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

by Neil Shubin

  Mangold’s dissertation work was ultimately to win the Nobel Prize, but not for her. Hilde Mangold died tragically (the gasoline stove in her kitchen caught fire) before her thesis could even be published. Spemann won the Nobel Prize in Medicine in 1935, and the award cites “his discovery of the Organizer and its effect in embryonic development.”

  Today, many scientists consider Mangold’s work to be the single most important experiment in the history of embryology.

  At roughly the same time that Mangold was doing experiments in Spemann’s lab, W. Vogt (also in Germany) was designing clever techniques to label cells, or batches of them, and thus allow the experimenter to watch what happens as the egg develops. Vogt was able to produce a map of the embryo that shows where every organ originates in the egg. We see the antecedents of the body plan in the cell fates of the early embryo.

  From the early embryologists, people like von Baer, Pander, Mangold, and Spemann, we have learned that all the parts of our adult bodies can be mapped to individual batches of cells in the simple three-layered Frisbee, and the general structure of the body is initiated by the Organizer region discovered by Mangold and Spemann.

  Cut, slice, and dice, and you’ll find that all mammals, birds, amphibians, and fish have Organizers. You can even sometimes swap one species’ Organizer for another. Take the Organizer region from a chicken and graft it to a salamander embryo: you get a twinned salamander.

  But just what is an Organizer? What inside it tells cells how to build bodies? DNA, of course. And it is in this DNA that we will find the inner recipe that we share with the rest of animal life.

  OF FLIES AND MEN

  Von Baer watched embryos develop, compared one species to another, and saw fundamental patterns in bodies. Mangold and Spemann physically distorted embryos to learn how their tissues build bodies. In the DNA age, we can ask questions about our own genetic makeup. How do our genes control the development of our tissues and our bodies? If you ever thought that flies are unimportant, consider this: mutations in flies gave us important clues to the major body plan genes active in human embryos. We put this kind of thinking to use in the discovery of genes that build fingers and toes. Now we’ll see how it tells us about the ways entire bodies are built.

  Flies have a body plan. They have a front and a back, a top and a bottom, and so on. Their antennae, wings, and other appendages pop out of the body in the right place. Except when they don’t. Some mutant flies have limbs growing out of their heads. Others have duplicate wings and extra body segments. These are among the fly mutants that tell us why our vertebrae change shape from the head end to the anal end of the body.

  People have been studying abnormal flies for over a hundred years. Mutants with one particular kind of abnormality got special attention. These flies had organs in the wrong places—a leg where an antenna should have been; an extra set of wings—or were missing body segments. Something was messing with their fundamental body plan. Ultimately, these mutants arise from some sort of error in the DNA. Remember that genes are stretches of DNA that lie on the chromosome. Using a variety of techniques that allow us to visualize the chromosome, we can identify the patch of the chromosome responsible for the mutant effect. Essentially, we breed mutants to make a whole population where every individual has the genetic error. Then, using a variety of molecular markers, we compare the genes of individuals with the mutation to those without. This allows us to pinpoint the region and the likely stretch of chromosome responsible for the mutant effect. It turns out that a fly has eight genes that make such mutants. These genes lie next to one another on one of the long DNA strands of the fly. The genes that affect the head segments lie next to those that affect the segments in the middle of the fly, the part of the body that contains the wings. These bits of DNA, in turn, lie adjacent to the ones that control the development of the rear part of the fly. There is a wonderful order to the way the genes are organized: their position along the DNA strand parallels the structure of the body from front to back.

  Now the challenge was to identify the structure of the DNA actually responsible for the mutation. Mike Levine and Bill McGinnis, in Walter Gehring’s lab in Switzerland, and Matt Scott, in Tom Kauffman’s lab in Indiana, noticed that in the middle of each gene was a short DNA sequence that was virtually identical in each species they looked at. This little sequence is called a homeobox. The eight genes that contain the homeobox are called Hox genes. When the scientists fished around for this gene sequence in other species, they found something so uniform that it came as a true surprise: versions of the Hox genes appear in every animal with a body.

  Hox genes in flies and people. The head-to-tail organization of the body is under the control of different Hox genes. Flies have one set of eight hox genes, each represented as a little box in the diagram. Humans have four sets of these genes. In flies and people, the activity of a gene matches its position on the DNA: genes active in the head lie at one end, those in the tail at another, with genes affecting the middle of the body lying in between.

  Versions of the same genes sculpt the front-to-back organization of the bodies of creatures as different as flies and mice. Mess with the Hox genes and you mess with the body plan in predictable ways. If you make a fly that lacks a gene active in a middle segment, the midsection of the fly is missing or altered. Make a mouse that lacks one of the genes that specifies thoracic segments, and you transform parts of the back.

  Hox genes also establish the proportions of our bodies—the sizes of the different regions of our head, chest, and lower back. They are involved in the development of individual organs, limbs, genitalia, and guts. Changes in them bring about changes in the ways our bodies are put together.

