Humans have asked where we come from for thousands of years, across all cultures. But only recently have we started to address the mystery of the evolution of the human brain — the organ that's the source of those existential questions, not to mention our evolutionary success itself.

Top image: Hubis/Shutterstock.com

Our brains are each made of billions of cells, called neurons, that link together to form living circuit boards that control everything from our thoughts to our behaviors to the rhythm of our breathing. We aren't the only creatures with brains, but our brains are unique in terms of their size relative to our bodies, and in terms of their complexity. Just how did incremental changes to ancient animal brains, over millions of years, eventually result in this most sophisticated of living, computing machines?

A schematic of the connections between neurons in the human brain, based on an MRI dataset from living humans. Thomas Shultz.

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Unfortunately, the soft consistency of brain tissue has robbed us of our ability to directly reconstruct the origins of this defining human feature. Bones, buried in the right geological layer, can turn into fossils that last eons. But brains disintegrate quickly, leaving almost no trace behind.

While fossils can't show us exactly what ancient brains looked like, fossilized skulls can hint at what was required to protect and house ancient brains. Similarly, though the common ancestors of most species are extinct, the many surviving species that populate the planet, known as extant species, are useful for inferring the incremental changes that advanced the brain forward. For example, amongst extant vertebrates (animals possessing spines and spinal cords), it's satisfying to see brains grow in size and complexity as animals evolved from swimmers to crawlers to walkers.

(Remember, though, that comparing extant species in this way only provides an indirect view of evolutionary history: modern fish have also evolved, over millions of years, from their last common ancestor with humans.)

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But the story of the human brain stretches even further back than what we can see in our animal relatives.

In fact, the story predates even the first neurons, which we often think of as the building blocks of even the simplest brains. To understand where brains come from, we have to reach back to the first examples of life forms capable of successfully reacting to their immediate environment. The evolution of the human brain begins with bacteria.

Even bacteria can think (sort of)

Obviously, single-celled organisms like bacteria utterly lack neurons, let alone brains. Modern genetics increasingly shows, however, that bacteria possess a unit of human brain structure even more microscopic than neurons: ion channels.

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Ion channels are large proteins that selectively allow ions (electrically-charged molecules) to flow in and out of cells. In the human brain, as well as in the neurons of even the smallest-brained animals, ion channels are vital for communication, or signaling, between neurons. Ion channels allow for messages to travel down the lengths of individual neurons, somewhat analogous to electric charge traveling down an electrical wire. This signaling is the basis for every computation the brain carries out.

Intriguingly, many of these ion channels found in human neurons are also present in ancient organisms such as bacteria, because the genes providing the instructions for building ion channels in human neurons are also found in bacteria.

But why would bacteria need ion channels if they don't have neurons? Some bacteria possess mechanically-sensitive ion channels, as well as microscopic propellers that drive movement, giving them a rudimentary sense of touch and the ability to move. Within a single bacterial cell, sensation, information processing (you could call it a simple form of 'memory'), and reaction can be coordinated, partially thanks to the same ion channels responsible for human brain signaling. Eons before more complex organisms would use neurons to build nervous systems, ion channels were aiding bacteria in their quest to interact with their surroundings.

Bacteria demonstrating their ability to move in a petri dish. This movement isn't as random as it seems, as bacteria are capable of sensing their environment and reacting appropriately, partially thanks to ion channels.

As a species of tinkerers, we sometimes mistakenly assume that complex biological structures, like neurons, explicitly evolved to carry out brain signaling. But evolution's only goal as an 'tinkerer' is to promote the survival of an existing species, not necessarily to build complex structures for future species.

Bacterial ion channels demonstrate an important lesson of modern evolutionary theory, as articulated by Richard Dawkins in his book, The Extended Phenotype, with reference to newly-evolved traits:

Not only must the end product get off the ground; so must every intermediate along the way, and each intermediate must be superior to its predecessor.

Ion channels on their own needed to be useful for the first organisms that possessed them, in order to be inherited by future generations. Thus, primitive forms of bacterial 'thinking' actually predated the very structures we consider necessary for our own thoughts (neurons and brains). Bacterial ion channels suggest that the ability to sense and react evolved slowly, in very simple organisms lacking neurons, only to eventually be consolidated into the specialized neurons we now see in animals.

