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He gave many invited lectures including the Wilde (University of Oxford), Riddell Newcastle University, Boutwood University of Cambridge, Scott Holland University of London, Bicentary Georgetown University.
He served on various commissions including the Archbishops' Commission on Doctrine (1977-86). He was appointed Vice-President of the Institute on Religion in an Age of Science in 1980.
Bowker has written and edited many books on world religions. He has also taken a deep interest in science and religion and in particular the relationship of biology and psychology to religion.
In 1983 he edited Violence and Aggression and 1987 he wrote Licenced Insanities: religions and belief in God in the contemporary world.
In 1992 and 1993 he gave lectures at Gresham College analysing in detail the claim by Richard Dawkins that belief in God was a kind of mental virus. In the scientific parts he collaborated with Quinton Deeley, a student of his whose dissertation on biogenetic structuralism led to his deciding to re-train as a doctor and is now a published psychiatrist. He suggests that this "account of religious motivation . . . is . . . far removed from evidence and data." and that, even if the God-meme approach were valid , "it does not give rise to one set of consequences . . . Out of the many behaviours it produces, why are we required to isolate only those that might be regarded as diseased? And who . . . decides, and on what grounds, what is diseased? . . . there is nothing here as objective as the observation of chicken-pox . . . the observer . . . is highly relative".
In his 2005 book The Sacred Neuron: The Extraordinary New Discoveries Linking Science and Religion he suggests that it is incorrect to view faith and reason as opposing functions. he argues that recent discoveries in the neurosciences are revealing startling facts about the workings of the human mind and how certain ideas are processed into beliefs. His publishers assert that "John Bowker shows that faith and belief are not separate or distinct from reason, but are actually rooted in it. And science—especially neurophysiology—is the key to unlocking how we think about God, about the relationship between different cultures and religions, and about the processes of the human mind that influence our behavior. When rationality and faith are viewed as complementary a new understanding of the human mind can serve as a basis for resolving conflicts between religions and cultures. This discovery has stunning implications for the world."Palgrave MacMillan description
His most recent book Conflict and Reconciliation: The Contribution of Religions (Coming Fall 2008) is unique in supplying the material and resources in the great religions of the word which could be brought to bear on the pursuit of peace and reconciliation after a conflict. Other books including this one point out the extent to which religions are involved in conflicts, but this book alone shows the ways in which religions are under obligation to seek peace.
The Targums and Rabbinic Literature: an Introduction to Jewish Interpretations of Scripture,
Cambridge (Cambridge University Press), 1969 (2nd edn. 1979).
Problems of Suffering in Religions of the World, Cambridge, (Cambridge University Press),
1970 (2nd edn., 1975; 3rd edn., 1990).
Jesus and the Pharisees, Cambridge (Cambridge University Press), 1973.
Uncle Bolpenny Tries Things Out, London (Faber and Faber), 1973.
The Sense of God: Sociological, Anthropological and Psychological Approaches to the Origin of
the Sense of God, Oxford (Oxford University Press), 1973 (2nd edn., with new Introduction, Oxford (One World), 1995).
The Religious Imagination and the Sense of God, Oxford (Oxford University Press), 1978.
Worlds of Faith: Religious Belief and Practice in Britain Today, London (Ariel Press), 1983.
Ed. with Introduction, The Origins, Functions and Management of Aggression in Biocultural Evolution, Zygon, Florida (Winter Park), 1983.
Licensed Insanities? Religions and Belief in God in the Contemporary World, London (DLT),
1987; US edn.
Is Anybody Out There?, Westminster (Christian Classics), 1988.
The Meanings of Death, Cambridge (Cambridge University Press), 1991 (awarded the biennial Harper-Collins Prize for the best book in the academic section).
A Year to Live, London (SPCK), 1991.
Hallowed Ground: Religions and the Poetry of Place, London (SPCK), 1993.
Joint editor (with Jean Holm), Themes in Religious Studies (10 volumes on different themes), London (Pinter), 1994.
Is God a Virus? Genes, Culture and Religion, London (SPCK), 1995.
Voices of Islam, Oxford (One World), 1995.
What Muslims Believe, Oxford (One World), 1998.
‘A’ For Ethics: An Alphabet of Action, Philadelphia (University of Pennsylvania), 1996.
The Oxford Dictionary of World Religions, Oxford (Oxford University Press), 1997 (2nd revised edn., 1999).
World Religions, London (Dorling Kindersley), 1997 (2nd revised edition, 2003).
The Concise Oxford Dictionary of Religions, Oxford (Oxford University Press), 2000.
The Complete Bible Handbook, London (Dorling Kindersley), 1998 (Benjamin Franklin Award, 1999).
The Cambridge Illustrated History of Religions, Cambridge (Cambridge University Press), 2002.
God: A Brief History, New York (Dorling Kindersley), 2002.
The Sacred Neuron, London (I.B. Tauris), 2005.
Beliefs That Changed the World, London, (Quercus), 2007.
Aerial Atlas of The Holy Land: Discover the Great Sites of History from the Air, London (Mitchell Beazley), 2008.
Knowing the Unknowable: Science and Religions on God and the Universe, London (I.B.Tauris), 2008.