On the other hand, about a month ago I was in a conversation with a person who told me that science can't prove anything, and he must be skeptical of everything that scientists say. He believes that he is justified in rejecting many of the commonly accepted-as-true theories in the scientific world in favor of one that the scientific community, as a whole, has rejected. He claims that this is a humble and honest approach to science (implying that all other approaches to science are dishonest, and only skepticism promotes scientific progress).
Both of my friends illustrate extremes of the boundaries of the scientific method. It is true that the scientific method can give us knowledge (the boundary taken to the extreme by my first friend); however, it is also true that that knowledge is open to be challenged at any point that contrary evidence comes around (the boundary taken to the extreme by my second friend).
As many are aware, the scientific method deals with observation and evidence; proof requires 100% certainty (knowledge of all observables and all evidence), and no person knows everything. Since no human or the entire human race can possess all knowledge (even via the scientific method), it cannot be said that the scientific method can actually "prove" anything (where my first friend went wrong). The best we can do is get to a level of certainty that may approach 100%, but will never reach it.
But does this limitation warrant the level of skepticism of my second friend? The answer is, no. Because the scientific method offers evidence, the more evidence that we have that supports a specific theory, the more likely it is to be true- meaning that our certainty level of its truth rises with every confirming discovery. If the majority of the evidence points toward the truth of one theory, then that theory is to be preferred as being true. If the evidence points against one theory being true, then that theory is to be rejected as being false. Both of these situations can be over-turned; however, more evidence for the truth or falsity of a theory that we find indicates that its truth or falsity is unlikely to be over-turned.
Since the scientific method does not have the capability to give us 100% certainty, my first friend is not justified in saying that God's involvement has been scientifically proven unnecessary. Likewise, my second friend is not justified in being skeptical of theories that the vast majority of evidence supports or being confident of the truth of his theory that the majority of evidence is against.
Many scientists hold to a specific belief that they know the evidence is against. The lack of certainty that what they believe to be false is true is what gives them room to continue investigating; while the possibility that evidence of the truth of what they don't want to believe can still be over-turned drives them to continue investigating. Any claim to certainty here has the possibility to stifle investigation- both theists and atheists have stifled research and promoted research. It just happens to be in-step with what they do and do not believe to be true. (Of course, scientific progress is not only continued based on the drive to over-turn evidence for personal vindication. Finding evidence that supports one's view is quite exciting, but every piece of evidence tends to ask more questions that need to be investigated).
Both extreme approaches described come with a lack of humility and honesty. The first is a claim to complete knowledge when it is not possible- a dishonest claim that leads to unwarranted pride. The second is claiming to know something for certain that is against the majority of the evidence. It is prideful because of the unstated claim to certainty and dishonest because it ignores evidence.
By avoiding both extremes we avoid both pride and dishonesty. We neither directly nor indirectly claim to have all knowledge (thus preserving humility and honesty), and we can allow the evidence to guide our investigations and conclusions (thus preserving honesty).
Both sides need to look honestly at the other. If we automatically assume that the other side is trying to "hide" something, then there is no way that constructive dialog can take place. We also need to justify others' thinking this of us. We need to not be hiding something. If our view is correct, then it will withstand scrutiny and the majority of the evidence will point toward its truth. If the majority of evidence points against our belief, why are we even holding it? What good is it going to do us?
I have often seen friends like #1 point to friends like #2 as justification for rejecting Christianity. I have also seen friends like #2 point to friends like #1 as justification for rejecting science. Both cite "dishonesty" and "pride" in the other's approach for their disdain for it. Christianity and the scientific method are not mutually exclusive; there is no need for the Church nor unbelievers to enforce the idea that it is.
Here is a great conversation on the scientific method from Apologetics.com: God and the Scientific Method
Here are some links to other posts that help bring more clarity to this post:
Nature Vs. Scripture
Do You Rely On Authorities?
The Power of the Cumulative Case
The Danger of Overstating Conclusions