does not exist. When these skeptical argu-
ments have been criticized, we shall have better motivation to examine current research into
genomics in the following sections.
Current research into molecular biology has dashed all hope of a simple molecular imple-
mentation of the Mendelian gene. If we had hoped that genes would supervene on simple,
contiguous, easily identiable stretches of DNA, then we must at least lower our expectations.
Although classical genetics makes use of notions of dominant or recessive genes, it is now well
understood that such concepts are, at best, useful but severe idealizations. Genes (if they ex-
ist) are neither implemented in a simple, straightforward manner, nor are they inherited in a
simple, straightforward manner.
It is fromthese uncontroversial premises that skeptics about the gene including John Dupr
and David Hull make their arguments. These arguments draw upon premises that are often
pressed into service for anti-reductionist arguments concerning the gene. Indeed, I shall argue
that these arguments are too closely related to these anti-reductionist arguments.
According to these skeptical arguments, the term gene is supposed to refer to whatever en-
tity implements the mechanisms of inheritance in a way that approximates classical Mendelian
theory about inheritance. So genes exist only if there is something that does implement inher-
itance in such a way. But when we begin to investigate how various segments of DNA imple-
ment the mechanisms of inheritance, we quickly discover that there is no simple story to be
told. The same, or functionally same, phenotypic characteristics are famously understood to
be multiply realized by many different possible segments of DNA [26]. Furthermore, owing to
complications arising fromdevelopmental facts, identical segments of DNAmay instantiate dif-
ferent phenotypic characteristics. The point is a familiar one fromanti-reductionist arguments,
namely, that the relationship between genotype and phenotype is hopelessly many-many, not
capable of any simple characterization by any nite set of bridge laws.
It should strike us as odd that these premises which are typically the premises of anti-
reductionist arguments shouldbe pressed into service to support a non-existence claimabout
genes. After all, reductionist theses are typically understood as conclusions about explanations
and terms; that is, reductionism is a linguistic thesis. But existence claims are obviously onto-
logical theses. Alan Garnkel puts the point succinctly:
So reductionism, which is on its face an ontological question, is really a question
about the possibility of explanation: to say that something reduces to something
else is to say that certain kinds of explanations exist. [5, p. 443]
2
Thus, it might appear at rst glance to be a non-sequitur when Hull and Dupr argue that genes
do not exist by providing premises of anti-reductionist arguments. So it is important to try to
reconstruct this line of reasoning in more detail.
It is well appreciated that during the Modern Synthesis, it was Mendels work on the mech-
anisms of inheritance that allowed Darwins theory of evolution by natural selection to be put
on a solid theoretical foundation. Although he had no way of guessing as to the physical im-
plementation of inheritance, Mendels insight was to recognize that the observed facts of in-
heritance could be explained by positing theoretical entities called genes that would somehow
inuence the development of organisms, while also following simple rules of transmissionfrom
parent to offspring.
Mendels rules of inheritance assumed that these posited entities would fall into various cat-
egories, including dominant and recessive, that each gene would have an equal probability
of being passed along from parent to offspring (the so-called independence of assortment as-
sumption), and that they would affect the development of the organism in a straightforward
manner. Of course, none of these assumptions have been borne out in the long run inheri-
tance, for example, can be affected by so-called driving genes, and the mechanisms of assort-
ment are severely affectedby the locationof particular stretches of DNAalong the chromosome.
Specically, if two stretches of DNA are close together on the chromosome, then the probability
that one will be inherited by the offspring is positively correlated with the inheritance of the
other. So these Mendelian assumptions have turned out to be false.
Skeptics about the gene have used these complications in a deceptively simple argument.
If the theoretical term gene refers to an entity that controls inheritance, and which assorts
independently, then there simply is no such thing that answers to that description. Hence, the
termgene fails to refer to anything at all; therefore, we are to conclude that genes do not exist.
Hull puts the argument in an interesting way. According to Hull, we have to distinguish two
possible scenarios that could play out in a reduction of one theory to another. On the one hand,
it may turn out that the reduced theory is discovered to be incorrect in some relatively minor
ways; thus, in order to carry out the reduction, we wouldhave to rst correct it in order to bring
it into line with the reducing theory. Such would presumably be the case when we discover how
to reduce (e.g.) Newtons law of cooling to statistical mechanics whereas we originally had
a deterministic and non-probabilistic theory, we correct it by introducing statistical factors
into the theory. But according to Hull, this is not a problematic case, because the theory is
recognizably the same both before and after the reduction has been carried out.
