The scientific method does not deal in certainties: it offers the best possible explanation of observed phenomenon, and allows for the fact that future scientists may offer a better explanation. This attitude of never being certain leads to use "The Theory of .." to describe a body of science that is accepted as being the best explanation by all scientists, but may one day be overturned.
The Theory of Gravity, of relativity, of evolution may one day be found to be lacking some essential element that overturns completely our understanding of the how and why of such things.
Let me take you through a case example of the scientific method at work. It involves the work of Scott Persons, a researcher at the University of Alberta, who has been studying oviraptors, an animal that was vegetarian despite its flesh-ripping sounding name.
It is accepted by paleontologists that the earliest feathered dinosaurs did not fly (the feathers might have been a device for staying warm in cold regions) and the earliest flying dinosaurs did not have feathers (their wings were made of reptile-like leather).
The novel thing that Persons observed was that the final vertebrae were fused together forming a ridged, blade-like structure called a pygostyle. The fusing is known to modern biologists - for they appear in the tails of birds to hold its tail feathers. A complicated structure that allow individual feathers to be fine tuned for aerial maneuvering, and, in a number of birds, as part of mating rituals.
A dinosaur known as the Caudipteryx had no pygostyle but did have a fan of symmetrical feathers which were probably used in social display. It could not fly, and there seems to be little other purpose for such a fan except as something for display purposes. This reptile precedes the oviraptors by tens of millions of years.
So the question that Persons asked was why did the oviraptor have a pygostyle when no feathers had ever been unearthed near one? Well - feathers are very tricky to fossilize (even though some did) : the majority of dinosaur feathers turn up in amber (famed for being the source of DNA for the Jurassic Park films). The absence of feathers attached to oviraptor fossils does not prove that they did not have any, just that, as expected, no feathers survived to modern times.
So Persons made a leap of faith, but one of evidential faith. If a dinosaur had all the tail mechanisms found in a peacock for a peacock to made its mating ritual, what was its use? All realistic answers are that it had tail feathers. In a species that had a history of using tail feathers for social display. The hypothesis is that oviraptors did have feathers, and used them for mating or other social display.
An idea that has a lot of credence to it. Does that mean oviraptors had feathers? No - just that it seems, with all our current evidence, that they probably did.
Will the matter ever be resolved, one way or the other? No - we have no way of predicting future finds. But it is not impossible that the case may one day be proven.
In the meantime, we have some confidence that oviraptors had feathers, but no certainty.
Which fits the agnostic philosophy on just about every topic you wish to raise. We have some degree of confidence in believing that something is true or false, but accept that we might one day be persuaded to change our mind. So - do we live in "The Matrix": that gets about a 0.0000001 chance - or smaller. Did the moon landings take place? 99.99999 certain (sorry, conspiratists, your arguments fail to persuade. Is free will an illusion? Which comes in pretty solidly at about 0.500.
Those with a dualistic outlook on life are, by definition, designed to plump for a yes or no on all issues. Take all the evidence available and make a decision that will hold until an epiphany takes it away.
Is there a god? 100% yes claims the theist, for non-evidential faith is the heart of theism. 100% no says the atheist, for evidential-faith is the heart of disbelief.
And the Agnostic? Most agnostics will opine that the absence of any evidence that a god takes a personal interest in the life time affairs of man makes the probability exceedingly small - so close to zero as to put it near to par as being a pod in "The Matrix". But no gods at all? Not proven one way or the other, so, depending on personality, the probability sways around the 0.5 mid point.