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Scientific ideas ideally progress through from hypothesis to theory. A hypothesis is a possible explanation for some observed phenomena. Its most important feature is that it makes testable predictions. If those predictions are validated through repeated experiment...
...the hypothesis eventually graduates to theory.

The word "theory" confuses a lot of people, because it's used in a multitude of ways.* Most commonly, it's used to express an untested, unverified idea someone's come up with to explain something he's observed.
e.g. "I have this theory that mice are actually superintelligent and are performing experiments on US." Obviously, that's just a wild idea that hasn't been scientifically tested. That's not at all what scientists mean by the word "theory," and is much more like a hypothesis.
In science, a theory is a scientific explanation for natural phenomena that has been thoroughly tested and verified. That part is REALLY important. A good example would be Einstein's general theory of relativity, which has been repeatedly tested and has (so far) never failed.
Einstein's theory is reliable science, because it accurately describes things we observe in the natural world, and no serious contradictions to the theory have been found.

It was about a century ago that Einstein's theory replaced Newton's longstanding theory of gravity...
...so does that mean Newton's theory was bad science? Does it show how transient and untrustworthy science is? No. Newton's physics was sufficient to get astronauts to the Moon, so obviously it works. But we've since learned that Newton's theory was limited...
...it only applies under certain conditions, which was not obvious to people until the 20th century. If you're an engineer working under earthly conditions, all you need are Newton's laws. But if you're working on something like satellite technology, you need Einstein.
What I would therefore caution Christians against is making too much of any particular scientific theory. If a theory has been properly tested and reflects observed reality, even within some narrow limits, it's good science. But it probably doesn't reflect the whole of reality.
As we learned with Einstein's relativity, there's probably a bigger picture, a grander reality, than we can currently imagine. The natural world is knowable, but not infinitely knowable. That's not surprising, given what we know of the God who created it all.
And since God is the good, wise, lawful, unchanging author of both scripture and nature, it's not unreasonable to expect them to be both consistent with each other and knowable, at least within our limited human means to know them.
There may be times when theories appear to be in conflict with each other, or to be in conflict with parts of scripture. It's almost always temporary, and just reflects the rocky road we travel on to understand the world in our limited human way. Have faith...
...and wait for the resolution. It almost always comes, and often leads to new ways of looking at the world that in my mind glorify God even more.

* Let us return briefly to the word "theory"...
...As if things weren't confusing enough, there's another way "theory" is used, within science. In my field (astrophysics) it's also used to distinguish scientific work based on mathematical models from the type of work I do, which is observational or experimental science.
Theory vs. experiment/observation is a subtle distinction used within physics. For instance, theoretical astrophysicists use computer modeling to try to figure out the detailed and complex physics of supernova explosions. These are constantly tested against observation, but...
...until the models make predictions that are repeatedly tested and verified through observation and experiment, they're not theories. (Confused yet? Sorry.)
Getting back to the main thread... If a scientific theory is GOOD, that is, it has been thoroughly tested and verified, and there are no serious challenges, you can trust it. And we can learn important things from trying to reconcile these theories with scripture.
Mostly these will be subtle lessons we learn, and we'll come to find out that perhaps we missed an important nuance in the translation of a passage of scripture. I doubt very much anything we discover scientifically will ever contradict the core tenets of Christianity...
...and this is especially true, since modern science is a direct product of Christianity. The academic scientists of Newton's time were mostly ordained priests and they considered scientific inquiry a form of true worship. As long as science is conducted with integrity...
...I don't have any concerns that science represents a threat to Christianity or that it can't be used to sharpen our understanding of the Creator of the natural world. For me, it's only affirmed what I read in scripture and magnified my awe of what He has done.
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