Did sea sponges grow the first synapses?

Bacteria, and their single-celled cousins (archaea), comprised all of Earth's life for a few billion years, until some of their ilk banded together to form early multicellular organisms. With this advancement, life boomed as never before.

Nick Hobgood

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Sea sponges represent the beginning of the tidal wave of multicellular diversity that swept across the planet about 600 million years ago. While sea sponges consist of colonies of very simple cells (their bodies contain no organs or nervous systems whatsoever), these cells aggregate using proteins on their cell membranes to communicate with one another. Surprisingly, these same cell communication proteins are also vital for building synapses in the human nervous system. Synapses are the junctions between neurons that allow for neurons to transmit signals from one to another.

Similar to the presence of ion channels in bacteria in the absence of neurons, these 'synaptic' proteins were present in sponges in the absence of synapses themselves. It's likely that nervous systems (brains and nerves) arose from this novel application of pre-existing parts. Scientists call this process "exaptation," and it is one of the lesser-appreciated ways in which species evolve. Think of it as the upcycling of the evolutionary process.

While an adaptation becomes prevalent through natural selection, an exaptation reflects how an organism can recommission an inherited trait for a new purpose. The feathers that allow birds to fly today probably evolved for a completely different purpose. Early proto-feathers likely aided dinosaurs with their mating displays. It was only through exaptation of feathers that birds were able to take to the skies. Likewise, nervous systems evolved out of simpler systems that merely existed to coordinate multicellularity, or basic sensation.

An example of some of Ramon y Cajal's 19th-century drawings of neurons.

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Still, scientists disagree vehemently over the origins of the first neurons. It's appealing to imagine a single cell, capable of sensing and behaving just like a bacterium, separating its functions into two cells, a neuron and a muscle cell, that communicate on an intimate, molecular level. But it's also hard to dismiss the possibility that these cells arose independently and figured out how to talk to one another, something that is seen during the development of nearly all animals. Lacking a fossil of the first neurons, however, all this scientific musing is likely to remain speculation for some time to come.

The first neurons were a hit for animal life

A mere 50 million years after the appearance of sea sponges, various marine worms and jellyfish had evolved. These multicellular creatures had actual neurons, complete with both ion channels and synapses, loosely organized into nerve nets. These nerve nets, consisting of handfuls of individual neurons, were sparsely spread around the mouths of these simple marine creatures, very unlike the concentrated masses of neurons in our brains. The nerve nets enabled simple predatory behaviors like hunting, which allowed animals to get food a lot more easily. Having even a simple nervous system, it turned out, was highly advantageous for animals on Earth.

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As these new animals diversified, so did their nerve nets. Just one group of organisms with nerve nets evolved into three very different groups: cephalopods (octopus, squid, cuttlefish), gastropods (sea slugs), and bivalves (clams). Cephalopods have complex, large brains, and gastropods have concentrated groups of neurons, called ganglia, in their heads. Meanwhile, bivalves possess just simple nerve nets. You might think that bivalves came first, while the cephalopods emerged later, because simple brains should, in theory, predate complex brains.

A coconut octopus, a cephalopod known to 'tip-toe' and carry around shells for shelter. Nick Hobgood

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But DNA tells a different story. By analyzing the genomes of animals from all three groups, scientists found out that cephalopods had actually branched away from the gastropods and bivalves quite early during evolution.

Brain complexity evolved independently in each of these animals, a discovery that contradicted traditional ideas about brain evolution. It also raised the possibility that brain devolution may have allowed the bivalves to shed the more complicated nervous systems of the mollusk common ancestor of all three groups, in favor of a sleeker neural net better suited to the bivalve lifestyle.

Suffice to say, the question of how neurons and brains first evolved is still an open question. The more we learn about animal ancestries from genetic data, the more it seems that brains may not come from a common origin, but instead evolved separately in many animal groups. Given the right building blocks, evolution may have come up with a similar solution to the same problem multiple times.