  Different kinds of creatures have different numbers of Hox genes. Flies and other insects have eight, mice and other mammals thirty-nine. The thirty-nine Hox genes in mice are all versions of the ones that are found in flies. This similarity has led to the idea that the large number of mammalian Hox genes arose from a duplication of the smaller complement of genes in the fly. Despite these differences in number, the mouse genes are active from front to back in a very precise order just as the fly genes are.

  Can we go even deeper in our family tree, finding similar stretches of DNA involved in making even more fundamental parts of our bodies? The answer, surprisingly, is yes. And it links us to animals even simpler than flies.

  DNA AND THE ORGANIZER

  At the time when Spemann won the Nobel Prize, the Organizer was all the rage. Scientists sought the mysterious chemical that could induce the entire body plan. But just as popular culture has yo-yos and Tickle Me Elmo dolls, so science has fads that wax and wane. By the 1970s, the Organizer was viewed as little more than a curiosity, a clever anecdote in the history of embryology. The reason for this fall from grace was that no one could decipher the mechanisms that made it work.

  The discovery of Hox genes in the 1980s changed everything. In the early 1990s, when the Organizer concept was still decidedly unfashionable, Eddie De Robertis’s laboratory at UCLA was looking for Hox genes in frogs, using techniques like Levine and McGinnis’s. The search was broad and it netted many different kinds of genes. One of these had a very special pattern of activity. It was active at the exact site in the embryo that contains the Organizer, and it was active at exactly the right time of development. I can only imagine what De Robertis felt when he found that gene. He was looking at the Organizer, and there in the Organizer was a gene that seemed specifically to control it or be linked to its activity in the embryo. The Organizer was back.

  Organizer genes started popping up in laboratories everywhere. While doing a different kind of experiment, Richard Harland at Berkeley found another gene, which he called Noggin. Noggin does exactly what an Organizer gene should. When Harland took some Noggin and injected it into the right place in an embryo, it functioned exactly like the Organizer. The embryo developed two body axes, including two heads.

  Are De Robertis’s gene and
Noggin the actual bits of DNA that make up the Organizer? The answer is yes and no. Many genes, including these two, interact to organize the body plan. Such systems are complex, because genes can play many different roles during development. Noggin, for example, plays a role in the development of the body axis but is also involved with a host of other organs. Furthermore, genes do not act alone to specify complicated cell behaviors like those we see in head development. Genes interact with other genes at all stages of development. One gene may inhibit the activity of another or promote it. Sometimes many genes interact to turn another gene on or off. Fortunately, new tools allow us to study the activity of thousands of genes in a cell at once. Couple this technology with new computer-based ways of interpreting gene function and we have enormous potential to understand how genes build cells, tissues, and bodies.

  Understanding these complex interactions between batteries of genes sheds light on the actual mechanisms that build bodies. Noggin serves as a great example. Noggin alone does not instruct any cell in the embryo about its position on the top–bottom axis; rather, it acts in concert with several other genes to do this. Another gene, BMP-4, is a bottom gene; it is turned on in cells that will make the bottom, or belly side, of an embryo. There is an important interaction between BMP-4 and Noggin. Wherever Noggin is active, BMP-4 cannot do its job. The upshot is that Noggin does not tell cells to develop as “cells on the top of the body” instead, it turns off the signal that would make them bottom cells. These off-on interactions underlie virtually all developmental processes.

  AN INNER SEA ANEMONE

  It is one thing to compare our bodies with those of frogs and fish. In a real sense we and they are much alike: we all have a backbone, two legs, two arms, a head, and so on. What if we compare ourselves with something utterly different, for example jellyfish and their relatives?

  Most animals have body axes defined by their direction of movement or by where their mouth and anus lie relative to each other. Think about it: our mouth is on the opposite end of the body from our anus and, as in fish and insects, it is usually in the direction “forward.”

  How can we try to see ourselves in animals that have no nerve cord at all? How about no anus and no mouth? 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. While that odd arrangement may be convenient for jellyfish and their relatives, it gives biologists vertigo when they try to compare these creatures to anything else.

  A number of colleagues, Mark Martindale and John Finnerty among them, have dived into this problem by studying the development of this group of animals. Sea anemones have been remarkably informative, because they are close relatives of jellyfish and they have a very primitive body pattern. Also, sea anemones have a very unusual shape, one that at first glance would seem to make them worthless as a form to compare to us. A sea anemone is shaped like a tree trunk with a long central stump and a bunch of tentacles at the end. This odd shape makes it particularly appealing, since it might have a front and a back, a top and a bottom. Draw a line from the mouth to the base of the animal. Biologists have given that line a name: the oral–aboral axis. But naming it doesn’t make it more than an arbitrary line. If it is real, then its development should resemble the development of one of our own body dimensions.

  Martindale and his colleagues discovered that primitive versions of some of our major body plan genes—those that determine our head-to-anus axis—are indeed present in the sea anemone. And, more important, these genes are active along the oral–aboral axis. This in turn means that the oral–aboral axis of these primitive creatures is genetically equivalent to our head-to-anus axis.

