The human brain is arguably the most complex object in the known universe. It contains roughly 86 billion neurons woven together by an estimated 100 trillion synaptic connections. It is responsible for everything that makes us human — our memories, emotions, personalities, dreams, and consciousness itself. And despite decades of research, billions of dollars in funding, and some of the greatest scientific minds in history dedicated to studying it, we still barely understand how it works.
This isn’t a small gap in our knowledge. It’s a chasm. And the story of how science tried — and largely failed — to crack the brain is one of the most fascinating and humbling episodes in modern scientific history.
The Billion-Dollar Bet That Didn’t Pay Off
In January 2013, the European Commission made one of the most audacious bets in the history of science. It awarded neuroscientist Henry Markram and his team €1 billion — roughly $1.3 billion at the time — to build a complete working computer simulation of the human brain within a decade. The project was called the Human Brain Project, and it was launched with extraordinary fanfare.
Markram’s vision was deeply personal. His son Kai had been diagnosed with autism, and he wanted to simulate his son’s brain to understand how he experienced the world. In a celebrated 2009 TED Talk, he told a global audience that simulating the entire human brain on a supercomputer would be possible within ten years. Politicians, press, and public were captivated.
It didn’t go as planned. Almost immediately, the project was engulfed in controversy. By 2014, nearly 800 neuroscientists — including Nobel Prize winners — had signed an open letter questioning the project’s scientific foundations and calling for a complete overhaul. The critics argued that the simulation approach was premature because too little was known about the different types of neurons in the brain and how they were wired together. As neuroscientist Zachary Mainen put it, trying to build a simulation without this foundational knowledge was like trying to repair a broken watch by putting incompletely understood components together at random. As MIT Technology Review later reported, the billion-dollar enterprise was characterised more by infighting and shifting goals than by breakthrough science.
By 2016, Markram had been removed from leadership. The project’s goals were drastically scaled back. When it finally wrapped up in September 2023 after consuming around €600 million and the work of approximately 500 scientists, the honest verdict from Nature was that its achievements were significant in certain narrow technical areas — but fell far short of the original vision. As one participant noted, the final results were deeply disappointing relative to the massive funding and the promises that had been made.
Across the Atlantic, the US had launched its own brain mapping initiative. In April 2013, President Obama announced the BRAIN Initiative — the Brain Research through Advancing Innovative Neurotechnologies programme — calling it the “next great American project.” The goal was to map the firing of every neuron in the human brain simultaneously. A decade and several billion dollars later, the project was winding down. Some progress had been made — new tools for studying the brain had been developed, optogenetics had been advanced, and researchers achieved the remarkable feat of recording more than one million neurons firing simultaneously across the mouse cortex. But the original ambition — to understand how neural firing produces complex human thought — remained as distant as ever.
Why We Can’t Even Understand Simple Brains
Here is a fact that puts the whole challenge in perspective. The lab roundworm — technically known as Caenorhabditis elegans — has exactly 302 neurons and 7,000 connections between them. Scientists have known this for decades. They have painstakingly mapped every single connection. And as Christof Koch, Chief Scientist of the Allen Institute for Brain Science, points out, we still don’t fully understand how those 302 neurons work together to produce the worm’s behaviour.
The human brain has 86 billion neurons and 100 trillion connections. If we can’t figure out the worm, what hope do we have with the most complex object in the known universe?
Koch — who is one of the world’s leading neuroscientists — is refreshingly blunt about where the field stands. “We don’t even understand the brain of a worm,” he says. The sheer number of components is only part of the problem. Scientists don’t yet have a comprehensive “periodic table” of brain cell types — a clear catalogue of all the different kinds of neurons and what each one specifically does. Without knowing the building blocks, building a theory of the whole is essentially impossible.
What Nobody Can Explain
Of all the mysteries the brain presents, none is more fundamental — or more baffling — than consciousness.
Right now, you are reading these words. You are experiencing them. There is something it is like to be you, in this moment, reading this article. That subjective inner experience — the redness of red, the feeling of joy, the ache of grief — is what philosophers call “qualia.” And nobody in the history of science has come close to explaining how physical brain processes give rise to it.
This is what philosopher David Chalmers famously called “The Hard Problem of Consciousness” — a term he coined in 1995 that has become central to neuroscience and philosophy of mind. As Chalmers describes it on Scholarpedia, the hard problem is not about explaining how the brain processes information or categorises stimuli — those are the “easy problems” (which are themselves enormously complex). The hard problem is explaining why any of that processing is accompanied by subjective experience at all. Why is there something it is like to be us?
In 2023, a famous scientific wager came to an end that illustrated just how stuck the field is. In 1998, Koch had bet philosopher David Chalmers that a consciousness circuit would be identified in the brain by 2023. Koch lost. After 25 years of dedicated research, neuroscience has identified many neural correlates of consciousness — brain regions that activate during conscious experience — but has not found anything that explains why those activations feel like anything. The question remains completely open.
