[QUOTE=kowalskil]I still do not know what can be done to eliminate endless conflicts between theists and atheists. But comments collected at several websites prompted me to compose a short online paper at:
http://pages.csam.montclair.edu/~kowalski/theo_sci.html  http://pages.csam.montclair.edu/~kowalski/theo_sci.html
(It seems tome you are confusing the science/religion debate with the atheist/theist debate. Atheists are not necessarily scientists, by any means, and religious people are not t^necessarily theists and so on.)
At first reading, the obvious point that seems to be overlooked is that mathematics and science cooperate happily because science is concerned with improving the quality of prediction of real world events, whereas mathematics has no concern with the real world at all. Therefore the two cannot clash.
Thus Pythagoras' theorem is provable given certain assumptions formalised by Euclid and assuing a 'flat' space. However whether it applies to triangles in the real world, and therefore real world space is flat is something for the scientist to test. If it turns out to be curved, and Riemannian or hyperbolic geometry turn out to produce better predictions, mathematicians are unconcerned.
I've played with the mathematics of abstract spaces in economics, and while one may hope to find one of practical use, the mathematical side is valid (unless I make logical errors) irrespecitive of where scientific 'truth' may lie.
That contrasts strongly with the clash of science and theology, where each of them claims in one way or another to be describing something 'out there' that actually exists or actually happens.
Such a clash  though there's no reason it cannot be a polite one  is therefore frequently associated with the field the scientist works in: a biologist may happily go along with theorlogical views of the origin of the cosmos; a cosmologist may happily go along with religious theories of evolution. In their own fields however they are likely to be more sceptical.
So arguments that science and religion essentially deal with 'different things' are on the whole incorrect: they overlap considerably.
And my initial answers to the three questioons would be:
Is it desirable to end such confrontations?
I'm not sure. It would be desirable to end violent, aggressive and intolerant confrontations, but without them people might not learn to be tolerant.
Is it possible to end them?
Only if one or the other gives up trying to do what it is trying to do. Argument from revealed truths and argument from empirical observation have no meeting ground, merely opposition.
If yes, then how? God knows. Or not as the case may be.
 Citizen of AnkhMorpork.
Never believe anything until it has been officially denied  Sir Humphrey Appleby, 1984.
