Your Inner Fish

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Your Inner Fish Chapter 3 Summary & Analysis

Summary
Analysis
While Shubin and his team dig up fish fossil bones, Randy Dahn at the research lab at the University of Chicago looks at the embryos of sharks and skates (a smaller cousin of a shark. Dahn is investigating the affects of Vitamin A on limb development in sharks, hoping to explain part of the way that our DNA directs body cells to form a functional body. Dahn’s experiments look to compare the DNA “recipe” for shark fins to the “recipe” for human hands.
Dahn’s work points both to the ways that animal bodies are similar enough that sharks can stand in for humans, and the ways that scientific research builds on the past and looks towards the future. Dahn does not expect to change the world with his research, but the information about shark development he finds may be useful for other scientists looking at human hands.
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Experiments on DNA fill in an important gap that fossil study can’t address, as fossils are rare and cannot be manipulated to change specific variables or answer certain questions. Dahn wants to prove that the genes for fish fins and human hands are virtually identical by manipulating shark embryos to make part of the fin look like a hand.
Aside from the bones that Shubin compared between fins and limbs, the genetic code that builds these structures may prove to be very similar. If the directions for building limbs and fins are the same, it is more likely that fins and limbs share the same developmental path in the history of life.
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Though the human body is made up of hundreds of different kinds of cells, every cell in an individual human’s body has the exact same DNA in its center. Different organ cells develop differently because only certain genes are active in each cell. Understanding what switches a gene on or off in a particular cell helps explain what genes are involved in specific body systems. Isolating the genetic differences between the code for a fin and the code for a hand gives Shubin likely places to look for a switch that allowed an animal like Tiktaalik to start making the bones for a hand instead of a fin.
Though Shubin set up the argument that fins and limbs have the same basic genetic directions, a key part of Dahn’s research is actually looking for differences between hands and fins. These small changes will point to the ways that the “basic” fin recipe may have turned into a more complex limb. Even if fins and limbs do not have the exact same genetic code, finding that they share some information would be evidence that limbs developed from fins.
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Making Hands. Hands have three dimensions: top to bottom, pinky side to thumb side, and base to tip. Shubin looks for the genes that make a pinky look different from a thumb as a “key” to the genetic recipe that controls hands. In the embryo, limbs develop from the third to eighth week after conception. First, tiny buds extend from the body, then form into little paddles. The tips of these paddles are the millions of cells that will become the limb’s skeleton nerves and muscles. Scientists study limbs that have gone wrong because it is easier to identify genetic mutations that differ from the “normal” DNA recipe.
Comparisons between DNA continue to be important, as Shubin explains how Dahn compares not only fin and limb DNA, but normal limb and mutated limb DNA to look for what is the same and what is different. Places of difference point to structures unique to that specific animal, while places of similarity suggest a shared past between all of these structures. From a very simple paddle, complicated limbs form.
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To study embryonic limbs, scientists need an organism that is big enough to see and manipulate and that has readily available, fairly cheap embryos. In the 1940s and 50s, chicken eggs were the perfect candidate. Edgar Zwilling and John Saunders, two scientists that studied embryos, cut into chicken embryos and surgically removed small patches of tissue in the limbs to see what would happen. They discovered that a small zone of tissue is responsible for the development of the entire limb. Removing it at different times in the embryo’s life stops limb development at different junctures.
Scientific research always has to contend with what is practical for the time period and the location as well as what will best fit the question that scientists like Zwilling and Saunders want to investigate. Shubin does not address any ethical concerns that might arise from surgically experimenting on embryos of any species, though chicken eggs are easy for most people to approve of sacrificing for scientific good. The small patch of tissue that Zwilling and Saunders found is another example of simple starts that can blossom into huge results, as Shubin explains throughout his book.
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Mary Gasseling, a member of John Saunder’s embryo lab, transplanted limb tissue to different places on the limb to see how manipulating the place affects limb development. Taking a small patch of tissue from the “pinky” side of the limb bud and transplanting it to the “thumb” side early in development actually causes the embryo to develop a limb with a full duplicate set of digits, arranged as a mirror image of the normal set. Injecting vitamin A into the chicken egg during development produces the same result. The patch of tissue that controls limb development was named the zone of polarizing activity (ZPA).
Gasseling continues Saunder’s experiments and builds on them in another example of collaborative scientific work. His experiments help clarify the complicated process of building a hand, as Shubin breaks down the many factors at play in the work of the ZPA. While the ZPA is not wholly responsible for building an entire hand, it is the initiator of hand development. This small patch of tissue yields huge results in the mature animal.
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The ZPA controls the formation of fingers and toes by controlling the concentration (amount) of a certain molecule in the cells that will become the limb. The cells closest to the ZPA have a high concentration of the unknown molecule and respond by making a pinky finger. The cells farther away from the ZPA have a low concentration of the molecule and respond by making a thumb. The cells in between have varying concentrations of the molecule that correspond to making the second, third, and fourth fingers.
