YIF: Chapter 11

This chapter is the final chapter in the book Your Inner fish and is appropriately titled "Meaning of it all." In this chapter Shubin first tells us about evolution and how our genetic tree has developed over the past billion years. This is crucial for the rest of the chapter where he will talk about specifics that did not fit in the last 10 chapters. He relates our speech to that of primates and how they evolved together. Then talks briefly about how our fish and tadpole "ancestors" evolved and how we evolved from them and that is how we have hiccups. He explains that how hiccups are beneficial to fish in their breathing, whereas they are neither beneficial nor harmful for us humans. Lastly he talks about how our shark "ancestors" can help us, especially males, relate to getting hernias. The overall basis for these points in this chapter is the biological "law of everything" that states every living thing on the planet has had parents. The most important idea in the section was how we can link ourselves to each other and how all humans are related, no matter where from on earth, because we all evolved from a common point. The part I find intriguing is how we can tract this relationship with others. To do this we use a method similar to cladograms, except it is almost reversed. We look at a family tree of yourself and you can, for the most part, tell where another person that you have meet would fall. This process is much more complex than I gave it credit for, but that is essentially what happens. However this so called "family tree" would have to go back hundreds of generations of you, so it is not practical for the average person to do. This chapter reverts back only to the first Big Idea of biology that states: The process of evolution drives the diversity and unity of life. This is a very evolution heavy chapter and essentially this Big Idea relates to the chapter because Shubin keeps going back to the point that we have all descended from a common ancestor and thus these evolutionary links can be establish between us and other races. An essential question to take from this chapter would be: "How can characteristics from other species tell us more about our own bodies?"

YIF: Chapter 10

The chapter entitled "Ears" or chapter 10 is about the biology of the human ears and relating the middle ear and inner ear to biological ancestors. Shubin is quick to make the remark that the external ear that we humans have, is a trait that is unique to mammals although some amphibians and reptiles do have a somewhat external ear. The man component of the human ear that has been linked to other ancient organisms is the middle ear, composing of the stapes, malleus, and incus. These three ear bones have been linked to gill arches, the stapes in the second gill arch and the malleus and incus in the first gill arch. Through the brilliant minds of Karl Reichert, Ernst Gaupp, and W. K Gregory the link to fish as well as mammal-like reptiles has been discovered, because the three ear bones found in humans is strongly tied to the anatomy of these organisms. Next Shubin writes about the biology of the inner ear, a topic that fascinated me the most. He talked about how the ear works with the brain and the eyes to determine sound, position or acceleration. What was most fascinating was the part of the ear that is the main component in determining these three things. There is a gel like substance in the ear that is touched by hair cells. When one moves or shifts their body, the gel like substance shifts, and tiny rock like objects on top of this gel exaggerate the shift, causing hair cells to detect the movement and ultimately send signals to the brain. This chapter relates the most to Big Idea #3 and Big Idea #4. Big Idea #3 states Living systems store, retrieve, transmit, and respond to information essential to life processes. It is fairly obvious that the three parts of the ear, the inner, middle, and external ear all work to gather in order to obtain knowledge about the position of the person, their current velocity, and hearing sounds. Big Idea #4 states: Biological systems interact, and these systems and their interactions possess complex properties. And like mentioned before, not only does the three parts of the ear work together, but the ear as a whole works with the eye to get the most accurate information of the current environment that one is in. An essential question that can be formulated based on this chapter would be: How do ancient organisms with no ear at all come to evolve to create complex ear systems?

YIF: Chapter 9

This chapter called "Vision" is mainly about the biology of the eye and a little history of the eye. There are several fascinating experiments that scientists have done on eyes, but the evolution of the eye was not mentioned much. After all "[e]yes rarely make it into the fossil record." (Shubin 149) First the author talks about the biology of the human eye and talks about the molecules involved in light reception. Later he talks about these molecules being incorporated with tissues. Finally, Shubin went into detail of the genes in multiple eyeless genes, and showed how flies, mice, and humans have similar genes that turn on and off the eye genes. This last part was my favorite part of this chapter. Walter Gehring compared the genes of of flies, mice, and humans that all had a similar eye disorder. He found a similar gene in all three in of these organisms, and tested with the eyeless gene in flies and Pax 6 gene in mice and found that if he put the Pax 6 gene any where on a fly, an extra fly eye grew there. This showed the very close relationship between the eye genes found in these organisms. The only Big Idea in biology that relates to this chapter is Big Idea #3, which is  living systems store, retrieve, transmit, and respond to information essential to life processes. Brains respond to information that the eyes receive from their environment and transmit to the brain. The rods and cones are the main parts of the eye that pick up the light from the environment and the brain picks up these signals from various nerve cells. The brain then interprets the light information from the eye and acts accordingly. An essential question that can be made from this chapter is "How do we put variation to use in understanding how our ability to see developed over time?"

