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Finding Your Inner Fish



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    1.Explain why the author and his colleagues chose to focus on 375 million year old rocks in their search for fossils. Be sure to include the types of rocks and their location during their paleontology work in 2004.

    The author and his colleagues specifically chose to focus on 375 million year old rocks in their search for fossils because this was the time frame that provided fish that would be useful to study from. The 385 million year old rocks provided fish that look too similar to the ones we have now and the 365 million year old rocks have fossils that don’t resemble fish. The 375 million year old rocks, however, provide fossils that show the transition between fish and land living animals. Sedimentary rocks are the type of rock that preserves the fossils. Limestone, siltstone, shale, and sandstone are examples of this. The reason why these rocks are the best at preservation is because they are formed by a process that includes the movement of lakes, rivers, and seas. A rock in a body of water has the potential to fossilize because after the gradual compression on the layers in the body of water forming, chemical processes are still happening.

    2.What major paleontological prediction does the Tiktaalik fossil confirm?

    In a Tiktaalik, the head is completely free of the shoulders. This feature is shared with mammals, including humans. In this way, the Tiktaalik fossil confirms the major paleontological prediction that almost all the body parts (ribs, ears, and wrists) are similar to ours and therefore that we can be traced back to this fish.

    3.Explain why Neil Shubin thinks Tiktaalik says something about our own bodies? (in other words – why the Inner Fish title for the book?)

    Neil Shubin basically thinks Tiktaalik shows the link between our bodies in the present and the history of the organisms we evolved from. The discovery of Tiktaalik shows us how we are related to fish in many ways that were hard to prove in the past. The title comes into play because although we our much more complex than our fish ancestors, everyone’s bodies comes from a long line of evolution that once contained fish.

    Chapter 2 – Getting a Grip
    1.Describe the “pattern” to the skeleton of the human arm that was discovered by Sir Richard Owen in the mid-1800s. Relate this pattern to his idea of exceptional similarities.

    Sir Richard Owens, the scientific leader, noticed that there was a pattern to the human arm. There was one bone in the upper arm, two bones in the forearm, a group of nine little bones in the wrists, then a series of five rods that make the fingers. The idea of exceptional similarities was among all creatures. It was the idea that all creatures with limbs have a common design. This design is one bone, the humorous in the arm or the femur in the leg, articulates with two bones, which attaches to a series of blobs that connect with fingers or toes. The only difference is the size and shape of bones along with the number of blobs, fingers, or toes.

    2.How did Charles Darwin’s theory explain these similarities that were observed by Owen?

    Charles Darwin theory explained Owens theory of exceptional similarities by stating that the skeletal patter of the limbs is there because the creatures share a common ancestor. In this way, Charles Darwin’s work also helped to validate Sir Richard Owen’s work. 3.What did further examination of Tiktaalik’s fins reveal about the creature and its’ lifestyle?

    Further examination of Tiktaalik’s fins revealed that the fish had a wrist. At the end of the fin bone there were spaces for four other bones. When they took the fin apart, they noticed that all the joints were exceptionally well preserved. This discovery reveals new information regarding Tiktaalik’s lifestyle. Tiktaalik was able to do push-ups, for example; another reason for why this fish is similar to humans. Chapter 3 – Handy Genes

    1.Many experiments were conducted during the 1950s and 1960s with chick embryos and they showed that two patches of tissue essentially controlled the development of the pattern of bones inside limbs. Describe at least one of these experiments and explain the significance of the findings.

    In one of the experiments, Mary Gasseling took a little patch of tissue, early in development, from what would be the pinky side of a limb bud. She took that tissue and put it on the opposite side right beneath where the first finger would form. The chick would develop and form a wing; the new fingers were also copies of the normal set. Basically, the tissue (more specifically some molecule or gene inside the tissue) was able to direct the development of the pattern of the fingers. This led to further experiments that defined the ZPA, or the zone of polarizing activity. This patch of tissue is able to determine the difference between the pinky side and the thumb side. 2.Describe the hedgehog gene using several animal examples. Be sure to explain its’ function and its’ region of activity in the body.

    Hedgehog is a gene active in ZPA. ZPA is only located in little clusters and with this hedgehog gene, it creates a mirror image in limbs for the development and growth. The gene creates digits that are clearly different from one another depending on how close they are to the ZPA. The chicken version of the hedgehog gene was named Sonic hedgehog and it activates once Vitamin A is injected. All creatures have the Sonic hedgehog and they all can be activated by injecting Vitamin A. When tested on a skate, the Sonic hedgehog turned on at the same time as a chicken, it also turned into a patch of tissue that makes genes active on the other side; this resulted in duplicate fins. Chapter 4 – Teeth Everywhere

    1.Teeth make great fossils – why are they “as hard as rocks?”

