An Ear Distinction

On page 158, Shubin begins discussion on ears. Explain why "some of the most distinctive traits of mammals lie inside the ear"(159). What is similar and different between mammalian inner ears and the inside of ears of other animals. How does the theme of evolution tie into the differences we see?

Matt Kim

(matthewkim0803@gmail.com)

Amphioxus

On page 94, Shubin describes Amphioxus, which is an invertebrate. Describe the evolutionary significance of Amphioxus and how it and others like it provide a window into our past. Include how it is unique and why it is studied.

Germ Layers

On page 98-99, Shubin talks about how chickens, frogs, and fish limbs all look very similar at the start of development. Shubin also states that three germ layers are all the same in these animals. Yet later in development, trillions of cells form very different animals. Describe how this can be used against the creationist argument and describe the similarities and differences of the general process of development using the three germ layers in frogs, chicks, and humans.

Fontanelles

In chapter 5, Neil Shubin discusses the plates, rods, and blocks that make up the cranial structure for human heads. Infants are born with fontanelles which clearly provide no protection for the brain. Discuss how fontanelles are key in the formation of the human skull and how a lack of fontanelles would effect the formation of a human.

hydroxyapatite and the rest

In chapter 4 Neil Shubin addresses the hydroxyapatite within teeth. The hydroxyapatite was initially suggested for internal use against deterioration due to chemical and mechanical digestion that occurs in the mouth. Furthemore, conodants are mentioned as the first organisms to have teeth. When was hydroxyapatite introduced and how does the time relate to the formation of chitin and calcium carbonate throughout evolutionary history? Discuss the chemical composition of hydroxyapatite.

The Cells That Make Us

In Chapter 7, Shubin describes all of the different kinds of cells that together make up the different organs and parts of the body. All of these cells that constitute all of these different organs has a distinct role in bodily functions. "What happens when 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... say from the heart or brain? You could end up with a dead human" (117). Why are some of these cells more important than others when it comes to bodily functions? Which type of cells are more important for our body to continuously function properly? Why is it so important for cells such as skin cells to be sloughed off and continuously renewed, and why does our skin become wrinkly when we grow old if our skin cells are constantly able to produce new cells and replace our old ones?

(Sujin Ko, sujinko93@gmail.com)

DNA not the same in every cell in our body?

On page 45, Shubin writes, “there is a deep similarity among every cell inside our bodies: all of them contain EXACTLY the same DNA”. If this is true, then how do muscle, tissue, and bone develop within our bodies? Explain using what we have learned throughout the year about DNA and gene expression.

Matt Micucci (coochqbk@sbcglobal.net)

History? Gross!

In the last chapter of the book, Shubin discusses and explains several examples of "Why History Makes Us Sick" (184). The idea behind the persistence of these evolutionary artifacts is that, as our ancestors have evolved and used old parts in new ways, some undesirable side-effects of our past have remained as a result of our extensive physiological adaptations, such as hiccups and hernias.

In general, one would expect the process of natural selection, however, to remove these negative effects over the course of evolutionary time. Why has this not happened? Why have there not been favorable mutations that have removed the diseases Shubin mentions that make us sick? Are there examples of diseases that have been selected against since humans' evolution from amphibians?

Explain why certain diseases persist in humans and why others do not. Explain the connection between your responses and evolution, the relationship between structure and function, and/or continuity and change.

- Vincent Fiorentini
(vincent@panatechcomputer.com)

Handy Genes

On pages 44-46 of Your Inner Fish, Shubin begins to discuss "handy genes." Give an in-depth explanation of DNA and gene expression. Include in your discussion the important role that "genetic switches" play in the biological assembly and make-up of humans and other organisms.

Matt Kim

(matthewkim0803@gmail.com)

Sense of Smell

Shubin describes the sense of smell as a "lock and key". Are there any other "lock and key" relationships that we have observed earlier in the year? What similarities and differences exist between smell and this relationship? Describe the evolution of smell in fish, amphibians, reptiles, and mammals.

Those Darn Hernias

Shubin states that the reason that humans have hernias is because humans were morphed from fish bodies into mammalian bodies (193). Describe why this occurs in terms of evolution and how this evolution relates to reproduction in mammals.