Onthe other hand, it is possible to discover that the reduced theory must be modiedbeyond
recognition in order to bring it into line with the reducing theory. In such a case, we cannot
simply say that we are correcting the reduced theory instead, we are replacing it. As Hull puts
the point regarding the reduction of classical Mendelian genetics:
3
My intuitive impression continues to be that the differences between the cor-
rected and uncorrected versions of these theories are too numerous and too
fundamental to consider the relationshipbetween the two corrected theories re-
duction in the formal sense of the term. Pre-analytically, the relation between
Mendelian and molecular genetics is a paradigm case of theory reduction, but
from the point of view of the logical empiricist analysis of theory reduction, it
looks more like replacement. [8, p. 660]
However, the simplicity of that argument belies a deep difculty concerning the reference of
theoretical terms. For nowhere else do we tie a terms denotation to its original intensional
meaning. For example, although it is certainly true that the term atom was originally intro-
duced to refer to an indivisible thing, and that there is no such (known) indivisible thing, we
do not conclude that atoms do not exist. Rather, we simply recognize that the original con-
ception of the atom was in error. Indeed, if any theoretical term is unrecognizable from the
perspective of its original meaning, the termatom is.
In general, we feel free to allow the sense of a theoretical term to shift under the inuence
of new information concerning that term. Thus, as we discovered that atoms were indeed ca-
pable of being divided into component parts, we simply allowed the term atom to continue
to refer to those entities, in spite of the fact that they turned out not to answer to their original
conception. This strategy is underwrittenby the causal theory of reference, attributedprimarily
to Quine [25] and Kripke [15]. According to the causal theory of reference, proper names and
theoretical terms may initially have their reference xed with the help of a connotative deni-
tion, their reference is in fact xed by virtue of a causal chain which runs from the user of the
term (e.g. a practicing scientist) back through a series of experiences which may include con-
versation, writing and so on. That chain will eventually terminate in some causal inuence that
the entity in question had on someone who xed the referent of the term by stipulation. The
upshot of the causal theory of reference is that it is this causal relationship, and not a set of
necessary and sufcient conditions, that xes the referent of a theoretical term. In this way, we
are able to account for the continuity of a scientic theory in the face of radical theory change.
For although the meaning of a theoretical term may eventually change to the point at which it
is unrecognizable to its original users, the causal chain leading from that entity to the users of
the termremains.
For the present purposes, the lesson is straightforward. We do not attempt to defend the
view that the Mendelian concept of the gene is alive and well. But we ought to question Hulls
assumptionthat there is any cut-off point after which the termhas been so dramatically revised
that it loses its ability to refer to the same entity. We should not expect the meaning of the term
gene to remain xed in the light of ongoing scientic research any more than we should expect
4
the term atom to retain its original connotation. It is a mistake to assert that any set of con-
ditions can be attached to the term that are necessary for that term to refer. Specically, con-
tiguity of the chromosome, independence of assortment, a simple developmental story from
genotype to phenotype, and all such other conditions are not necessary (singly or jointly) for
the termgene to refer.
2.1. Indispensability. According to a line of argument that has become widely accepted, we
are justied in claiming that a theoretical term refers to a real entity if the use of that term is
indispensable in explaining observed phenomena. Normally, however, when we are able to for-
mulate bridge laws relating some supervenient entity A to its underlying physical implemen-
tation B in a straightforward, suitably non-disjunctive way, then that reduction may be taken
to show that we can replace any mention of A in our explanations with a translation into the
language of B. In other words, when we have a successful reduction in hand, that is taken to
show that the reduced entity is dispensable. Thus, if a reduction is evidence at all concerning
existence, then it should speak against the existence of the reduced entity. Conversely, when
we nd that we are unable to carry out a reduction, then we will typically assume that we are
correspondingly unable to eliminate the term in question. Thus, the use of that term is more
likely to be indispensable.
