The rising tide of religious maximalism has set in motion a new wave of religious minimalism. Maximalists (aka fundamentalists) insist on bringing their holy books and their faith into the public realm. Minimalists (aka secularists) not only insist on keeping organised religion outside the affairs of the state, they are also beginning to insist on a rational examination of the content of religious dogmas themselves. In the words of philosopher Daniel Dennett, the prime mover in American atheism, time has come to "break the spell" of the supernatural and to embark upon a "forthright, scientific, no-holds-barred investigation of religion as one natural phenomenon among many."

Such a new atheist movement is most welcome and, particularly in America where I live, much needed. The de-godification of the public sphere is not sustainable in the long term without a de-godification of our mental and emotional landscape. As we have seen through the two Bush administrations, the public sphere shrivels when faith drives politics. Secular politics requires respect for evidence and critical thinking, applied across the board, not excluding faith itself.

But as secularists have begun to take on religion there is a danger that in calling for a rigorous evidence-based examination of one area they leave other areas untouched. In banishing religion from the front door some of these secularists are happily letting other forms of supernatural thinking in through the back.

Countless sociological studies have revealed the growth of a holistic milieu in western societies where many varieties of do-it-yourself spirituality and esoteric practice (belief in reincarnation and astrology, yoga, transcendental meditation, "vibration therapies") are flourishing. The attitude of most rationalists on matters of spiritualism has usually been of benign neglect, or even indulgence. It all appears so harmless and it might even have some positive contributions to make to one's health and tranquility of mind. Attacks by feminists, environmentalists and others on the sins of "reductionist western science" have created a positive aura around 'holistic science' which, it is claimed, overcomes the gap between the subject and the object. It is easy to debunk faith. Faith is by definition a relationship of trust regardless of evidence. Spiritualism has learned to dress up its metaphysical abstractions in the clothes of empiricism, neuro-physiology and quantum physics. In contrast to the obvious irrationality of believing in an all-powerful, all-knowing invisible being, belief in 'spiritual energies' which can be 'directly experienced' by anyone simply by altering the state of their consciousness can appear so much more rational, even 'scientific'.

The problem is that rather than subjecting this mystical realm to the same rigourous analysis as that of religion, the new atheism seems convinced by it's pseudo-scientific claims, and even acts as a cheerleader for this spurious way of thinking. The holistic world view trades on three core misconceptions. First, that mysticism is a rational alternative to faith and somehow consonant with the scientific method and theories of mind and matter. Second that mystical experience can lead to 'direct experience' of the spiritual substance that underlies the visible material world. Third, spiritual practices lead to peace and harmony. By merging your soul with the "world soul", you are supposed to develop a sense of kindred-ness with all beings big and small, and be less inclined to hurt them.

This thinking has cast its spell even on those who profess to be militantly rationalist and atheist. The hardcore of the new atheists are distinctly soft on holism. A case in point is Sam Harris, the author of The End of Faith, widely celebrated in America these days as a fearless iconoclast and an uncompromising rationalist. Harris's Pen Award winning best-seller gleaned approving endorsements from the likes of the New York Times and The Economist, and from prominent atheists like Richard Dawkins (whose quote "Read Sam Harris and wake up" adorns the book jacket). Harris, now a columnist for Free Inquiry, America's most prominent secularist journal, is the young, reliably militant pin-up for rationalism.

Yet Harris declares "the end of faith" only to celebrate the beginning of a new age of spirituality. That such a prominent rationalist is prepared to reclaim spiritualism in the name of science matters. When spiritualism, or mysticism, claims the status of rational knowledge or science, it ends up transforming what is essentially an ecstatic emotional experience into a knowledge claim about the nature of reality. These issues are not just theoretical. In countries like India, where spiritualism enjoys the blessings of the highest religious authorities, metaphysical beliefs that follow from mystical experiences exert a great deal of social influence. While India has a fairly large and advanced scientific workforce, science has not succeeded in displacing the authority of metaphysical truths from the cultural sphere. An idealistic, spirit-centered metaphysics continues to structure the worldview of ordinary people, while intuitive and certain knowledge of the 'absolute truth' of 'pure consciousness' is still the culturally hegemonic paradigm of knowledge and truth.

Moreover, the notion that such knowledge is rational and scientific is routinely used by Hindu nationalists to assert the superiority of Hinduism over Islam and Christianity, which they condemn as being superstitious in terms not dissimilar to those used by Harris. A rationalist endorsement of mysticism could have dire consequences for the development of a rational scepticism adequate to the challenge of fundamentalism.

