There were and are materialisms which explicitly talk about multiple levels of reality. Someone who believes that the brain is made of atoms but that consciousness is “strongly emergent” is still a materialist—at least compared to someone else who believes in a separate soul-substance
The problem with “strong emergence” is that it can be used to “explain” anything and is thus worthless.
If evolutionary biology could explain a toaster oven, not just a tree, it would be worthless. There’s a lot more to evolutionary theory than pointing at Nature and saying, “Now purpose is allowed,” or “Evolution did it!” The strength of a theory is not what it allows, but what it prohibits; if you can invent an equally persuasive explanation for any outcome, you have zero knowledge.
The problem with “strong emergence” is that it can be used to “explain” anything and is thus worthless.
Eliezer Yudkowsky http://lesswrong.com/lw/kr/an_alien_god