Yes, that's the main failure mode of ethical naturalism. "You must die, because SCIENCE!"
My libertarian shard says it's the main failure mode of politics: "You must die, because POWER!"
What would the progressive atheist's answer be to the challenge of producing virtue from matter?
No idea, but mine is game theory coupled with compassion — a System 2 mathematical insight and a System 1 intuitive and trained response. Ethics comes down to symmetry among agents: my good is no more or less The Good than your good. Humans can recognize this both as a matter of explicit mathematical-philosophical reasoning, and using intuitive-emotional responses (which can be trained). Virtuous humans both recognize and feel that symmetry, and vicious humans do not recognize or feel it.
The basic ethical failing that leads to atrocities is not usually the lack of System 2 ethical reasoning, but the sentiment (or System 1 trained reaction) that those people are not really people; they are some sort of mockery of people who do not deserve compassion. See Rorty, "Human Rights, Rationality, and Sentimentality".
What we see in the history of eugenics politics is the notion that society can progress by freeing itself from having to care about certain kinds of people — so that they can be subjected to medical violation, mutilation, or extermination. But this is the same thing that we see in religious antisemitism or any number of other sources of the dehumanization meme. Dehumanization works the same evil whether it's couched in the language of progressive science, the Lutheran language of Nazi antisemitism, or in the order to the Albigensian crusaders: "Kill them all; God will know his own."
Rorty's critique of ethics since Plato has a weird echo when we're talking about eugenics, though:
It would have been better if Plato had decided, as Aristotle was to decide, that there was nothing much to be done with people like Thrasymachus and Callicles and that the problem was how to avoid having children who would be like Thrasymachus and Callicles.
But speaking of science and ethics, I think it's really kinda weird that humanity had the Golden Rule from traditional sources since antiquity, but didn't invent the math to describe it until the mid-20th century — the same time frame in which engineering gave to politics the ability to destroy the world.
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