10 Puzzles of Evolution That Scientists Still Can’t Explain

Evolution has shaped life on Earth for billions of years, gradually refining species through natural selection and adaptation. Yet despite everything we know about the process, there are still considerable gaps in our understanding. Some biological traits appear too complex to have evolved gradually, others seem to contradict traditional evolutionary principles, and a few remain so baffling that scientists still can’t agree on how they came to be.

Scientists have proposed intriguing theories to answer these questions, but many remain unresolved and hotly debated. While we may one day unravel these mysteries, for now, they stand as some of the most fascinating puzzles in the history of evolution. Here are 10 evolutionary mysteries that continue to stump scientists.

Related: Top 10 Weirdest Products of Evolution

10 The Origins of Complex Eyes

Eyes are among the animal kingdom’s most sophisticated and varied organs, appearing in at least 40 different evolutionary lineages, including insects, mollusks, and vertebrates. The widely accepted theory is that eyes evolved from simple, light-sensitive cells, gradually developing into complex, image-forming structures through incremental changes. However, what baffles scientists is how this process occurred so many times in such different species and seemingly so quickly.

The Cambrian explosion, a period about 540 million years ago, saw the sudden emergence of highly advanced eyes in creatures like trilobites and early mollusks. This rapid development is difficult to explain because eyes require many different biological components to function together, including the lens, retina, optic nerves, and the brain’s ability to process visual information. Evolution is thought to favor gradual changes, but a functional eye is useless unless all of its parts develop at once.

Why did eyes evolve so many times in so many different ways yet always converge on a handful of similar structures? And how did some creatures—like deep-sea fish—develop eyes that work without light at all? These unanswered questions continue to fuel scientific debate about the evolution of vision.^[1]

9 The Mystery of Left-Handedness

Roughly 90% of people are right-handed, while only 10% are left-handed, a ratio that has remained consistent for thousands of years. This is unusual because, in most animal species, there is no such strong preference for one side over the other. The question remains: Why does left-handedness persist, and why hasn’t evolution eliminated it or made it more common?

One theory suggests that left-handedness is an advantage in combat or competition. Left-handers often have an edge in sports like boxing, fencing, and baseball because their movements confuse right-handed opponents who aren’t used to facing them. In prehistoric times, this may have applied to hand-to-hand combat and hunting, making left-handers unexpectedly effective warriors.

Another hypothesis links left-handedness to brain asymmetry, which may enhance creativity, problem-solving, and divergent thinking—qualities that could have benefitted innovation and survival. However, left-handedness has also been linked to higher risks of neurological disorders and shorter lifespans on average, making it even more puzzling why evolution has preserved it. If natural selection typically weeds out traits that don’t offer strong advantages, why has left-handedness remained at a steady 10% for thousands of years?^[2]

8 Why Do We Yawn?

Yawning is one of the most mysterious involuntary behaviors seen across the animal kingdom. Nearly all vertebrates yawn, from humans and dogs to birds and even fish. Yet scientists still can’t agree on why we do it. The most popular theory was that yawning helps increase oxygen levels in the blood. However, multiple studies have debunked this, showing that oxygen intake doesn’t increase significantly when we yawn. If yawning isn’t about oxygen, then what is its purpose?

One hypothesis suggests that yawning helps regulate brain temperature, cooling it down and improving mental function. Another idea is that yawning increases alertness, acting as a signal to the brain and body that it’s time to wake up. But the strangest aspect of yawning is how contagious it is. Seeing, hearing, or even thinking about yawning can trigger it involuntarily. This effect is so strong that even some animals—like dogs and chimpanzees—can “catch” yawns from humans.

Contagious yawning may have evolved as a social bonding mechanism, helping groups synchronize their sleep cycles or increase vigilance in dangerous environments. But if that’s the case, why do we also yawn when we’re alone? And why do fetuses yawn in the womb before they’ve even interacted with others? Yawning remains one of the biggest biological enigmas.^[3]

7 How Butterflies Evolved Their Metamorphosis

Metamorphosis is one of the most dramatic transformations in nature, allowing caterpillars to completely dissolve into a liquid state before emerging as butterflies or moths. The fact that this process works at all is remarkable, but what’s even stranger is that scientists still don’t fully understand how or why it evolved. While we can trace the evolutionary history of butterflies and moths, no known transitional fossils show how the metamorphosis process developed step by step.

One theory suggests that insects gradually evolved different life stages to reduce competition between juveniles and adults—caterpillars and butterflies eat completely different foods, meaning they aren’t fighting for the same resources. Another idea proposes that metamorphosis evolved due to ancient parasitic relationships.

Some researchers believe early caterpillar-like larvae lived inside plants or other animals, only emerging later in life to reproduce, similar to how some modern insects hijack hosts before reaching adulthood. But the biggest mystery is how an organism can completely liquefy itself, rebuild its body, and somehow retain memories from its caterpillar phase. Metamorphosis seems almost too radical for evolution to produce gradually, yet we still don’t know how it emerged.^[4]

6 The Origin of Human Consciousness

Human consciousness is one of the most profound mysteries in biology. At some point in evolution, our ancestors developed the ability to reflect on the past, plan for the future, and think in abstract terms. This level of self-awareness is far beyond what we see in even the most intelligent animals, like dolphins or primates. But how did this ability evolve, and why did it appear in humans but not in our closest relatives, like chimpanzees or Neanderthals?