A twist in the story

Around the same time that mollusks were diversifying, other animals were evolving spinal cords and distributing nerves throughout their bodies. This new organization of the nervous system, featuring internal, bony structures full of nerves running up our backs, turned out to be a remarkable twist in brain evolution.

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UC Berkeley developmental biologist Phil Abitua studies the evolution of one cell type, the "neural crest," which spurred the development of the vertebrate nervous system. His lab, the Levine Lab at UC Berkeley, was on a hunt for ancestral neural crest cells and the origins of the vertebrate nervous system.

Neural crest cells are incredibly powerful. They "have the potential to give rise to all the pigment in your body, the majority of your peripheral nervous system, the cranium and the cartilage of your head," Abitua tells io9.

These cells accomplish so many tasks by playing an important role in fetal development, migrating from the growing head of an animal to areas throughout the body. Neural crest cells also form the jaw, a key development for vertebrates who hunt to survive.

A lancelet, the fish-like animal that was falsely believed to be the closest extant relative of vertebrates. Hans Hillewaert

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For years, scientists believed lancelets, which look like long, thin fish, were one of the most recent pre-vertebrate ancestors. The Levine lab, however, was interested in a less-familiar organism, the sea squirt, which is known to spray unsuspecting tidepoolers with sea water.

"Even though cephalochordates [like lancelets] look more like vertebrates, sea squirts are more closely related, based on a broad analysis of their genetics," Abitua explains. If the sea squirt was a better example of a vertebrate ancestor than the lancelet, maybe the sea squirt harbored that unidentified ancestor of neural crest cell.

A Polycarpa aurata sea squirt. Nick Hobgood

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But how could studying sea squirt neural crest cells — present only in growing embryos — illuminate the origins of the vertebrate nervous system? Why study development, if you're just interested in the evolution of the final product — the brain?

Over the past few decades, developmental biologists have convincingly shown that genetics and development can teach us many things about evolution. Certain genes are expressed, or 'turned on', at certain times during development, causing specific features, like a hand or a brain, to grow at the correct time.

It turns out that similar patterns of gene expression are responsible for early development in all animals, and these early genes are highly conserved, or shared without variation across many types of organisms. The same genes that spur eye development in fish spur eye development in other vertebrates, including humans.

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Somewhere deep in the evolutionary tree, the common ancestor of fish and humans possessed a conserved eye gene — and potentially, an ancient, rudimentary eye.

Along these lines, Abitua noticed that a slew of genes known to define neural crest cells in vertebrates were also being expressed in developing sea squirts. However, the cells marked by this group of genes did not migrate like neural crest cells in vertebrate fetuses, nor did they show the potential to become anything more than pigmented cells. What was holding these 'neural-crest-like' cells back from behaving like actual, vertebrate neural crest cells?

Abitua found an intriguing genetic difference between the two cell types: a gene called twist, conspicuously absent in the sea squirt 'neural crest' but present in the known vertebrate neural crest. Could twist be responsible for the migration and diversification of vertebrate neural crest cells not seen in the sea squirt?

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Using a decades-old technique, pioneered by the Levine lab, that allows for foreign genes to be introduced into specific cells in sea squirt embryos, Abitua expressed twist in early sea squirt 'neural crest' cells, and waited.

Amazingly, this single gene sparked new life in these cells. They migrated from their usual position and even differentiated into another cell type. Not only was the sea squirt neural crest similar in its original gene expression to the vertebrate neural crest, but adding in a vertebrate gene demonstrated the potential of the sea squirt neural crest to behave as if it were from a vertebrate. Abitua had succeeded in evolving the sea squirt neural crest forward.

"[Expressing twist] isn't necessarily the way it evolved, but it does show you the power of single genes," he says. "You could imagine that some early ancestor originally had little pigmented spots. Then, through two whole rounds of gene duplication, it was able to express twist in that pigmented spot, and those cells divided and spread throughout the animal. Now, the neural crest can provide this advantage that protects these animals from harmful UV rays."