The End of Faith is a rationalist jihad on jihadi theology. Disturbed by the rise of religious violence around the world, especially the 9/11 attacks on America, Harris has taken on the traditional theological beliefs about God and afterlife that motivate some to kill innocents. Brushing aside political and historical factors that have contributed to religious extremism, Harris singles out theological beliefs as the primary and pretty much the sole cause of religious violence. He saves most of his venom for the Koran, condemning it as intrinsically violent and intolerant, a manual of war. The problem is not extremism, but the religion itself. In short, it's the theology stupid!

Throughout Harris can barely curb his enthusiasm for George Bush's "war on terror", announcing gleefully that "we are at war against Islam" – not at war against violent extremists, mind you, but against the very "vision of life prescribed to all Muslims in the Koran." He finds tortured justifications for torturing suspected terrorists in America's gulag. He goes further: "some propositions are so dangerous that it may even be ethical to kill people for believing them.... Certain beliefs place their adherents beyond the reach of every peaceful means of persuasion, while inspiring them to commit acts of extraordinary violence against others."

While he has some harsh things to say about Christians and Jews as well, he spares them the wars and the torture, for unlike the Muslim barbarians, they have had their reformations and their enlightenments.

But this bilious attack on faith – the aspect of the book which has received all the attention – only sets the stage for what seems to be his real goal: a defense, nay, a celebration of Harris' own Dzogchen Buddhist and Advaita Vedantic Hindu spirituality. Spirituality is the answer to Islam's and Christianity's superstitions and wars, he tells us. Spiritualism is not just good for your soul, it is good for your mind as well: it can make you "happy, peaceful and even wise". Results of spiritual practices are "genuinely desirable [for they are] not just emotional but cognitive and conceptual".

Harris describes the mystical experience as tuning, or focusing, the mind through meditation, fasting, chanting, sensory deprivation or psychotropic drugs, that enables it to overcome, or dissolve, the sense of the self that stands separate from the objects of its consciousness. The goal is to "experience the world perfectly shorn of self… to lose the subject/object perception… to continue to experience the world, but without the feeling that there is a knower standing apart form the known. Thoughts may arise, but the feeling that one is a thinker of these thoughts vanishes." Harris is describing the classic all-is-one and one-is-all experience that mystics and spiritualists have reported throughout history.

I would have no argument with Harris if he were only recommending spiritualism as means for mindful relaxation. Indeed many wise mystics have realised that the mystical experience does not confer existential status on its content but can be enjoyed and valued for the experience itself. Unfortunately Harris loads spiritual practices with metaphysical baggage. While he tries to distance himself from the more extravagant fads, he ends up endorsing fundamental New Age assumptions as rational alternatives to traditional religiosity.

He celebrates the growing popularity of western and eastern occult traditions, everything from "shamanism, Gnosticism, Kabbalah, Hermetism and its magical Renaissance spawn (Hermeticism) and all the other Byzantine paths whereby man has sought the Other in every guise of its conception." He rejects a naturalistic understanding of nature and the human mind and sets consciousness free from such mortal things as brains and bodies, allowing the possibility of pan-psychism, the doctrine of immanence of awareness or consciousness throughout the universe. For someone studying to be a neuroscientist, Harris holds rather unconventional views. He scoffs at the physicalism of the mainstream of scientists who believe that our mental and spiritual lives are wholly dependent upon the workings of the brain. He gives full credence to reports of near death experience and leaves open the possibility that a disembodied soul can survive the death of the body, claiming that we don't know what happens after death. After denying that consciousness is a product of our physiology, he presents it as a fundamental ingredient of nature, "a far more rudimentary phenomenon than living creatures and their brains." This is nothing but good old spiritual monism, the first principle of all New Age beliefs. The problem is not that Harris holds these beliefs, but that he wants to convince us that they are the very height of rationality.

Harris believes that spiritual experiences are knowledge experiences which can "uncover genuine facts about the world". He buys into the basic idea that what mystics "see" in their minds actually has an ontological referent in the world outside their minds. Or to put it in the vocabulary he prefers, when the gap between the subject and object vanishes, "pure"awareness of one's subjectivity can tell us something about the objective reality.

In all this Harris falls in to the trap that William James described in The Varieties of Religious Experience: "Mystical states seem to those who experience them to be also states of knowledge… as a rule, they carry with them a curious sense of authority." James goes on to dismiss claims that such experiences can be thought of as revealing objective or verifiable truth: "mystical states… are absolutely authoritative over the individuals to whom they come. But mystics have no right to claim that we ought to accept the deliverance of their peculiar experiences…. Non-mystics are under no obligation to acknowledge in mystical states a superior authority."