One theory is that consciousness emerged as a byproduct of complex social interactions, allowing humans to predict the behavior of others, build alliances, and communicate effectively. Another possibility is that consciousness developed in tandem with language since the ability to process and understand speech may have required higher-order cognitive abilities. But the true mystery is when the “switch” happened.

Did early hominins have some form of rudimentary self-awareness, or was there a specific moment when the human brain made the leap into reflective thought? Neuroscientists still can’t pinpoint where consciousness resides in the brain, and some philosophers argue that it’s not just a biological process but something deeper. Even with advancements in brain science, the exact origin of consciousness remains one of the biggest unanswered questions in human evolution.^[5]

5 The Evolutionary Purpose of Dreams

Humans and many animals experience vivid, often bizarre dreams, but scientists still don’t fully understand why. Sleep itself is clearly essential for survival, aiding in memory consolidation, brain detoxification, and energy restoration. But why do our brains create elaborate dream scenarios rather than just resting?

Some researchers believe dreams help with problem-solving, simulating real-world challenges so the brain can “practice” solutions. Others suggest dreams are a form of emotional processing, allowing the mind to work through fears, anxieties, and past experiences in a way that’s less threatening than reality. The biggest mystery, however, is why dreams are often so illogical and surreal.

If dreaming serves an evolutionary function, why aren’t dreams more practical? Why do we dream about flying, being chased by impossible creatures, or losing our teeth instead of running through realistic survival scenarios? And then there’s lucid dreaming, in which people become aware that they’re dreaming and can control their dream environments. If dreams are meant to be passive processes, why does the brain sometimes allow conscious control? While theories abound, the true evolutionary purpose of dreaming remains unknown. ^[6]

4 Why Do Whales and Dolphins Sleep with Half Their Brain?

Most animals sleep in complete, unconscious states, but whales, dolphins, and some birds do something completely different—they sleep with only one-half of their brain at a time. This process, known as unihemispheric slow-wave sleep, allows marine mammals to swim, surface for air, and remain alert for predators while getting the rest they need. But why did evolution select for this unique sleep pattern, and why haven’t other animals developed it?

One theory suggests that early marine mammals faced constant threats from predators, requiring them to remain partially awake at all times. Another idea is that sleeping too deeply underwater could lead to accidental drowning, forcing species like dolphins to evolve a built-in safety mechanism. What’s puzzling is why other aquatic animals, such as fish and reptiles, don’t require this adaptation.

If it’s so beneficial, why hasn’t evolution made half-brain sleeping more common across the animal kingdom? The biological mechanisms behind unihemispheric sleep remain an ongoing mystery, and it’s still unclear how whales and dolphins manage to switch between hemispheres without cognitive impairment.^[7]

3 The Existence of Altruism in Nature

Evolution is often framed as survival of the fittest, where animals are expected to act in self-interest to ensure their own survival. However, throughout nature, we see countless examples of self-sacrificing behaviors that don’t seem to offer any clear evolutionary advantage. Vampire bats regurgitate blood to feed unrelated colony members, dolphins protect sick or injured companions, and meerkats stand guard to warn their group of predators—even when it puts them at risk.

One explanation is kin selection, where animals help relatives to ensure the survival of shared genes. But this doesn’t explain why altruism occurs between non-related individuals, as seen in vampire bats or certain bird species. Another theory, reciprocal altruism, suggests that animals help others, expecting future favors in return, but many observed cases of animal altruism don’t fit this model either.

Why do certain species engage in costly, seemingly irrational acts of kindness while others never develop such behaviors? And why do humans, in particular, show extreme levels of selflessness, even when it doesn’t benefit them personally? Despite decades of research, the roots of altruism remain one of evolution’s biggest mysteries.^[8]

2 Why Some Species Haven’t Evolved Much at All

The vast majority of species on Earth have changed dramatically over millions of years, adapting to new environments, predators, and food sources. Yet some species—such as horseshoe crabs, coelacanth fish, and certain sharks—have remained almost identical to their ancestors from hundreds of millions of years ago. These “living fossils” challenge the idea that all species must evolve constantly to survive.

One explanation is stabilizing selection, where some species find a nearly perfect survival strategy early on and don’t need major changes. But this theory doesn’t explain why these species weren’t wiped out by competitors who did evolve. If rapid adaptation is so beneficial, why have horseshoe crabs survived for over 450 million years with barely any changes?

Did they simply luck into an ideal ecological niche, or is there a deeper reason why certain organisms resist evolutionary pressure? Some scientists believe these species may evolve in ways we don’t yet recognize, such as through biochemical adaptations rather than physical ones. But as of now, the persistence of “unchanging” species remains a fascinating evolutionary puzzle.^[9]

1 Why Life Evolved at All

The biggest evolutionary mystery of all is why and how life began in the first place. Scientists believe life originated around 3.5–4 billion years ago, but how non-living chemicals assembled into the first self-replicating molecules remains unknown. The leading hypothesis is abiogenesis, where the right mix of elements, energy, and environmental conditions leads to the formation of simple organic molecules that eventually develop into early life forms. But how did these molecules suddenly transition from random chemical interactions to self-sustaining, evolving organisms?

Some theories suggest life began in deep-sea hydrothermal vents, where mineral-rich environments could have provided the perfect conditions for early biochemistry. Others propose that life didn’t originate on Earth at all, but instead came from organic molecules on asteroids or comets—a concept known as panspermia. While scientists have managed to recreate some of the basic building blocks of life in lab experiments, they’ve never been able to jump from simple molecules to an actual, self-replicating organism. The question of how lifeless chemistry gave rise to evolution itself remains the ultimate mystery of biology. ^[10]