The naturalistic fallacy was described and named by G.E. Moore at the beginning of the 20th century.
But have there been pre-enlightenment philosophers who have treated the concept?
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As the Wikipedia entry on the naturalistic fallacy notes, this fallacy is related to and often confused with the is-ought problem first articulated by David Hume (1711-1776). They are similar, though distinct, arguments about common failings with respect to what is taken for granted within an ethical analysis.
I'll suggest the Euthyphro Dilemma by Plato as an example of this issue. In my thinking, Plato used the Euthyphro Dilemma to bring to light a problem with believing that gods are actually just human expressions rather than true-in-fact supernatural authorities.
The dilemma (as reworked by Leibniz) goes:
Is what is morally good commanded by God because it is morally good, or is it morally good because it is commanded by God?
Neither choice seems OK, but especially not if you don't accept claims by Abrahamic believers in "The I Am" about the nature of God as the sole originator of both physical and moral reality.
If gods really are just human contraptions, then this dilemma feels like a paradox and thus anticipates the naturalistic fallacy without expressing it as such.
WHAT IS THE NATURALISTIC FALLACY ?
In his Principia Ethica G. E. Moore argued that whatever definition was given of an ethical property such as 'goodness' in terms of some scientific or metaphysical property X, it would not be a correct definition. If 'goodness' meant the same as 'X' then 'What has X is good' would be a triviality, and Moore thinks that such a sentence is never a triviality. Moore thinks that whatever characteristic X is, whether that of being approved by the speaker, by most men, by fully informed observers, or being conducive to evolution, being pleasant, being as like the eternal as it is possible for a temporal being to be, or whatever else is suggested, it is always a significant question as to whether what has X is good. (J.J.C. Smart, 'Prior and the Basis of Ethics', Synthese, Vol. 53, No. 1 (Oct., 1982), 4.)
Ralph Cudworth (1617-88), the Cambridge Platonist and definitely a pre-Enlightenment figure, is credited by Arthur Prior with a clear anticipation of the naturalistic fallacy : 'Prior relates how in the seventeenth century Ralph Cudworth used a Moore-like argument against the view that goodness is just obedience to the will of God or to the civil sovereign'. (Smart, ibid.)
Parenthesis : Hume's relation to the naturalistic fallacy is a complex matter, not at all straightforward. But the emphasis on 'pre-Enlightenment' in the Question as originally worded indicates an assumption that the Enlightenment could be jumped because Hume, an Age of Enlightenment figure, so plainly belongs to the naturalistic fallacy's history. But does he ?
... by the 1930s Moore’s alleged naturalistic fallacy had come to be regularly conflated with a more standard sort of unwarranted inference, from “is” propositions to “ought” prescriptions—usually traced back to David Hume’s argument blocking inferences from factual to moral judgments. The former were made by the faculty of reason and pertained to “the real relation of ideas, or to the real existence of matters of fact”; the latter by the passions, which perceive matters of fact as virtues and vices, which “may be compar’d to sounds, colours, heat and cold” and other secondary qualities in the mind rather than its objects. Although he did not use the word “fallacy,” Hume condemned such inferences as logical errors and indicted almost all moral systems for committing them. There is no indication that Hume thought matters of fact were exclusively natural, and he offered a nuanced discussion as to how virtues and vices may be deemed natural or unnatural, depending on how those terms are defined.
How then did Hume’s argument come to be identified with Moore’s alleged fallacy— especially since by Moore’s lights Hume himself was guilty of the naturalistic fallacy in deriving moral judgments from the passions? This is a genuine puzzle. A 1939 article by the University of Michigan philosopher William A. Frankena (who had studied with Moore at Cambridge) that valiantly attempted to sort out the conceptual mess provides valuable clues. Noting what strange bedfellows Hume and Moore made, Frankena pointed out that all they really seemed to share was a “bifurcationist” ontology of ethical judgments: just as Hume bifurcated “is” and “ought” propositions, intuitionists like Moore asserted that “ethical characteristics are different in kind from non-ethical ones.” There the analogy ended' ( Lorraine Daston, 'The Naturalistic Fallacy Is Modern', Isis, Vol. 105, No. 3 (September 2014), 581.)
G.E. Moore, Principia Ethica, Cambridge : CUP, 1903.
W.K. Frankena, 'The Naturalistic Fallacy', Mind, 39 (1939), 464-77. [Widely reprinted.]
A.N. Prior, Logic and the Basis of Ethics, Oxford : Clarendon Press, 1949.
J.J.C. Smart, 'Prior and the Basis of Ethics', Synthese, Vol. 53, No. 1 (Oct., 1982), pp. 3-17
Lorraine Daston, 'The Naturalistic Fallacy Is Modern', Isis, Vol. 105, No. 3 (September 2014), pp. 579-587.