First Principles and the Brain

First Principles and the Brain

An Engineer’s Journey into Neuroscience

Joseph P. McFadden Sr.

with Claude (Anthropic) as Collaborator

Engineer | Educator | Author

www.McFaddenCAE.com

February 2026

Part of the Building Intuition Before Equations Series

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I am an engineer. I solve problems by understanding how things work, and more importantly, why they fail.

For over four and a half decades, that instinct has served me well in the world of materials, structures, and systems. When a component fails, you do not just replace it and move on. You ask why. You trace the failure back to its root cause. You examine the environment, the loads, the material’s history. You look for the mechanism, not just the symptom.

A few years ago, I turned that same instinct toward something far more complex than any engineered system I had ever analyzed. I turned it toward us. Toward the human brain, human behavior, and the question that kept surfacing in my classroom, in my mentoring, in the news, and in the mirror: Why do we do what we do?

This essay is the story of that journey. Not the conclusions I have reached, because the puzzle is far from complete. But the path I have walked, the tools I have used, and the methodology behind the work that has become my “Neuroscience of...” series. I am writing this because I believe the journey itself matters, and because I want anyone reading my work to understand what stands behind it.

It Started with a Pattern

Teaching engineering at the university level, you see patterns. Students who are bright, capable, and motivated will consistently choose the path of least cognitive resistance. Given the choice between a multiple-choice exam and an essay, they pick multiple choice every time. Not because they cannot write. Because it costs less. Less energy. Less uncertainty. Less exposure to being wrong.

I noticed it in myself, too. That pull toward the easier assessment, the quicker conclusion, the gut reaction that feels like wisdom but might just be reflex. I noticed it in colleagues, in public discourse, in the way people argue about politics without ever questioning why their convictions feel so urgent, so personal, so threatening to examine.

As an engineer, I do not accept “it is what it is.” That answer is lazy, and in engineering, laziness gets people hurt. So I went looking for the mechanism.

Starting with Why: The Philosophical Foundation

My first instinct was not to pick up a neuroscience textbook. It was to go back further. If I wanted to understand why humans behave the way they do, I needed to start with the people who spent their lives asking that question before brain imaging existed.

I read Carl Jung, who mapped the architecture of the unconscious mind and showed how archetypes and shadow elements drive behavior we do not recognize as our own. I read Nietzsche, who dismantled the comfortable assumptions we build our moral lives upon and asked what remains when you strip away the inherited narratives. I read Aleksandr Solzhenitsyn, who demonstrated through the most extreme human conditions that the line between good and evil runs through every human heart, not between groups of people.

These were not casual reads. They were deliberate. Each one peeled back a layer. Jung showed me that the machinery operating beneath conscious awareness is sophisticated and patterned. Nietzsche showed me that our explanations for our own behavior are often post-hoc rationalizations. Solzhenitsyn showed me that under sufficient pressure, the same human hardware can produce heroism or atrocity, and that the difference is often thinner than we want to believe.

I was building a foundation. Not of answers, but of better questions.

From Philosophy to Physical Architecture

Philosophy gave me the questions. Neuroscience gave me a place to look for answers.

I dove into the physical science of the brain. Not the pop-science summaries that dominate social media, but the actual architecture. Neurons, synapses, and the action potential. How signals propagate. How networks form, strengthen, and prune. The latest research on dendritic computation, which is rewriting our understanding of how individual neurons process information, suggesting they are far more than simple on-off switches.

I learned that the brain consumes roughly twenty percent of the body’s energy while comprising only two percent of its mass. That single fact reframed everything. This organ is expensive. Phenomenally, biologically, thermodynamically expensive. And anything that expensive is under constant evolutionary pressure to find shortcuts, conserve resources, and do as little deliberate work as possible.

Suddenly, the patterns I was seeing in my students were not character flaws or generational decline. They were the predictable behavior of an energy-hungry system doing exactly what evolution designed it to do: minimize metabolic expenditure while maintaining survival.

The Evolutionary Lens

Understanding the brain’s physical hardware was necessary but not sufficient. I needed to understand the software, and more importantly, the environment that wrote it.

Evolutionary psychology provided that context. Our brains were shaped on the savanna over hundreds of thousands of years in an environment where speed beat accuracy every time. The organism that paused to carefully evaluate whether a shadow in the grass was a predator did not survive long enough to pass on its genes. The organism that reacted first and asked questions later lived to reproduce.

We inherited that system. The amygdala, our alarm system, fires roughly six times faster than the prefrontal cortex can even begin deliberate analysis. The feeling arrives first. The thinking arrives second. And in that gap between feeling and thinking, we find jumping to conclusions, tribal behavior, confirmation bias, and most of the interpersonal and societal dysfunction we struggle with today.

This is not a flaw. It was a brilliant survival strategy. But the world has changed faster than our biology, and we are running Pleistocene software in a twenty-first-century environment.

The Thermodynamic Thread

Here is where the journey took a turn I did not expect. As I studied the brain through the lens of physics and biology simultaneously, a pattern kept emerging that I recognized from my engineering work: thermodynamics.

In materials science, I teach my students that every material has a personality, characteristics revealed under pressure. Steel bends before it breaks. Glass shatters without warning. These are not random responses. They are the material’s relationship with energy, playing out according to thermodynamic principles. The material is not just passively receiving stress. It is actively navigating an energy landscape, seeking the configuration that minimizes free energy.

The brain does the same thing. Every cognitive shortcut, every reliance on pattern recognition over deliberate analysis, every preference for the familiar over the novel is the brain navigating its own energy landscape. The second law of thermodynamics does not care whether the system is a polymer chain or a neural network. Energy flows downhill. Systems move toward lower energy states. And brains, consuming extraordinary resources, are under relentless pressure to find the path of least metabolic resistance.

