PDF Summary:Your Inner Fish, by Neil Shubin

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Ancient fossils like Tiktaalik, plus embryos and DNA, provide clues to a story of human development stretching back 3.5 billion years.

Casting new light on the human family tree, Your Inner Fish became a popular PBS series.

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1. Rocks the right age
2. Rock types conducive to preserving fossils
3. Rocks that are exposed

Rocks can be dated because they’re arranged in layers going back billions of years, with the oldest rocks in the lowest layers and more recent ones on top. Earthquakes and faults can push some older layers over younger ones, but scientists can usually figure out the correct order.

The fossils in rock layers also follow a progression from the oldest on the bottom to younger fossils in higher layers. The lowest layers show little evidence of life; then there’s a progression from jellyfish-like creatures; to animals with skeletons, limbs, and organs such as eyes; to vertebrates.

Lessons from the Zoo

Every species fits into a complicated classification system or taxonomy that helps paleontologists identify what they’re looking at and predict what they’ll find.

A trip to the zoo illustrates how the system works. The system organizes species and organisms by grouping them according to traits they share, like a set of Russian nesting dolls with smaller groups encompassed by larger ones.

Every species in a zoo has a head and two eyes; another group or subset has a head,...

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Discoveries going back further led closer to the origin of fingers and toes:

• Between 1929-1934, a Swedish paleontologist found a fish fossil from the Devonian period on the east coast of Greenland. Called Ichthyostega soderberghi, it had fully developed fingers and toes on its fin-limbs.
• Another fossil of a limbed creature, found by the same paleontologist, was a mystery until 1988, when paleontologists found additional fossils of it at the same site showing full limbs with wrists, fingers, and toes but no webbing.

But it wasn’t until the 2004 discovery of Tiktaalik—a creature with a yet more primitive form of hands, feet, wrists, and ankles—that the sequence for limb development could be put together.

Wrist Bones in Fish

In 1995, Shubin and colleagues found a 365-million-year-old fin fossil (lacking the rest of the skeleton) in a highway construction area in Pennsylvania. The fin had webbing and scales like a fish but also the bone structure of a limb: one bone at the base, attached to two bones with eight bones extending like fingers. Without a full skeleton, however, researchers couldn’t determine whether it showed the origin of limbs.

That discovery...

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To learn about the process, scientists experiment with genetic mutations that make limbs malform. In the fifties and sixties, scientists experimenting with chicken embryos uncovered a key mechanism—a patch of tissue—that controls development of the bone pattern of limbs. By removing the patch, they could stop limb development at various points. They called the patch, which causes the little-finger side of a hand to differentiate from the thumb side, the ZPA, or zone of polarizing activity.

Moving the ZPA from the little-finger side of the limb bud to the thumb side caused the embryo to develop a duplicate set of digits mirroring the normal set on that side.

The ZPA controls development of fingers and toes by varying the concentration of a molecule in the cells building the limb. The cells nearest to the ZPA have a high concentration of the molecule and make a little finger. The cells farther away from the ZPA have a lower concentration of the molecule and make a thumb. The cells in between have varying concentrations and make second, third, and fourth fingers.

The DNA Recipe

In the 1990s, with new molecular techniques, researchers looked at DNA in flies to identify...

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After finding the tritheledont (an intermediate mammal), researchers found various new mammal species with new kinds of occluding teeth suited to new diets. But the tritheledont paved the way for diverse eaters, including us.

The Origins of Teeth

The most unique feature of teeth is that they’re harder than other body parts because they have a crystal molecule called hydroxyapatite, particularly in the enamel. The same molecule appears in lesser concentrations in other parts of the teeth, bones, and other tissues.

Our hydroxyapatite-containing tissues contribute to our ability to eat, breathe, move, and metabolize minerals. The substance—which we share with fish, reptiles, birds, amphibians, and mammals—traces back to a common ancestor.

The first teeth, 250 million to 500 million years old, were found in the 1830s and belonged to jawless fish or lamprey-like creatures. However, scientists found the teeth before they found the fish the teeth belonged to. The teeth were so ubiquitous—they showed up on every continent— that scientists initially thought they were separate creatures, which they called conodonts. However, 150 years later, researchers discovered...

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• First arch: Cells from the first arch form the upper and lower jaws and two of the ear bones.
• Second arch: Cells from this arch form the third ear bone, a throat bone, and facial muscles.
• Third arch: These cells form bones, muscles, and nerves in the throat that are used to swallow.
• Fourth arch: This arch forms the deep part of the throat, including the larynx and its surrounding muscles and vessels.

The arches dictate the routes of the key cranial nerves. The trigeminal nerve serves the body systems (jaw and ear) formed by the first arch. The facial nerve serves structures developed by the second arch. The nerves corresponding with the third and fourth arches follow the same pattern.

The human body is segmented. Each vertebra in the body represents a segment. The nerves corresponding with each body system exit the spinal cord at a specific point, according to their segment. For example, our leg muscles are served by nerves exiting the spinal cord at a point below the nerves serving our arm muscles. The head is also segmented, as determined by the arches. This is why, for instance, both the trigeminal nerve and the facial nerve travel to...

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Experimenting With Embryos

In an effort to learn more about how embryos develop body structures and organs, early scientists experimented with them by cutting, grafting, and treating them with chemicals.

