Some of the weekend’s speakers alluded to the turmoil at the council, where several longtime employees have resigned or been laid off. But in general they emphasized unity: They shared common enemies, like religious fundamentalism and “Intelligent Design.” And they believed morality was possible without God.

The presenters did differ on where a secular morality might come from. In his new best seller, “The Moral Landscape,” Mr. Harris argues that morality is a product of neuroscience. (The good, he argues, is that which promotes happiness and well-being, and those states are ultimately dependent on brain chemistry.) Others believe morality is bequeathed by evolution, while still others would argue for ethics grounded in secular philosophy, like Immanuel Kant’s or John Rawls’s. But all agreed that nonbelievers are at least as moral as believers, and for better reasons.

The disagreement was not, then, between atheism and humanism. It was about making the atheist/humanist case in America. A central question was, “How publicly scornful of religion should we be?”

Here even the humanists got less humane, as each side stereotyped the other. Those trying to find common ground with religious people were called “accommodationists,” while the more outspoken atheists were called “confrontationalists” and accused of alienating potential allies, like moderate Christians.

At the liveliest panel, on Friday night, the science writer Chris Mooney pointed to research that shows that many Christians “are rejecting science because of a perceived conflict with moral values.” Atheists should be mindful of this perception, Mr. Mooney argued. For example, an atheist fighting to keep the theory of evolution in schools should reassure Christians that their faith is compatible with modern science.