We don’t even know definitively which parts of the brain are responsible for consciousness. We know of patients with severe brain damage who retain full conscious experience. We know of cases of terminal lucidity — where patients with severely deteriorated brains suddenly regain full consciousness shortly before death — that defy existing models entirely. The Wikipedia list of unsolved problems in neuroscience devotes an entire section to consciousness, with dozens of sub-problems each of which remains completely unresolved.
We Know Where It Isn’t, Not Where It Is
Memory is one of the brain’s most fundamental and mysterious functions. We know that memories are not stored in one place — decades of research have proven that. We know that the hippocampus plays a critical role in forming new memories. We know that sleep appears to be essential for memory consolidation.
But we don’t actually know what a memory looks like at the physical level. We don’t know exactly how a memory is encoded, stored, or retrieved. We don’t understand why some memories persist vividly for a lifetime while others fade in minutes. We don’t know why emotional experiences seem to be stored differently from neutral ones. And we certainly don’t understand the mechanism behind the most mysterious memory phenomenon of all — why we cannot access memories from our earliest years of childhood, a phenomenon called infantile amnesia.
As the Discover Magazine deep dive on unsolved brain mysteries notes, even the baseline activity of the resting brain — the brain’s default mode when you’re not actively doing anything — may be one of the most important aspects of our mental lives, yet it remains almost completely unexplored. The brain uses 20% of the body’s total oxygen despite making up just 2% of its mass, even when you’re doing nothing. What is it doing with all that energy? We genuinely don’t know.
The Language We Can’t Read
Every time you pick up a cup of coffee, your brain sends a cascade of electrical signals to your muscles. Neurons fire in precise patterns that somehow encode the information needed to coordinate that action. This underlying language of the brain — the system by which neurons encode and transmit information — is called the neural code.
We know almost nothing about it.
We know that neural information is not stored in one place — even simple tasks like picking up an object involve multiple distributed brain regions firing together. We can observe neurons firing. We can record which neurons activate during which tasks. What we cannot do is read the code. We don’t understand what the pattern of firing actually means or how the brain interprets it. It would be as if you could see that Morse code was being transmitted but had no idea what any of the symbols meant.
Researchers at the Allen Institute are now able to observe tens of thousands of neurons firing simultaneously in real time — a massive leap from recording just a few hundred at a time in earlier decades. And their finding so far? The more they look, the more complex it gets. There doesn’t appear to be any simple underlying principle. As Koch puts it, “Evolution doesn’t care about elegance. The brain doesn’t care if you understand it.”
Why Is This So Hard? The Scale of the Problem
Part of the problem is pure scale. Recording the activity of all 86 billion human neurons simultaneously is so far beyond current technology that it borders on the unimaginable. Early BRAIN Initiative researchers described it as watching a TV one pixel at a time — trying to understand a film’s entire plot from a tiny fraction of the screen.
But scale isn’t the only obstacle. There’s also a fundamental theoretical vacuum at the heart of neuroscience. Unlike physics — which has quantum mechanics and general relativity as organising frameworks — or genetics — which had the double helix and then the human genome as its foundation — neuroscience doesn’t have a comprehensive theoretical framework for how the brain works at all. As Nautilus notes, physicists knew what they were building the Large Hadron Collider to find. Genome researchers knew what DNA was before they mapped it. The Human Brain Project was trying to simulate something without any agreed-upon theory of how it works — which is part of why it was doomed from the start.
In 2025, Harvard released a book by neuroscientist Dwayne Godwin and cartoonist Jorge Cham titled Out of Your Mind: The Biggest Mysteries of the Human Brain, which captures both the wonder and the frustration at the heart of the field. For all our advances, the central mystery remains intact.
What We Have Managed to Learn
None of this is to say neuroscience has accomplished nothing. The advances of the last 30 years are genuinely remarkable.
Brain imaging technology — particularly fMRI and EEG — has allowed scientists to watch the brain in action in ways that were simply impossible before. We have mapped broad functional regions of the brain with considerable precision. We understand the basic electrochemical mechanisms by which neurons communicate. We have made significant progress on specific diseases — treatments for epilepsy, new understanding of stroke, advances in neurodegenerative disease research. Optogenetics — using light to control individual neurons — has opened entirely new research possibilities. And the 3D digital brain maps produced by the Human Brain Project, despite its failings, represent a genuine scientific contribution.
After decades of effort and billions of dollars spent, neuroscience finds itself in a paradoxical position. We know more about the brain than ever before. And yet the more we learn, the more we realise how much we don’t know. Every answer seems to generate ten new questions. Every new imaging technology reveals new layers of complexity that previous models failed to anticipate.
The brain remains, as the Allen Institute’s Koch once said, the most complex object in the known universe. Perhaps the most honest thing science can currently say about it is this: we are at the very beginning of understanding something that may take centuries to fully comprehend.
And that, in its own strange way, is one of the most exciting things about being alive right now.
