All of this is true but completely misses the point. We're talking about starting with an effect and extrapolating back to the original cause. This is where miracles really throw a monkey wrench into things. We look at the current evidence and then from there retrace the natural steps (processes) as they would have gone according to their natural way.
Here's a simple example.
When we look at bullet holes, we can determine from those holes the trajectory of the shot. But if the bullet was deflected supernaturally, and was caused to change direction, science would be ineffective in detecting this merely from the hole. Only testimonial evidence could tell of a miracle in which a shooter aiming in one direction was thwarted by some supernatural force. The scientist with purely naturalistic presuppositions would be unable to discover the reality in this situation. He would conclude from the physical evidence that a shot was fired from a particular direction. Yes he would see the effect of the miracle, but misinterpret the details about it.
The same holds true when science attempts to determine the duration of events. If a bullet is fired from say 1000 feet away and becomes embedded into a wall, scientists can tell by the depth of the penetration how far back the shot was fired from, how long it traveled, etc.. A shot closer up would naturally penetrate deeper. But if a supernatural force slowed the bullet down from a close range shot before it struck the wall, the scientists observing the effect (the hole from the bullet) would come to wrong conclusions about the distance and time the bullet traveled. They would see the effect, but misinterpret it.
This is why the concept of
methodological naturalism is so essential to science. Science must always assume before investigation even starts that natural processes were working normally. There is no possible way around it.
So yes, miracles have effects, and yes we can observe them. We just can't interpret them properly using science alone. The example I gave was just a single simple supernatural intervention of a bullet. Imagine all the confusion all the interventions listed in Genesis 1 would cause! It boggles the mind. Imagine how much confusion the interventions in the Flood account would cause. Sure we see the affects of the Flood, but the naturalist must compare those to the effects of natural floods we observe today. We really have no idea what mechanisms God used to start it, sustain it and end it. We just know God did it! Creationists have come up with quite a few
models, but these include the biblical testimonial data, which includes supernatural interventions. Naturalists don't like this and cry foul. But the real foul is a bias in presuppositions.
So for someone to ask me to reinterpret Genesis because science demands it is quite irrational in my view. The explicit and implicit miracles of the creation account are vast in both number and scope. God created a fully functioning world instantaneously for all practical purposes. It doesnt surprise me in the least that scientists, without biblical presuppositions, are so confused.