Meditative experiences can bring about a feeling of having touched something far deeper and more vivid than what is normally experienced by the five senses. This conviction itself becomes a source of validation of the objective reality of what they have seen: what they see in their minds, they assume, must exist outside. Vision gets fixed into metaphysical systems built on super-sensory entities and processes. The experience of losing the boundaries of one's ego, the feeling of having transcended time and space, gives the feeling of becoming one with the universe.

Neurosciences are revealing the biological grounds for why mystical experiences feel as if they are actually uncovering genuine facts about the world. Andrew Newberg and Eugene D'Aquili, in Why God Will Not Go Away, offer a clue. They believe that the ontological fallacy stems from the process of reification – "the ability of the brain to convert a concept into a concrete thing, or more succinctly, to bestow upon something the quality of being real or true. Reification refers to the power of the mind to grant meaning and substance to its own perceptions." On this account, meditative practices slow down the transmission of neural information to the posterior superior parietal lobes of the brain, which controls spatial orientation, resulting in the sensation of pure awareness which is incapable of drawing boundaries between the limited personal self and the external material world.

What neurosciences seem to be telling us is that while the neurological processes that give rise to mystical experiences are real, they prove nothing about the ultimate nature of reality or God. Just because we can study the neuro-physiology of mysticism in a scientific manner, does not make the experience scientific or rational in any way. (We can study schizophrenia in a scientific manner, but that does not mean that schizophrenics are rational). Harris argues that there is an analogy here with scientific consensus, but this is untenable. In science (Thomas Kuhn notwithstanding) anyone with functioning senses, adequate training and right apparatus can see the same star, the same DNA molecule, the same electron. But not everyone with adequate training in meditation techniques, and the right atmosphere, sees the same mystical reality: some see God, some see nothing at all and some, without any meditation at all, see what the mystics see. The mystical beliefs which Harris so approves of are every bit as unscientific, untestable and unverifiable as the religious belief he so aggressively attacks.

Harris's effort to keep religious and mystical belief separate really comes unstuck in relation to the issue of violence. He trots out the widely shared view that Abrahamic faiths encourage violence against man and nature, while eastern spirituality promotes peace and harmony with fellow creatures.

At the root of all wars, Harris tells us, lies the separateness, or the dualism, between human beings, between the 'I' and the non 'I': "Every problem we have can be ascribed to the fact that human beings are utterly beguiled by their feeling of separateness". He ascribes this to the Abrahamic tradition itself which has demanded faith in a God who remains separate from his creation. The more ordinary people can divest themselves of the feeling they call 'I', he tells us, the more they feel themselves connected to the universe, the less they will have the feelings of fear and anger. Love and compassion will follow.

Even if one were to play along with Harris's badly flawed, theology-centered diagnosis of religious extremism, it is simply not true that spiritual, non-dualistic eastern religions are free from violence. Violence and authoritarianism run deep in societies which worship at the altar of 'one-ness.' Harris, who is so alert to the 'inherent' violence of the Koran, is completely blind to the religious sources of violence in the 'spiritual east'.

The Jains of India may not be committing acts of suicide bombings, as Harris reminds us repeatedly, but can one honestly say that Jains and pious Hindus have shown any 'one-ness' with the Muslims, Christians and other religious minorities in India? Has their Hinduism prevented Tamil Tigers from conducting suicide bombings against the equally 'spiritual' Buddhists of Sri Lanka or the Buddhists from discriminating against the Tamils? Didn't Zen Buddhists actively and enthusiastically support Japan's ultra-nationalism in the brutal imperialist wars against China and Korea? There is a complex history of nationalism, spiritualism and violence behind each one of these historical episodes.

Harris appears oblivious to the authoritarian implications of the one-ness he worships. Shedding one's 'I-ness' is a recipe for group-think and authoritarianism. The individual in her everyday life is treated as an illusion of no consequence when seen from the mystical highground of one-ness. Of course the Gnostic vision of one-ness is not supposed to be available to all. The enlightened have always constituted a spiritual aristocracy in deeply unequal Eastern societies. When one-ness is made into the highest religious ideal you get the 'holism' of caste society.

I grew up as an observant Hindu. My experience of the deep connections between Hindu metaphysics and Hindu nationalist politics underpins my scepticism and naturalistic world view. All knowledge claims should be subjected to an equally rigorous test of reason and evidence. To launch a stinging attack on certain forms of irrational belief, while seeking spiritual shelter elsewhere, is to sell out the rigourous materialist ideals which underpin science and are a vital weapon in the profoundly political battle against ignorance and violence.

Meera Nanda is a philosopher of science and author of Breaking the Spell of Dharma and Prophets Facing Backwards