Naturalism — philosophy based on a natural philosophy or ontology — has had a problematic history. In the history of science, in the general history of thought. In the last 50 – 100 years, arguments for naturalism have been strengthened by two major developments: empirical cosmology and the concept of emergence. This has happened despite the fact that the theory of evolution is not accepted by a lot of people (even by some pubic school science teachers ).
Empirical cosmology has strengthened the case for naturalism due to the weakening of the case for our uniqueness in the cosmos. Our planet is a tiny speck. For humanity’s, man’s, homo sapiens’ place in the universe based on the anthropic principle. Emergence has strengthened the case for naturalism by weakening (or revising) the argument against classical reductionism. Let’s unpack these two trends more.
Western ontology had long entangled religion with theism; and theism had incorporated views of cosmology, some dating back to ancient times, from early Greek philosophers. Modern science (a relatively new way of thinking) had pushed back on outdated cosmology convincingly. (How many people still believe the earth is at the center of the universe and surrounded by a heavenly sphere?)
Christian theology, of course, had struggled with arguments for the existence of God each time entangled cosmology evolved. For example, the struggle with the Ptolemaic model. Copernicus, Galileo. All too familiar now. Then the theory of evolution. Psychology as well (Freud, Jung, etc.). Quantum mechanics. Somewhere recently I noted that the Pope officially closed the problem of faith and cosmological revisionism by defining a proper, inviolate domain for theism.
I started reading about emergence in physical and biological systems / processes even before grad school. In such systems we see properties which cannot be explained by the component, simpler elements. Is this a question of our ignorance of those systems or processes? Is this a question of our use of language for different descriptive domains or sciences? Is this evidence for some “spark” at some level of complexity?
Sean Carroll talks a lot about emergence, directly or indirectly, in his book The Big Picture. His argument (proposal) is bolstered by use of the term in many disciplines other than physics, e.g., information theory. But I need to further explore his place in the spectrum of reductionism-emergentism . [TBS quotes here.]
Emergence provides a framework to avoid classical reductionism. A natural framework which can explain the rise of novelty which appears not to be predictable (solely or in part) from subsystems / subordinate elements/entities or describable using the language of those subsystems / subordinate elements/entities. Adopting an adaptive “multilingual” stance and Bayesian logic, the goal of a unified natural philosophy/ontology is to smooth out the boundaries of those domains as we learn more about the universe. It’s a work in progress. Which makes it tough on those who claim absolutes or want ready closure or 100% certainty — on those which cannot accept a provisional outlook.
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 In addition to the issue of acceptance, the theory of evolution is not even really understood in general, as opposed to the public distortion of Darwinism. Like the distortion of determinism as social determinism. Also, as to the strengthening of the case for naturalism, there’s been progress in anthropology, e.g., the case for higher-order thinking in other animals (including primates) and even use of tools and language. And generally a broader penetration of Bayesian reasoning for the credence of philosophical claims. Other than academic progress, the passing of generations and some questions losing their vitality — perhaps younger generations ignorance of past philosophical battles and reaction to strident hypocrisy. Yet, in daily life, a coherent intellectual outlook is not all that common — it’s a lot of effort! — especially without a broad social and institutional support structure. A compartmentalized, inconsistent intellectual and emotional framework (think of a Venn diagram with no overlapping or only partially intersecting circles) remains authentic.
Having encountered the “Void” in seminary and grad school, I felt that I understood the pain and distress that a non-theistic and organism-centered cosmology presented to traditional “believers.” Yet, I failed to appreciate the pushback in the coming decades from the faith-based movement, both philosophically and politically.
For example, I had quite a visceral experience on this subject when I taught public school. A “wake-up call,” indeed. As a math teacher, I had worked with some science teachers to get a grant for an interdisciplinary project: SEPRE (Students Educated to Propagate Respect for their Environment). One of that project’s outputs was a video on the life of Darwin. At least one of the science teachers was tangibly distressed regarding that task, requiring some workarounds. So, that’s why I resonate with statements [TBS quotes] by Sean Carroll about science’s responsibility to address all the questions which religion has addressed — a vibrant, meaning-full framework for living. No small task!
See also: Karl Popper, Thomas Kuhn.
 “Emergent properties are not identical with, reducible to, or deducible from the other properties. The different ways in which this independence requirement can be satisfied lead to variant types of emergence.” [https://en.wikipedia.org/wiki/Emergentism] Carroll may hold a relational model of emergence (which might bypass issues with some flavors of physicalism and materialism), but there appears to be a hierarchical point of view as well. He does seem to say that our choice of language to describe different domains is a matter of convenience.