Teeth and the food web

In chapter 4, Shubin explains the different sort of teeth starting from the incisors, continuing with the molars, etc. He also goes on to say that the mineral hydroxyapatite is what gives teeth its “hardness.” Finally, Shubin ends by saying on page 79, “We would never have scales, feathers, or breasts if we didn’t have teeth in the first place.” Clearly, teeth are one of the most important features of an animal’s anatomy, but explain the transition from teeth within a fish to teeth within a terrestrial animal? What role does hydroxypatite play in teeth as you move up the food chain (such as the example Shubin provided with clams and lobsters having calcium carbonate and chitin instead)? Finally, why exactly would we never have scales, feathers, or breasts if teeth didn’t exist?

-Michelle Layvant, mlayvan2@students.d125.org

Genes and Gill Slits

During development, humans are known to have gill slits for a certain period of time. The gill region of humans and sharks are shown in the diagram, on page 91. As described by Neil Shubin, the purpose of these slits is to form jaw bones, ear and throat structures, vocal cords, etc. Why is it that the gill slits in sharks do not close but the gill slits in humans close and “disappear” after a certain time in development? What signals or genes command the gill slits in sharks to stay open and for the gill slits in human embryos to close even though the gill region serves as the same purpose in both species?

Chandrika D.

(shiningstar0393@gmail.com)

Smells Good

Chapter 8 of Neil Shubin's book talks about how scents are created, through connections with your brain. He explains that a 'lock-and-key' mechanism is used for smelling, with molecules that connect to receptors in your nose, which send signals to your brain. How does this 'lock-and-key' system work and how does it relate to other topics we've learned previously in the school year? Why is this mechanism necessary for certain functions to work properly? How would these functions be different without this mechanism? Explain using Shubin's knowledge, Campbell, or other sources.

External Ear

In chapter 10, Shubin discusses ears. There are three parts to the ear: the external, the middle, and the inner. Shubin says that "the part of the ear that we can see... is a relatively new evolutionary addition to bodies" (159). Why did this part of the ear come to be? What is the purpose of the external ear? Also, mammals are the only animals that have pinna (a flap of the external ear). Earlier animals, like bony fish, amphibians, and reptiles don't have this pinna. Fish don't even have an external part to the ear. Why are mammals the only animals with pinna, and what is the purpose of this? Danielle Webb (dwebb456@gmail.com)

Hand Evolution

In the vertebrate unit, we learned about phylogenetic trees. There are two ways to make a phylogenetic tree. One way is to separate animals based on physical characteristics. The other way is to base the tree of molecular characteristics. There is an important distinction between the two. For example, we could make a tree that separated humans from birds because we have hands and birds have wings. However, we can't separate the two groups based on ZPA and Sonic hedgehog because both birds and humans possess them. Explain the importance between the distinction of the two types of trees and the evolutionary significance.

Evolution of Teeth

In chapter 4, Shubin discusses the importance of teeth. He notes the importance of the structure of an animal's teeth in understanding the life of the animal. Using your knowledge of evolution, explain how teeth have evolved from the first oceanic life all the way to humans.

Cell recognition

On page 123-124, Shubin describes the cell's ability to recognize each other in order to form larger masses such as tissues or bodies. In between cells can lay different kidns of collagen and proteoglycans that help attach cells. What causes the cell to be able to recognize other cells to attach to each other? How does this communication relate to the function that the cells must perform in the body? Relate this ability to recognize other cells to the function of DNA in expressing genes.

Discovering Disease

On page 198, Shubin discusses a method employed by European scientists to study a mitochondrial disease. The team studied a microbe known as Paracoccus denitrificans and were able to create the same human mitochondrial disease in the bacterium by changing certain genes. How might this method, using evolutionary history to identify genetic mutations that cause disease, be further expanded and applied to other aspects and characteristics of human life, even beyond disease? Would it be useful? Why or why not? vickram.pradhan@yahoo.com Vickram Pradhan 1/2a

Evolution of Eye Positions and Neck

The diagram on page 24 lays out the transition of an aquatic animal, fish, to a land-living animal, tetrapod. There were changes in the presence of neck, head shape, and eye positions. Just like any other animal, fish also need to be aware of their 360 degree surroundings. Why is it that fish had eyes only on their sides and no neck? Wouldn’t it seem logical that a neck would help them move their head to get a better view? What factors/adaptations led these fish to develop a neck and a “flat head [with] eyes on top” (24) and why is this a better advantage than having eyes on the sides? Compare the advantages and their adaptations of animals with eyes on the sides as opposed to eyes on the top of the head.