In 1903, German embryologist Hans Spemann determined that more than one individual can come from a single egg—he pinched apart a newt embryo making two clumps of cells. Each clump formed a newt, showing that embryonic cells can build a whole body.

In the 1920s, another researcher, Hilde Mangold, grafted a bit of newt embryo tissue containing all three germ layers onto an embryo of another species. The transplanted tissue developed a full newt body on the back of the second embryo. Scientists called the bit of tissue, which directed other cells to form a complete body, the Organizer.

Another researcher figured out how to label cells so their development into body parts could be traced. This led to an embryo map showing where every organ begins.

All mammals, birds, fish, and amphibians have Organizers, which initiate the bodybuilding process, telling each clump of cells in the embryo to follow the body plan for that animal. The key is that the Organizer contains DNA...

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Bodies with advanced features like hands and sense organs haven’t been around all that long. Life consisted of single-celled organisms for much of Earth’s 4.5-billion-year history. If that history were compressed into a calendar year, single-celled organisms (like algae and bacteria) would be the only life until June. Animals with heads would show up in October and the first human would appear on December 31.

Rocks illustrate this immense time scale: those older than 600 million years show evidence only of colonies of algae, which are far from being bodies. In the 1920s and ‘30s, paleontologists found evidence of possibly the earliest bodies but didn’t realize what they were. The impressions looked like disks and plates—they may have been primitive algae or jellyfish.

Scientists found more impressions of disks, ribbons, and fronds in Australia in 1947. But they didn’t understand until the 1960s, when the rocks were accurately dated, that the impressions were of some of the earliest bodies. Some resembled today’s simple sponges and jellyfish; others were unlike anything that existed.

So multicellular creatures lived in the seas 600 million years ago. Some bodies had...

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In 1991, researchers identified a large family of genes that create our sense of smell. They made three assumptions, which proved to be correct: that human genes for smell resemble the odor genes in mice, that the genes are active only in the tissues associated with smell, and that a large number of genes are involved with smelling.

They determined that 3% of the human genome is involved in detecting odors, which is a lot for one function. Each of these genes creates a receptor for an odor molecule. Other researchers found odor receptor genes in other species, which helped trace the transition in animals from sensing smell in water molecules to sensing it in air molecules.

Lampreys and hagfish have receptors that can handle both water and air molecules, indicating they emerged before the odor-detecting genes split into the two types, for water and air. These fish also have a fairly small number of odor genes.

The number of odor genes in animals increased over time (humans and mammals have over 1,000)—apparently, as animals became more complex, so did the sense of smell. The more odor genes an animal has, the greater its ability to detect different odors. Mammals (think...

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1. The molecules that gather light
2. The eye tissues
3. The genes that direct eye development

1) Light-Gathering Molecules

The molecule in the eye that collects light breaks into two parts after absorbing light: Vitamin A and a protein called an opsin that starts a chain reaction sending an impulse to the brain.

Humans, like all animals, need three different opsins to see color and one to see in black and white. Every animal that can see light (including humans, insects, clams, and scallops) uses the same kind of opsin molecule to do so.

Opsins transmit messages by carrying a chemical across the membrane of a cell, then helping the chemical follow a convoluted path through the cell to the nucleus. This same tortuous path exists in certain molecules in bacteria, meaning that, in a sense, we have modified pieces of an ancient bacteria inside our retinas, helping us see.

Examining opsins and eye development in different animals—for instance, the development of color vision in primates—offers further clues to human eye development.

Primates’ (and humans’) vivid color vision comes from a change in the gene that makes light receptor molecules. Primates have three...

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In 1913, a paleontologist connected the dots between:

• The theory that the malleus and incus bones moved from the jaw in reptiles to the ear in mammals.
• The discovery that dog-sized South African reptiles with mammal-like teeth also had bones at the back of the jaw resembling mammal ear bones. A series of fossils of the evolving reptile showed that these bones in the jaw got progressively smaller over time and moved toward the ear.

Indeed, the malleus and incus in mammals evolved from reptile jawbones. So mammals ended up with three middle-ear bones (remember, reptiles and other animals had only one). Having three enabled mammals to hear higher-frequency sounds. Improved hearing was developed by repurposing bones originally used by reptiles for chewing.

The Stapes

While two bones in our middle ear came from reptiles, the third ear bone (the stapes) came from fish.

As noted earlier, the second arch produces the stapes in mammals; the second arch also produces a large bone (hyomandibula) connecting the upper jaw to the brain area of fish and sharks. In both species, these two bones—in the mammal ear and shark jaw—are served by the same second-arch nerve, the...

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• The first and third generations share a red nose, while the second and third generations share red noses and big feet.

Actual human traits can be traced the same way, although it’s more complicated because humans and animals typically change more than one trait with each generation. It’s even possible to trace a lineage of shared traits through humans, animals, and back to the earliest life forms.

Revisiting the Zoo

A trip to the zoo helps show how scientists trace relationships among humans and other creatures.

Humans share many features with other animals, but we have more in common with some animals than others. For example, we have more in common with polar bears (two eyes, neck, four limbs, hair, mammary glands) than we have with turtles (two eyes, neck, four limbs). But we have more in common with turtles than we have with fish.

In the same way that generations of the clown family passed down additional traits, different subsets of animals add features. Individuals with the most shared features are the most closely related. Humans and polar bears share more features, so they should share a more recent ancestor than humans and turtles do.

While it can’t zero...