Atomism has a long and interesting history in Indian philosophy as well, and an anti-reductionist version was developed within the Nyāya-Vaiśeṣika tradition (named for two systems which arose independently but later blended together). Some key arguments were worked out in response to rival, reductionist brands of atomism defended within certain schools of Buddhism. They can be found in the Nyāya-sūtra and the commentarial tradition based on it, relevant texts from which can be found in the very useful recent collection , edited by Matthew Dasti and Stephen Phillips.
An important larger theme in the Nyāya-sūtra (which covers a wide variety of metaphysical topics) is the self-defeating character of skepticism. The commentators deploy this idea against Buddhist reductionist atomism as well. (Cf. pp. 100-3 of Dasti and Phillips.) Both sides make reference to ordinary objects, such as a clay pot. Both sides agree that the pot is ultimately made up of unobservable atoms. But the Buddhist reductionist says that those atoms are really all that exist, that there is no such thing as a composite whole over and above them.
The Nyāya-Vaiśeṣika commentators argue that the position that results from this is incoherent. The Buddhist position presupposes that we can know that there are atoms, but claims that the composites we take to be made up of atoms are unreal. If they are unreal, then of course we cannot be said to know of them through perception. But the atoms are not perceptible either. So how could the Buddhist know of them any more than he knows the purportedly unreal composites? In fact it is only through the composites that we can know the atoms that make them up. Hence the composites must be real.
This argument focuses on our knowledge of objects, but a second, related point made by the commentators focuses on our active engagement with them. Composite objects can be grasped and pulled, and sometimes pulled merely by virtue of getting hold of a part of them. This could not be done if there were no composite over and above the whole. Consider how, if you spill a pile of sugar on the counter, you can’t remove it merely by grasping one side of the pile and thereby pulling the whole pile. The argument is that if the atoms were all that really existed and the composite whole did not, then you couldn’t pull on a pot (say) any more than you could pull on a pile of sugar.
The commentators consider possible objections the reductionist might raise. (Cf. pp. 103-6 of Dasti and Phillips.) Consider an object made of bits of straw, rocks, and wood glued together. You could pull on it just by virtue of pulling some part of it, but the Nyāya-Vaiśeṣika anti-reductionist would not want to consider this random object a true composite the way a pot is. The commentator Uddyotakara responds by biting the bullet and allowing that this odd object should be counted as a composite. (Here we see how Nyāya-Vaiśeṣika anti-reductionism, though something with which an Aristotelian hylemorphist is bound to sympathize, is not quite the same position. For the Aristotelian, we need to draw some important distinctions here. The random object in question would have a merely accidental form rather than a substantial form, and thus not count as a true substance, even if it is a composite of some kind.)
Another possible objection to the Nyāya-Vaiśeṣika position that the commentators consider goes like this. If you look at a forest from far enough away, it can appear to be a single, unified whole. But this is a misperception, and in fact there is nothing more there than the trees that make up the forest. Similarly, where we take there to be an everyday composite like the pot of our earlier example, there is really only the atoms that make it up.
The Nyāya-Vaiśeṣika response to this objection is that the analogy is a false one, because atoms, unlike the trees that make up a forest, are not observable. In the case of the forest, it makes sense to say that we are really perceiving trees, and simply mistaking them for some larger whole. We do, after all, really see the trees. But in the case of an object like a pot, it does not make sense to say that we are really perceiving atoms, and simply mistake them for a pot. For again, as both the Buddhist reductionist and the Nyāya-Vaiśeṣika anti-reductionist agree, we can’t perceive atoms at all, even in a distorted way.
The commentators also consider the suggestion that the features of a composite can be accounted for entirely by way of factors like the proximity and contact between atoms, and that the “conjunction” of atoms that yields a purported composite is nothing more than that. (Cf. pp. 106-7.) The commentator Vātsyāyana responds that there has to be more to it than this insofar as “new entities” with distinctive properties can arise out of the conjunction of atoms. He seems to be presenting a variation on the theme familiar from contemporary anti-reductionist views (including contemporary hylemorphism) that wholes have causal powers and properties that are irreducible to the sum of the powers and properties of the parts. Indeed, Uddyotakara illustrates this idea by noting that “yarn is different from the cloth made from it, since the two have different causal capacities” (p. 107).
He also argues that yarn must be different from the cloth made from it insofar as the former is a cause of the latter (Ibid.). And he distinguishes this cause from the cloth’s “other causes,” such as “the weaver’s loom.” Here we might seem to have an implicit distinction between what Aristotelians call material cause (the yarn) and efficient cause (the weaver’s loom). But Nyāya-Vaiśeṣika speaks of a thing’s “inherence cause” rather than material cause, i.e. that in which the qualities of the composite inhere. And the notion of an inherence cause is broader than that of material cause, since it can include things other than matter (e.g. a location).
Important differences aside, the Nyāya-Vaiśeṣika position, like other anti-reductionist positions in the history of philosophy, converges in key ways with Aristotelian hylemorphism. At the very least, it seems clearly to amount to a kind of non-reductive physicalism, and perhaps even approximates what is today sometimes called “structural hylemorphism” (which differs from traditional Aristotelian-Thomistic hylemorphism by taking parts to exist actually rather than virtually in wholes – thereby, from the A-T perspective, abandoning the unicity of substantial form).
As I argue in chapter 3 of Maintaining a coherent anti-reductionism requires going the whole Aristotelian hog., these varieties of anti-reductionism are ultimately unstable attempts at a middle position between reductionism on the one hand and A-T hylemorphism on the other.