Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body

by Neil Shubin

It turns out that being a paleontologist is a huge advantage in teaching human anatomy. Why? The best road maps to human bodies lie in the bodies of other animals. The simplest way to teach students the nerves in the human head is to show them the state of affairs in sharks. The easiest road map to their limbs lies in fish. Reptiles are a real help with the structure of the brain. The reason is that the bodies of these creatures are often simpler versions of ours.

Typical summers of my adult life are spent in snow and sleet, cracking rocks on cliffs well north of the Arctic Circle. Most of the time I freeze, get blisters, and find absolutely nothing. But if I have any luck, I find ancient fish bones.

Dwight D. Eisenhower’s famous remark about warfare: “In preparing for battle, I have found that planning is essential, but plans are useless.”

For billions of years, all life lived only in water. Then, as of about 365 million years ago, creatures also inhabited land.

In fact, the fossil sequences in the world’s rocks can be predicted by comparing ourselves with the animals at our local zoo or aquarium.

Every species in the zoo and the aquarium has a head and two eyes. Call these species “Everythings.” A subset of the creatures with a head and two eyes has limbs. Call the limbed species “Everythings with limbs.” A subset of these headed and limbed creatures has a huge brain, walks on two feet, and speaks. That subset is us, humans. We could, of course, use this way of categorizing things to make many more subsets, but even this threefold division has predictive power.

The order of fossils in the world’s rocks is powerful evidence of our connections to the rest of life. If, digging in 600-million-year-old rocks, we found the earliest jellyfish lying next to the skeleton of a woodchuck, then we would have to rewrite our texts. That woodchuck would have appeared earlier in the fossil record than the first mammal, reptile, or even fish—before even the first worm. Moreover, our ancient woodchuck would tell us that much of what we think we know about the history of the earth and life on it is wrong. Despite more than 150 years of people looking for fossils—on every continent of earth and in virtually every rock layer that is accessible—this observation has never been made.

My colleague Jenny Clack at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins, conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.

Like a fish, it has scales on its back and fins with fin webbing. But, like early land-living animals, it has a flat head and a neck. And, when we look inside the fin, we see bones that correspond to the upper arm, the forearm, even parts of the wrist. The joints are there, too: this is a fish with shoulder, elbow, and wrist joints. All inside a fin with webbing.

It took us six years to find it, but this fossil confirmed a prediction of paleontology: not only was the new fish an intermediate between two different kinds of animal, but we had found it also in the right time period in earth’s history and in the right ancient environment. The answer came from 375-million-year-old rocks, formed in ancient streams.

This figure says it all. Tiktaalik is intermediate between fish and primitive land-living animal.

All creatures with limbs, whether those limbs are wings, flippers, or hands, have a common design.

A seemingly trivial pattern in the fins of these fish had a profound impact on science. The fins of lungfish have at their base a single bone that attaches to the shoulder. To anatomists, the comparison was obvious. Our upper arm has a single bone, and that single bone, the humerus, attaches to our shoulder. In the lungfish, we have a fish with a humerus. And, curiously, it is not just any fish; it is a fish that also has lungs. Coincidence?

Our fin had a full set of webbing, scales, and even a fish-like shoulder, but deep inside were bones that corresponded to much of the “standard” limb. Unfortunately, we had only an isolated fin. What we needed was to find a place where whole bodies of creatures could be recovered intact. A single isolated fin could never help us answer the real questions: What did the creature use its fins for, and did the fish fins have bones and joints that worked like ours?

the earliest creature to have the bones of our upper arm, our forearm, even our wrist and palm, also had scales and fin webbing. That creature was a fish.

The basic skeleton of our hands and feet emerged over hundreds of millions of years, first in fish and later in amphibians and reptiles.

Unlike fish and amphibians, our knees and elbows face in opposite directions. This feature is critical: think of trying to walk with your kneecap facing backward. A very different situation exists in fish like Eusthenopteron, where the equivalents of the knee and elbow face largely in the same direction. We start development with little limbs oriented much like those in Eusthenopteron, with elbows and knees facing in the same direction. As we grow in the womb, our knees and elbows rotate to give us the state of affairs we see in humans today.

The DNA recipe to build upper arms, forearms, wrists, and digits is virtually identical in every creature that has limbs.

The “inner fish” that Randy found was not a single bone, or even a section of the skeleton. Randy’s inner fish lay in the biological tools that actually build fins. Experiment after experiment on creatures as different as mice, sharks, and flies shows us that the lessons of Sonic hedgehog are very general. All appendages, whether they are fins or limbs, are built by similar kinds of genes. What does this mean for the problem we looked at in the first two chapters—the transition of fish fins into limbs? It means that this great evolutionary transformation did not involve the origin of new DNA: much of the shift likely involved using ancient genes, such as those involved in shark fin development, in new ways to make limbs with fingers and toes.

Carnivores, such as cats, have blade-like molars to cut meat, while plant eaters have a mouth full of flatter teeth that can macerate leaves and nuts.

You might recall lampreys from biology class—these are very primitive fish that have no jaws. They make their living by attaching to other fish and feeding on their bodily fluids.