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Now, the pigment in your skin might not seem to be important for organizing your nervous system or your brain, but Abitua's discovery shows how seemingly unrelated features of an organism can derive from common, evolved changes in gene expression. In the sea squirt, neural crest cells are stuck in the head of the animal. Even if sea squirt neural crest cells gained the potential to become, say, the neurons that wire up vertebrate limbs with the spinal cord, those neurons would be useless without the ability to migrate down to their target location.

The advent of twist in an ancestral vertebrate may have first given neural crest cells the ability to migrate and become pigmented cells, a feat that provided an immediate advantage for early vertebrates. Only later, as evolution proceeded, would those now-mobile neural crest cells have gained the ability to also become the neurons of the vertebrate nervous system, another example of exaptation.

In the same way that sea sponges originally used synaptic proteins simply for cell aggregation, early vertebrate neural crests may have originally been used simply to protect animals from UV rays. Proving, once again, that evolution doesn't try to dictate the structure of the organs in hypothetical future organisms — it only encourages functionality, and thus survivability, in organisms that exist right now.

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In case you were wondering, in addition to primitive neural crest, sea squirts also have intriguing brains. The sea squirt brain is "not that impressive, not contemplating its existence," Abitua jokes. But "even though it's small compared to the mammalian brain, it's patterned similarly. It has a forebrain, midbrain and hindbrain, but no gigantic telencephalon." Perhaps one day we'll discover the origins of the vertebrate brain itself in the unassuming, immobile sea squirt.

The closer we get to our own brain, the less we get to peek inside

Given the uncertainty surrounding the origins of neurons, early brains, and vertebrate brains, you'd be correct in guessing that the brain's predicted path from sea squirt to fish to reptile to mammal is similarly riddled with false floors, dead ends, and hidden surprises.

While biologists can easily grow sea squirts in labs and genetically engineer them to probe early brain evolution, the direct study of vertebrate brain evolution is limited to the few inbred model organisms that are standard in biology: fruit flies, zebrafish, frogs, and mice. Anything closer to humans is relegated to more 'old-school' techniques, like paleontology and anatomy.

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Luckily, the complexity of the human brain forces us to simplify the questions we dare to ask about its evolution. For every handful of genes that controls the neural crest in the sea squirt, at least a half-dozen handfuls control the human neural crest. The human brain is even more complex — and of course there's no ethical way to test brain evolution hypotheses on developing human fetuses.

The biggest question surrounding human brain evolution is disarmingly simple. Knowing that brain size correlates roughly with intelligence in animals, how did we end up with such disproportionately large brains for our body size, relative to other similarly-sized mammals?

Brains of various mammals, to scale.

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Drew Halley, an anthropologist at UC Berkeley, has taken a novel approach to addressing this question. Anthropologists have long wondered why primates, out of all the mammals, have such large brains. While speculating about the cognitive needs of primates can provide fodder for dinner table discussion, it's not something that's easy to investigate scientifically.

"There are theoretically a priori reasons why [a larger brain] should give you more intelligence," Halley tells io9. "Maybe you have extra neurons — you're not using your entire brain to run your body, so you have a little bit of extra space for better memory or cognition. There are some experiments in animal behavior that support these ideas, but the specifics are a little hazy."

Halley has turned instead to development to address the issue of primate brain size. Like Abitua, Halley studies early animal development. But Halley must track down rare specimens, instead of growing them. His sources range from the American Museum of Natural History, in New York City, to stranding networks on the West Coast, which handle the remains of deceased marine animals that wash up on beaches.

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He looks for well-preserved primate embryos, non-typical mammalian specimens (like pregnant dolphins), or histological slides that can date back nearly one century. He is interested in the timing of brain growth in primates relative to other mammals. And he's investigating an interesting quirk of the primate brain.

While some mammals, like whales and dolphins, have relatively large, complex brains, the brains of all primates — including humans — get a substantial head start in their growth. For nearly all mammals, growing fetuses have a normalized brain to body ratio of 6%, a ratio that holds steady during most of gestation. Surprisingly, developing primates maintain a brain to body ratio of 12%, says Halley — "That's dramatically bigger, twice as large the entire time you gestate."

Although size is not everything for a brain (the sperm whale brain weighs a whopping 17 lbs, compared to the average human brain of 3 lbs), a brain size discrepancy of 100% throughout all of development might be something worth noting. Developmental biologists have known for quite some time that while adult animals come in all shapes and sizes, they look uncannily similar early in development — and proportions tend to be conserved.