For example, suppose that a metaphysical argument is proposed that only basic substances
such as subatomic particles exist, but not the ordinary objects such as tables and chairs that we
ordinarily take to be composed of those basic substances. Such metaphysical arguments typi-
cally proceed by showing that there is no explanation or causal power possessed by tables and
chairs that cannot be fully explained by the causal powers of the particles that (we ordinarily
take to) compose tables and chairs. Thus, the argument goes, we can at least in principle re-
place any talk of these ordinary objects with talk of basic substances. And so, the dispensability
of these entities is taken as defeating any reason to believe that they do exist.
So regarding the gene, we nd that there is a tension between antireductionist arguments
and arguments purportedly establishing that genes do not exist. For normally, the premises
of antireductionist arguments are taken to imply that the unreducible entity is indispensable,
and that we therefore have reason to believe that the entity exists. On the other hand, if the
entity in question can be reduced, then the use of that term is dispensable, and we thereby
lack at least some important justication for saying that the entity exists. But if we were to
accept the arguments of Hull and others, thenthe gene is completely different. For they take the
premises of antireductionist arguments to show that genes do not exist. This tension between
antireductionism and indispensibility provides a further reason to question such arguments
purporting to show that the gene does not exist.
5
3. FUNCTIONAL CHARACTERIZATION OF GENES?
In the best of all possible worlds, we could simply dene each particular gene as a particular
sequence of nucleic acids, locatedin a specic place on the chromosome. It is a point not worth
belaboring here that such a denition is hopeless [26]. Obviously, if genes do exist, then there
will be numerous small changes to the particular sequence of nucleic acids that will not affect
the identity of the gene. Furthermore, as philosophers of biology have long understood, the
same gene type may be tokened at two or more different locations on the chromosome without
affecting the identity of the gene. Indeed, suchshifts appear to play a crucial role inevolutionary
processes, and the reconstruction of the history of such changes gives us valuable insight into
the evolution of various species.
1
For a philosopher of science, when a physical characterization fails, the obvious next step is
to try for a functional characterization. That is, for any particular gene, we may try to dene it
using the following schema:
(3.1) Gene X =
def
any nucleic acid sequence performing function F
Unfortunately, as is also well-appreciated by philosophers of biology, it is common for a par-
ticular sequence that performs one function in some species to perform a different function in
another species. Intuitively, we would like to be able to claim if we were to have a workable
gene concept that the same gene performs two different functions. However, schema (3.1) will
not countenance such a claim. Of course, one could always hold out for a disjunctive version
of schema (3.1), but there is no a priori way to set an upper limit on the number of possible
functions that a gene could perform. One could reasonably suspect, in fact, that without set-
ting an arbitrary limit on the number of possible contexts in which a particular sequence might
appear, that there is no upper limit to be had at all. Thus, it looks as if neither a physical and
reductive denition, nor a functional non-reductive denition will work for dening the gene.
No wonder, then, that philosophers of biology have despaired of coming up with a workable
denition of the gene.
4. CAUSATION AND THEORETICAL TERMS
At this point, we have a trio of problematic proposals regarding the reference of the theoret-
ical term gene. First, we have the traditional Mendelian gene concept, which is well-known
to be incorrect, or at least to be so severely idealized that it is not to be found in the genome.
Second, we have the philosophical positions advocated by Hull and Dupr, according to which
the term gene simply fails to refer at all. But as I have argued above, their negative arguments
ultimately fail because they rely upon problematic theories about the reference of theoretical
terms. Third, we have the possibility that a functional characterization of the gene concept can
1
See below, in section 6.
6
be made out. But for familiar reasons having to do with multiple realizability, this approach
fails as well.
These difculties may properly be considered symptoms of a deeper problem regarding the
gene concept. For the question of whether the gene exists should be interpretedas the question
of whether the theoretical term gene successfully refers. Thus, the question of whether the
gene exists is primarily a question for the philosophy of language and specically for the theory
of reference. And the gene concept provides a particularly difcult test case for a theory of
reference.
As I have argued above, it is too quick to argue that the term gene fails to refer merely be-
cause our current understanding of genetics demonstrates that the Mendelian gene concept is
inadequate. For such an argument implicitly depends upon a theory of reference that xes that
reference of a term by giving something like a denite description of it. And such a picture has
been long recognized to be inadequate for the task of accounting for theory change. Thus, we
should not be surprised to nd that such a theory of reference turns out to be inadequate for
characterizing as complex a theory as that of genetic inheritance. Accordingly, a defense of the
gene concept requires (at least an outline of) a defense of a theory of reference that is plausible
on its own, while remaining compatible with the view that the termgene successfully refers.