Conodonts were originally found isolated. Then, as whole animals became known, we learned that many of them functioned together as a tooth row in the mouths of these soft-bodied jawless fish. Ostracoderms have heads covered with a bony shield. The microscopic layers of that shield look like they are composed of little tooth-like structures.

Teeth, breasts, feathers, and hair all develop from the interactions between layers of skin.

This example is akin to making a new factory or assembly process. Once plastic injection was invented, it was used in making everything from car parts to yo-yos. Teeth are no different. Once the process that makes teeth came into being, it was modified to make the diverse kinds of organs that lie within skin. We saw this taken to a very great extreme in the ostracoderms. Birds, reptiles, and humans are just as extreme in many ways. We would never have scales, feathers, or breasts if we didn’t have teeth in the first place.

The gill region of a developing human and a developing shark look the same early on.

The parallels go deeper still: equivalent nerves in sharks and humans supply similar structures, and they even exit the brain in the same order

Amphioxus lacks a backbone, but like all creatures with backbones, it has a nerve cord that runs along its back. In addition, a rod runs the length of its body, parallel to the nerve cord. This rod, known as the notochord, is filled with a jelly-like substance and provides support for the body. As embryos, we have a notochord, too, but unlike Amphioxus’s, ours breaks up and ultimately becomes part of the disks that lie between our vertebrae. Rupture a disk and the jelly-like substance of what was once a notochord can wreak havoc when it pinches nerves or interferes with the ability of one vertebra to move along the next. When we injure a disk, a very ancient part of our body plan is rupturing. Thanks a lot, Amphioxus.

The fish, amphibian, and chicken embryos were like nothing I had ever seen before in biology. They all looked generally alike. All of them had a head with gill arches. All of them had a little brain that began its development with three swellings. All of them had little limb buds.

In really rare cases, the blastocyst is expelled into the mother’s body cavity, the space between her guts and body wall. In even rarer cases, these blastocysts will implant on the outside lining of the mother’s rectum or uterus and the fetus develops to full term!

Eventually, as tissues move and fold, we become a tube with a folded swelling at the head end and another at the tail. If we were to cut ourselves in half right about now, we would find a tube within a tube. The outer tube would be our body wall, the inner tube our eventual digestive tract. A space, the future body cavity, separates the two tubes. This tube-within-a-tube structure stays with us our entire lives. The gut tube gets more complicated, with a big sac for a stomach and long intestinal twists and turns. The outer tube is complicated by hair, skin, ribs, and limbs that push out. But the basic plan persists. We may be more complicated than we were at twenty-one days after conception, but we are still a tube within a tube, and all of our organs derive from one of the three layers of tissue that appeared in our second week after conception.

The names of these three all-important layers are derived from their position: the outer layer is called ectoderm, the inner layer endoderm, and the middle layer mesoderm. Ectodermformsmuch of the outer part of the body (the skin) and the nervous system. Endoderm, the inside layer, forms many of the inner structures of the body, including our digestive tract and numerous glands associated with it. The middle layer, the mesoderm, forms tissue in between the guts and skin, including much of our skeleton and our muscles. Whether the body belongs to a salmon, a chicken, a frog, or a mouse, all of its organs are formed by endoderm, ectoderm, and mesoderm.

versions of the Hox genes appear in every animal with a body.

Creatures like jellyfish, corals, and sea anemones have a mouth, but no anus. The opening that serves as a mouth also serves to expel waste.

Take the entire 4.5-billion-year history of the earth and scale it down to a single year, with January 1 being the origin of the earth and midnight on December 31 being the present. Until June, the only organisms were single-celled microbes, such as algae, bacteria, and amoebae. The first animal with a head did not appear until October. The first human appears on December 31.

In the fossil record, we see nothing but microbes for the first 3.5 billion years of earth history. Then, suddenly, over a span of perhaps 40 million years, all kinds of bodies appear: plant bodies, fungal bodies, animal bodies; bodies everywhere.

Timing is everything. The best ideas, inventions, and concepts don’t always win. How many musicians, inventors, and artists were so far ahead of their time that they flopped and were forgotten, only to be rediscovered later? We need look no further than poor Heron of Alexandria, who, perhaps in the first century a.d., invented the steam turbine. Unfortunately, it was regarded as a toy. The world wasn’t ready for it.

They took an alga that is normally single-celled and let it live in the lab for over a thousand generations. Then they introduced a predator: a single-celled creature with a flagellum that engulfs other microbes to ingest them. In less than two hundred generations, the alga responded by becoming a clump of hundreds of cells; over time, the number of cells dropped until there were only eight in each clump. Eight turned out to be the optimum because it made clumps large enough to avoid being eaten but small enough so that each cell could pick up light to survive. The most surprising thing happened when the predator was removed: the algae continued to reproduce and form individuals with eight cells. In short, a simple version of a multicellular form had arisen from a no-body.

If an experiment can produce a simple body-like organization from a no-body in several years, imagine what could happen in billions of years. The question then becomes not how could bodies arise, but why didn’t they arise sooner? Answers to this puzzle might lie in the ancient environment in which bodies arose: the world may not have been ready for bodies.