  One axis down, another to go. Do sea anemones have anything analogous to our belly-to-back axis? Sea anemones don’t seem to have anything comparable. Despite this, Martindale and his colleagues took the bold step of searching in the sea anemone for the genes that specify our belly-to-back axis. They knew what our genes looked like, and this gave them a search image. They uncovered not one, but many different belly-to-back genes in the sea anemone. But although these genes were active along an axis in the sea anemone, that axis didn’t seem to correlate with any pattern in how the adult animal’s organs are put together.

  Jellyfish relatives, such as sea anemones, have a front and a back as we do, a body plan set up by versions of the same genes.

  Just what this hidden axis could be is not apparent from the outside of the animal. If we cut one in half, however, we find an important clue, another axis of symmetry. Called the directive axis, it seems to define two distinct sides of the creature, almost a left and a right. This obscure axis was known to anatomists back in the 1920s but remained a curiosity in the scientific literature. Martindale, Finnerty, and their team changed that.

  All animals are the same but different. Like a cake recipe passed down from generation to generation—with enhancements to the cake in each—the recipe that builds our bodies has been passed down, and modified, for eons. We may not look much like sea anemones and jellyfish, but the recipe that builds us is a more intricate version of the one that builds them.

  Powerful evidence for a common genetic recipe for animal bodies is found when we swap genes between species. What happens when you swap a body-building gene from an animal that has a complex body plan like ours with one from a sea anemone? Recall the gene Noggin, which in frogs, mice, and humans is turned on in places that will develop into back structures. Inject extra amounts of frog Noggin into a frog egg, and the frog will grow extra back structures, sometimes even a second head. In sea anemone embryos, a version of Noggin is also turned on at one end of the directive axis. Now, the million-dollar experiment: take the product of Noggin from a sea anemone and inject it into a frog embryo. The result: a frog with extra back structures, almost the same result as if the frog were injected with its own Noggin.

  Now, though, as we go back in time, we are left with what looks like a huge gap. Everything in this chapter had a body. How do we compare ourselves with things that have no bodies at all—with single-celled microbes?

  CHAPTER SEVEN

  ADVENTURES IN BODYBUILDING

  When I wasn’t out in the field collecting fossils, much of my graduate career was spent staring into a microscope, looking at how cells come together to make bones.

  I would take the developing limb of a salamander or a frog, and stain the cells with dyes that turn developing cartilage blue and bones red. I could then make the rest of the tissues clear by treating the limb with glycerin. These were beautiful preparations: the embryo entirely clear and all the bones radiating the colors of the dyes. It was like looking at creatures made of glass.

  During these long hours at the microscope, I was literally watching an animal being built. The earliest embryos would have tiny little limb buds and the cells inside would be evenly spaced. Then, at later stages, the cells would clump inside the limb bud. In successively older embryos, the cells would take different shapes and the bones would form. Each of those clumps I saw during the early stages became a bone.

  It is hard not to feel awestruck watching an animal assemble itself. Just like a brick house, a limb is built by smaller pieces joining to make a larger structure. But there is a huge difference. Houses have a builder, somebody who actually knows where all the bricks need to go; limbs and bodies do not. The information that builds limbs is not in some architectural plan but is contained within each cell. Imagine a house coming together spontaneously from all the information contained in the bricks: that is how animal bodies are made.

  Much of what makes a body is locked inside the cell; in fact, much of what makes us unique is there, too. Our body looks different from that of a jellyfish because of the ways our cells attach to one another, the ways they communicate, and the different materials they make.

  Before we could even have a “body plan”—let alone a head, brain, or arm—there had to be a way to make a body in the first place. What does th
is mean? To make all of a body’s tissues and structures, cells had to know how to cooperate—to come together to make an entirely new kind of individual.

  To understand the meaning of this, let’s first consider what a body is. Then, let’s address the three great questions about bodies: When? How? And Why? When did bodies arise, how did they come about, and, most important, why are there bodies at all?

  HABEAS CORPUS: SHOW ME THE BODY

  Not every clump of cells can be awarded the honor of being called a body. A mat of bacteria or a group of skin cells is a very different thing from an array of cells that we would call an individual. This is an essential distinction; a thought experiment will help us see the difference.

  What happens if you take away some bacteria from a mat of bacteria? You end up with a smaller mat of bacteria. What happens when you remove some cells of a human or fish, say from the heart or brain? You could end up with a dead human or fish, depending on which cells you remove.

  So the thought experiment reveals one of the defining features of bodies: our component parts work together to make a greater whole. But not all parts of bodies are equal; some parts are absolutely required for life. Moreover, in bodies, there is a division of labor between parts; brains, hearts, and stomachs have distinct functions. This division of labor extends to the smallest levels of structure, including the cells, genes, and proteins that make bodies.

  The body of a worm or a person has an identity that the constituent parts—organs, tissues, and cells—lack. Our skin cells, for example, are continually dividing, dying, and being sloughed off. Yet you are the same individual you were seven years ago, even though virtually every one of your skin cells is now different: the ones you had back then are dead and gone, replaced by new ones. The same is true of virtually every cell in our bodies. Like a river that remains the same despite changes in its course, water content, even size, we remain the same individuals despite the continual turnover of our parts.