PDF Summary:On the Origin of Species, by Charles Darwin

A foundational work in the field of biology, On the Origin of Species revolutionized the way we look at life on Earth. Published in 1859 by the naturalist Charles Darwin, this work explains and argues for the theory of evolution—that organisms weren’t created separately in their current forms, but that each species evolved gradually from other species over the course of millions of years.

Our guide explains the key mechanisms behind evolution and explores how it shapes the world. We’ll take a closer look at the objections raised against Darwin's theory by his colleagues and at Darwin's rebuttals. We’ll also explore why animals in Australia are all different from those in Asia, what happens when you try to breed two closely related species, and why human embryos have gill slits. Finally, we’ll extend Darwin's theories with updates from contemporary biology.

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(Shortform note: Darwin theorized that all life on Earth is descended from a single common ancestor—but some researchers have suggested the possibility that life on Earth could have had multiple origins. If simple life arose once, could it have happened two or three times on the same planet? However, research supports Darwin's hypothesis of universal ancestry: All life on earth shares certain basic building blocks, including universal proteins and amino acids. Statistical analysis of the possible courses of evolution supports the view that these similarities likely originated in a universal common ancestor.)

In this section, we’ll first explore Darwin's arguments that species have descended from earlier species. Then, we’ll discuss his evidence that modern species are related through shared ancestry.

The Descent of Species

Darwin advances four kinds of evidence that species have descended from earlier species: changes in domesticated species, leftover characteristics, intermediate species found in the fossil record, and the role of natural barriers.

Evidence Type 1) Changes in Domesticated Species

To support his argument that species change over time, Darwin highlights the ways humans have changed domesticated plants and animals through selective breeding. He observes that many domesticated organisms have become highly specialized to provide more value to humans. For example, domesticated strains of berry vines grow much larger fruits than their wild counterparts. This occurs because humans select for these desirable traits when breeding domesticated species. Based on this evidence, Darwin concludes that trait selection has the power to gradually change the characteristics of a species.

(Shortform note: Researchers have tried to understand what happens in the evolution of domesticated animals that return to the wild. Do feral organisms simply revert to their earlier forms in a kind of “reverse evolution”? Or do they retain characteristics selected for by humans? Some research reveals that they keep evolving from their domesticated forms, but they evolve in new directions as they face different pressures of selection in the wild. Studies of feral chickens in Hawaii reveal they’re distinct from both domesticated and wild chickens—the feral chickens are a new kind of hybrid with a mix of domesticated and wild characteristics. This supports Darwin's broader view that organisms are shaped by their entire histories of selection, regardless of the conditions for selection.)

Evidence Type 2) Leftover Characteristics

Darwin explains that organisms have taken on multiple forms over the course of their evolution. He argues that we can find evidence for this by looking at structures that’ve been modified from earlier forms. He identifies two types: vestigial characteristics and repurposed characteristics.

Vestigial characteristics are features that served a purpose in earlier versions of a species but are slowly disappearing due to disuse. For example, some species of blind cavefish still have eyes, even though they no longer work, and whales have pelvises and femurs even though they have no legs. These characteristics suggest that their ancestors once used these features. Darwin argues that these characteristics wouldn’t exist unless species had evolved from older species.

Repurposed characteristics are features that evolved to serve one purpose and then became adapted to a second. For example, many insects communicate by rubbing their legs or wings together to make noise. These body parts likely evolved for movement before the insects started using them for communication. The fact that some body parts have taken on secondary purposes suggests that they evolved to fulfill one need and were then adapted for another, supporting the view that organisms developed in stages.

(Shortform note: Researchers have found that organisms retain characteristics from previous versions due to a tendency toward "irreversibility." Once an organism has evolved a structure or characteristic, it can't simply revert back to earlier forms. This principle—named Dollo's law of irreversibility—was first put forward in 1890. Research has revealed some exceptions to Dollo's law: Lizards have lost and regained toes, insects have lost and regained wings, and bacteria have gained and lost resistance to antibiotic compounds. However, these exceptions are extremely rare. In general, researchers have found that the more complex an organic structure is, the harder it becomes to "un-evolve.")

