Just when I think I’m pretty smart, I go to the evangelical outpost and read one of Joe’s postings, like this three part series on Christian theory making – here’s the links.
What can we learn from Joe’s waxing? 

1. Religious beliefs and other suppositions most certainly are part of theory making, in all disciplines of knowledge, including math and science

For each of these four philosophers what was considered to be divine (“just there”) had a significant impact on how they answered the questions about the nature of the simple equation. For Leibnitz it was mathematical abstractions; for Russell it was logic; for Mill is was sensations; and for Dewey it was the physical/biological world. On the surface we might be able to claim that all four men understood the equation in the same way. But as we moved deeper we found their religious beliefs radically altered the conceptual understanding of 1 + 1 = 2.

2. The argument that religious suppositions are disallowed in theory making is foolish, arrogant, and wrong, because all theories must eventually find ground in assumptions about the Ultimate.  Even if that belief is atheistic, it is just that – a BELIEF

A belief is a religious belief, says Clouser, provided that (1) It is a belief in something(s) or other as divine, or (2) It is a belief concerning how humans come to stand in relation to the divine. The divine, according to Clouser, is whatever is “just there.” Whether we refer to it as being self-existent, uncaused, radically independent, etc., it is the point beyond which nothing else can be reduced. Unless we posit an infinite regress of dependent existences, we must ultimately arrive at an entity that fits the criteria for the divine.

Different traditions, religions, and belief systems may disagree about what or who has divine status, but they all agree that something has such a status. A theist, for instance, will say that the divine is God while a materialist will claim that matter is what fills the category of divine. Therefore, if we examine our concepts in enough detail, we discover that at a deeper level we’re not agreeing on what the object is that we’re talking about. Our explanations and theories about things will vary depending on what is presupposed as the ultimate explainer. And the ultimate explainer can only be the reality that has divine status.

3. Most of the outlooks that exclude God and limit our knowledge may be categorized as "reductionist", and end up being discredited

Examine any theory from the social or natural sciences that were later discredited and you will find a common thread: they all reduce at least one aspect of reality to another and treat one aspect as primary. The problem with this, as philosopher Roy Clouser notes, is that it assigns some part of creation the role of lawgiver to creation. Because the non-theists denies a role for a self-existent creator and sustainer, they must invoke some aspect of creation to perform those essential functions.

What all of the explanations have in common, what all non-theistic views share, is a tendency to produce theories that are “reductionist” — the theory claims to have found the part of the world that everything else is either identical with or depends on. This is why the Christian view on math, science, and everything else must ultimately differ from theories predicated on other religious beliefs.

4. Christian theory making is as good or superior to atheistic, naturalistic theory making because it does not deify created objects which can not really be considered deity.

But Christians – members of the true “reality-based community” – have the ability to set the theories aright. Unlike the reductionists, we do not “deify” nature and so are not forced to deny some essential aspect of the natural world. We have the freedom to produce robust and coherent theories about the natural realm because we are not forced to square circles.