Most Enlightenment thinkers believed that the World’s order (as ultimately based on divine laws) is good and thus every gain of knowledge will have good consequences. Scientific process was assumed to entail moral progress. In fact some moral progress did occur in the Western civilization and science contributed to it, but it is widely incommensurate with the progress of science. The Enlightenment’s concept of a concerted scientific and moral progress proved largely wrong for several reasons. (1) Public morality and science evolve largely independently and may either enhance or inhibit each other. (2) There are no objective values to be read in the World’s order and simply followed. Instead, our real, subjective values and the moral systems they fuel have all been generated and shaped by evolution rather than designed to be universally good, and thus ought to be managed rather than simply followed. (3) Our evolved morality is flawed, deficient, prone to doctrinal manipulation and refractory to progress. (4) The majority of people show metaethical incompetence in failing to take a reasoned critical stand toward the principles and assumptions of received morals. This makes moral progress largely dependent on those who reach metaethical competence by transcending the conventional stages of moral development.