YIF: Chapter 8

This chapter titled "Making Scents" is, like the chapter suggests, about the nasal passage and smelling. Shubin spend time talking about the evolution of smelling and how this is relevant to the evolution of smelling to animals and even us humans. Shubin makes a remarkable statement that "our sense of smell allows us to discriminate among 5000 to 10,000 odors." It is very fascinating that out of all the molecules in the air we are able to pick out "up to one part per trillion." The connection to evolution is that "3% of our entire genome is Devoted to genes for detecting different odors." You can trace back to the genes for smelling out from the history of animals. This can be seen by looking at which genes are being expressed in fossils that are extinct or in animals that are still alive. What I found most interesting was how we smell. We smell by tiny molecules in the air which will actually attach themselves to neurons in our nasal passages. The complexity of these neurons is incredible. We have thousands of genes that express for the nerve cells that enable us to detect odors. And apparently we lost many of these genes throughout our evolution. According to Yoav Gilad "primates that develop color vision tend to have large numbers of knocked out smell genes." Going with the assumption in this book that we are we, as humans, are ancestors from primates, we can tell that we have lost large numbers of smell genes for our color vision. This chapter relates a lot to big idea one and four. For big idea one the process of evolution for smelling shows the diversity of life. As we saw in this chapter dolphins had blowholes and lampreys had a nostril and we, humans, have external and internal nostrils. As we look throughout our evolutionary history we see that the amount of genes for smelling has been increasing, this attributes to the diversity of life. For this chapter's connection to big idea for we see the molecular system of smelling and how our brain interacts with this. We see that small amounts of molecules enter through our nose and attach themselves to neurons and our Nasal passages. The book goes on about how the brain interprets these neurons and all of which is explained in great detail in this chapter. An essential question that can be made from this chapter would be, "How does an organism gain or lose the ability to smell?"

YIF: Chapter 7

            In this chapter of Your Inner Fish, the author does a lot of explaining about the history and organisms with different types of bodies, organs, and the way they make their bodies. The author explained about the collagens and other molecular chemicals that are found in bodies organisms, and how even some primitive organisms, like sponge, have these. The author did not say too much about this and its evolutionary connection with humans, but he did write about how the in the timeline of the Earth that there weren’t bodied organisms until about 1 billion years ago. He said that when bodied organisms started to appear on the Earth that the life that Earth had was forever changed. This explains why humans and animals of all kinds are bodies, which was the point of the entire chapter. My favorite part of the chapter was the short story about the evolutionary experiment that was performed by Martin Boraas. In this experiment he let single cell alga organisms thrive in a controlled environment. After 1000 generations, he let a single celled creature with a flagellum into the environment where it thrived off eating the other organisms. After less than 200 generations the alga organisms evolved into an eight celled ball where each of the cells could get light to photosynthesize, and where it wouldn’t get eaten by the predator. This is my favorite part because it describes an experiment that shows that evolution of an organism is very possible and it supports the author’s belief of evolution. The Big Ideas of biology that are connected to some ideas that are present in this chapter are:  living systems store, retrieve, transmit and respond to information essential to life processes, biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis, and the process of evolution drives the diversity and unity of life. The first Big Idea has connection to this chapter, and it is that when the author was talking about the timeline of the bodied organisms he mentioned that the organisms might have become bodied in response to predators eating them, also that the sponges respond to the outside environment with the information around them. The second Big Idea’s connection to this chapter is that the single celled biological systems utilized the energy from oxygen and the sun to become bodied and then the homeostasis of the prey was stabilized. Lastly the third Big Idea’s connection to this chapter is that all bodied organisms are diverse but at the same time united by the fact that they are multicellular and certain cells have certain roles, and also that all the bodied organisms are bodied due to the change in the way of life and body-building. An essential question that can be made from this chapter would be, “How (chemically) does one cell evolve to become an organism with two trillion cells?”

