Science, like religion, begins with observation and speculation, but science does not stop there. Newton speculated that a single universal force, gravity, might account for the observed motion of planets encircling the Sun. He guessed that a central force, operating between all constituents of matter, and directly proportional to the product of masses and inversely proportional to the square of the separation distance would do the job. This guess was made long before Newton actually constructed his famous theory of universal gravitation. Indeed, he had to invent a new mathematics, differential calculus, in order to formulate a theory that could be used to make precise testable predictions.
Even though the set of differential equations that comprise his theory of gravitation was marvelously successful in accounting for the observed motions of the planets, and even though these same equations are employed today to guide spaceships, it must be remembered that one can never really prove a physical theory, but only subject that theory to perpetual rigorous testing. Possible limitations of the theory in question will be revealed by predictions that are not in accord with observations and experiments.
The revelation of such limitations is the very essence of science. Thus, it eventually became evident that there was a slight discrepancy in the predicted orbit of the planet Mercury, something of the order of six miles per month. This discrepancy, a puzzle for a very long time, was finally explained in 1916 by Einstein's entirely different general theory of relativity, the origins of which are explained elsewhere on this website.
Einstein's theory was also based upon differential equations, but it involved not Euclidean space and absolute time but rather Riemannian curved spacetime. The predictions of Einstein's theory and Newton's theory agree in general for phenomena that are readily accessible to even the most casual observer, but Einstein's theory accounts for the perihelion shift of Mercury at well. The same theory also predicts the bending of light rays from distant stars as the rays pass close to the Sun. More than one expedition to photograph the stars behind the Sun during a solar eclipse verified this prediction of Einstein's theory. Later the Hubble telescope provided us with spectacular pictures revealing the bending of light from distant galaxies as it passed by nearer galaxies on its journey to the earth.
Scientific theory evolves through the attempt to remove inconsistencies between existing theories and observations, as well as between theories, each of which has a established track record. Today, we know that there is an unresolved conflict between general relativity and quantum field theory. Many ideas have been presented in the hope of resolving this conflict, but (using a metaphor) thus far the child of this pair of theories has not been born. One thing is certain, however; the child will possess DNA contributed by both parents. I shall be very surprised if it turns out to be anything other than a truly beautiful baby.
It might well be said that scientists, more than anyone else, recognize the "intelligent design" of the universe. Indeed, it is the fascination with the complexities of the universe that motivates scientists to devote their lives to an attempt to understand more completely the workings of that universe.