Religion is highly personal for some believers, and it can be pervasive in every aspect of their lives. Cultural norms are heavily influenced by religious beliefs and practices, and many religions place a heavy focus on a person's individual relationship with a deity. Even people who are not otherwise affiliated with organized religions may feel strongly about their personal relationship with God. 



The problem with using these personal relationships as proof of God's existence is that they are inherently subjective experiences. A person's experience and the emotions it causes can be genuine without the cause of that experience being based on anything outside of his or her mind. For example, near-death experiences, the experience of being disconnected from your body or moving down a tunnel toward a bright light is common and feels very real for the person experiencing it. However, studies have shown that near-death experiences are caused by chemical reactions within the brain ⁽¹⁾. The same can be true for many religious experiences.

The Temporal Lobe and Religious Experiences

When some people talk about their personal relationship with God, it's in fairly nebulous or metaphorical terms. They might discuss the way that praying makes them feel more peaceful or how reading certain passages of their preferred holy book sends chills down their spine. Others, though, use this description much more literally. Some people report having visions, hearing the voice of God or otherwise having a sensory experience. 



Of course, emotional effects of prayer do not necessarily have to have a supernatural origin, and religious people are not the only ones that can have seemingly paranormal sensory experiences, and these experiences can occur in obviously secular situations. For example, mental illness and drug use can disrupt normal sensory experiences. In fact, certain hallucinogenic substances have been used in religious ceremonies for centuries among certain cultures ⁽²⁾. 


Recent scientific discoveries have helped to explain some of the chemical reactions behind religious experiences. Part of this research began by examining people with temporal lobe epilepsy, a neurological condition which can frequently trigger religious hallucinations in addition to seizures and sensory disruptions ⁽³⁾. The basic conclusion we can draw here is that, although someone may have an extraordinary feeling or experience, the cause of that experience is not necessarily supernatural. As we know, the same types of experiences and feelings can be brought on by entirely natural and explainable causes.


Seeing What You Want to See

The human brain is hard-wired to spot patterns, even in random noise ⁽⁴⁾. This patternicity, as science historian Michael Shermer calls it, plays a heavy role in how religious experiences occur. People who are raised within a religious culture will generally have experiences that mirror the expectations of that culture. This means that an unexplained sensory experience might be attributed by a religious person to be a message from God. The same experience felt by another person might be variously attributed as a ghost, a demon, telepathy, alien abduction or hallucination depending on that person's individual experiences and expectations.

This creates a feedback loop, where people see what they want to believe, which then supports the beliefs they already hold. While all of this can be powerfully persuasive for the person experiencing it, none of it constitutes evidence of a deity.

The Burden of Proof

Science is uncovering a better understanding of the neurological basis behind many religious experiences ⁽⁵⁾. At the same time, science cannot nor is it expected to disprove claims based on every subjective experience a person may have. The burden of proof is always on the person making a claim, not on the person that the claim is being made to. So in order for an individual's personal relationship with God to act as proof of God's existence, it's up to the person making this claim to substantiate it. 



Imagine, for example, that a person claims that an angel came down from heaven for a visit at their home to share a cup of tea and plate of biscuits. This is a far-fetched claim, and before you believe it, you’d likely want some proof: Did anyone see the angel? Did it leave behind any evidence of its presence? Without evidence, an explanation fitting the known laws of the universe makes more sense: Either the person is lying or he is delusional or mistaken about what happened. 


Assume that two different people make such a claim. One hallucinated the entire experience, while the other was actually visited by an angel. Without any evidence, the two experiences are indistinguishable from the perspective of an outsider. We have no reason to believe this claim or any other third-party account of personal experience. 


A person's experiences are personal and ultimately unfalsifiable. We cannot see other people’s dreams or hear the voices inside their heads. If a person makes the claim that her personal experiences reflect physical reality, she needs to be prepared to back up those claims with actual evidence. Subjective experiences and anecdotal evidence are not sufficient to provide proof of a deity's existence, and wanting to believe something does not make it true.

References:

1. Blanke, Olaf, and Sebastian Dieguez. "Leaving body and life behind: Out-of-body and near-death experience." The neurology of consciousness: Cognitive neuroscience and neuropathology (2009): 303-325.
2. 

Pinchbeck, Daniel. Breaking Open the Head: A Psychedelic Journey into the Heart of Contemporary Shamanism. New York: Broadway Books, 2002.
3. 
Ramachandran, V. S., Sandra Blakeslee, and Oliver Sacks. Phantoms in the Brain: Probing the Mysteries of the Human Mind. New York: William Morrow, 1999.
4. Shermer, Michael. The Believing Brain: From Ghosts and Gods to Politics and Conspiracies---How We Construct Beliefs and Reinforce Them as Truths. St. Martin's Griffin, 2012.
5. Beauregard, Mario, and Vincent Paquette. "Neural Correlates Of A Mystical Experience In Carmelite Nuns." Neuroscience Letters 405 (2006): 186-90.