This insight connected my two worlds. The engineer who understood why materials behave under stress and the educator trying to understand why humans behave under cognitive and social pressure. The principles are not just analogous. They may be the same principles operating at different scales.

Reading Roger Penrose challenged me to consider consciousness itself through the lens of physics and quantum mechanics. Michael Levin’s work on bioelectricity opened another door entirely, showing that biological intelligence, the ability of systems to set goals and solve problems, extends far beyond the nervous system, down to individual cells navigating morphological space. Thermodynamics, it seems, participates not just in the behavior of brains but in the very mechanism of knowing.

The Tools: AI as a Socratic Partner

I need to address something directly, because it matters for credibility and for honesty.

I use artificial intelligence in my work. I use it extensively. And I am not remotely embarrassed about it.

But I need to be precise about how I use it, because there is a significant difference between asking a machine to think for you and using a machine to think with you.

My process works like this: I read the primary literature. I sit with it. I let connections form, sometimes over days or weeks, sometimes in the shower, sometimes in the car. When an observation crystallizes, when I notice a pattern or a contradiction or a bridge between two disciplines that I have not seen articulated, I bring that observation to a conversation with an AI partner.

Not one partner. Multiple. I work across different AI systems deliberately, because each one reasons differently, challenges differently, and finds different weaknesses in an argument. These are not brief exchanges. They are extended Socratic dialogues, sometimes spanning hours, where I present my observations, push back on the analysis, ask for contradictions, request the strongest counterarguments, and refine my thinking through sustained intellectual pressure.

The observations are mine. The connections are mine. The engineering intuition that says this pattern in brain behavior looks exactly like that pattern in material failure is mine, built over decades of working with both. What AI provides is what a brilliant graduate seminar provides: challenge, perspective, depth of reference, and the relentless willingness to keep asking “but why?”

When I then produce an essay, a posting, or an audiobook, I am not publishing the AI’s output. I am publishing the refined product of my thinking, tested and sharpened through a process that happens to include AI among its tools, alongside the primary literature, classroom observation, and decades of engineering practice.

I say this not defensively but as a matter of methodology. Because methodology matters. Because “where did this come from?” is a legitimate question, and the answer should be honest.

The “Neuroscience of...” Series

All of this work, the reading, the thinking, the conversations, the classroom experiments, converges in what has become my “Neuroscience of...” essay series, part of the larger Building Intuition Before Equations body of work.

The title format is deliberate. Each essay begins with neuroscience because I believe the path to understanding human behavior runs through the physical machinery that produces it. Not around it. Through it. If you want to understand why people jump to conclusions, you need to understand the amygdala. If you want to understand why passive learning leads to cognitive decline, you need to understand synaptic pruning and metabolic conservation. If you want to understand why we stop listening to people who disagree with us, you need to understand how threat detection, memory encoding, and executive function interact under social pressure.

The approach in every essay follows the same structure. First, I build the scientific understanding. What is actually happening in the brain, at the level of regions, networks, and neurochemistry. Then, I connect that science to observable human behavior, the kind of behavior my readers recognize in themselves and others. Finally, I offer practical tools and protocols, systems for working with your own neural architecture rather than being unconsciously controlled by it.

For younger audiences and students, I have developed a character framework that brings the brain regions to life. The amygdala becomes Amy, the hippocampus becomes the Hippo twins, and the prefrontal cortex becomes PFC. These are not cartoons. They are teaching tools that make complex neuroscience memorable and actionable. In engineering, we say a concept is not truly understood until it can be explained simply. The characters are my attempt to meet that standard.

The Incomplete Puzzle

I want to be explicit about something. I am not a neuroscientist. I am not a psychologist. I am not a philosopher. I am an engineer and an educator who has spent years doing what engineers do: looking at a complex system, breaking it into components, understanding the interactions, and building a working model.

My model is incomplete. Pieces are still missing. Some pieces I placed early on have shifted as I learned more. Some have been discarded entirely. That is not a weakness of the work. That is the work.

I describe myself as a purveyor of cognitive dissonance because I believe that discomfort, the productive confusion that comes from realizing your current understanding is insufficient, is where genuine learning lives. The brain would prefer certainty. It would prefer the settled, low-energy state of having already decided. But growth happens when you resist that pull and sit with the incomplete picture long enough to see new connections.

The puzzle is far from complete, and that is precisely what makes it worth doing. The deeper I dig, the more I discover. And the more I discover, the more joy I find in the digging. That is not a throwaway line. That is the entire point of everything I write.

An Invitation

If you have read my essays or listened to my audiobooks, I hope this piece gives you a clearer picture of what stands behind them. Not a prompt typed into a machine. A deliberate, years-long journey from first principles through philosophy, psychology, neuroscience, evolutionary biology, and thermodynamics, tested and refined through every tool available, including the most powerful Socratic partners ever built.

If you have not encountered my work before, consider this an invitation. Not to accept my conclusions, many of which I hold loosely and deliberately. But to adopt the methodology. Start with why. Go to the primary sources. Build from the ground up. Use every tool available, but make sure the observations, the connections, and the questions are yours.

The world does not need more people repeating what they have been told. It needs more people willing to do the expensive cognitive work of figuring out why things are the way they are. That is what engineers do. That is what students should be learning to do. And that is what I will keep doing, one essay at a time, as long as there are pieces of the puzzle still missing.

And I suspect there always will be.

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Be a driver, not a passenger.

Now go do the work.

Combating Engineering Mind Blindness, One Student at a Time.

Every failure tells a story.

www.McFaddenCAE.com

McFadden@snet.net