There is a quote attributed to Einstein that one should make scientific concepts as simple as possible but no simpler. His thought experiments are quite famous, especially the general relativity ones that deal with the concepts of uniform motion and simultaneity (ie, the speed of light and inertial frames of reference).
In fact, he uses a beautifully conceived image of a moving train in relation to the embankment: suppose two apparently simultaneous lightning bolts strike the embankment at two distant places, A and B; if you're at the exact halfway point (on the embankment), the two strikes would appear simultaneous for all intents and purposes; but, if you're on the moving train (at or near the speed of light) there'd be a slight difference in the timing of the two strikes (Walter Isaacson, 2007, p. 123).
Then there is that less-intuitive illustration of the "twin paradox" - also dealing with the impossibility of absolutely-defined notion of time: one twin travels into space (again, at or near the speed of light) while the other stays behind. By the time the space-travelling twin returns the other has aged considerably while the space-twin has barely aged at all.
The thing about Einstein's thought experiments like the two examples above is that he never doubted the physical meanings of the constants that define the functional relations of the equations. What is important is not the parochial illustrations but the speed of light in vacuum space (denoted as c) and how that relates to two distinct frames of reference (and why the notion of absolute time is an untenable notion).
Let's say the two points in space are: the sun and the earth. The sun is at least 8 light minutes away from the planet Earth. If, heaven forbid, the sun spontaneously blew out, it would take the stream of photons from that point in space at least eight minutes before we realized on Earth that there was no more sun.
The beauty of Einstein's genius (and Isaacson's book provides great examples of this) is that he never took for granted the physical implications/meanings of the mathematical constants that correct for errors in observed data and he saw these not as mere accounting devices but as having physical significance.
For example, where Planck saw his own famous constant (denoted h, the unit of quantum) as a "mathematical contrivance" (Isaacson, p. 99) Einstein saw it as having a physical reality that explains how photons are emitted and absorbed when interacting with matter (ie, as discreet allowable packets of energy called, quanta, whence "quantum theory" gets its name). -both Planck and Einstein (towards the end of their lives) remind me of F Scott Fitzgerald's aphorism: "show me a hero, and I'll write you a tragedy" but the story is best told in Isaacson's excellent book that I've been quoting.
The take-away from this entry (I hope) is that the truly scientific pursuit of knowledge has nothing "auto-magical" and/or wishy-washy about it, but is, in fact, built-up from findings before it. It is a rational accounting/explanation of what practitioners find in their explorations that founds the eyes of geniuses like Einstein and Newton.
I don't see these advancements in human knowledge as reasons for abandoning my beliefs in spiritual matters but confirms to me yet again that opening lines of Psalm 19:
The heavens declare the glory of God;
the skies proclaim the work of his hands.
Day after day they pour forth speech;
night after night they reveal knowledge.
They have no speech, they use no words;
no sound is heard from them.
Yet their voice goes out into all the earth, their words to the ends of the world.
In terms of my own spiritual beliefs I try and take the Einsteinian attitude that there must always be a link between what we believe to be true and our existence within that reality. The true, inscrutable mysteries of G*d as creator and saviour (ie, the justification for our evolutionary process to (spiritual) maturity) is about perspective rather than a thing to be figured out definitively:
He has shown you, O mortal, what is good. And what does the Lord require of you? To act justly and to love mercy and to walk humbly with your God. (Micah 6:8)
I leave the preaching to others; the essential mitzvot, as commanded by our Lord Saviour, I will meditate upon and try my best to actualize in my remaining life.