Collagen requires a relatively large amount of oxygen for its synthesis and would have greatly increased our ancestors’ need for this important metabolic element. But the problem was this: levels of oxygen on the ancient earth were very low.

For billions of years, microbes developed new ways of interacting with their environment and with one another. In doing so, they hit on a number of the molecular parts and tools to build bodies, though they used them for other purposes. A cause for the origin of bodies was also in place: by a billion years ago, microbes had learned to eat each other. There was a reason to build bodies, and the tools to do so were already there. Something was missing. That something was enough oxygen on the earth to support bodies. When the earth’s oxygen increased, bodies appeared everywhere. Life would never be the same.

Extracting DNA from bodies is incredibly easy, so easy you can do it in your kitchen. Take a handful of tissue from some plant or animal—peas, or steak, or chicken liver. Add some salt and water and pop everything in a blender to mush up the tissue. Then add some dish soap. Soap breaks up the membranes that surround all the cells in the tissue that were too small for the blender to handle. After that, add some meat tenderizer. The meat tenderizer breaks up some of the proteins that attach to DNA. Now you have a soapy, meat-tenderized soup, with DNA inside. Finally, add some rubbing alcohol to the mix. You’ll have two layers of liquid: soapy mush on the bottom, clear alcohol on top. DNA has a real attraction to alcohol and will move into it. If a goopy white ball appears in the alcohol, you’ve done everything right. That goop is the DNA.

We humans are part of a lineage that has traded smell for sight. We now rely on vision more than on smell, and this is reflected in our genome. In this trade-off, our sense of smell was deemphasized, and many of our olfactory genes became functionless.

From studying the other primates that have color vision, we can estimate that our kind of color vision arose about 55 million years ago. At this time we find fossil evidence of changes in the composition of ancient forests. Before this time, the forests were rich in figs and palms, which are tasty but all of the same general color. Later forests had more of a diversity of plants, likely with different colors. It seems a good bet that the switch to color vision correlates with a switch from a monochromatic forest to one with a richer palette of colors in food.

Reichert proposed a notion that even he could barely believe—that parts of the ears of mammals are the same thing as the jaws of reptiles. Things get more difficult when we realize that Reichert proposed this several decades before Darwin propounded his notion of a family tree for life.

The origin of mammals involved not only new patterns of chewing, as we saw in Chapter 4, but new ways of hearing.

Keep your eyes fixed in one place as you move your head. What happened during this experiment? Your eyes stayed fixed on a single point while your head moved. This motion is so commonplace that we take it for granted, but it is incredibly complex. Each of the eight muscles in both eyes is responding to the movement of the head. Sensors in your head, which I’ll describe in the next section, record the direction and velocity of your head’s movement.

When we drink too much, we are putting lots of ethanol into our bloodstream, but the fluid inside our ear tubes initially contains very little. As time passes, however, the alcohol diffuses from our blood into the gel of the inner ear. Alcohol is lighter than the gel, so the result of the diffusion is like the result of pouring alcohol into a glass of olive oil. Just as the oil moves around in the glass as the alcohol enters, so the gel inside our ear swirls. The convection wreaks havoc on the intemperate among us. Our hair cells are stimulated and our brain thinks we are moving. But we are not moving; we are slumped in a corner or hunched on a barstool. Our brain has been tricked. The problem extends to our eyes. Our brain thinks we are spinning, and it passes this information to our eye muscles. The eyes twitch in one direction (usually to the right) as we try to track an object moving from side to side. If you prop open the eyes of someone who is stone drunk, you might see this stereotypical twitch, called nystagmus. Police know this well,

A primitive version of part of our inner ear is embedded in the skin of fish. Small sacs—the neuromasts—are distributed around the body. When they bend, they give the fish information about how the flow of water is changing.

Here I was, in the hallowed halls of academe, listening to seminars on taxonomy. You know, taxonomy—the science of naming species and organizing them into the classification scheme that we all memorized in introductory biology. I could not imagine a topic less relevant to everyday life, let alone one less likely to lead eminent senior scientists into apoplexy and the loss of much of their human dignity. The injunction “Get a life” could not have seemed more apt.

Take the body plan of a fish, dress it up to be a mammal, then tweak and twist that mammal until it walks on two legs, talks, thinks, and has superfine control of its fingers—and you have a recipe for problems. We can dress up a fish only so much without paying a price. In a perfectly designed world—one with no history—we would not have to suffer everything from hemorrhoids to cancer. Nowhere is this history more visible than in the detours, twists, and turns of our arteries, nerves, and veins. Follow some nerves and you’ll find that they make strange loops around other organs, apparently going in one direction only to twist and end up in an unexpected place. The detours are fascinating products of our past that, as we’ll see, often create problems for us—hiccups and hernias, for example. And this is only one way our past comes back to plague us. Our deep history was spent, at different times, in ancient oceans, small streams, and savannahs, not office buildings, ski slopes, and tennis courts. We were not designed to live past the age of eighty, sit on our keisters for ten hours a day, and eat Hostess Twinkies, nor were we designed to play football.