Evidence Type 3) Intermediate Species in the Fossil Record

Darwin asserts that the fossil record provides examples of transitional species. These ancient ancestors provide links that show one species transitioning into another.

For example, biologists believe that birds evolved from reptiles because fossil evidence shows hollow-boned dinosaurs like Coelophysis, which were likely ancestors to modern birds. Biologists also believe that whales descended from land-dwelling mammals because there are fossils of transitional species like Ambulocetus, a whale-like mammal with webbed feet that could still walk on land.

(Shortform note: Paleontologists caution that transitional fossils can only provide us with a rough outline of evolutionary development—they don’t necessarily prove direct ancestry from any one particular species. This is because transitional fossils may represent members of a larger family of organisms, some of which became the ancestors of modern species and some of which died out. For example, the Archeopteryx is a prehistoric animal that shares characteristics of both birds and reptiles, supporting the view that birds evolved from reptiles. However, we don't know whether birds evolved from Archaeopteryx or from a relative that hasn't been preserved through fossilization.)

Evidence Type 4) The Role of Natural Barriers

Darwin also argues for the descent of species by highlighting the role of natural barriers in shaping populations and ecosystems. He points out that species look very different from each other on opposite sides of natural barriers like oceans and mountain ranges. Darwin explains that this occurs because natural barriers isolate breeding populations from each other: Organisms that live on either side of a natural barrier evolve to become distinct from each other because they no longer interbreed.

For example, lemurs—a long-tailed, tree-dwelling primate—diverged from other early primates over 60 million years ago by becoming isolated on the island of Madagascar. The natural barrier of water between Madagascar and the African mainland allowed lemurs to evolve separately from the ancestors of modern monkeys.

What Evolution Teaches Us About Ancient Geography

Biologists have discovered that the pattern of organisms evolving in areas with natural barriers is consistent enough to teach us about barriers that existed in the ancient past.

One of the most famous examples of wildlife emerging on opposite sides of a natural barrier is found in the Wallace Line. Recall that Alfred Wallace was a contemporary of Darwin who independently came up with a similar theory of evolution. He discovered an invisible line running through the Malay Archipelago: All of the flora and fauna on one side of the line consisted of Asian species and their descendants, while the organisms on the other side were all Australian species and their descendants.

Scientists have since discovered that this boundary was caused by plate tectonics. The islands on each side of Wallace's line had been connected to the ancient continents of Sunda and Sahul, which were slowly pushed together to form the Malay Archipelago.

The Relatedness of Modern Species

Darwin's theory of evolution maintains that organisms are related to each other through a family tree of descent. This happens because one highly successful ancestor species is capable of seeding multiple descendant species.

Recall that the individuals in every species carry inherited traits from their ancestors (heritable variations). That means a single population may have multiple traits that are useful for particular purposes. These traits can accumulate in distinct groups within the species. Over enough time, the groups become distinct from each other, turning into two different species.

For example, a species of wolf has a variation that allows for one of two types of foot pads. One type of pad allows the wolves to move more silently, perfect for stalking small prey. The other type of pad helps the wolves run faster, making it easier to chase down large prey. Over time, these variations accumulated in two different groups that split off from each other, leading to two new species of wolves.

(Shortform note: Researchers have found that speciation—the process of one species seeding multiple new species—is largely influenced by population size and geography. One study of Anolis lizards on the Caribbean Islands found a consistent relationship between the size of an island and the number of different lizard species. Larger islands had more species because they could support larger populations and allowed lizards to spread across a greater area. As the lizards spread out, they had more opportunities to become isolated and form new independent species. Therefore, the number of distinct lizard species is proportionate to the area of the island.)

Darwin argues that all species today have ancient ancestors in common. He draws on two major types of evidence: similarity of traits and hybridization.

Evidence Type 1) Similarity of Traits Between Related Organisms

Darwin argues that shared traits between organisms reveal their relatedness. For example, all mammals have four limbs, warm blood, and three inner ear bones. These shared traits suggest that all mammals are descended from a common ancestor which had these traits.

