This is actually a good post.
The key word is the "tool box" that we have, which is science.
There two paths we can focus on from this point.
First - The tool box of science works to a certain extent - after that is another box that holds "human logic, intelligence and common sense" (let's call this tool box as "HIC"). This box also gives us some direction and some perceived information (not necessarily always correct though) and this box also works only to a certain extent, and THEN, there is the inevitable, throwing the white towel of "I don't know" or "we don't know".
The final box of "I don't know" is held by both Atheists and Theists, and it's the exact same box.
And I think the crux of our discussion lies in the box of "HIC". Because this tool box is not exact the same for every person (unlike the tool box of Science and the tool box of "I don't know".
This box of HIC may vary from person to person. This box may also have a common ground between Theists and Atheists but this tool box may also have uncommon ground between the two groups.
So lets begin with the first tool box.
I fully support the tool box of science - but we see that the immediate bone of contention between both camps is "Theory of evolution" - a topic not so encouraged to be discussed in this forum - so we have to surpass it.
So lets stick with the tool box of science and move beyond the Theory of human evolution - and we come to this post that I wrote earlier which moves us from the tool box of science to the tool box of HIC where all the action lies.
If you haven't read it before, please read it again. Slow and easy so you could understand my train of thoughts.
Remember the above in quotes is the step BEFORE we throw in the white towel of "we don't know".
Now to continue with this HIC box if X is what started it all then X is probably a force with intelligence because creation and design (as we observe in the natural universe) requires intelligence and force.
I think to some extent, believers can say X is God.
Atheist can say, X is just nature that has designed and created it all.
What is X and where it come from?
Both parties throw in the white towel of "I don't know".
*BUT* is probably a fact that exists.
As the great Einstein put it,
Try and penetrate with our limited means the secrets of nature and you will find that, behind all the discernible laws and connections, there remains something subtle, intangible and inexplicable. Veneration for this force beyond anything that we can comprehend is my religion. To that extent I am, in fact, religious.”
In my personal opinion, if you are an Atheists and you can be all the Atheists you want but if you are also a believer in the knowledge of science then it will probably be unfair to outright deny the existence of this "force" - NOT because you have more scientific knowledge than Eisenstein and you can prove him wrong but look at what's going on here?
He (a non religious and perhaps the greatest scientist) believes in the existence of "force" that he cannot provide the evidence of it's existence.
Sounds familiar?
Perhaps believers label this "force" as God.
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The second path that we can take from the tool box of science that I would like to shed just a little light on is, "What should be our intention behind using this, very useful, tool box"?
In my opinion, exploration of scientific knowledge that benefits humanity MUST be continued on - I 100% support it. If that was not the case, I would've not gotten a Masters in Science, and neither would have encouraged my wife pursue a double PhD in science.
IMO, when it comes to the scenario of "Science and Religion coming face to face", THEN, believers should use the knowledge of science to appreciate X as to how this force created things under our research and exploration.
And Atheists should simply continue with their research and exploration in the field of science that benefits humanity WITHOUT belittling those who would like to appreciate X.
This way, both camps can join forces and move even faster in expanding the knowledge of science that is beneficial to all.