For years I speculated about the soul, consciousness and free will. Was the supernatural required to explain these things. If so, how does it act on the natural (material)? How do you explain free will in a clockwork universe? Since, we are too large for the laws of quantum mechanics (QM) to apply and since QM may be more likely to account for free will, could consciousness be a subatomic particle? This would explain animism.
However, everytime I looked into neuroscience, I would discover that a new aspect of what we consider ourselves to be was a function of the brain. Eventually, I found the evidence to be overwhelming.
Personality and Morality
The story of modern neuroscience begins with the story of Phineas Gage. In 1848, while Gage was working as a railroad construction foreman he was tamping dynamite into a hole in a rock when the dynamite went off. It blew the tamping rod through his skull damaging his left frontal lobe.
His personality changed to such a degree that his friends said he was no longer Gage. The frontal lobes control our emotions and is the seat of personality. This is why the frontal lobotomy was such a cruel procedure.
Here is an account of the changes in Gage as reported by the Bulletin of the Massachusetts Medical Society,
“His contractors, who regarded him as the most efficient and capable foreman in their employ previous to his injury, considered the change in his mind so marked that they could not give him his place again. He is fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows, impatient of restraint of advice when it conflicts with his desires, at times pertinaciously obstinate, yet capricious and vacillating, devising many plans of future operation, which are no sooner arranged than they are abandoned in turn for others appearing more feasible. In this regard, his mind was radically changed, so decidedly that his friends and acquaintances said he was “no longer Gage”.”
Over time due to the plasticity of the brain and due to social influences, he was able to regain some of who he was before.
Clearly, the damage affected his morality: “irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows, impatient of restraint of advice when it conflicts with his desires”
Damage to the anterior prefrontal cortex in children affects their ability to develop moral reasoning.
Emotions and Desires
in the 1920’s, by using electrical stimulation of various places in the brain of a cat, Swiss physiologist Walter Rudolf Hess could elicit rage, hunger and sleepiness. 
John Fulton reported in 1935 how he was able to make a violent chimp calm after destroying the prefrontal lobes. He was disturbed when he found out that Egas Moniz was using his procedure on psychotic mental patients. He later embraced the use of psychosurgery on mental patients. 
Emotions and Behaviors
Jose Delgado was a physiology professor who was horrified at the use of lobotomy on mental patients. In the 1950’s he began experimenting with electrical brain stimulation to elicit emotions and physical responses. He used a feedback loop to train the brain of a chimp named Paddy to be less anxious.
His most famous experiment was when he placed electrodes in the brain of a bull. He entered a bullfighting ring with the bull. When the bull charged him, he flip a switch on his transmitter and the bull walked away. Here is a video of this experiment: https://www.youtube.com/watch?v=23pXqY3X6c8 
Self Control and the Sense of Self
Tests of emotional regulation have shown that the inhibition of emotions is performed by the ventromedial prefrontal cortex.
Studies suggest that the medial prefrontal cortex and the medial posterior parietal cortex are involved in the recall of knowledge about oneself.  The posterior cingulate cortex, the Cortical Midline Structures and the the insula are involved in self reflection.
In his book, Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts, Stanislas Dehaene details experiments that show we can take in information subconsciously that we aren’t conscious of. He describes further experiments that show that information we only registered subconsciously can affect our conscious perceptions of the things we see soon after.
This is one I used to puzzle over a lot. It is difficult to see how one’s consciousness arises from neurons. I even speculated a subatomic particle that created consciousness.
My idea is that it was as fundamental to nature as the electron. This was easier for me to accept than it being an electrochemical process. However, this just moves the question from neuroscience to physics. Nothing more was accomplished by this idea than making me feel better.
Consciousness is altered through chemical substances. For example, you lose consciousness from anesthesia. Your consciousness can be restricted by sedatives. Some say hallucinogens alter consciousness. I actually suspect that consciousness remains unaltered while the perceptions are altered.
Whether due to drinking, a drug overdose or mental illness, one can have blackouts. This is where one continues to go about her or his activities, but having no recollection of performing them. Post-blackout, you may find evidence of your activities. Sometimes the evidence is strange because your behavior was out of character. Were you conscious at the time and later forgot what you did? If not, who was in control?
Brain trauma that diverts blood flow away from the frontal lobes affect self-awareness. An epileptic seizure will cause dissociation and hallucination–a so-called altered state of consciousness.
In his book, Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts, Stanislas Dehaene observes that the moment a perception becomes conscious a large number of neuron spanning many areas of the brain fire.
In 2014, Mohamad Koubeissi director of the Epilepsy Center at George Washington University’s School of Medicine and Health Sciences published a paper about an experiment where he used electrical stimulation to disable consciousness. 
Many experiments have been conducted in neuroscience in order to understand free will. A complete model has not been developed. There are still a lot of contentious issues. One of which is free will may be an illusion. I for one hope not. I would have to abandon Buddhism and convert to Ājīvika or follow the philosopher Richard Taylor.
Patrick Haggard has proposed that prior intention and deliberation are functions of the medial prefrontal cortex. This is merely a proposal, however those things we consider most human originate in the prefrontal cortex, so I wouldn’t be surprised that free will would originate there as well.
Since mechanisms in the brain for emotions, desires, behaviors, sense of self and the subconscious are well known and understanding of brain structures involved in consciousness have come a long way, it didn’t make sense to me to invoke the supernatural just to explain free will. It is for this reason I became a materialist.