George Romanes' 1892 copy of Ernst Haeckel's embryo drawings.

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Just as gene expression is often conserved across species during early development, only to diverge as animals gain their species-specific features, the anatomy of different species often takes time to diverge as well. Every vertebrate possesses a tail as embryos, but notably, humans lose our tails as we develop. Identifying when species begin to diverge in their genetic or anatomical similarity during development can help explain how organisms evolved with new features, like an abnormally-large brain.

The implications aren't too shabby. "You can't really build a human brain if you haven't set up a primate brain in the first place," says Halley. All primates have large brains, but humans in particular have even larger brains, partially thanks to our gigantic frontal lobes — the part of your brain that lies directly behind your forehead and provides you with advanced decision-making skills, and your beautiful personality, amongst other things. Without that head-start on brain growth as fetuses, we may never have had the time to grow even larger frontal lobes.

Look around and thank an extinct hominid.

We've finally reached the chapter of human brain evolution that is perhaps most emblematic of our identity as humans: the jump from primate to human. Chimpanzees are our closest living relative, but our last common ancestor with chimps probably lived about 13 million years ago. Lacking fossilized brain tissue, all of our knowledge about human brain evolution in the past 13 million years comes from studying fossilized skulls of various extinct primates, leading up to the hominids, of which we are the remaining extant member.

Christopher Walsh - Harvard Medical School

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Hominids emerged about 2 million years ago, and humans (Homo sapiens) are thought to have evolved about 200,000 years ago. Though the limited fossil record shows that the brain sizes of hominids increased over that 1.8 million year span, we lack experimental techniques for finding the changes in gene expression or developmental timing that allowed this to occur.

In fact, our best hypotheses come from analyzing when and where in the world hominids managed to thrive, and whether other hominids were around to compete with them.

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After all, evolution is not a one-branched tree. Neanderthals, our closest relatives in the Homo genus, thrived for hundreds of thousands of years, only to die out about 40,000 years ago. Neanderthals had larger brains than we did on an absolute scale, though their brains were slightly smaller than ours relative to their body weight. Why Neanderthals died out, and why we survived, remains an open question, though experts are fairly certain that Neanderthal extinction coincided with our own migration into Neanderthal territories.

Human vs Neanderthal skull - hairymuseummatt

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But Neanderthals were not our only competition, tens of thousands of years ago, and new discoveries continue to reshape our understanding of hominid evolution. Just ten years ago, anthropologists discovered a dwarf-sized hominid that lived as recently as 12,000 years ago in modern-day Indonesia. Experts were shocked that a hominid with such a small brain (about one-third the size of that of a human) could have survived until that recently. The last hominids with such small brains had been dated to millions of years ago.

Reconstruction of Homo floresiensis, the 'hobbit' hominid, by John Gurche; photograph by Tim Evanson.

Humans are the only living hominins left - but increasingly it looks like our isolation within our genus is a recent development. Peter Brown, one of the first experts to inspect the so-called 'hobbit' fossils, noted just how much the discovery had influenced his thinking in a recent interview with Nature.

From Nature:

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Brown: Now I'm more open to the idea that very small-bodied and small-brained bipeds moved out of Africa at a much earlier date, maybe 3 million years ago, or earlier. I'm more open to the idea that there were lots of failures in the evolution of bipeds. Some were successful, some weren't. It's a very branchy tree, and it just so happens we've survived.

Although hominid brain sizes increased overall over the 2 millions years of hominid evolution, brain sizes within Homo sapiens alone actually shrunk from about 20,000 years ago until 100 years ago. In the past 100 years, some scientists believe brain sizes in the developed world have started to increase again. Problem is, we can't test our best guesses for why our brains grow or shrink from generation to generation. The burdens and advantages of civilized life likely play a role, as well as variations in our genes, but the true ending to this story is anyone's bet.

We're just a branch on the tree of life — that is now decked out with LED lights in every color. We'll never know for certain where our brains came from, but we do know our large brains were never a foregone conclusion.