I agree, at least in part, that the progress of the modern era was indeed due to both modern science and the principles of the enlightenment. However, I do believe that the success of both modern ethics and science can ultimately be attributed the advent of emergent phenomenon (of which capitalism is the economic sort), which is the eventual conclusion of free society.
In the case of science, this is the idea of the "marketplace of ideas" that is often talked about today, but really coincided with the enlightenment. Scientific ideas compete in the literature for dominance, and that grow the most acceptance over time eventually dominate. Both Newton's calculus and gravitational theories proved to be subject to quite a bit of criticism (from Gottfried Leibniz and Robert Hooke, respectively), and of course Newton's gravitational theory has become dominant, though I have heard that the calculus we learn today is closer to that of Leibniz than that of Newton. Likewise, Darwin's theory of natural selection was subject to intense a persistent criticism for nearly 100 years -- Darwin's Theory of Natural selection was published in 1856 and the Scopes trial was not decided until 1925, and the Supreme Court only struck down laws outlawing teaching of evolution in 1968. Today, of course, countless scientific theories are competing for dominance in the scientific literature across the world -- a process that has been fundamental to the monumental scientific gains we have made since the time of Newton.
Likewise, secular theories of morality have been almost entirely emergent in nature. Adam Smith first proposed that morality was the consequence of compassion, learned by each of us as we grow up and figure out that making others happy makes us happy, and seeing misery makes us unhappy (he called this "mutual sympathy of sentiments"). He claimed that as we grow, each of us comes up with our own moral code based on what we discover to cause mutual sympathy of sentiments, and that society's moral sense is derived from each of our individual moral codes. In fact, Adam Smith first used the term "the Invisible Hand" in his "The Theory of Moral Sentiments" to describe how societal morality is derived from individual moral codes. An example of this in our lifetime is the growing acceptance of lgbtq people in the west, or in the generations before us, the about face in the moral attitude towards race. Today, that arguments is carried on by the likes of Steven Pinker, who claims that our sense of morality is continually moving towards acceptance and away from violence, which he attributes to commerce (which forces people to interact with each other), and centralized government, by forcing people to act as people of a court rather than as warriors -- though I might prefer the term civilized government.
That said, none of these ideas are even slightly novel. Lucretius first expounded on them in his "De Rerum Natura", and obviously the giants of classical liberalism explained them in much greater depth. Charles Darwin was brought up in the tradition of the Scottish enlightenment thinkers, and very much surrounded himself with the ideological successors to classical liberalism and, in particular, David Hume. In the economic sphere, Hayek devoted his entire life to the idea of emergent phenomenon. And lastly, most of the examples here are taken from "The Evolution of Everything" by Matt Ridley.