Thinking is a full body activity, problem, not just a brain activity

In earlier posts, we have discussed concepts like “self,” “qualia,” and “free will.” We claimed they are illusions created by our brain/body thinking mechanism — very convincing illusions, but scientifically invalid.

The March 14th issue of New Scientist Magazine contained an article that bears on this subject. The opening line of the article captures a major shift in thinking about Alzheimer’s disease:

Alzheimer’s may start outside the brain. Inflammation in organs like the skin, lungs, and gut during midlife may trigger Alzheimer’s disease in later years.

“Alzheimer’s disease has long been viewed as something that originates inside the brain. But an in-depth genomic analysis suggests it may initially be triggered by inflammation in distant organs such as the skin—perhaps decades before a person’s memory starts to decline.

This radical reframing of the condition may explain why Alzheimer’s drugs have been disappointing to date, because they act too late in the disease progression.”

Thinking Isn’t Only in Your Brain — It’s in Your Entire Body

One of our most basic assumptions about thinking is wrong. Thinking does not begin and end in the brain. The whole body thinks. We may imagine the brain as the command center. But the entire body is a vast network of continuous two-way communication.

Immune signals rise and fall; Hormones circulate and alter behavior; The gut communicates with the brain; The skin constantly senses and reports. Signals are always moving—back and forth, across the entire organism.

What we call “thinking” is not located in one organ. It is the ongoing pattern of responses across the whole system.

Instead of “the brain thinks,” consider: stimulus → organized response → integrated response → ongoing chain

This thinking applies to the entire body. The brain is a major hub, yes—but it is not the origin of thought. It is part of a larger process.

An Alzheimer’s patient may not realize how deeply the disease has altered his thinking; his perceptions are distorted; his conclusions may be wrong;. his memory is unreliable

Yet he still feels: “I am thinking. I am deciding.” From the inside, the process still feels like control. Like all of us, he believes he has free will.

We also: Do not perceive the mechanisms behind our thoughts, Do not see the countless signals shaping every belief
Do not experience the lifelong accumulation of stimuli driving our responses. 

Yet we too conclude: “I am in control. I have free will.”

If inflammation in the skin can begin altering thought decades before symptoms appear, then the same principle applies more broadly: Our thoughts are the result of processes we neither see nor control.

Hit your thumb with a hammer. Eat an orange. Have a conversation. Experience a loss. Each event alters the system—chemically, electrically, structurally.

Years later, you may hold a belief , make a decision, express a preference, without the slightest awareness of the chain of events that produced it.

The illusion of self and free will

From this perspective, the “self” is not a controller. It is the ultimate illusion — the story the system tells about its own activity. It’s a useful story—but still just a story.

Just as an Alzheimer’s patient cannot see how inflammation has reshaped his thinking, a healthy person cannot see how a lifetime of stimuli has shaped his. The difference is not in kind, but in visibility.

In the same way, the feeling of control does not prove the existence of a controller. The bottom line: Everything responds to stimuli. In living systems, those responses become organized, integrated, continuous over time

What we call thought, belief, desire, and self are patterns within that process. The Alzheimer’s patient shows us what happens when the system breaks down. The rest of us experience how convincing the system is when it holds together. 

You may feel that you have free will, but consider these familiar stimuli, many of which you may have experienced