Unfortunately, the subject of the reference of theoretical terms is far too complex for the cur-
rent paper. However, I think that it is possible to argue that a causal theory of reference allows
us to retain a meaningful gene concept. That gene concept is one that emerges as a result of
current research into genomics. Furthermore, standard objections to the causal theory of ref-
erence as it is applied to theoretical terms are problematic. This will be the subject of the
current section.
4.1. Ostension and Theoretical Terms. The obvious alternative to a theory of reference that is
based on denite descriptions or other intensional meanings is a causal theory. Indeed, the
causal theory of reference has become the received viewfor theoretical terms precisely because
it is capable of accounting for how terms maintain their reference while their sense changes
signicantly. Thus, adopting a causal theory is a promising strategy for accounting for the gene
concept.
However, we immediately run into difculties if we try to straightforwardly apply the causal
theory to this case. For on a standard picture of the causal theory, a term acquires its reference
through an initial baptism, in which a demonstrative is used to x the reference of a term. For
example, a parent may x the reference of the term Joe by indicating a child and using the
demonstrative, that child shall be called Joe from now on. Thus, the reference of a name may
be xed without having in mind a denite descriptionof the object named. Furthermore, when
a person uses the name to refer to the object, she may successfully do so despite the fact that
her own understanding of the objects properties are quite incorrect. So long as their use of the
7
name is explained by an appropriate causal history leading back to the initial baptism, the term
refers.
Following Kripke, Quine, and Putnam [15, 24, 25], the causal theory of reference is applied to
natural kind terms in a similar way. But instead of naming a particular token object, we use the
initial baptismto refer to a class of entities. For example, I may ostendto a cat and say, the word
cat shall refer to things like that. In so doing, I x the reference of the term cat, and I may do
so even without having any useful theoretical knowledge of cats. Likewise, another person may
refer to cats using the term cat, even while lacking any correct understanding of what a cat is,
so long as their use of the term is causally connected in the right way to the original baptism.
An immediate difculty that arises for the causal theory of reference applied to theoretical
terms is that there are obvious cases in which the theoretical termcannot be xed by ostension.
That is, there are cases in which we cannot simply point to a token of the thing because it is an
unobserved or unobservable entity. For example, we cannot simply point to a token of the type
electron, since electrons cannot be directly observed. Instead, only the effects of such entities
can be observed. Accordingly, the initial baptism for such theoretical entities is modied; in-
stead of by ostension, we baptize those entities by attributing causal powers to them. Thus, we
say that (e.g.) an electron is whatever causes such-and-such observable effects. In general we
say:
(S): The referent of termX is whatever type of entity that is the cause of .
where is some directly observable phenomenon.
Much has been made of the distinction between so-called ostensible entities whose names
may givenby ostension, andnon-ostensible entities whose names are givencircuitously through
something like schema (S). Berent En [2] and Robert Nola [18], for example, have offered the-
ories of reference according to which the reference of ostensible and non-ostensible terms re-
quire different conditions. In particular, both argue that non-ostensible terms have their ref-
erence xed partially by intensional concepts in a way that is not required for the reference of
ostensible terms.
Luckily, it is not necessary to get into the details of these arguments here for my purpose
here is not to offer a general account of the reference of theoretical terms, but to clear away
apparent difculties concerning the reference of the theoretical term, gene. Accordingly, I
propose that we consider theories of reference as falling along a spectrum dened by the role
played by non-causal elements of the reference xing event. Thus, on one end of the spectrum,
we have (what Nola calls) the bare causal account, in which the reference of all names (and ev-
ery other termthat behaves like a name, including theoretical terms) is xed by ostension or by
schema (S). At the other end of the spectrum are theories according to which the intension of
the term is used to x the reference, instead of causal facts. The theory of denite descriptions
would be an example of a theory occupying the latter position on the spectrum. In between
8
are what we might call hybrid theories, which are causal, but require intensional information
about at least some of the terms in order to x their reference the theories of En and Nola are
examples of this kind of hybrid theory.