YIF: Chapter 6

            This Chapter does a lot of explaining of evolution in terms of embryos yet again. But instead of the connection between humans and other animals being gill arches it is about the body plan of the embryo in the very early stages of development. Karl Ernst von Baer did experiments with the embryos of chickens and other animals and noticed some very strong similarities. And his ultimate conclusion was this: “Every animal organ originated in one of [the] three [germ] layers. Significantly, the three layers formed the same structures in every species.” This discovery is found in humans as well, the three layers being the ectoderm, mesoderm, and endoderm. This shows that von Baer’s conclusion of the evolution is relevant to human evolution because since most animals have it, then it is likely that we descended from the same ancestors. When the book was talking about the human embryo stages of development was my favorite part of the chapter. I loved how it talked about the early timeline of the fetus in the mother’s body and how childbirth is such a wonderful thing. It was also very fascinating to know and understand what the fetus looks like before it has any distinguishing features. I think the most interesting part of this section of the chapter would be when the author talked about the three germ layers, the mesoderm, endoderm, and ectoderm and how they will all develop into separate organs, like the mesoderm into the body cavity and other organs and the endoderm into the digestive tract and other organs. The Big Idea that has connections to this chapter of the book is the process of evolution drives the diversity and unity of life, because the author lectures about the genetics and embryonic similarities between species so that he can convey that they are unified and also diversified. This is one specific example that was used in this chapter but there are many more connections that can be found as well. An essential question that can be made from this chapter would be “What can similarities in genetics cause to be similar between two creatures?”

YIF: Chapter 5

            This chapter was in some ways irrelevant to evolution. It took a little while for the author to tie what he was saying into the evolution of human. What he was mainly talking about was the head of mammals, fish, worms, and humans. What was special and what he said that they all have in common, yes even the headless worms, was that they all had something called the four gill arches. Each of the four categories of animals that I listed not long ago all have these arches and they look similar to each other when each of these animals is an embryo. It is when they develop further along into the stages of their embryo that they separate and look different from each other and each of the gills forms into something different. The author didn’t relate the four gill arches to the evolution of humans until he mentioned that the essence of our heads goes back to worms, such as the Amphioxus, who didn’t even have heads, and this is because these worms have the same gill arches, but when they develop they form separate organs that humans do and it is believed that these headless worms are part of the origin of the arches that we have. The most interesting part of this chapter was when the author said that “we can manipulate the identity of the gill arches almost at will, by changing of the gills inside.” (Shubin 94). This fascinated me more so than other parts of this chapter because it kind of reminded me of the ZPAs that we heard about a few chapters ago, in that we can manipulate the genes to change the embryo when it fully develops. In the book the author used the example of manipulating the gill arches of frogs by turning off some of the genes in the gill arches. The outcome of this was that the frog ended up with two jaws. That is simply interesting, however this does have much to do with evolution, and it only deals with the biology of embryos. This chapter has connections with two Big Ideas in biology, one being biological systems interacts, and these systems and their interactions possess complex properties, and the process of evolution drives the diversity and unity of life. The first idea makes a connection with this chapter because of the insane complexity of the four gill arches and how they develop into something so specialized and they interact with each other to make the organism better functioning. The second Big Idea makes a connection with this chapter because of the idea that the headless worms that existed millions of years ago share the same gill arches that several different animals, ranging from sharks to humans, have the same arches, but they develop into organs with different functions. This idea means that the diversity of the mammals can be unified by using the perspective of this one evolutionary aspect.

YIF: Chapter 4

            This chapter encompasses the evolution of animals by taking the perspective of teeth. The evolution starts at conodonts, then, ostracoderms, all the way up to humans. Teeth are a powerful window into an animal’s lifestyle, especially their diet. Also the author talks about teeth and how they are preserved well and why, which is because teeth contain something called hydroxypatite. This is why teeth are more preserved than other bones and tissue. The evolution history of humans can be explained by something as small as teeth because of the type of teeth, their size, and their alignment. For example our mammalian way of precise chewing, emerges in the fossil record from around the world that ranges from around 225 million to 195 million years ago. My favorite part of the chapter was the largest portion of the chapter; it was the story of the author’s first expedition and the first two expeditions that he led with his colleagues. This story was well written and grasping and intriguing, after each page that I read, I wanted to react more because it was intertwined and showed a progression in wisdom and experience. It made it seem realistic and the effort that was put into the expeditions could be easily seen. Also I love how he sets up each expedition is a many story by making a sort of suspense by talking about his failure, what he did to improve and then him getting better, and then finally him finding something special to both him and something that is very relevant to the purpose of the book. The Big Idea of biology that makes a connection to this chapter is the same as all the others, and that is the process of evolution drives the diversity and unit of life. The reason being is that once again this proves that multiple animals that are seemingly different can be classified in the same category as humans due to a common ancient ancestor. One essential question that can be made for this chapter would be, “How can mammal teeth show the relationship between two species?”

