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In the early modern period, theological propositions and natural philosophical propositions both formed part of the same scientific mosaic, and thus [[The Zeroth Law|one needed reconciliation with the other]]. [[CiteRef::Barseghyan (2015)|p. 190-196]] One specific theological criticism of Descartes was that his mechanistic corpuscular natural philosophy could not be easily reconciled with the Catholic ''doctrine of transubstantiation''. This doctrine had been proposed by Thomas Aquinas as an Aristotelian explanation for the Christian dogma of the ''Real Presence''. The dogma maintained that in the sacrament of the Eucharist, Christ is really (as opposed to metaphorically or symbolically) present in the bread and wine. Aquinas had posited that the Aristotelian substance of the bread and wine were replaced with the body and blood of Christ, while their forms (that of bread and wine) remaining unchanged. In Descartes' corpuscularism, bread and wine differed from flesh and blood because they had a different arrangement of corpuscles. There is no obvious way that one could appear as the other. Anglican Christians did not accept the ''doctrine of transubstantiation'' and thus Cartesianism did not face objections based on it, and became accepted at Cambridge University by 1680. Catholic Paris didn't accept it until 1700. Many solutions reconciling Cartesianism and the ''Real Presence'' were, by then, proposed. Barseghyan speculates that the one accepted by the Parisian community was that proposed by Antoine Arnauld in 1671, in which Christ's presence in the Eucharist was due to a miracle beyond human comprehension, and outside the ordinary course of nature described by Cartesianism.[[CiteRef::Barseghyan (2015)|p. 194]]
Another sort of objection raised in commentaries on Descartes had to do with the fact that corpuscular explanation involved hypothetical unobservable entities, and the supposition that this invisibly small world could be understood by analogy with larger objects. Descartes countered that "there is nothing more in keeping with reason that we judge about those things that we do not perceive, because of their small size, by comparison and contrast with those that we see" [[CiteRef::Clarke (1992)|p. 267]] He felt that a plausible model, though potentially incorrect due to the unobservability of its fundamental parts, was better than none at all. The role of unobservable entities and metaphysics in the physical sciences was to remain a matter of prolonged debate. The positing of unobservably small entities in explanations of observable phenomena has become an accepted practice of modern physics, and in other modern fields such as molecular biology.
One particularly notable objection came from Princess Elizabeth of Bohemia (1618-1680), who questioned Descartes’ theory of substance in a letter dated the tenth of May, 1643. In it, she asks “Given that the soul of a human being is only a thinking substance, how can it affect the bodily spirits, in order to bring about voluntary actions?”[[CiteRef::Descartes (2009)]] Descartes would never gives a satisfactory answer to this central question over the course of the correspondence. In 1747, in his ''L'Homme machine''(''Machine Man'') Julien Offray de La Mettrie (1709-1751) raised another simple, but devastating objection to Descartes' supposition that human reason must be due to an immaterial mental substance. He noted that reason can become impaired by material causes such as drunkenness and fever. [[CiteRef::La Mettrie (1996)]]. In the nineteenth century, Princess Elizabeth's objection became far more poignant with the formulation of the law of the conservation of energy which implied causal closure of the physical world to influence by a mental substance. In the early twentieth century, the mathematician Alan Turing (1912-1954) showed that it was possible to construct a general purpose machine capable of performing any possible mathematical computation, thereby demonstrating that a general purpose machine was possible and refuting Descartes' core argument against a mechanical understanding of human reason. By the end of the twentieth century, the relevant scientific communities of neuroscience and cognitive science had rejected the idea of a mental substance and sought a mechanistic physical explanation for the mind [[CiteRef::Bechtel (2008)]], though there was still no agreement as to whether consciousness could be explained in this fashion. [[CiteRef::Chalmers (1996)]]