The reference of the termgene is threatened under any hybrid theory of reference, since the
intension of the term has obviously changed a great deal in the history of genetics. However,
hybrid theories of reference face difculties because the distinction between ostensible and
non-ostensible terms is extremely problematic. This is simply because the ability of an entity to
be directly observed just is a particular kind of causal power the entity possesses. Thus, even an
entity that is directly ostensible is ostensible because it has the causal power to affect our sense
organs in a particular way. This is apparent in Kripkes discussion of the term heat, where he
describes the causal powers of molecular motioninterms of their ability to create certaineffects
inour nervous system. Incharacterizing the manner inwhichwe ostensibly refer to heat, Kripke
seems to equate reference by direct ostension with reference by more indirect methods:
At any rate, we are able to identify heat, andbe able to sense it by the fact that that
it produces in us a sensationof heat. It might here be so important to the concept
that its reference is xed in this way, that if someone else detects heat by some
sort of instrument, but is unable to feel it, we might want to say, if we like, that
the concept of heat is not the same even though the referent is the same. [15, p.
131]
In short, because the ability to be observed is an instance of a causal power that could gure
into the use of the schema (S), it is far from clear how to draw a distinction between ostensible
and non-ostensible terms.
2
But even if we put aside this difculty for the time being, we can still
identify two two general types of cases that have traditionally been used to motivate a hybrid
account of how the reference of theoretical terms is xed. These two cases are:
(1) cases in which the intensional meaning of a term is inadequate for xing its reference,
and
(2) cases in which we are more likely to abandon the term rather than radically revise its
intensional meaning.
My contention here is that by attending to these cases, we are led to a better modication of the
theory of reference for theoretical terms, and that this modication makes sense of the contin-
ued use of the termgene. I shall discuss each in turn, before outlining the positive proposal.
2
The difculty of distinguishing between ostensible and non-ostensible terms is parallel to the familiar difculty
of distinguishing between observable and non-observable entities. For direct observation requires the observed
thing to exert a causal inuence uponour sense organs and a (perhaps implicit) theory of howthe resulting sensory
impressions reveal facts about it. In fact, I think it is reasonable to suspect that the distinctions between ostensible
and non-ostensible entities on the one hand, and observable and unobservable entities on the other, stand or fall
together.
9
4.2. Thales and the amber. Nola has contended that if the bare causal theory were correct,
then people would be in a position to x the reference of theoretical terms when they clearly
lack the necessary level of understanding to do so. In particular, anyone who was in a position
to observe the effects of some theoretical entity would be able to stipulate a name for whatever
it is that happens to be the cause of those effects. But according to Nola, it is clear that (at least
in many cases) more is required.
For example, Nola recounts a story about Thales, who observed (what turned out to be) the
buildup of electrical charge on a piece of amber after it had been rubbed. If the bare causal the-
ory were correct, thenThales wouldhave been ina position withno further informationabout
electricity to stipulate a termfor whatever it is that causes the attractive effects of amber after
it has been rubbed, and would thereby have xed the reference of a term upon electricity. But
according to Nola, this sort of case should strike us as wrong it attributes too much scien-
tic prescience to Thales in the absence of any theory about the itemso picked out [18, p. 516].
Rather, in order for Thales to have successfully picked out electricity, he would have had to have
had some theory about how the entity causally brings about its effects.
However, even if we share Nolas intuitions about Thaless alleged inability to x the reference
of any term upon electricity, there is still a difcult problem with requiring that Thales would
have to have had a theory about how electricity causes the attractive powers of the amber. This
difculty can be brought out as a dilemma, for we must either require that the theory be correct
(or nearly correct), or we must waive the requirement. It should be clear that the rst horn of
the dilemma is unattractive for two reasons. First, it is plainly too demanding, and would put
the cart before the horse in that it often turns out that it is necessary to x the reference of a
term before engaging in the kind of research that could lead to the correct theory about the
entitys causal powers. Second, if we require a correct theory of the entitys causal powers, then
we are treading too closely to a denite description theory of reference for the correct theory
could simply be used to x the reference of the theoretical term without having to worry about
a causal theory of reference at all.