Lack of sleep: One bad night and people become irritable, pessimistic, and impulsive. The same person, same “self,” produces different conclusions about life. A rested brain plans long-term. A tired brain seeks immediate relief.
Hunger: Low blood sugar leads to anger, impatience, and poor decisions. Eat a sandwich, and suddenly the world looks reasonable again.
Caffeine: A cup of coffee can increase focus, confidence, even risk-taking. The “you” before and after caffeine is measurably different.
Gut bacteria: can have a profound influence on your thinking. Certain gut bacteria are linked to depression and anxiety. Change the gut, and mood can change. Gut microbes influence what you want to eat — sugar, fat, specific foods. You think you want it. Your gut may be nudging you. It’s one reason why dieting can be so difficult. Fecal transplant studies show that transferring gut bacteria from one animal to another, and can transfer: anxiety levels, boldness vs. caution, and even social behavior. Same brain structure. Different gut → different behavior.
Pain: A headache or back pain narrows attention and reduces patience. Chronic pain sufferers often develop different outlooks on life.
Prescription drugs: Antidepressants, anti-anxiety meds, even blood pressure drugs can alter mood, motivation, and decision-making.
Hormones: Testosterone, estrogen, cortisol — all affect aggression, attraction, stress response, and confidence.
Illness and inflammation
Even a mild infection can cause “brain fog,” fatigue, and pessimism. The immune system is quietly rewriting your thinking.
Noise: Your concentration drops, errors increase, frustration rises.
Heat and cold: Extreme heat increases aggression and reduces cognitive performance. Cold slows thinking and reaction time.
Lighting: Dim light can reduce alertness; bright light can improve mood and focus. Brain states → different “selves”
Time of day: Morning vs. late night thinking can be radically different. Ideas that seem brilliant at 2 a.m. often look foolish at 8 a.m.
Stress: Under stress, the brain shifts toward quick, survival-oriented thinking — less nuance, more certainty, more error.
Peer pressure: People will say things they know are wrong just to align with a group.
Authority influence: If a “trusted expert” says it, people believe it — even when it conflicts with their own experience.
Repetition (the “illusion of truth”): Hear something often enough, and it begins to feel true. Consider the thought processes of people who watch Fox News vs. people who listen to public radio.
Optical illusions: You see something that is not there — and you cannot “decide” to see correctly.
Advertising and framing: The same information, framed differently, leads to different decisions. Every salesperson knows this.
Childhood experiences: Early rewards and punishments shape adult beliefs and preferences.
Trauma: A single event can permanently alter risk perception, trust, and emotional reactions.
Habits: Repeated actions become automatic responses — what feels like “choice” is often just rehearsal.

Then, there are all the diseases that affect our thinking. In addition to the aforementioned Alzheimer’s, we have”

Other Neurological diseases affecting memory, judgment, personality — all progressively change.
The person does not choose confusion. It is imposed.
Parkinson’s disease, hnown mainly for movement problems, but also causes: depression, apathy, and impaired decision-making.
Stroke: A small area of brain dFamage can eliminate speech, alter personality, change emotional responses
Mental illnesses cause depression, anxiety disorders. (harmless situations feel dangerous, bipolar disorder (the same person cycles between grand certainty (“I can do anything”) and deep despair;
Urinary tract infection can cause confusion, hallucinations, personality changes
Encephalitis / brain infections can rapidly alter cognition, behavior, and identity.
Hormonal and metabolic diseases: Thyroid disorders (hypothyroidism leads to sluggish thinking, depression) (hyperthyroidism leads to anxiety, agitation)

Every one of these examples shows the same thing: Change the inputs, change the body, and you change the thoughts. If microbes in your intestines can alter your mood, influence your cravings, and change your stress response, then the idea of a self-contained, independent “thinker” is simply wrong.

You  often might say: “That wasn’t really me — it was the caffeine.” or “That wasn’t my belief — it was the lack of sleep.”

If alcohol can change judgment; hunger can change temperament; noise can change reasoning; hormones can change desire; inflammation can change cognition, then what we call “free will” is simply the name we give to decisions whose real causes we don’t recognize.

You may think you have free will — we all experience that feeling — but it is just nature’s illusion.

What commonly are termed “consciousness” and “free will” are nothing more than stimuli leading to responses which lead to more stimuli/responses, in an endless chain. There is no magic. It’s all physics. It’s all stimulus → organized response → integrated response → ongoing chain.

You aren’t “conscious.” You are responsive.

Rodger Malcolm Mitchell

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