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The rightful legacy of SPE includes the naturalism, internalism and nativism found also in Chomsky's syntactic work.⁴ By naturalism, we refer to the idea that language, including phonology, can fruitfully be studied as a natural object (see especially Chomsky 2000). Chomsky has labeled the resistance to naturalistic inquiry of language among certain philosophers “methodological dualism.” As James McGilvray sums up the idea in the introduction to Chomsky (2009b), certain philosophers “might have anything from a reasonably clear to a very good […] idea of what naturalistic scientific methodology is, but they clearly refuse to hold that language and concepts could be investigated using this methodology” (p. 22) and “when it comes to crucial features of the mind, the empiricists abandon not just internalism and nativism, but the methods of the natural sciences” (p. 21).

We detect a related methodological problem within contemporary phonology which also seems tied to neglect and/or ignorance of foundational arguments concerning internalism and nativism. Phonology has seen a number of widely adopted innovations in recent decades, such as the use of more complex graph‐theoretic representations for both segment‐feature relations (e.g., Sagey 1986) and higher‐order units like syllables (e.g., Zec 2007), that are consistent with a trend towards increased rigor and explicitness expected in science. However, phonology has a long way to go before it can be considered a mature science in practice. The rejection of radical internalism has lead to the biggest problem that characterizes much of phonological reasoning since SPE, the notion of markedness, which results in forms of teleological reasoning that, we hold, have no place in modern scientific inquiry. Markedness‐based empiricist phonological theories are trying to be theories about too many things at the same time—not only phonological competence, but also typological trends concerning the distribution of patterns in the languages of the world; verbal behavior factors related to speech rate; inter‐ and intra‐speaker variation related to dialect and register differences; and even the intelligibility of the speech of young children.⁵ In trying to do too much, such work fails to adopt the normal strategies of natural sciences like isolation, idealization and simplification.

Probably a majority of working phonologists believe that “Many if not most phonological phenomena [are] characterizable in terms of output restrictions” (Tesar 2014), or else that phonological grammars manifest “conspiracies” for “reoccurrence of a common output factor” as Kager's (1999, p. 56) OT discussion summarizes Kisseberth's (1970) early post‐SPE work. McCarthy's (2011, p. 2) discussion of Kisseberth asserts that a conspiracy involving two rules ensures that “[f]inal vowel deletion cannot create bad syllables in surface forms, and epenthesis exists to eliminate” bad syllables. In some work, the purpose is expressed in terms of pathologies: phonological computation has to “cure” a “condition” (Yip 1988). Phonology is said to contain “principles of well‐formedness (the laws) that drive it” (Prince and Smolensky 1993, p. 216), taking input representations and making them somehow better, more harmonic or optimal. Such passages, demonstrate that phonology has not, in general, achieved the rigor of a natural science—naturalism is not explicitly rejected, but such teleological rhetoric makes it clear that it hasn't been universally embraced either.

Markedness and other expressions of “surface‐orientation” in phonology are reminiscent of Appelbaum's (1996) critique of the protean reference to “gesture” in the motor theory of speech perception (e.g. Liberman and Mattingly 1985) and Articulatory Phonology (Browman and Goldstein 1989): “By leaving the referent of ‘phonetic gestures’ ambiguous between an articulatory interpretation and a neural one, proponents of the motor theory try to exploit the theoretical benefit of each interpretation, without incurring the theoretical burden of either.” In a similar vein, surface‐oriented, output‐driven phonology oscillates between actual phonetics (sound and articulation) and the output of the grammar (surface phonetic representations). For example, McCarthy and Prince (1995, p. 88) refer to an OT constraint as the “phonologization of Boyle's law.”⁶ There is no way that Boyle's law, or the Bernoulli effect or details about tongue and lip position of actual articulation can motivate the computation between input and output of the grammar. Yet this is exactly what the copious work in OT, Natural Phonology, and various repair‐based models of phonology proposes. If grammar is internal, then external facts like the behavior of gases under pressure or the properties of the muscles controlling the lips, are not directly available to the grammar (although they may play some role in filtering the kinds of data that learners can have access to).

For a particularly egregious abuse of phonetic motivation, consider the parameterized constraints of McCarthy (1996, p. 223), e.g. “the meaning of this constraint is this: the constraint is violated if a surface stop, or its underlying correspondent is immediately preceded by a vowel.” In other words, phonetic (articulatory or acoustic) motivation is supposed to explain bans on potential sequences of segments across levels of representation: a stop consonant should not appear in a surface representation if its correspondent in the underlying representation is preceded by a vowel. In contrast to this approach referring to marked or banned potential structures, SPE handles such phenomena by treating a language's phonology as a function composed of multiple rules. As in mathematics and logic, the order of composition matters. There are no teleological conspiracies to repair, cure or optimize representations; no attempts by the grammar to facilitate articulation or comprehension according to vague claims about the “communicative function” of language (see papers in Hayes et al. 2004, for examples of this view). In the SPE tradition, grammar models “dumb,” mechanical computation—that's a good thing, since grammars don't have goals and desires, even if people do. The SPE arguments given against building markedness into the formal theory are consistent with the idea of phonology as naturalistic inquiry, and these convincing arguments are only reinforced by the inconsistencies in markedness‐based approaches.