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Prof. Ninan was born in Kozhencheri, Kerala, India in a Syrian Christian Family which claims descent from one of the four families to whom St.Thomas the apostle of Jesus entrusted the gospel. His father Late.M.M.Mammen, was a publisher Freedom fighter and Christian Reformer. His eldest Brother is the well known theologian Late Dr.M.M.Thomas, who was the Chairman of the World Council of Churches, the Governor of Nagaland, India and the Chairman of the Christian Institute of Study of Society and Religion. He belongs to the Malankara Mar Thoma Church, a reformed church holding the theology of the Eastern Churches which claims a 2000 year old heritage.
He is by profession a Professor of Theoretical Physics and had been a teacher in various universities around world including Ethiopia, Ghana, Jamaica, Sudan, Yemen, India and United States of America. He retired as the President of the Hindustan Academy of Engineering and Applied Sciences, Affiliated to University of Bangalore, India
He was the first Moderator of the International Christian Fellowship, Sanaa, Yemen and the Co-founder, Sudan Pentecostal Church. He has published several studies on the influence of Christianity in the formation of Hindu religion and religious scriptures.