Chandrika D.

(shiningstar0393@gmail.com)

Making Scents

In chapter 8, Neil Shubin discusses the differences between "water-based receptors in [a fish's] nasal neurons" and the "air-based ones" (Shubin 145) in mammals and reptiles. Elaborate more on the specific differences between these two receptors. Is there some sort of advantage between these two different apparatuses? Is one able to be more accurate or identify more odors than the other? What would be the possible evolutionary advantage of each type of receptor? Kathy Li, kathy2132@gmail.com

From Blobs to Bodies

Ch. 6 and 7 explain how bodies emerge from clumps of cells and the factors that shape them. Also, it is explained when bodies began to form, instead of blobs without complex systems. As humans, we have multiple systems that control the way we live. Why did bodies start forming and how did they change life on Earth? How do our separate systems (Circulatory, digestive, nervous, etc.) give us a selective advantage in our daily processes? Compare and contrast the human body plan with those of other organisms referencing Shubin, Campbell, and any other sources.

Austin Lee

austinklee7@gmail.com

Limb Development

Ch.2 of Neil Shubin's book discusses the evolution of limbs starting from prehistoric organisms to modern day animals. A diagram on page 31 shows an interesting diagram of the bone structures of limbs from different animals, shaded to show how they are similar to one another. This chapter explains how even fish fins are related to our own arms, using Tiktaalik as the bridge between the two. Describe the relationships between our limbs and those of other animals all around us, and explain how fish limbs developed into the limbs of terrestrial animals. Use specifics given by Your Inner Fish and class material, as well as outside sources if necessary.

Austin Lee

austinklee7@gmail.com

The Bozo Family

From the polar bear to the turtle to the human, we're all related to some degree (179). Shubin discusses the "pattern of relatedness" in the organisms of the Earth and the commonalities we share even with the strangest of animals. For instance, polar bears and humans both share hair, mammary glands, four limbs, a neck, two eyes, etc. (179). To conclude, the polar bear would be more closely related to the human than the turtle or the fish who shares less common characteristics (179-180). This is how ancestry and relatedness is deciphered by paleontologists or other scientists.

Understanding this concept, if Tiktaalik shares many more structural characteristics than the average fish, how would they relate to the human as far as ancestry goes? And, if Tiktaalik was the bridge between limbless organisms and limbed organisms, then why do we see more fish without these appendages today rather than fish like Tiktaalik? What caused fish without the appendages that Tiktaalik had to prevail in the oceans?

Sonia Doshi soniadoshi7@gmail.com

The Evolution of Smelling and Seeing

Chapters 8 and 9 discuss the structure, function, and evolution of the olfactory system and vision. In humans, many different genes are employed to detect odors where each gene forms a separate receptor. On the other hand, the human eye uses multiple genes that work together to form one organ that recognizes different images via several receptors. Both use numerous genes that together form one sensory organ. Compare and contrast the evolution of these two sensory organs. How do their differences in evolution reflect their differences in structure and function? Sami Kopinsky sami_kopinsky@yahoo.com

In Chapter 6, Shubin explains the relationship between our body plans and the body plans of other organisms. Specifically, he compares our body plan with a sea anemone’s. But how is it possible for these to be even remotely similar considering that we have bilateral symmetry while a sea anemone has radial symmetry? Explain by using what is said in Your Inner Fish and what we have learned in class.

Matt Micucci (coochqbk@sbcglobal.net)

TEETH (humans vs. reptiles)

In the chapter titled "Teeth Everywhere," Shubin describes the detail and precision of human teeth, having "upper and lower cusps, basins, and ridges match closely." (61) Unlike humans, reptiles, such as crocodiles, snakes, and lizards, have teeth that are all very similar to each other; a blade-like shape with the only difference being the size of the teeth. Why is it that reptiles are able to successfully survive without precise upper and lower teeth that fit together when humans cannot? What are the selective advantages of reptiles having a basic, similar structure for all teeth? what are the selective advantages of humans having precisely matching teeth? Explain with specific, detailed examples.