    Teeth are “as hard as rocks” due to the enamel within them. Teeth enamel contains something known as mineral hydroxyapatite, and the enamel has large quantities of it. Teeth are exceptionally hard because of the mineral. Teeth can consequently be preserved for many time periods. Teeth can tell us several things such as diet, which can show how feeding came about. 2.Shubin writes “we would never have scales, feathers, and breasts if we didn’t have teeth in the first place.” (p. 79) Explain what he means by this statement.

    When Shubin says this, he is linking all organs to the same process. Although there are many different organs, they are more similar than they are different. This is because when there are interactions between skin, teeth, breasts, feathers, scales and hair they all develop but in variations. Teeth are formed by the interaction of two layers of tissue, and this process is similar for all of the aforementioned organs. Shubin likens it to plastic being used in a factory and the process for everything being changed around this new development. The same is true with teeth. Teeth revolutionized how the body produced its organs. Chapter 5 – Getting Ahead

    1.List the structures that are formed from the four embryonic arches (gill arches) during human development.

    The first arch tissues form the upper and lower jaws, two tiny ear bones (the malleus and incus), and all the vessels and muscles that supply them. The second arch forms the third small ear bones (the stapes), a tiny throat bone, and most of the muscles that control facial expressions. The third arch forms bones, muscles, and nerves deeper in the throat; we use these to swallow. The fourth arch forms the deepest parts of our throat, including parts of our larynx and the muscles and vessels that surround it and help it function. 2.What are Hox genes and why are they so important?

    Each gill arch has a different compliment of Hox genes active in it; basically the Hox gene is located behind where the first gill arch forms, with this information, we can map our gill arches and the constellation of genes active in making each. This is what makes Hox genes so important.

    3.Amphioxus is a small invertebrate yet is an important specimen for study – why? Be sure to include characteristics that you share with this critter!

    Amphioxus is a worm, an invertebrate, but has nerve cord that runs along its back. It also has a rod like structure that runs the length of the body
    parallel to the nerve cord. The rod known as a notochord is filled with a jelly like substance that provides support. Humans also have a notochord, but it breaks up and turns into disks and if one of these disks break/injure, our body plan will begin to rupture. It is a severe part of our body. We also share gill arches with these worms. The cartilage that we have in our jaws, ear bones, and voice box are also in the Amphioxus, but the Amphioxus has an arch associated with a bar of cartilage.

    Chapter 6 – The Best Laid (Body) Plans

    1.Early embryonic experiments in the 1800s led to the discovery of three germ layers. List their names and the organs that form from each.

    The outer layer is the ectoderm which forms the skin and nervous system. The inner layer is the endoderm which forms in the digestive tract and glands associated. The middle layer is the mesoderm which forms tissue in between the guts and skin, including much of our skeleton and our muscles. No matter what creature it is, they all need these 3 layers to form the organs in their body.

    2.Describe the blastocyst stage in embryonic development.

    A blastocyst forms during fertilization. This is a cell ball of 16 calls because the egg cell begins to divide and forms these cells. The blastocyst has thin walls in a shape of a sphere and still doesn’t have a body plan. This “blastocyst stage” doesn’t contain organs or tissues. The ball later sticks to the mother’s uterus and joins the mother’s bloodstreams. This ball doesn’t resemble any kind of organism yet. 3.What type of gene is Noggin and what is its function in bodies?

    Noggin is a gene that has bits of the DNA that make up the organizer. Noggin interacts with other genes to organize the development of the body axis but also is involved with a host of other organs. It acts in concert with several other genes to instruct any cell in the embryo about is position on the top-bottom axis. Another interesting fact about Noggin is that wherever it is active, BMP-4 (bottom gene) can’t do its job. Chapter 7 – Adventures in Bodybuilding

    1.Refer to the timeline on p.121 in Your Inner Fish – what is most surprising to you about the timescale? Explain your choice.

    What I found most surprising was the time difference in between the first life and first bodies. This is because to me, it is extremely curious that on Earth, there were so many different kinds of bodies. I would at least think that it would take around 500 million years or more but in fact, it actually took a couple billion years. Additionally it is interesting how “quickly” (relatively speaking) development occurred after the first bodies appeared. 2.What is the most common protein found in the human body? Name it and describe it.

