Individual Origin
Supernatural concepts are heavily attached to humans' intuition. This intuitive and imaginative ability was first evolved circa 30.000-50.000 years ago, during the Upper Paleolithic, the final end of Stone Age. That time, arts (like petroglyphs, cave paintings), funerary*) artifacts, and more sophisticated and diverse rock tools begun to bloom. This intuition led to "agency detection," that is the tendency to "feel" or register the presence of agency even though there is only inconclusive evidence. "Agency detection" coupled with humans innate desire to find and seek meaning and other novel things led them into primordial supernatural concepts. When primitive humans, for instance, see lightning, which is outside their capability to explain (unlike now, we know how lightning can be formed.) and given its destructive power, loud sound of thunder, and majestic appearance of the lightning, it's easily to ascribe lightning as something that comes from God, or even that there is God of lightning. If this intuitive capability is somehow diminished, then people will be less likely to believe in God or other supernatural concepts. There are at least three studies to support this:
1. The study that shows that people with autism are less likely to believe in God. It tells us that that religious belief relies on being able to intuitively conceptualize deities as intentional agents with mental states who anticipate and respond to human beliefs, desires and concerns, a capacity known as "mentalizing." Autistic people, lacking the ability to imagine what other people are thinking, are having difficulty in conceiving the notion of a concerned God, and therefore less likely to believe in it.
The development of science to replace religion as something that can satisfy human's desire to find meaning and purpose, pushes religion even further. Creationism and intelligent design are challenged by cosmology, physic, and evolutionary biology. The infallibility of Holy Book like Qur'an or Bible is challenged by historical study and textual criticism. The claims of miracle are challenged by chemistry, archaeology, anthropology, and medical science. One thing is left: that belief in God is a subjective experience (thus, there is no way to prove to disprove it.) However, recent developments in evolutionary biology and neuroscience***) have tried to decode the thought process that gives birth to the notions of God and religion. One day, when human mind is finally mapped and it turns out that religion is just a mundane brain phenomenon and there is nothing supernatural or holy about it, what is left from religion? We don't know. But are we ready?
**) It has been suggested that religious figures like Moses (on Exodus 3 and Exodus 19), Saint Paul (on Acts 9:1-19a, Acts 22:3-16, Acts 26:9-18, and perhaps 2 Corinthians 12:7), and Seventh-day Adventists Church founder Ellen White (who once had brain trauma when she was 9) all had temporal lobe epilepsy, which may cause hallucination. This hallucination could be mistakenly perceived as religious vision or divine encounter. Some even wilder theory suggests that Moses was under the influence of psychedelic plants when Ten Commandments were given.
***) - For instance, the "light tunnel" vision during near death experience/NDE (in which some people ascribed that with a journey to the afterlife) can be explained by hypoxia/cerebral anoxia (lack of oxygen to brain.) When a person enter clinical death, brain is deprived of oxygen supply and higher brain areas (frontal lobe, parietal lobe, occipital lobe, and temporal lobe) in the cortex quickly blank out. The more primitive lower brain area (medulla, pons, midbrain, thalamus, hypothalamus) remains active for several minutes, causes "neural noise," or an overload of information sent to the brain's visual cortex, creating an image of a bright light that gradually grows larger, which may be interpreted as going through a tunnel. NDE can also be explained by a sudden REM sleep state while brain is still awake, that is triggered by extreme stress or trauma. Since the higher brain (to process spatial sense, logic, and bodily perception) is malfunctioning during NDE, sensory inputs that come from lower brain (in which also regulate memory) are not processed, resulting in out-of-body experience (OBE), "traveling in extra dimensions," and encounter with angel, demon, God, or dead people. NDE also triggers brain to release endorphin as coping mechanism, which may cause the tranquil, calm, heavenly sensation. Sensory malfunctioning and euphoric sensation from the endorphin together can be simply mistakenly perceived as "afterlife." See also God helmet.
- OBE or astral projection itself can be explained by malfunctioning in temporal parietal junction, causing brain unable to distinguish what is real or not.
- Transcendental feeling when people are meditating is now linked with increased activity in frontal lobes (makes people having more attention and focus.) The thalamus also shuts down normal sensory input during meditation. The parietal lobes (which regulate our spatial and temporal perception) is also less active. Add to that increased flow of endorphin, giving the sensation of having a sense of timelessness, a suspension of self, a feeling of bliss and being "united with universe."
- Speaking with tongue (glossolalia) is associated with lower activity in frontal lobes - the thinking, willful part of the brain through which people control what they do, as were the language centers. This gives the impression for the speaker that God is taking control of her body, and manifested in some unknown speeches.
- Ghost sighting is liked with infrasonic sound. Because the brain is not used to registering frequency so low (since it's not what is usually heard in normal situation,) it cannot associate such frequency to any object/definition, causing spooky feeling. The low frequency can also cause eyeballs to vibrate slightly due to resonance, and it might alter the vision for split seconds, creating ghostly images.