Shubin makes the complex process of digit formation very simple by focusing only on the ZPA and the concentration of molecules, even though there are many other genes and protein interactions at work. This is a good basic understanding that lets the average person grasp enough of limb development for the purposes of Shubin’s book, and learn more if they are interested.
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The DNA Recipe. In the 1990s, scientists were better able to look for the molecular mechanisms that the ZPA uses to differentiate fingers. Cliff Tabin, Andy MacMahon, and Phil Ingham decided to look at flies for the answer. Genetic experiments in the 1980s had already mapped out the gene activity that guides fly development from front to back, with different genes active in the front head than the back wings. Tabin, MacMahon, and Ingham identified another gene that controlled the body regions of the fly.
The fact that Tabin, MacMahon, and Ingham can look at flies for a process originally found in chickens again points to the underlying similarities between all creatures. Yet Tabin’s group must modify their research to the fly’s body instead of its limbs, as fly limbs do not have different digits. The process of differentiating body segments is very similar to the development of different digits in a limb.
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Tabin, MacMahon, and Ingham named the gene that controls differentiating body segments in flies the hedgehog gene, because flies that have a faulty hedgehog gene look like little bristly hedgehogs. In chickens, this gene is called “sonic hedgehog” (named after the video game character). Sonic hedgehog is only active in the ZPA of chicken embryo limbs. After experiments that confirmed that hedgehog does the same limb production in flies, chickens, and mice, Dahn began to look for a sonic hedgehog gene activity in sharks.
Though chickens also have different body segments, it seems that the specific “sonic hedgehog” gene is only active in chicken limbs, whereas a more general version of the gene has a much larger role in the fly body plan. Yet Shubin does not explicitly say that flies developed before chickens in this case, or use this as evidence for a shared developmental path, only commenting on the similarities between flies and chickens as they are now.
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Sharks and their smaller cousins, skates, have embryos in eggs that are remarkably similar to chicken eggs, with some adaptations for life in water. Looking for sonic hedgehog activity in skate embryos would prove that this basic recipe for limb development goes far further back than just land animals in the history of life on earth, as the earliest shark fossils are dated to 400 million years ago. Sharks and humans are distantly related, and obviously look very different on the surface. Shark bones are even made out of a different material than human bones. All of these differences make it even more useful to use sharks to see if sonic hedgehog is unique to limbed animals or if it is active in all animals with appendages.
The comparison between skate sonic hedgehog and chicken sonic hedgehog is much cleaner than the earlier comparison between chicken limbs and fly bodies, because these experiments are considering the same body structure and the same specialized limb version of the hedgehog gene. If the gene is the same in such different appendages, the similarities between sharks and chickens would be deep enough to suggest a developmental path from water creatures like sharks to land creatures like chickens.
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Dahn started by looking for the sonic hedgehog gene in shark embryos. Once he found that sonic hedgehog was indeed present, he started to run through all the experiments that Tabin’s team had done on chicken eggs. In each instance, the shark fin reacted the same way as chicken limbs – to the point of producing a duplicate fin when the shark ZPA was treated with Vitamin A.
Dahn basically reenacts the earlier experiments on chickens, building on this earlier research that explained how limbs developed and pushing it to help find the origin of limbs. The fact that the shark ZPA shows the same signs as the chicken ZPA supports the idea that fins and limbs are fundamentally the same structure.
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Dahn went further to see if the shark ZPA could be influenced with the protein that the sonic hedgehog gene produces in mice. Normally, the rods in a shark’s fin are all the same. When Dahn inserted the mouse sonic hedgehog protein, the rods of the shark fin developed to be different sizes and shapes from each other, just like mouse fingers do.
Dahn’s experiment was a success, based on the goal that Shubin stated earlier in the chapter of developing fins into hands. Dahn was able to introduce genetic material from a mouse, have it be accepted by a shark (proving that genetic material is similar enough across these two species to even have effects) and force the shark fin to develop like a limb with differentiated fingers.
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Dahn’s experiments prove that all appendages, whether fins or limbs, develop the same way from the same basic DNA recipe. Shubin argues that this means the transition from fins to limbs did not involve any new DNA, but simply using the ancient genes for fin-making in new ways. Ultimately, experiments on flies, chickens, mice, and sharks show the similarity between all animals with appendages and give insight to the genes responsible for the development of human limbs.
Shubin focuses on the significance of tying fins and limbs together with the same genetic recipe. While this is certainly evidence that supports connections between all animals, Shubin does not fully explain why certain species would begin using the DNA that allowed them to build fins for another purpose—a question that has more to do with environment than with fossils and DNA.
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