For most of its history, atheistic materialism has gone about its business with a rather aggressive macho swagger. When Leucippus and Democritus invented the idea of atomism in the fifth century BCE, they seem to have spent more time ridiculing the idea that the world is governed by gods and providential purposes than constructing a positive natural science based on the motions of tiny inanimate particles. And their follower Epicurus made his reputation by inviting the students who gathered in his beautiful Athens garden to sneer at the multitude with their empty and ignorant superstitions.

Two thousand years later, when Galileo, Descartes and Newton started to deliver on the scientific promise of atomism, the smug and raucous tone made itself heard once again. If the human body was simply an automatic machine controlled by the brain, it was easy for radical materialists like La Mettrie to conclude that traditional notions of morality and free will were nothing but a warm blanket of rhetoric concealing the harsh and uncomfortable truth: that we are nothing but a fleeting infestation on the surface of a medium-sized planet, signifying nothing.

Seen in this perspective, the publication of Darwin's On the Origin of Species in 1859 marked not so much the end of an agreeable old form of theism as the beginning of an agreeable new form of atheism. Naturalism after Darwin was no longer intent on dissing our fondest hopes; instead it promised to provide them with a new foundation. Compared with our 'allies' amongst the primates, as Darwin put it, we had as a species "undergone an extraordinary amount of modification". Our big brains might be mere by-products of natural selection, but we could take pride in them nevertheless.

It took a long time for Darwin's cheerful message to get through. When EO Wilson's Sociobiology came out in 1975, there were still plenty of self-styled 'humanists' who regarded the idea that society has biological roots as an outrage against the pieties of progressive thought.

Luckily those days are now past, and in this attractive and informative new book the Yale psychologist Paul Bloom brings us up to date on the many graces of human existence that can now be explained, at least approximately, in evolutionary terms. Descartes, as Bloom recalls, believed that we are all born with a kind of complimentary starter pack, a little kit of 'innate ideas' to aid us in our first attempts at making sense of the world. Descartes' Baby summarises masses of experimental evidence to prove that our innate endowments are far more extensive than Descartes ever dreamed.

Few would now deny Noam Chomsky's claim that we are all born with some kind of 'language organ' – a faculty which, while it does not give us knowledge of any particular language, enables us to analyse the languages we are exposed to in infancy and learn them in what would otherwise be an unbelievably short space of time.

If Bloom is right, then recent research suggests that Chomsky's argument needs to be taken much further. We are, in the first place, innately scientific, not in the sense of being born with specific scientific knowledge, but because even as tiny babies we presume that physical things have a relatively stable 'essence', which accounts for their outwardly observable changes in behaviour. In addition, we are all born with a capacity for 'empathy' which, when generalised by the powers of reasoning that we naturally develop as adults, will lead us to develop a sense of moral responsibility not only for our closest kin but for the human race as a whole. Hence there are, according to Bloom, good biological reasons for believing in moral progress, and for being 'morally optimistic materialists'.

Bloom's grandest claim is also his most paradoxical. The evidence he presents suggests that we have an innate tendency to divide the world into two domains: bodies and souls. We are 'natural born dualists', and it is not surprising that so many of us have ended up believing in disembodied spirits and the possibility of surviving our bodily deaths. But the biases and prejudices of our natural constitutions are not always justified, and we can sometimes correct them by making use of our equally innate capacity to reason.

It is not always easy, of course: Bloom acknowledges that, however rational we are, we may still be reluctant to eat a sweet that has been moulded to look like a dog-turd. He also recounts an experiment in which atheists were invited to sign a contract selling their soul to the Devil, and many of them refused. Not all of them however: reason can sometimes prevail, as Bloom hopes it will in the case of a biologically-based science of consciousness.

There is one notable gap in this remarkably comprehensive tour of the natural science of humanity. Bloom passes over the fact that our reasoning capacities can scarcely be exercised in social isolation – that they cannot function properly unless they are integrated into communities of language and reason that transcend us, and that allow each generation to take advantage of the wisdom of its predecessors.

One of the remarkable things about human beings (and certain primates too) is that we can benefit from the fruits not only of biological evolution but of cultural accumulation too. Without access to such historically evolving traditions, Descartes's babies may flourish, but they will never grow up.