Well, if you want to take an original angle, you can blur the distinctions a bit. Check out current research into quantum philosophy and such. The movie "What the Bleep Do We Know" is a good crash course. For a more in-depth look the book the Holographic Universe is interesting. The first two chapters are fairly scientific, the rest is heavily speculative. The problem is that the research the author tries to explain is...questionable, to say the least. But the ideas it presents make it a decent source book for psudoscientific ways to justify just about anything. This has been such a fringe area that only recently has serious scientific work been done on it. A physicist attempting to measure the level of dark energy or whatever in the univers was one of Popular science's top 10 most interesting a few years back. For an interesting look at something fairly rational though only bordering on hard science (and not claiming otherwise) there is the "Global Conciousness Project."

 

link noosphere.princeton.edu/

 

See especially the section linked to from "The Primary Results." For example scroll down to the analysis of the data from September 11 2001. Crazy stuff.

 

Other thoughts on religious war: have you read the Dune books by Frank Herbert?

Here is an idea based on my suggestion above. Intellegent Design advocates in the US end up being extremely successful, and ID becomes the over-riding paradigm in the scientific community. This has two unintended consequences. The first is that when the traditional wall between science and religion is broken down, the big winners are quantum philosophy advocates who provide a scientific rationale for bridging the gap between science and religion. The second consequence is that although the ID advocates want to acknowledge that there is a Designer and stop there, the scientific community insists on going further. Like the hypothetical anthropologist who finds a statue and concludes that it must have been designed, the scientific community looks at the artifact and begins reasoning backward to investigate the nature of the Designer. The inescapable conclusion is that there is no human anatomical system--nervous, endocrine, muscular, skeletal, etc--that exhibits any indication of an absolute and unchanging threshold value. Thus the equally inescapable consclusion is that if the human being is designed the designer could not have held much importance in such things--that the designer was not a designer that had any use for "thou shalt nots."

5) The NoR has a religion which says that dying in combat (for their God) will get them sent to heaven

 

6) The NoS guys have read too much Fukuyama and engage in warfare for the practical reason that humans who don't have anything to fight about lose their humanity

7) . . .etc

 

See, there are lots of reasons why two nations would go to war.  You just have to scrounge around in history a bit.  You can also confuse the issue all you want.

This is an idea I thought of for a conflict in a story, which I am writing. But I do not know how it could start out. How can I make a war between a nation of science between a nation of religion? What should cause the war to begin? Plus how should I make it not similar to Halo? I think Halo deals with Science fighting against religion. The humans use scienctific knowledge as the aliens use religious knowledge. I really want some good advices for my story.

Two possible plot lines:

1)  The Nation of Religion (NoR)  fanatics deside that it is their duty to keep the Nation of Science (NoS) people from going to hell and demand that they convert and submit to being ruled by the priests of the NoR.  When the NoS refuses NoR sleeper cells mount a series of escallating terrorisst attacks to force compliance. [War on Terror]

 

2)  NoR undergoes a schism, splitting into multiple groups which compete to see which group can kill the heretics (i.e. all the other groups).  Conflict results in breakdown of agricultural system and mass starvation.  NoS attempts humanitarian mission, which becomes center of conflict when each group tries to steal relief supplies for itself.  [Somalia]

 

 

fundamentally of course the god-naggers are going to lose the technological high ground,

look at irag-astan at the moment. we kep inventing clever ways to kill the murdering jihadists..

and they keep inventing new jihadists for us to kill