The Problem with Understanding the Mind by Studying the Brain

Gabriel A. Silva
5 min readMar 10, 2020


When I was a kid I sometimes imagined that everyone I knew were actually alien beings that would put on human looking masks whenever they interacted with me. Whenever I wasn’t paying attention they would take off their masks and look, well, however it was they looked like in their natural state. It was as if I was at the center of some strange alien experiment that revolved around tricking me about the true nature of reality. My own personal Truman Show long before the movie ever came out. Of course, I never really believed it was real. But it occurred to me that even though I knew it was not true, I had no real empirical or objective way of proving it to myself. If it was true and alien beings really were putting on masks, by the very nature of how I set this up in my head I couldn’t catch them in the act. And if it wasn’t true, well, I couldn’t prove that it wasn’t because I couldn’t separate from the condition that it was.

This was my first exposure to questions about self awareness and the nature of reality. It also made me realize the dichotomy between what I could prove and understand in relation to what I could observe. Fast forward to today. A similar struggle exists between my drive to understand the brain as an engineered system, and the mind as the output of that system. For our purposes, the mind is the functional output of what the brain produces, including consciousness and self awareness. But why is the mind is so difficult to understand by studying the brain?

In every other physical system that we now of the “thing” being studied, the physical object or process — or even just an idea that we are trying to understand, is observable or measurable. And if it isn’t it is at least conceptually or intellectually accessible in the sense that the end goal, the understanding we are trying to achieve, can be described or speculated about in a way we can share and communicate to others. In other words, we can at least write down “what” we are trying to understand, even if actually observing or probing it may be difficult or even impossible. If nothing else, the problem itself is understandable.

Consider this in the context of some of the most challenging topics in science that we presently know of.

Black holes are arguably one of the strangest and most mysterious objects in the universe. They are impossible to observe directly beyond their event horizon. Beyond this point the gravity of a black hole is so severe that it bends space-time to such an extreme degree that no matter in what direction you travel everything moves towards the singularity at the center of the black hole. Nothing can escape past this point, not even light. No information can be practically retrieved, even though it it is not destroyed. The physics at the singularity is a complete unknown. We don’t understand or have the right physical laws and mathematical equations to describe or predict what happens. Yet, despite all this, we at least know where our understanding of the physics breaks down. We can in a very real way explain the problem, the physical system itself, even though we can’t observe it or know what the answer is.

Another good example is quantum mechanics. As mysterious as it is, having no natural intuition about how or why things behave the way they do at quantum scales, the mathematics has never failed to properly explain any experimental result. The interpretation of what it all means remains the subject of intense philisopical debate, but the physics itself is very accessible. And importantly, arguments about how to interpret quantum mechanics are also accessible. What we are attempting to understand and make sense of is the weirdness of quantum mechanics that the experiments and mathematics show us.

In the outer fringes of pure mathematics abstract ideas born from pure thought strain the imagination and attempts at following the threads of logical progressions from axioms to theorems. Yet, the objects of interest and study are those ideas themselves. They are also accessible.

This is not so with the brain and mind. But why? What is so fundamentally different about the brain and how the mind emerges from it that differentiates it from other physical systems? After all, the brain must also follow physical laws. In fact, we know quite a lot about its its genetics, molecular biology, biophysics, and physiology. And we understand and can describe how these different components come together to varying degrees of detail. There’s a lot about the brain we can measure, observe, and model. Yet, there is something fundamental about the outputs of the brain that escapes us — that resists understanding. When it comes to the mind, we can’t even come to a consensus on what the right questions are. Hypotheses, ideas, and speculation among neuroscientists, philosophers, and arm chair observers abound of course, but even a cursory read of the literature will quickly convince you how little agreement there is.

Here’s the problem: The mind, as a product of the brain, is completely self-referential and closed from the outside world and everyone and everything else in it. We don’t actually know what the physical world looks and feels like. We create internal perceptual models of what we think it is from information taken in from our five senses and our internal creativity in how we put all that information together. For example, I can describe to you in detail what the color red looks and feels like to me. And you can do the same for me. But you will never know what red really means to me, nor I for you. Your mind is literally a singularly unique personal experience. It is precisely this fact that makes studying the brain to grasp the mind is so difficult.

We want to understand the mind, but can only observe, measure, and think about the brain. For example, the electrical patterns we measure in the brain and the connectivity of the networks that make it up are things we can measure, model mathematically, and discuss how the genetic and molecular details that produce them underlie the neural code — the internal language the brain uses to represent and process information. But there exists a gap, a chasm really, between this and the emergence of self-awareness and consciousness because of the self-referential nature of the mind. And to a theoretical neuroscientist, this fact is both my greatest source of motivation and drive, and my greatest defeat and frustration. On a positive note though, it also represents perpetual job security.



Gabriel A. Silva

Professor of Bioengineering and Neurosciences, University of California San Diego