presentism and the conflict thesis

Even the most well-founded, well-argued, and well-intentioned ideas about science and religion are liable to later change or eventual rejection. The same is true for historiographical positions, including, of course, the complexity thesis itself.
David Wilson, 'The historiography of science and religion'

Wilson's essay in the Science and Religion collection is certainly more thought-provoking than the previous one, though the view is much the same - that a conflict thesis has operated largely among non-historians, and particularly among scientists, but that historians of science have largely come round to a 'complexity thesis'. Again, though, its many examples point to a complexity of understandings of both science and religion between individuals, and often within particular individuals, particularly in the seventeenth and eighteenth centuries. The fundamental philosophical issues are not discussed.
Having said that, Wilson does highlight some important themes. Particularly pertinent is the issue of 'presentism'. Wilson explains it in contrast to contextualism. I'll provide a lengthy explanatory quote from early in the essay:

Although historians have espoused various approaches to the past, it will make our subject more manageable if we concentrate on the polar opposites around which views have tended to cluster. One approach has been to examine past ideas as much as possible in their own context, without either judging their long-term validity or making the discussion directly relevant to present issues. Another approach has been to study past ideas from the perspective of the present, taking full advantage of the hindsight provided by later knowledge to judge which ideas have proven to be valid. The second approach has apparent advantages. It does not exclude current knowledge that can assist us in the historical task. It also keeps present issues to the fore by insisting that historians draw lessons from the past that are relevant to current issues. However, historians have tended to regard the second approach as precariously likely to lead to distortion of the past in the service of present concerns. Dismissing this as 'presentism', therefore, historians of science have come to favor the first, or contextualist, approach.

 Presentism isn't a term I've heard before, but the problem is familiar enough. we find it in fiction too, of course, when we find modern writers of historical romances getting not just the tone but the whole seventeenth century context wrong - sometimes deliberately. Or we have new dramatic interpretations of such perennial faves as Jane Austen which 'tease out' feminist undertones claimed to be found in the original. It raises the obvious question of whether we can ever really recapture the context of the times [I think of Borges' character writing an exact replica of Don Quixote which critics find disturbingly other than the previous version]. Here, though, the distortions of presentism are said to feed into a progressivist view of science and knowledge, what historian Herbert Butterfield called 'the whig interpretation of history' [he published a book with this title in 1931]. 

Were I a historian, I would heed the warnings, while also recognising, for example, that the rigorous exclusion of non-natural explanations in the sciences [meaning, essentially, a tightening of the definition of scientific praxis] has been a great boon in the advancement of knowledge over the past few hundred years, an advancement that has been truly sensational. We should indeed guard against what Maurice Mandelbaum called 'the retrospective fallacy', in which we lose sight of the groping, uncertain nature of the past as it was lived for those who felt it as present and future. For that would be to destroy empathy and to judge harshly. Many great past scientists 'transcended' their times, but only to a limited extent, and to see them as our contemporaries would be to do them a great disservice. Sometimes, in reading them or reading about them, we wish we could free them from the context of their times and show them how times have changed, partly as a result of their own achievements. That's only human, but it's fantasy, after all. 

So, it's true that the earliest practitioners of what we 'retrospectively' call modern science were not atheists, secret or otherwise, and that they were seeking to comprehend the glory of their god's creation, but I'm not so sure that it's a 'presentist' distortion to point out that they were, in fact, contributing to a loosening of the grip of theology and religion upon our modern understanding of how the world works, to a degree that, a few hundred years later, that grip is but a memory trace in the collective scientific consciousness. Or is that going a bit too far? 

Again the point I'm making is that there's plenty of complexity in the relations between and among scientists and believers, but science and religion have ceased to mix sociably since science has refused to, or forgotten to, keep to its circumscribed territory, and has shrugged off its dress-up as some deity's hand-maiden.