First of all, I hope you realize that atheists and secularists do not derive their morals from "Darwinism." We can use evolution (both biological and social) to explain where our morals come from, to some extent at least, but I don't think anyone would argue that the tenets of the theory of evolution somehow form a moral basis.
Secondly, I agree with your basic point. I think in many ways science and technology have had devastating consequences on the natural environment. The power of science has allowed us to destroy swaths of ecosystems and pollute our air. It has also allowed us to poison the soil to maintain our grain food supply with pesticides and artificial fertilizers. Most troubling for me, science has led to the industrialized treatment of food animals—there is no word to describe our treatment of cows, pigs, and chickens except "torture." We treat them as protein machines. And, of course, science has also helped us create unimaginably terrifying weapons of war.
But on the other hand, I think science and technology have underpinned most of the moral advances throughout history. You could not have laws or religion without the technology of writing. Islam, in particular, could not exist without the technology of the codex. Slavery would still be common were it not for the industrial revolution. And it would be impossible for you and I to be having this conversation were it not for the vastly increased powers of communication that the internet has brought us.
I don't think science is good or bad. It is a method of gaining knowledge about the natural world, just like mathematics is a method of gaining knowledge about abstractions, and it can be used for both "good" and "evil." But at the same time, I don't think you can separate science from morality, because science leads to technology, and all throughout history our societies have been shaped by technology. And we derive our morals from society.
This is, I think, why Westerners are often called "progressive"—because we see morality as changing as society changes, as we learn more about the world and about each other. People used to believe that blacks were racially inferior to whites, and that women were intellectually inferior to men. We know better now, and so we've changed the way we treat blacks and women accordingly. Part of the moral experience of Western culture is to challenge the moral assumptions past generations have made and correct them if we've discovered that they no longer conform to reality or our experience. Even with all of our mistakes and moral atrocities, I do believe that things are getting better in Western society; I would certainly rather live now than in any other era, and I'm eagerly looking forward to what the future brings.
Religious people, on the other hand, believe that morality is permanantly rooted in a certain point in history, when a god supposedly handed down his revelation onto mankind.
The problem with the religious position, as I see it, is that you can't separate morality from society and you can't separate society from technology. Morality, society, technology, and science, are all ultimately part of the same fabric. So if you want your culture to keep its morality rooted in a certain era, it shouldn't come as a surprise that the rest of your culture—its scientific and social advancements—also remain rooted to that era as well.






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