Some of the most striking similarities between organisms reveal themselves through embryos (when the organism is in its earliest stages of prenatal development). For example, many land-dwelling vertebrates—including humans—develop gill slits and tails in the embryo stage. This trait not only suggests descent from fish but also suggests a common ancestry for all land vertebrates.

The Role of Genes in Embryonic Similarities and Differences

Biologists have ample evidence that embryonic similarity results from shared genes. The basic DNA instructions for how to make features like eyes, backbones, and legs may be the exact same genes across many organisms. But what then accounts for the differences in development between organisms?

Researchers believe the differences in how organisms develop may have less to do with having completely different genes and more to do with the timing and duration of those genes’ activity during embryonic development. The instructions for producing a particular type of cell will be active or inactive for different durations depending on how many cells of that particular type an organism needs.

That means an organism with large eyes may have the same instructions for growing eye cells as an organism with small eyes, but it develops bigger eyes by simply repeating those instructions more times. Researchers have even discovered molecular “counters” which accumulate or deplete proteins to trigger the next stage in embryonic development.

Evidence Type 2) The Breeding Characteristics of Hybrids

The breeding characteristics of hybrids reveal relatedness between certain species. Darwin explains that breeders of plants and animals have found that individuals from similar species can sometimes reproduce with each other, but with mixed results. Some hybrids only rarely produce offspring, some produce infertile offspring, while still others can sometimes produce fertile offspring and yield new hybrid varieties.

Darwin argues that the range of outcomes refutes the idea of sharp delineations between species. Organisms that can produce hybrid offspring together are distant relatives whose reproductive systems are gradually evolving to become incompatible with each other. This further supports the view that these organisms all had ancestors with a common reproductive system.

What Causes Hybrid Incompatibility?

Researchers have attempted to identify the exact source of reproductive incompatibility between hybrids to better pinpoint how and when species diverge. Research on fruit flies suggests a variety of factors.

• One experiment identified two genes that conflict with each other, resulting in the death of male offspring. When these genes are "turned off," the male offspring survive.

• Other researchers have identified a divergence in gene function that dooms hybrid offspring: A gene will serve one purpose in one species and a second purpose in another. The offspring then struggle to survive because the same gene can't perform two functions at once.

• Further research has identified an imbalance in proteins, rather than genes, that prevents successful reproduction.

Part 3: Arguments Over the Theory of Evolution

Darwin's theory of evolution was controversial in its time, even among scientists. In the final edition of On the Origin of Species, released in 1872, Darwin responds to the three main objections raised by skeptics of his theory of evolution. Here, we’ll review these objections and Darwin's rebuttals in defense of his theory.

Objection #1: “Lower” Organisms Continue to Exist

Darwin cites critics who argue that the continued existence of simple creatures challenges the claim that sophisticated organisms evolved from simpler ones. If some simple organisms evolved into more complex ones, why didn't all of them evolve that way? Darwin provides two explanations.

Rebuttal 1) Natural Selection Doesn’t Always Favor Complexity

First, Darwin argues that natural selection isn’t biased in favor of sophistication. Instead, species accumulate adaptations that allow them to continue reproducing. Therefore, a "simple" organism may still be well suited to its environment. For example, biologists have estimated that the earth contains about 2.5 million times as many ants as it does humans. Even though their bodies are simple, ants are still highly successful at surviving and reproducing.

(Shortform note: Some organisms, like goblin sharks, horseshoe crabs, and chambered nautiluses have earned the nickname "living fossils'' for staying relatively the same for millions if not hundreds of millions of years. Why, when most organisms change, do some stay the same? Some evolutionary biologists attribute this to "stabilizing selection," a form of natural selection that selects against extremes and in favor of an average characteristic. For example, snails with excessively thin shells are vulnerable to predators, but snails with excessively thick shells are less mobile. Therefore, evolution selects for shells of medium thickness. Thus, competing evolutionary pressures can stabilize each other, keeping traits consistent, sometimes for millions of years.)

