But if you believe in supernatural entities, whether you band together with others of that ilk or not, your reasoning is, in my opinion, flawed.
In my opinion, nearly all reasoning is flawed, including my own.
I am not therefore certain that the reasoning of all people of religious faith is any more flawed than that of people who do not profess a religious belief.
Alister Crowley said some time ago,
"We place no reliance on virgin or pigeon; our method is science, our aim is religion."
Not many people seem to have figured out what the old Beast was on about, but I think I've got him sussed out pretty well.
We place our faith (yes, faith) in science, and it treats us pretty well, on the surface. It has laws and they work, mostly. We certainly have come to depend upon them continuing to work as we believe they should for our modern lives, and they do. But that is for the layperson. What goes on behind the scenes for the scientist is a roiling, bubbling, never-ending series of upheavals and arguments and dust-ups and brouhahas and donnybrooks of Brobdingnagian proportions, over all manner of things, great and small, and from time to time, we laypersons may even hear of one or two of them. E=MC2 and String Theory and Grand Unified Theory and so on, as it pops up on the Discovery Channel or for the bluebloods, Nova.
We still have no idea whatsoever of the answers to any of the really big questions (except for Douglas Adams, of course, blessed be His Name).
We do not know what the original cause for The Singularity was. We do not know what existed before it brought all space-time, energy, and matter into being. We do not know if the universe has boundaries. We do not know if it will continue to fly apart forever, or if it will one day collapse upon itself. We do not know where most of the mass of the universe has gotten itself off to, which based on our best theories, ought to be there and doesn't appear to be.
We do not know what the purpose of our type of intelligence is from an evolutionary standpoint.
We do not know what the smallest unit of matter is, or what causes gravity.
We do not know what constitutes life, or if a virus is a living creature.
We do not know how life began.
And, importantly, in the
'Age of Reason', we have placed science as it was understood at that time upon the mantle of correct thinking, and worshiped (yes, worshiped) it as if it were unchanging truth. We have ridiculed and terrorized, tortured and imprisoned people for daring to challenge science - exactly as an earlier age of religion did to men of science.
Ironically, we have at each step of our knowledge proclaimed our knowledge to be complete, and we have taken special pains to root out those who disagreed that we had reached the pinnacle and had anything left to learn, even minority-viewpoint scientists, from crackpots to those whose theories have fallen out of favor in the scientific community.
In the 1300's, we
knew that the sun revolved around the earth, in the 1700's, we
knew that rocks did not fall from the sky, and now we know...what? Everything, apparently. And those of us who profess that science does indeed have every answer or can go fetch it like a good dog, and that therefore it is
not a faith like unto religion to trust in it without understanding - those people will
quietly refuse comment when, in five minutes or five years, one or more of their cherished truths becomes invalidated by newer scientific proofs.
At every moment in the days, months, and years to come, those who place their, um,
'not faith but belief rooted in fact' will continue to scoff at those who place their faith in religion (or supernatural if you prefer), but as scientific knowledge continues to advance, and change, and be refined and redefined, most of those who claim to believe in it won't even know about the big-ticket items being debated around them, won't be aware that the scientific bedrock upon which they stand is prone to earthquakes and mudslides. They're smug, they're content - why, they're just like smug, content, believers in the supernatural.
Yes, the supernatural is, by definition, beyond the ken of man, and thus cannot be defined as true or false, which gives those who believe in science the willies, since science cannot grasp it.
Yes, science is a good and loyal friend, and even when we do not understand gravity, we know that it works, since we do not simply float away off the face of the earth. We can observe the effects of gravity in a way that we cannot observe the effects of a deity.
And yet, each set of assumptions - for those who dislike the term 'faith' applied to what it is that they choose to believe - has parts in it that are self-evident, and parts in it which are subject to change and which defy understanding to date. Each is very much like the other when defined as a set of things we know versus a set of things we do not know. Each is very much like the other when defined as a set of operating principles that seems to have valid application to our everyday lives and how we interact with each other.
And each is often utterly at each other's throat, as if the one somehow threatened the existence of the other. Believers in science claiming they never attack, only defend, as they hurl blow after blow, believers in religion saying the same thing. Each pointing out the worst flaws in the opposite camp, whilst proclaiming that the flaws attributed to their own camp apply only to a shabby minority of fringe thinkers, not the mainstream.
And yet, some of us can see both sides of the river, and do not think it impossible to travel from one side to the other and back again.
Science says, with reference to The Singularity, the moment before (if the word 'moment' has meaning here) all space-time, matter, and energy came into being, that there was nothing, a void.
In the beginning God created the heaven and the earth. And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters.
And then, there was an explosion. In a fraction of a fraction of a second, all energy, all matter, all space-time, came bursting into being and exploded. From the energy there was light and heat, from the matter there was shadow wherever light did not strike.
And God said, Let there be light: and there was light. And God saw the light, that it was good: and God divided the light from the darkness. And God called the light Day, and the darkness he called Night. And the evening and the morning were the first day.
And as the mass congealed, drawn together inexorably together by gravity, planets and stars were formed, and galaxies, and everything began to spin and hurtle away from each other. Planets formed and began to cool.
And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. And God called the firmament Heaven. And the evening and the morning were the second day. And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so. And God called the dry land Earth; and the gathering together of the waters called the Seas: and God saw that it was good.
Well, it goes on like that for awhile. I see no great disparity there. It seems to me that there isn't much difference, philosophically, from saying
"the universe was created and we don't know how," and
"the universe was created and God did it on purpose." Even supposing that science someday does think it knows how the universe was created, experience has shown that it will eventually change its mind, and what was once settled fact will again be in a state of flux.
I believe in God. I can't prove the existence of God, and I have some serious doubts that any of my beliefs are
'the right ones' concerning any particular creator. I don't really care. It does not keep me up at nights, although it can make for some fascinating debates and late-night coffee conversations.
I also believe in science. I think that science has done a wonderful and amazing job of explaining and understanding the universe we find ourselves in, and I trust that scientists will continue to explore, discover, refine, and otherwise learn about our reality and to share that information in meaningful and useful ways with the rest of us.
I do not suspect that there will someday be any great harmonic convergence of religion and science. They operate on different principles and their language of description is completely different. They're also too much alike to ever get along.
But for those of my friends who believe that science is not based in a belief system, and that religion is necessarily based on falsehoods because it cannot be proven...we'll find out, one day. Pity none of us will be able to share our 'ah-ha' moment with the others.
Until then, shalom. I think that's all I've got.
While, as you’ve pointed out, in the remote past we have had certain knowledge that proved to be wrong, there’s usually room in the way 21st century science operates for that to occur without that absolute certainty you speak of- most scientist recognize that they’re operating from models, and that the models are flawed. Our job is to improve the models with more data and theorizing. 
