Although Newtonian philosophy dominated intellectual life in the 1700s, objections lingered among a few influential writers. The English philosopher George Berkeley (1685-1753), an Anglican Bishop, articulated a philosophical objection that wove together his religious and scientific concerns, and we can place his opposition to Newtonianism within a broader defense of revelation. He also doubted the ability of human reason to truly fathom divine wisdom, as so confidently asserted by the followers of Newtonian rationalism. This led to his challenge to the authority that Newtonian natural philosophers and physicians were beginning to claim in the moral realm.

The typical Deist position was far more accepting of the value and possibility of a Newtonian science built upon the ideas of matter and its mathematical modeling. Newtonian Deists followed a standard that was commonly held in doing their science, to produce from empirical work the most reasonable conclusion.  But for Berkeley, this unity about a vague conception of God the Creator was not enough (as well as dangerous to the institution of the Church as necessary).

Berkeley's counter-arguments reveal the range of speculations derived from the new science and philosophy. Attracted to questions of physics and metaphysics by the work of Descartes and John Locke, Berkeley took a quite different view of matter and actions as the ultimate basis of knowledge. External things are known only in perception, and thus the universe is only conceivable through mind. For Berkeley, these experiences are produced by an external will (divine intelligence) and are not the results of inert matter. They have causes and order, in a universe regulated by divine mind. Thus nature is the work of God and partakes of divine mind, but human understanding is still limited. Science tries to understand nature but our minds are limited in our ability to interpret the divine. The approach taken by mathematical physics, to model inert matter and forces as the ultimate expression of knowledge, was for Berkeley a dangerous path to skeptical atheism. The Scholastics saw science as the elucidation of causes; Descartes reduced it to tracing efficient causes alone. This was insufficient for Berkeley, and his own view was that science does not find true underlying causes. Rather, by examining signs in nature, it discovers the regularities of nature. In practical terms, that is enough.

More narrowly for Newtonian physics, Berkeley questioned the theory of forces acting through a vacuum. He thought that making power a property of matter was a limit to divine agency. Such theories of mechanism without spirit led, he concluded, to atheism. This was an astute judgment, when one considers how radical discussions of religion were becoming in the 1700s. In place of the mechanical philosophy, Berkeley envisioned an animistic, interconnected cosmos. He rejected what he saw in mechanism: the spiritual sterility of an objectively measuring observer in a detached universe.

Berkeley also objected to the mathematical methods of the Newtonians. One of his most pointed treatises, The Analyst; or, a discourse addressed to an infidel mathematician (1734), was addressed to (perhaps) Halley as a critique of Newtonian mathematics. Berkeley's worry was with "freethinkers" -- the term for those opposed to the traditional Church. Berkeley describes them as "certain rigorous Extactors of Evidence in Religion, Men who pretend to believe no further than they can see" (p. 12). They argued that conviction has to be based upon reason, believing only what can be scientifically demonstrated. In an earlier treatise, Berkeley caricatured the free-thinker's logic, in a satirical dialogue describing the slippery slope of atheistical reasoning:

"First I must acquaint you, that having applied my mind to contemplate the idea of truth, I discovered it to be of a stable permanent, and uniform nature; not various and changeable, like modes or fashions, and things depending on fancy. In the next place, having observed several sects, and subdivisions of sects, espousing very different and contrary opinions, and yet all professing christianity, I rejected those points wherein they differed, retaining only that which was agreed to by all, and so became a Latitudinarian. Having afterwards, upon a more enlarged view of things, perceived that christians, Jews, and Mahometans had each their different systems of faith, agreeing only in the belief of one God, I became a Deist. Lastly, extending my view to all the various nations which inhabit this globe, and finding they agreed in no one point of faith, but differed one from another, as well as from the forementioned sects, even in the notion of a God, in which there is as great diversity as in the methods of worship, I thereupon became an Atheist; it being my opinion, that a man of courage and sense should follow his argument wherever it leads him, and that nothing is more ridiculous than to be a free-thinker by halves. I approve the man who makes thorough work, and, not content with lopping off the branches, extirpates the very root from which they sprung.

Atheism therefore, that bugbear of women and fools, is the very top and perfection of free-thinking."   (Acliphron, 1732, p. 30-31)

In Berkeley's eyes, dependence on rational and empirical demonstration alone would lead inevitably to atheism. Berkeley's argument about mathematics was that the Newtonian math contains false reasoning and even mysteries, which invalidates the logic of those depending on Newtonian rationality for their critiques of religion. In a famous quip, he says of the techniques of calculus:

"And what are these Fluxions? The Velocities of evanescent Increments? And what are these same evanescent increments? They are neither finite Quantities, nor Quantities infinitely small, nor yet nothing. May we not call them the Ghosts of departed Quantities?"  (Analyst, p. 59)

With such difficult contradictions in mathematics itself, Berkeley suggests that the freethinkers "who can digest a second or third Fluxion, a second or third Difference, need not, methinks, be squeamish about any Point in Divity" (p. 12). Dismissing the purely rational approach to religion, Berkeley accepted mystery (beyond reason) as essential to religion, but inappropriate in science -- thus separating science from theology.

Such critiques kept other philosophical and scientific options open during the dramatic expansion of Newtonian ideals, even if they had little impact on research programs.