How Do You Study the Organ that Named Itself?

We know surprisingly, or maybe not so surprisingly, little about the brain. While we have developed countless techniques to study the organs of the body, the brain remains stubbornly opaque. Known for its complexity, it is also uniquely inaccessible, constantly changing, and responsible for the very act of studying itself.

The Complexity of the Brain

The human brain is a marvel of complexity, both structurally and functionally. Composed of ~86 billion neurons, each capable of forming thousands of synapses, it creates a dense, high-dimensional network of interactions. And it’s not just which neurons interact, but how, when, and where; factors influenced by timing, receptor types, neurotransmitters, and whether signals are excitatory or inhibitory. These characteristics provide the framework for a seemingly infinite number of possibilities and patterns. Sound overwhelming? We’re just getting started. 

Perhaps the most elusive property of the brain is “plasticity”, the ability to rewire in response to learning, experience, and injury. Patterns that might seem stable one moment can shift the next. And while we often speak about the neurons, they’re just one part of the picture. The brain also includes glia, immune cells, and vascular structures, all of which play vital roles but are largely left out of mainstream narratives. 

Think about thinking…

What makes the brain truly different from other organs is that it produces “emergent properties”: consciousness, memory, emotions, and perception. These are not the result of individual neurons but of complex, dynamic networks. This makes the brain qualitatively different from the kidney for instance, whose function can be more directly traced to biochemistry and physiology. Consciousness in particular, presents a deep philosophical and scientific challenge. What does it mean to “think”? Some argue that advanced AI may now “think,” but thinking is not necessarily the same as experiencing. Philosopher Thomas Nagel once posed the question: “What is it like to be a bat?” His point was that consciousness is defined not by function, but by what it’s like to exist as a conscious being. An organism is said to be conscious if there is “something that it is like to be that organism - something that it is like for the organism”. It’s not something like a functional state because a robot can act like a human, even though it “experienced” nothing. Are you spiraling yet from thinking about how the brain is thinking? Welcome to neuroscience.

The Problem of Access

The brain is wildly complex and has an infinite number of patterns and possibilities to try and make sense of, but probably the biggest barrier to being able to study the brain is that it’s difficult to access directly and safely. Unlike a liver or a tumor, you can't just biopsy a healthy, functioning human brain. In the rare cases that we do get a sample, it is done on unhealthy tissue, making it problematic for studying normal brain structure. In a recent groundbreaking study, a small biopsy was obtained to access an underlying lesion. Google scientists were able to reconstruct a petavoxel of human cerebral cortex at a nanoscale resolution. 

The tools available to us have advanced rapidly over the years but they are still slow and the outputs are generally noisy. Non-invasive tools like fMRI and EEG offer glimpses into brain activity, but they’re indirect. For example, fMRI tracks changed blood flow, where increased blood flow to a brain region suggests increased activity, but this is not technically signaling. And while invasive studies are more common in animal models, like mice, these experiments are limited by species differences, variability, and interpretation challenges. After all, you can’t exactly ask a mouse how it feels.

Even something as simple as color perception reveals how tricky this is: how do you know that the “red” you see is the same red I see? We might agree on the label, but the internal experience could be wildly different. This is the heart of one of neuroscience’s “impossible” questions and remains an active area of research.

Brains Studying Brains: A Paradox in Progress

To begin understanding the brain, you must ask focused, specific questions. Neuroscience is a vast field, and depending on the question, researchers draw from different subdisciplines:

• Molecular and Cellular Neuroscience

What genes and proteins correspond to the different cellular mechanisms and functions? How are neurons sending signals in a specific context? Neurons send signals both electrically and chemically (neurotransmitters), again increasing the number of possible outcomes. 

• Circuit and Systems Neuroscience

How do different brain regions talk to each other and coordinate entire network signaling? What happens when they rewire (plasticity)? Your brain not only processes how you experience the world cognitively, but also physically. How are sensory signals processed?

• Developmental and Computational Neuroscience

How does the brain wire itself in embryos and then change and rewire through experience? Can we build algorithms that simulate brain circuitry and how it changes?