Origins science uses the principles of causality (everything that has a beginning has a cause) and analogy (e.g. we observe that intelligence is needed to generate complex coded information in the present, so we can reasonably assume the same for the past). And because there was no material intelligent designer for life, it is legitimate to invoke a non-material designer for life. Creationists invoke the miraculous only for origins science, and as shown, this does not mean they will invoke it for operational science.

Miracles are an addition to natural laws rather than a loophole within them. This is because natural laws are formulated in isolated systems. For example, Newton’s 1st Law of Motion states that objects will continue in a straight line at a constant speed — if no unbalanced force is acting. But there is nothing in the law to prohibit unbalanced forces acting—otherwise, nothing could ever change direction!
If God exists, there is no truly isolated system. Thus there is no basis for disallowing miracles unless you could prove that God doesn’t exist, but you can’t prove a universal negative. And if Jesus really were God Incarnate as I believe (see documentation), He could certainly bring other forces into play without violating science.
C.S. Lewis applied these concepts to the virginal conception of Christ: that is the zygote was made by the Holy Spirit’s action on Mary’s ovum, i.e. an addition to the system. But after that, the embryo developed in a normal manner.
Second, this comment treats natural laws as real entities. In reality, scientific laws are descriptive of what we observe happening regularly, just as the outline of a map describes the shape of a coastline. Treating scientific laws as prescriptive, i.e. the cause of the observed regularities, is like claiming that the drawing of the map is the cause of the shape of the coastline.
The Bible explains that: we are made in the image of a rational God (Genesis 1:26–27), God is a God of order not of confusion (1 Corinthians 14:33), God gave man dominion over creation (Genesis 1:28), and He commanded honesty (Exodus 20:16). Applying this, as well as a correct understanding of the nature of scientific laws as description, leads to a worldview that historically led to science without jettisoning miracles, as previously stated:
These [founders of modern science], like modern creationists, regarded ‘natural laws’ as descriptions of the way God upholds His creation in a regular and repeatable way (Col. 1:15–17), while miracles are God’s way of upholding His creation in a special way for special reasons. Because creation finished at the end of day 6 (Gen. 2:1–3), creationists following the Bible would expect that God has since mostly worked through ‘natural laws’ except where He has revealed in the Bible that He used a miracle. And since ‘natural laws’ are descriptive, they cannot prescribe what cannot happen, so they cannot rule out miracles. Scientific laws do not cause or forbid anything, any more than the outline of a map causes the shape of the coastline.
C.S. Lewis pointed out that arguing against miracles based on the alleged total uniformity of nature is actually circular reasoning (from Miracles):
No, of course we must agree with the empiricist, David Hume that if there is absolutely ‘uniform experience’ against miracles, in other words, they have never happened, why then they never have. Unfortunately, we know the experience against them to be uniform only if we know that all the reports of them are false. And we know all the reports are false only if we know already that miracles have never occurred. In fact, we are arguing in a circle.
Without a belief that the universe was made by a God of order and that we are made in the image of this God, the Logos, we have no basis for either an orderly universe or that our thoughts can be trusted. Atheists can treat these premises as axioms, i.e. accepted as true without proof, but they are theorems for Christians since they follow from the propositions of Scripture. Indeed, atheists can’t prove that the universe is orderly, because the proofs would have to suppose the order they are trying to prove. Similarly, they can’t prove that their thoughts are rational because the proofs would have to assume this very rationality. Yet evolution would select only for survival advantage, not rationality.
You cannot derive an orderly universe from the proposition ‘God does not exist’. Indeed, you need to accept an orderly universe as a ‘brute fact’, which ironically was actually plagiarized from the Christian world view.
This article has been adapted from an article by Jonathan Sarfati Miracles and Science on the website http://www.creation.com. First published 2/09/2006