I've been somewhat obsessed recently over the idea of weak emergence in understanding how all the layers of ontology fit into one another. This is an area that I think trips up so many people, both atheist and theist alike.
One reason why is that many people will think that naturalism entails that only the most fundamental layer of ontology has an sort of real status of existence. This view is known as eliminative materialism. Alex Rosenberg, a prominent atheist philosopher, told me back in 2015 that he thinks eliminative materialism is the logical and inevitable outcome of a naturalistic ontology. On this view only the most fundamental constituents that science tells us exist are real. Everything else is an illusion. That means people don't exist, color doesn't exist, solidity doesn't exist, and consciousness doesn't exist. In other words, all higher level phenomena has no ontological status whatsoever. If it isn't fundamental, it's an illusion.
Contrast that with the view that physicist Sean Carroll proposes, which he calls poetic naturalism. It's poetic because there are "many ways of talking about the world." We can talk about the universe in terms of fermions and bosons or we can talk about it in terms of people and societies. In other words, the emergent world of people, plants, animals, color, solidity, consciousness, countries, and economies—all the higher level phenomena—exist, at least in a certain sense. They don't "exist" in exactly in the same way that fermions and bosons exist. They exist as higher level emergent phenomena. However, some things really are illusions. Free will, souls, and the flow of time really are illusions, because they require certain things to exist fundamentally that don't; they can't truly be said to have any kind of real ontological status. Compatibilistic free will, which acknowledges that there isn't any real libertarian free will, is another matter. Bottom line, one has to understand how and why some emergent phenomena are or aren't illusions.
The major problems with this arise from our innate inability at understanding emergence; it's not at all intuitive and it's also extremely complex, generally requiring exceptional knowledge in both science and philosophy, which, let's be honest, most people don't have. And that's why so many people, both atheists and theists, even those reasonably knowledgeable in either science or philosophy, come to the conclusion that naturalism entails eliminative materialism.
River Out of Eden, saying, "In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won't find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference.” (p. 133)
Dawkins has gotten a lot of heat over this quote. Many theists have used it to show what a cruel and indifferent world naturalism entails. But I think they're taking it out of context. Dawkins was writing about how, from the perspective of nature, the blind forces of evolution are indifferent. The universe is amoral, the universe is blind, the universe is purposeless. But that doesn't mean on naturalism there can't be morality. On poetic naturalism, morality is a emergent property of evolved sentient beings, much in the same way that economics and culture is.
You will never find anything about economics in the fundamental laws of physics, nor will you find anything about morality. But concluding that therefore morality, economics, and culture doesn't exist would be foolish. This is where weak emergentism comes in: "a property is emergent if it is a systemic property of a system—a property of a system that none if its smaller parts share—and it is unpredictable or unexpected given the properties and the laws governing the lower-level, more fundamental, domain from which it emerged." Another way of looking at it is how Carroll himself put it, weak emergence
is simply the idea that there are multiple theories/languages/vocabularies/ontologies that we can use to usefully describe the world, each appropriate at different levels of coarse-graining and precision. I always return to the example of thermodynamics (fluids, energy, pressure, entropy) and kinetic theory (collections of atoms and molecules with individual positions and momenta). Here we have two ways of talking, each perfectly valid within a domain of applicability, but with the domain of one theory (thermodynamics) living strictly inside the domain of the other (kinetic theory).
Talk of morality is describing the universe at one particular level, that of us evolved social primates, us humans, and how we interact. But it is not found at the fundamental level. So a universe that is at heart, full of "blind, pitiless indifference" is no reason to cry for the death of morality from the naturalist's universe. Dawkins is just describing the universe at one level—the level of DNA—which is amoral. But zoom out a few levels past biology altogether and into the social sciences where ethics becomes relevant and you'll find a universe teaming with morality.