    The most common protein that makes up over 90% of the human body is collagen. Collagen fills much of the space between cartilage cells. Collagen gives strength along with the cartilage. An interesting fact about collagen is that it needs a large amount of oxygen for synthesis. 3.How do cells (generally) communicate with one another?

    In order for our cells to communicate, the cells must be right next to each other. The cells stick together as if they are bonded together by glue. The outer membrane of one cell is firmly attached to the outer membrane of the next cell and so on. All skin cells are next to other skin cells and all bone cells are attached to other bone cells and because of this, it keeps our body organized. The way cells “talk” to each other is by sending molecules back and forth to other cells. When a cells needs to give information to another cell, perhaps saying that the cell should start dividing, a molecule is sent out and attaches to the outer membrane of the cells that needs to receive the message. Once on the outer membrane, the molecule then send a chain reaction of molecules until it reaches the nucleus and tell the cell that it needs to divide. 4.What are choanoflagellates and why have they been studied by biologists?

    Choanoflagellates are single celled microbes. Most genes that are active in choanoflagellates are also active in animals. The genes that are active in these microbes are used for building bodies. Choanoflagellates gave the scientist a road map for comparing our body building apparatus to that of other molecules.

    5.What are some of the reasons that “bodies” might have developed in the first place? Include any environmental conditions that might have favored their evolution.

    Bodies may have arisen as a defense mechanism. This might have happened when the organisms found a way to eat each other instead of being eaten. This also might have caused them to continuously become bigger. Microbes feed by attaching to other microbes and engulfing them. Predator-prey interaction between microbes usually involve molecular cues, either signaling to back off or come closer which are maybe the same kind of signals that our bodies use to communicate with each other to help keep our bodies intact. A reason for why our bodies weren’t on Earth until a couple billion years later is because of the decreased amount of oxygen levels. There wasn’t enough oxygen to support the amount of bodies. Bodies need a large amount of oxygen considering that they have large amounts of collagen. Due to the chemistry of rocks, one is able to notice that a couple billion years ago, the Earth had an increasingly high amount of oxygen which was able to support the amount of bodies. This can now conclude the reason for the increase in bodies. Chapter 8 – Making Scents

    1.Briefly explain how we perceive a smell.

    As a human breathes, a tiny odor molecule suspended in the air will be sucked into one’s nostrils. From there, these odor molecules travel to an area behind the nose where they are caught in our nasal passages’ mucus lining. Millions of nerve cells, which have small projections into the mucous membrane, then bind with the aforementioned molecules. This sends a signal to the brain which is recognized as a scent.

    2.Jawless fish have a very few number of odor genes while mammals have a much larger number. Why does this make sense and how is it possible?

    The reason jawless fish have a very few number of odor genes while mammals have a much higher number is because mammals are highly specialized smelling animals. As animals have developed over time, the number of odor genes in animals has also developed. This makes sense because upon further inspection of the odor genes found in mammals, the genes are actually modified copies of the same odor genes found in jawless fish. A large number of rounds of duplication, therefore, is the answer for how there was such an increase in the amount of odor genes from jawless fish to mammals.

    Chapter 9 – Vision

    1.Humans and Old World monkeys have similar vision – explain the similarity and reasons for it.

    Humans and Old World monkeys have similar vision due to both relying on three different kinds of light receptors. Each receptor is basically programmed to a different kind of light. While most mammals have only two receptors and consequently cannot discriminate as many colors, humans and Old World monkeys share the ability to discriminate colors with greater accuracy. The reason this occurs is because many years ago, it is apparent that one of the genes in mammals that programmed for one of the two receptors duplicated, with the copies specializing over time. This is similar to the process described with odor genes in question 2 of Chapter 8. In fact, a change in the flora of the Earth millions of years ago might be the cause for this, due to the fact that monkeys would then be able to benefit from a better discrimination of colors for feeding.

    2.What do eyeless and Pax 6 genes do and where can they be found?

    Eyeless and Pax 6 genes control for an animal to not have eyes. The eyeless gene can be found on flies while Pax 6 genes can be found on mine. The discovery and experimentation with these genes were important because Walter Gehring was able to discover that the Pax 6 gene, from a mouse, could grow an eye on a fly if the gene was implanted there. Basically, Gehring had found a universal switch for eye development that was basically the same in a mouse and a fly.