But we cannot weaken the requirement of truth, either. For suppose that we require that in
order for Thales to be able to x the reference of the term, he need only have some theory or
other even a false one. Although it is certainly true that a term may have its reference xed
in spite of the fact that the intensional meaning of the term is wrong, it is strange to require
such a theory, while admitting that it might be totally false. To put the point rhetorically, it is
fair to wonder what a false theory adds to the reference-xing ability of Thales that cannot be
otherwise be met while being agnostic about howthe entity causes its observable effects. I thus
conclude that cases suchas this one do not pose a difculty for a bare causal theory of reference.
4.3. Phlogiston. We need now to consider cases in which the use of some term is abandoned
as we discover new information suggesting that the term fails to refer. The standard example
10
of this phenomenon is the failure of the theoretical term phlogiston to refer to any real entity.
En and Nola both argue that the reference of phlogiston was to have been xed partially in
virtue of the intensional meaning of the term; thus, when it was discovered that its intensional
meaning was not satised by any real entity, that discovery was tantamount to discovering that
phlogiston did not exist [2, p. 271].
But the interesting feature of this example, which makes it not good support for any hybrid
theory of reference, is that the intensional meaning of the termwas inextricably bound up with
the causal powers that were attributed to phlogiston. The following discussion from En is in-
structive:
For example, in the phlogistoncase, when the termphlogiston was introduced,
it was at least believed that whatever causes re can saturate air during combus-
tion and that when the air is saturated the re dies out... Furthermore, the belief
that this substance had the power to restore the metallic properties of calx and
to lead to death by suffocation... led to the belief that the substance in question
was a new kind of substance. [2, p. 271].
Thus, when these beliefs were discovered to be false i.e. that there is no substance meeting
that description scientists concluded that phlogistondoes not exist. Fromthis, En concludes
that in introducing a term, the scientist is not just naming whatever it is that is responsible for
such and such phenomena, he is rather naming a kind of object partially specied by the kind-
constituting properties he believes the object to have and by the context in which the object
plays its explanatory role [2, p. 271]. According to this argument, a bare causal theory would
have it that the scientists were referring to oxygen (since oxygen is what is responsible for com-
bustion), and they would merely have discovered that phlogiston actually refers to oxygen, but
that some of their other beliefs about phlogiston were false (for example, that it is responsible
for suffocation).
Kyle Stanford and Philip Kitcher call this the no failure of reference problem for the causal
theory [28]. In general form, the problem is that so long as the person who introduces the term
denes it as the cause of X, where X is some real effect of some cause or other, then the term
is guaranteed to refer to that cause, whatever it may turn out to be. But their intuition, which is
plausible enough, is that if the cause turns out to be totally different from what the introducer
of the termhas supposed it to be, then we are better off judging that the termfails to refer at all.
However, it is not so clear that the bare causal theory of reference really does lack the re-
sources to yield the correct judgment that phlogiston fails to refer. In short, I think it is fair
to say that those who use this particular episode in the history of science have cherry-picked
certain features of the example. To see this, consider a simplied and ctional case resembling
the historical example. Let us suppose that a scientist we shall call Williams
1
inquires as to the
cause of combustion, supposing that there may be some such substance, and he accordingly
11
denes phlogiston
1
as whatever substance causes combustion. Our ctional scientist may
develop all sorts of other beliefs about phlogiston
1
, many or all of which may be mistaken. He
may believe, for example, that it is emitted fromburning bodies or that it has a negative weight.
But let us suppose that his original reference-xing stipulation makes recourses only to the
particular causal property of causing combustion. When Levoisier discovers oxygen, Williams
1
may quite reasonably assert that phlogiston
1
is oxygen, in spite of the fact that many of his spe-
cic beliefs about phlogiston
1
will have to be revised or abandoned completely. And of course,
this is just what the bare causal theory would have be the case.
Now let us complicate the example somewhat. Suppose that another scientist Williams
2
inquires as to the causes of combustion and suffocation, hypothesizing that some substance is
the common cause of both. Then he stipulates that phlogiston
2
shall refer to whatever sub-
stance is the cause of combustion and suffocation. Like his counterpart, he may form a variety
of other beliefs about this new substance, but these play no role in xing the reference of the
term phlogiston
2
. Also like his counterpart, Williams
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stipulates the reference of phlogiston
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