Science, particularly the physical sciences, can be thought of as a search for causes. We want to understand how things work, the interactions and interdependencies between events so we can better understand and predict our world.
When some particular behavior or event (effect) is observed there’s an implicit assumption it was caused. We call this the Law of Causality (Cause and Effect); it’s so fundamental to the rational mind that violating it is absurd. It’s not only true — it’s formally true by definition: an effect is by definition something caused.
However, as we pursue probable causes to find an initial root cause, especially when examining historical events which we cannot replicate, we inevitably go back in time until we reach an event or state where there seems to be no possible natural cause: we then deduce that there must be an uncaused Cause. We call this observation the Kalam Cosmological Argument; it is formal proof of God’s existence.
One need not go all the way back to the beginning of Creation to find God causing effects: God has continued acting since Creation. (Jn5:17) While we should not presume God is the cause when we don’t yet understand how something works (God of the Gaps logical fallacy), we should be willing to acknowledge God as the Cause (a miracle) when this is implied by science itself: when any other probable cause violates scientific law.
Certainly, if we conclude a miracle has indeed occurred, we might later develop further scientific understanding and be able to explain it naturally, but this does not mean concluding an event is miraculous is unscientific any more than if we provide a plausible naturalistic explanation which later turns out to be false. In either case, we are being reasonable and honest based on our current understanding of science.
For example, a personal friend was shot in the chest multiple times at point blank range and survived. In analyzing his wounds, the attending surgeon found multiple instances where a bullet track terminated at the surface of a vital organ and the organ was undamaged; there was no bullet anywhere in the track, nor any alternate route found where the bullet might have exited the body. How does one explain the cause of such an event?
We may deduce the following: either [1] the surgeon lied (or was careless in his examination, which seems unlikely given his expertise, character and willingness to document and testify of the result – the x-rays are still available), [2] bullets ricocheted off vital organs and exited the body through the same path they entered (violating the physics of bullets fired at bodily organs), [3] the bullets vanished (violating the Law of Conservation Energy), or [4] this is a miracle.
Once we eliminate [1] by having multiple, authoritative witnesses interview the surgeon and examine the x-rays (which should be done with rigor, given the significance of the event), we must either conclude the laws of physics have been violated or accept this event as a miracle. (Jn 3:2)
Refusing to acknowledge the miraculous based on an a priori presumption of Philosophical Materialism is dishonest and irrational (Jn 12:37-38); it is simply a stubborn, willful refusal to acknowledge evidence, which is unscientific. Such bias will eventually be exposed as enmity against God by God Himself and punished accordingly. (Ro 1:18-21)
Yet a better question may be whether our desire to see a miracle or a sign from God is healthy and appropriate. God certainly does them from time to time, so there’s evidently good purpose in them when they occur, but is it ever right to ask God to perform a miracle or a sign to help us with our faith? or to be seeking signs and wonders, pursuing the miraculous as a manner of life?