    Chapter 10 – Ears

    1.List the three parts of the ear; what part of the ear is unique to mammals?

    The three parts of the ear are 1) the external ear, which is the visible part, 2) the middle, which contains the little ear bones, and 3) the inner ear, which consists of the sensory cells, the fluid, and the tissues that surround them. The flap of the external ear is only found in mammals making it unique. 2.An early anatomist proposed the hypothesis that parts of the ears of mammals are the same thing as parts of the jaws of reptiles. Explain any fossil evidence that supports this idea.

    Karl Reichert discovered that two ear bones that are present in mammals were part of the jaw of reptiles. The whole link between the two is found in three middle ear bones. Shubin concludes that, “the same gill arch that formed part of the jaw of a reptile formed ear bones in mammals.” (Page 160)

    3.What is the function of the Pax 2 gene?

    The Pax 2 gene plays an important role in the development and formation of the inner ear. Basically, the chain reaction that leads to the making of the inner ear is only initiated with the Pax 2 gene. Because of this, without the Pax 2 gene, major deformities can arise.

    Chapter 11 – The Meaning of It All

    1.What is Shubin’s biological “law of everything” and why is it so important?

    Shubin’s biological “law of everything” is that every living organism on the planet has a parent. When you think about it, it is one of the only true sweeping statements that can be made about every living thing on the planet. Because whether it is concerning a dinosaur or bacteria, it had a parent(s). This is so important because it means that every living thing is based off of the genetic information of their parent, in addition to the fact that even though there is a parent that doesn’t mean that the exact same traits will be passed down. Everything is a modified version of their parent, no matter the scale. This “law of everything” is also important because it allows scientists to view every organism on Earth as a part of a lineage.

    2.What is the author trying to show with his “Bozo” example?

    The author is simply trying to show heredity and the passing down of traits through a comical example. The importance of recognizing biological characteristics through lineage and family trees is what’s really being stressed. Although the Bozo is simply a human with clown features, imagine a primitive fish with a family tree stretching down all the way to us- humans! This is what the author is trying to show with the Bozo example. The question of how our first ancestors were created and who/what they were is still one of the greatest mysteries of science.

    3.This chapter includes many examples of disease that show how humans are products of a lengthy and convoluted evolutionary history. Choose three (3) of the problems listed below and briefly explain how ancient ancestors’ traits still “haunt” us:

    •Heart disease
    •Sleep apnea
    •Mitochondrial disease
    While humans are to blame for many of our health problems, we are still plagued by some diseased that are a result of our ancestors. Hemorrhoids are an example of this. The arrangement of our veins may have been suitable for our ancestors, but for people like truck drivers and others who sit for long periods of time, hemorrhoids remind us that humans did not always sit for so long. Obesity is a problem that is ever increasing in many parts of the world. The high-fatty foods we crave (due to their high energy) is another gift from our ancestors. Genetic diseases like diabetes also contribute to the problem of obesity. Sleep apnea is a disease that afflicts people when they’re sleeping. While one is asleep, one’s throat is relaxed and, for some people, this can mean a long period of time with no air passage. This is a possible obstruction of the airway that can result in death. This problem is a direct result of humans talking so much. A subtle reminder from our ancestors that we weren’t always as garrulous as we are today.

    Afterward (new findings re: Tiktaalik)

    1.Tiktaalik was a fish that lacked an operculum – what does this tell us about the animal?

    The operculum is simply a plate of bone the covers the gills in bony fish by forming a flap. The fact that the Tiktaalik didn’t have one tells us that Tiktaalik relied on breathing though the mouth. In addition, the absence of the operculum renders changes in the way Tiktaalik moved.

    2.Tiktaalik had a true neck – what did this allow the animal to do (advantages?)

    The fact that Tiktaalik had a true neck meant that Tiktaalik did not move the head and body to transport itself but rather move freely using the head to shoulder. The fact that it was able to move its head separately from its body was a bona fide advantage, allowing it to do things like support itself on solid ground.

    3.How was Tiktaalik able to survive in the cold Arctic environment? While Tiktaalik’s fossils were found in the arctic, Shubin does not believe that Tiktaalik lived in the arctic. Instead, he and his colleagues are of the opinion that Tiktaalik lived in a topical climate. This is because the climates of today’s world are not in the same places as they were 365 million years ago.

    Finding Your Inner Fish. (2016, Jul 17). Retrieved from

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