Rebuttal 2) Evolution Is a Work in Progress

Second, Darwin reminds critics that evolution is never completed and every moment in natural history is a snapshot of a work in progress. In the future, organisms may evolve to become even more sophisticated. For example, chimpanzees aren't as intelligent as humans now, but that doesn't mean they couldn't reach our current level in a few million years—a relatively short time in the scale of natural history.

Are Humans Still Evolving?

Researchers have tried to answer the question of whether humans are continuing to evolve. Some have theorized that humans have stopped evolving in the traditional sense: That is, low child mortality rates and effective birth control have made it so that individual choice, culture, and socioeconomics play a much larger role in reproduction than a person's genes. Therefore, genes are no longer selected for or against through natural selection, and our species' gene pool no longer changes in response to evolutionary pressure.

However, some research suggests that humans are continuing to adapt to the conditions of civilization. For example, one study found that the cultivation of dairy has led to natural selection for genes that aid in digesting lactose. This change has taken place only within the last 5,000 to 10,000 years.

Objection #2: Complex Features Are Difficult to Create Through Small Increments

Darwin explains that some naturalists found it difficult to believe that very sophisticated structures could arise through small increments. Organisms today have such highly developed structures and behaviors that it's hard to imagine a rudimentary version of them providing much value.

For example, bats hunt using echolocation. They emit high-pitched sound waves that bounce off insects and then they judge the distance and direction of the prey by listening to the echo. They do this fast enough to intercept insects in flight. That means echolocation needs to work at a high level of sophistication if it’s to work at all. It's hard to imagine a primitive bat just making noises and then trying to follow the direction of the echo.

Darwin provides two rebuttals to this argument.

Rebuttal 1) Evolution Repurposes Older Structures

Darwin argues that highly sophisticated structures and instincts can evolve incrementally, but they’re often repurposed from earlier structures. An earlier version of a species may evolve a structure for one purpose. Then, the organism finds a new use that allows the structure to continue evolving into greater complexity and sophistication.

Let’s return to the echolocation example. To echolocate, bats need highly sensitive directional hearing and the ability to make high-frequency sounds. These could’ve developed independently of each other before being repurposed into an echolocation system.

Bats may have started off like other nocturnal predators, such as owls, that hunt using highly sensitive directional hearing. They may also have communicated with each other using ultra-high-frequency squeaks that predators can’t hear, as many small rodents do today. Once early bats derived even a small advantage from using these abilities together in echolocation, evolution could then incrementally improve on this new usage.

The Mechanisms of Evolving Complex Organs

Researchers have named the process of repurposing structures exaptation. However, exaptation is only one of several processes that enable complex organs to evolve. Evolutionary biologists have identified several more key mechanisms for evolving complex structures.

• Duplication creates copies of genes and repurposes them. A complex structure may begin as a crude copy of another structure before adapting to a new function.

• Scaffolding allows structures to support the development of other structures before losing their functions—much like the scaffold in a construction project.

• Gene sharing allows one set of genes to take on multiple functions. This increases the complexity and range of organic structures that can be supported by an organism’s genetic code.

Rebuttal 2) The Natural World Shows Incremental Development of Complex Structures

Furthermore, Darwin argues that when we look at simpler organisms, we often find earlier versions of rudimentary structures that developed into much more complex structures over time. For example, the human brain is so complex that scientists are still discovering how it works. However, by understanding that the brain is a centralized collection of nerve cells in communication with each other, we can find the simplest examples of this structure in nature to reveal how it may have developed over time.

One of the simplest nerve cell structures belongs to jellyfish, whose nerve cells connect in a "net" that senses and processes information. One step up from this we find hydras, small freshwater relatives of sea anemones. These creatures also have a nerve net, but their nerve cells are more specialized, giving them something closer to a brain. Finally, in flatworms, these specialized nerve cells cluster together, forming a simple brain that can make decisions and even remember previous actions. By looking at these simple organisms, we can infer the origins of something as complex as a human brain.

Does Evolution Naturally Produce Complexity?

Some evolutionary biologists have theorized that evolution has a natural tendency to produce greater complexity, even without natural selection. They make their argument mathematically: Mutation is random, and randomness increases complexity. Therefore, mutation trends toward complexity.