Sujin Ko (sujinko93@gmail.com)

A Changing Life

In the chapter, "The Meaning Of It All," Shubin discusses how humans developed a sedentary lifestyle over time. With the advent of techonology, it appears that the human race may just become even more sedentary as time progresses. Describe certain characterisitcs of humans that evolved due to the hunter-gatherer lifestyle, and discuss how those characterisitcs might evolve in the future if the human lifestyle becomes more sedentary. vickram.pradhan@yahoo.com Vickram Pradhan 1/2a

Ancient Cellular Telephones

On page 119, Shubin discusses how in order for multi-cellular organisms to evolve, cells needed be able to communicate with one another. Various mechanisms were needed first to allow for the flow of such communication. Using your knowledge of primitive multi-cellular organisms such as sponges as well as your knowledge of more advanced multi-cellular organisms such as humans or zoo animals, compare and contrast the mechanisms available for communication and the ways in which these mechanisms are used. What selective advantage do some of these mechanisms provide that has allowed certain species to evolve? sami_kopinsky@yahoo.com Sami Kopinsky

Inside or Outside?

On page 74, Shubin tell us about animals with exoskeletons and animals like us with the skeleton on the inside of our body. Using our previous knowledge, what are the two different skeletons made of and what are the benefits to having this skeletal plan? Why do some animals have an exoskeleton and some have an endoskeleton?

Benny Jeong

bennyjeong218@gmail.com

Frozen Fossils?

The Arctic islands are one of the coldest places on the planet. People in Murmansk, Norilsk, and Vorkuta, which are three communities in Russia inhabit a portion of the Arctic Circle, along with people in Alaska, Russia, Greenland, and Scandinavia (“Arctic Circle”). According to the requirements laid out by Neil Shubin such as finding “rocks of the right age, rocks of the right type to preserve fossils, and rocks that are exposed at the surface” (5), is it possible to find fossils in these cold and snow/ice packed environments? In other words, can bones fossilize and remain preserved underground for hundreds of years even though the soil above them is not at normal temperature and the environment is not suitable for minerals such as apatite and fluorine in ground water? Apatite and fluorine are required for bones to fossilize. If it is not possible for bones to fossilize or remain fossilized for hundreds of years, what factors contribute to this?

Chandrika Darbha

(shiningstar0393@gmail.com)

“Arctic Circle”. Wikipedia. Retrieved March 28, 2011, from

http://en.wikipedia.org/wiki/Arctic_Circle

Throw Me A Bone!

In chapter 7, Shubin uses the analogy of a bridge to describe how our skeletons work (124). He details how the skeleton’s strength has to do with not just the size and shape of the bones, but their molecular properties, as cells are organized differently and have different characteristics. For example, some cells are separated by hydroxyapatite for strength, while others are separated by collagen. He further describes the skeleton by talking about how cartilage adds pliability to help make our joints run smoothly.

By making different kinds of molecules, it is possible for our bodies to create a mix between them to create a specific type of material. Why is it a selective advantage to be able to mix different ratios of hydroxyapatite, collagen, enamel, and proteoglycans to create different kinds of tissue? To close out the section, Shubin talks about how the cells in our body have to “stick together” to communicate, using molecular “rivets” (127). What kinds of rivets are Shubin talking about? What kind of signals do these cells communicate with? How would the body organize bone cells and other tissue cells using these methods of communication?

Eugene Bulkin (doubleaw002@gmail.com)

Gene Enigmas

On page 146, Neil Shubin says that genetic mutations sometimes cancel out the functions of certain genes. When these genes are not necessary for vital functions, such as sense of smell in dolphins, the mutation will continue to be passed on from generation to generation and the gene will cease to be expressed. Assess how this viewpoint may conflict with the statement that structure of a bodily mechanism must always be related to its function. Using information from our DNA and Biotechnology units, how is it possible for chromosomes to exist in the genetic makeup of an organism if they essentially "do nothing" as Shubin says? 



Christine Lin
choco_cat11@comcast.net

Hernias and Testes (Thanks A Lot Fish.)