YIF: Chapter 3

            This chapter brought embryos and eggs to show some of the biology of evolution that occurred. They did this by mentioning and describing and relating ZPAs, zones of polarization activity, which are essentially a patch of tissue that causes the pinky side to be different than the thumb side. Then the author went on and said that many animals, including humans, have the ZPA. Then scientists were curious so the wanted to see if the adding of another animal’s ZPA would cause to same result of adding the same animal’s ZPA to another ZPA and surprisingly it did. This was probably the part that most interested me as it justified, scientifically, the relationship of animals to each other using genetics. It is so intriguing to see that this was one of the first ways that scientists used to prove that different animals have similar genetic makeup. More specifically the part where they took a mouse’s ZPA and put it near the ZPA of a skate’s and the two reacted as if the two ZPA were from the same animal, which is an example, to what was mentioned above. This shows scientists that the genetic material of humans is similar to the animals that we already have seen similarities to. This just strengthens the fact that humans share a common ancestor to other animals. This is also the idea that can be drawn by relating this chapter to the Big Idea of biology, the process of evolution drives the diversity and unity of life. The overall essential question that can be made based off of this chapter is, “What is the relationship between genetics and evolution?”

YIF: Chapter 2

            This chapter was mainly focused on the origin and evolution of the hand and arm, and where they came about and how they were proven through multiple discoveries. Also, while going through what limbed animals have in common the topic of Owen came up. While the author was mentioning Owen, he talked about the patterns that he saw and how they were accurate and how they are related with all limbed animals. Those patterns would be: all creatures with limbs, have a common design; the differences between creatures lie in differences in the shapes and sizes of the bones and the numbers of blobs, fingers, and toes; and lastly, probably the most important pattern in the chapter, the skeleton of a human arm has one bone in the upper part of the arm, two bones in the forearm, several bones at the wrist, then the series of rods that are the fingers, and this arrangement is similar to all other limbed animals and the differences between different animals is explained in the second pattern. This overview shows scientist that we have similar characteristics to other animals, like frogs, horses, and seal, which show that the evolution of the human body and the evolution of these animals, and animals like them, are similar in many ways, only by looking at the arm. The most interesting part of this chapter was when the author when back to the fish that he discovered, the Tiktaalik, and analyzed it and told us how its fin has the same pattern that Owen described and it had similar bone structures to ours. And what was even more surprising was when he said that this fish had the ability to do pushups! It is simply amazing how a fish that existed so long ago has some human capabilities and that is possible that we could have gotten some of these abilities from this animal! The overall topic from this chapter can answer two Big Ideas of biology, one being the process of evolution drives the diversity and unity of life, and the other being biological systems interact, and these systems and their interactions possess complex properties. The first idea encompasses the obvious, that evolution of animals like Tiktaalik unify the limbed animals and us together. The second idea can be thought of how the interactions that occur in the hand from performing simple maneuvers make the hand have unique and complex properties. All in all, the chapter creates one essential question, “How does evolution of the same animal create separate species?”

YIF: Chapter 1

            This chapter does a great deal in mentioning the author’s, Neil Shubin, experience in fossil hunting and what they do to determine a great location for fossils which are the rocks’ age, sedimentary rocks (the types of rocks most ideal for preserving fossils), exposed rocks at the surface, and lastly serendipity. He explains how he used these four factors in his own expeditions, and he later describes the result of each expedition, how he was able to accomplish it, and what this tells us about the history of the evolution of limbed animals. His second expedition that he mentioned has the most relevance when talking about the Tiktaalik, a fish that he discovered in the Arctic, because this fish is an evolutionary intermediate between fish and primitive land-living animals, it is very important in understanding the evolution of humans. The most important conclusion that can be determined by analyzing this fish is determining how fish transitioned from living in water to living on land, which can be seen by analyzing its fins and head and shoulders and most of the rest of his body. This idea about the Tiktaalik was the most interesting to me because it was such a huge discovery and it involved so much to how reptiles and amphibians transitioned from fish which is just incredible. And what makes this discovery that much more amazing is that scientists predicted this type of fish would have existed and that they also were to give a relatively accurate period of time that this fish would have existed. This chapter makes the largest connection with the Big Idea of biology that is the process of evolution drives the diversity and unity of life. I will use the Tiktaalik again to describe this connection. This connection is that this fish leads people to conclude to the origins of life diverge. Because one can easily see that different land animals have similar body builds, with the same types of bones but in different locations and sizes, it can be determined that they all evolved from the same primitive land animal, and this discovery of the Tiktaalik shows that land animals evolved from fish which raises a lot of questions about the origin of land-animals but also answers a lot. Finally an overall question that can sum up all of the ideas from the first chapter of Your Inner Fish is, “How can fossils of the past help with our present?”