The modern great chain of being links scales from the size of the universe to the size of the most findamental particles we know. Explanation in terms of smaller simpler parts is the standard reductionistic method of science. Going backward, up the chain, involves emergence. "Weak emergence" is the claim that everything is reducible in principle, even non-obvious properties of complex systems --- but that such reduction is merely impractical. "Strong emergence" is the claim that some properties are irreducible --- that sometimes the whole is different than the parts, even in principle. This idea is much less accepted scientifically.
How was this chain assembled? The idea of atoms --- as ultimate unbreakable particles --- goes back to the ancient greeks, like Democritus. The roman poet Lucretius gives an account of the universe in terms of differently shaped atoms. But atoms actually came along much later via Chemistry. They were not really incorporated into Physics until the quantum revolution in the 1920s.
The real Physics synthesis behind the chain begins properly with Isaac Newton. He formulated the first "universal" laws and emphasized the idea of forces. His laws of mechanics and gravitation stood until Einstein modified them in the early 20th century. Most famously, Newton showed that his law of gravity resulted in orbits that are conic sections. Conic sections are a staple of ancient greek mathematics, once again showing the "unreasonable effectiveness of mathematics".
Class notes from the tablet are posted here. And here.