The scientific community can be bifurcated into regenerate and non-regenerate scientists. Regenerate scientists have put their faith and trust in the Lord Jesus Christ, while non-regenerate scientists have not. Any attempt to reconcile the worldviews of both groups is folly. The regenerate biblical scientist has access to three levels of knowledge: inherent, learned, and divine. The third being available through the indwelling of the Holy Spirit. The indwelling of the Holy Spirit gives the regenerate scientist an advantage that can and should be used to understand God's creation more fully. It is important for the regenerate creation science community to develop methodologies for and become proficient in incorporating miracles into their scientific studies. This paper proposes biblically-based scientific philosophies as well as providing suggested mechanisms for the development of a bible-based scientific model for the four major scientific communities (astronomy, biology, geology, and physics). It also gives specific examples of how miracles can and should be an integral part of creation science. A functional approach to science is introduced that can be used to integrate these various methods. The purpose of this paper is to encourage regenerate creation scientists to evaluate their scientific philosophical paradigm.