For example, imagine a very simple organism that’s made up entirely of one kind of cell. Any mutation at all—whether beneficial, detrimental, or neutral—could result in the organism having at least two kinds of cells, and therefore becoming more complex. The more mutations occur, the greater the cell diversity and subsequent complexity. Thus, evolution inevitably leads to complexity.

However, this theory remains controversial. Critics argue that organisms are always living under natural selection, and therefore it's difficult to prove that this (or any) force is truly independent of natural selection.

Objection #3: Why Aren’t There More Transitional Species?

Lastly, Darwin's critics argued that if species evolved from other species, then there should be more transitional species alive, or at least more evidence of them in the geological record. Darwin provides three rebuttals.

Rebuttal 1) Competition Destroys Transitional Species

Darwin argues that we don't see many transitional species alive today because competition between species would select against them. Recall that scarcity of food, habitat, and other resources puts species in competition with each other. Those that have evolved the best adaptations outcompete those that are less adapted. Therefore, transitional species are likely to die out.

For example, let's say there's a fish that eats two kinds of food: algae and smaller fish. Some of the fish in this population develop a mutation that gives them teeth that can scrape algae off coral, which allows them to eat algae faster. Others develop long, sharp teeth that allow them to catch small fish better. The optimized algae eaters eat most of the available algae, while the optimized fish hunters catch most of the available small fish. Now there’s less to eat for the parent population, which is optimized for neither algae nor small fish. They’ll likely die off, leaving two new species of fish.

(Shortform note: Studies of ovenbirds in South America have confirmed that closely related "sister species'' compete with each other by occupying similar niches. Researchers found that closely related species of ovenbirds that relied on similar food sources didn't live in overlapping territories due to "competitive exclusion." However, they found that once related species had evolved into distinctive ecological niches—some developed curved beaks for prying insects out of bamboo stems, for instance—then they no longer competed with each other and could share territory.)

Rebuttal 2) The Fossil Record Is Scarce

Darwin also explains that we don't find every example of a transitional species in the fossil record because the fossil record is very sparse. Most organisms never become fossils because fossilization is a rare process that requires very specific conditions. Our knowledge of the natural world before our time is very limited. Therefore, Darwin argues, the lack of transitional species in the fossil record poses little challenge to the theory of evolution.

(Shortform note: Paleontologists agree that the fossil record is extremely sparse. Some have estimated that less than 0.1% of species that have ever lived became fossils. Furthermore, the fossil record presents a biased sample because some organisms are more likely to fossilize than others. Organisms with bones or hard shells are more likely candidates for preservation. Creatures living in or near water are also overrepresented because water plays a vital role in the process of fossilization. Roughly 99% of all fossils discovered are the remains of marine organisms.)

Rebuttal 3) Transitional Adaptations Still Appear in Modern Species

Finally, Darwin argues that even though examples of transitional species may be sparse, we can still infer the course of evolution by studying the incremental adaptations in today’s natural world. Let's say we want to understand how whales evolved to swim, even though their ancestors walked on land. You could infer this evolutionary path by looking at the behavior of current aquatic and semi-aquatic mammals.

For example, raccoons and bears spend most of their time on land, but they occasionally venture into rivers to catch food. Muskrats and beavers spend even more time in water. Seals and walruses spend most of their time underwater, but they occasionally pass time on the shore. Finally, whales and dolphins spend all of their time in the sea. You could easily imagine the ancestors of modern whales progressively occupying each of these niches before finally leaving land. While we may never discover every intermediate species, Darwin argues that the natural world as it currently is furnishes more than enough evidence to support the evolution of one species into another.

(Shortform note: Researchers have found that modern organisms can tell us much more about evolutionary pathways than Darwin ever realized. By mapping genomes (complete sets of genes), biologists have identified similarities and shared clusters of genes that could imply common ancestry between organisms. Furthermore, researchers in an emerging field called phylogenetics are attempting to create hypothetical "family trees'' of organisms through DNA sequencing and mathematical models.)