1. What do you mean by 'selection factor'? I stand by my point.
If two sides are fighting for control of land, it doesn't matter whether they are seperated by religion, skin colour, or whether they are wearing a green or a purple scarf (a cookie for anyone who gets the reference), the issue they are fighting over is land, not anything else.
Carrying on with the Northern Irish example, you have the Catholics, who originated in Ireland and Northern Ireland, and the Protestants who came over from the rest of the UK. They aren't arguing over religion, they are arguing over land, religion is just a convienent seperation factor because it roughly divides the two sides. it is not, and never has been, a religious conflict.
2. Stalin's genocide was not caused by his atheism. Just because he was an atheist does not mean you can hold it up as a shining example of atheist extremism when it quite clearly was not.
And neither are most of the other wars you wish to claim have religious ties. Just because someone, or indeed a group of people, have different beliefs, does not mean they are fighting because of those beliefs. It's a double standard, either Stalin was an atheist extremist (because one of the selection factors he used was religion), or the wars seperated by religion but fundamentally about other issue are not religious. There is no way you can have your cake and eat it with this one.
3. What are these assumptions of scientific method? Nothing in science can be proven 100%. In a few hundred years, todays theories will probably seem laughable and outdated; however, we still see the benefits of them every single day and will continue. There will also be a well documented paper-trail showing how and why scientists believe the things they do.
How early do you want me to start with the assumptions?
Time moves forward
An effect always has a repeatable cause
An effect is always repeatable.
The simplest explaination is the most useful
Our observations are meaningful
Our observations are universe accurate, not just perception accurate
The universe behaves consistantly
Those are the obvious ones. If you wish to take science as being absolute, you then have to add a few more.
Absence of scientific evidence is equivilent to evidence of absence.
The simplest explaination is the correct one.
All of these assumptions make perfect sense in the context in which the scientific method was designed to operate, namely as a predictive and quasi-descriptive modelling approach to the universe. As a philosophy, they are all as unprovable as "in the beginning there was god", and no more valid.