In general, the "atheistic" materialist view coincides with formal operational thinking and abstract operational thinking, which focus on facts and data and derives connections from logic and evidence.
The vision of a conscious Kosmos usually coincides either with mythic believer's thinking, or with "vision-logic". Vision-logic begins with that same formal operational thought process, but also intuitively apprehends the nature of the whole (using multiple modes of knowing or intelligence).
There are several distinct levels of thought participating in this debate, often arguing in entirely different "languages". This topic can be explored in depth, but here I'll offer a simplified summary of the most important modes of thinking at play:
Mythic-rational thinking--often associated with religious belief and "intelligent design"
Mythic-rational thinking begins with a (usually shared) set of beliefs about the whole of reality and then views data (the "parts") through that lens. It is unable to see what fails to fit that view, and distorts data as needed to fit its culturally agreed-upon preconceived beliefs and conclusions. This is the thinking associated with the sort of religious beliefs and attitudes that Sam Harris so effectively condemned in his earlier books, The End of Faith, and Letter to a Christian Nation.
Early rational thinking-- often associated with aggressive "skeptics" asserting atheistic materialism
Some developmental researchers (such as Loevinger, Cook-Greuter and Torbert) have identified two distinct levels of rational thinking, the first of which is "abstract operational" thinking. Here there is the cognitive capacity to look at oneself, but with strong ultrarational defenses, gravitating toward oppositional battles with others who defend different positions. You can see this in web comment streams that have attracted atheists less sophisticated than Sam Harris. Individuals with this kind of thought pattern live in a world where things are sure and clear, and they feel entitled to impose their views on others. Thus they can seem argumentative and opinionated. Their logic begins with a conclusion -- the intention to advance or defend or glorify themselves. This mental mode is unable to synthesize complex systemic or metasystemic perspectives or to question its own presumptions. It is common among teenagers, bureaucrats, junior managers, and engineers, and can be found in almost every profession.
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