The recent Gifford lecture series here in Edinburgh by Peter Harrison back in February is now online (mostly).
It totals about 6 hours and is certainly not easy, but it provides an in depth review of the development of post-Enlightenment/Reformation thought on the development of 'science' and 'religion' as categories and so explores a lot of the origins of today's perceived contradictions between these two areas of study.
The level and depth of them won't be every ones natural cup of tea but they are well worth the investment of time and energy needed to take them in.
Summary of lectures
March 10, 2014
19 hours ago