And actually an atomic table is not largely space. Salt and sugar both have cubic crystals. And in crystallography one finds that the ions that make up these crystals are not only arranged in a cubic lattice, but also that although very slightly elastic they are virtually impenetrable. They do not behave at all like the empty spaces that Eddington dreamed about. It all depends on how you look at things. Long ago people thought of mountains as horrid places filled with hob-goblins and dragons; then in about 1540, Conrad Gesner climbed a mountain just for the fun of it, and was so charmed he told a friend he intended to climb a few mountains every year from then on. It depends how you look at things!
The mistake that Professor Eddington made was to think that the world, with which he had become familiar, was the real world; in other words was the uncreated world, in other words he equated his atomic particles with God, who alone is uncreated. His was an idolatry similar to the worship of wooden and stone idols by the Canaanites of old, or of the Israelites and the golden calf. He would not have acknowledged this; he was a professing Quaker; but that is what he was doing, whether he knew it or not. Atoms and molecules only exist in the world of space, time and matter; and one day that world will come to an end. The significant end may well be the Day of Judgement; but the physical end is likely to be when all matter has been changed to radiation, and entropy has increased so much that no radiation is of use any more. It will be a waste-land, ripe for extinction.
There is no insight into eternity, if it exists outside space and time, and can be none, unless you are an immortal person, and live an immortal life at least in a poetic sense. Atoms, molecules, the so-called Laws of Science (which describe in fact the way things work), the laws of logic, the beauty of musical harmony, and all the rest of the spiritual world, only came into existence when space, time and matter were created; and it is meaningless to ask what existed before. Just as it is meaningless to ask if your plan of battle is blue or green?