On page 193, Shubin talks about humans' propensity for hernias. Why is it that humans have a propensity for hernias near the groin? Discuss the arrangement of the reproductive system in males, including the testes, penis, scrotum and sperm. How did this propensity for hernias result from taking a fish body and morphing it into a mammal? Compare the organization of fish gonads and mammal gonads and explain how evolution has led to hernias developing in the groin area of humans. Hannah Kay (hgkay@aol.com)

Fossils vs. DNA

In chapter 3, Shubin talks about how he splits his laboratory into two sections: one section for fossils, and one for embryos and DNA. Shubin says that a disadvantage to working with fossils, is that you can't experiment on animals that have been long dead. What are some other advantages and disadvantages to working with fossils versus working with embryos and DNA? Danielle Webb (dwebb456@gmail.com)

Primitive Body Plans

In chapter 6, Shubin talks about body plans. He talks about how humans have front/back, top/bottom, and left/right. Humans, and other recent animals, have bodies that are symmetrical. However, Shubin also talks about animals like jellyfish. Their bodies lack a front and back, a head and tail, and a left and right. Why is it that primitive animals like the jellyfish have such different body plans than more recent animals like us humans? What other animals are like the jellyfish and have body plans that are difficult to compare with our basic design? Danielle Webb (dwebb456@gmail.com)

Talk Is Not Cheap

On page 189, Shubin discusses the price that humans have to pay for talking. What are some of the problems that humans face due to talking? Discuss how organs of the respiratory and digestive system may cause some of these problems. How does this price of talking relate to the larger theme of "why history makes us sick" or how evolution has caused some of these problems? Hannah Kay (hgkay@aol.com)

Shubin describes his trip to the Arctic in saying that "each winter, the temperature sinks to minus 40 degrees Fahrenheit. In the summer, when the sun never sets, the temperature rises to nearly 50 degrees." Given what we have learned pertaining to thermoregulation for animals and plants (especially the photoperiodic control), explain why so few species live in the Arctic. What sort of material adaptations do you think the Inuit people have developed in order to survive in such an environment? Finally, what sort of features do animals such as polar bears have that allow them to survive in the Arctic?

-Adnan Jahan

(adnanjahan@gmail.com)

Our fishy past

In chapter 11, Shubin connects our past to the active lifestyle of fish and includes many examples of disease that show how humans are products of a lengthy and convoluted evolutionary history. How do our ancestral traits relate to diseases such as heart disease, hemorrhoids, obesity, and hiccups? Please cite specific examples from the book and relate to our AP biology themes.

Adnan Jahan

(adnanjahan@gmail.com)

Eye see you

In chapter nine, Shubin talks about how our eyes allow us to see things. Explain what happens to the eyes on the molecular level when someone becomes near-sighted or far-sighted. Do animals' eyes also experience near or far-sightedness? If so, how do they adapt to this evolutionary disadvantage?

Anna Leng 2b-3 (annaissbananas@gmail.com)

Clowning Around with Genes

Descent with modification is the defining pattern of evolution, and Shubin points out that everyone we know and every organism we see has developed from some parental genetic information (174). Descent with modification “defines our family lineage” and thus allows us to reconstruct the genetic progression of mutations through generations just by looking at blood samples of individuals on a family tree.

Shubin illustrates this with an example of a couple having a child with a horrific genetic mutation that makes him look sort of like a clown, and he reproduces and his descendants become more and more clownlike. What kind of model could be used to plan this (think Mendelian inheritance!) and why would it be useful? How would genes pass on and mutate like this through multiple generations? How would a scientist be able to look at one of his descendants and determine a relation to him, if they only had their DNA to look at?

Eugene Bulkin (doubleaw002@gmail.com)

How are your teeth?

On page 61, Shubin mentions the development of teeth and the perfect match between the lower and upper set of teeth in the jaw. The opening and closing of our mouth is a precision advantage to chew our food. However, what happens when we have an underbite or an overbite? What causes us to have an underbite or overbite? How does having an underbite or an overbite affect our efficiency in chewing food?

Benny Jeong

bennyjeong218@gmail.com

Healthy Vitamins?

On page 50, it was found out that when a certain concentration of vitamin A at the right stage in embryonic development affects the growth of digits. The effect of vitamin A is to make a mirror-image duplication of the digits on the hands. The affected patch of tissue is known as the zone of polarizing activity. Why is it that vitamin A specifically affects the development of digits? How does the composition of vitamin A affect the tissue? What specific effects does vitamin A have?

Benny Jeong

bennyjeong218@gmail.com

Hic Hic

On page 190, Shubin discusses our relation to fish and tadpoles by talking about hiccups. He brings up the similarities between our respiratory system and the respiratory system of fish. He says that the brain stem-controlled breathing apparatus was taken from fish, and evolved into what we (as mammals) have right now (191).

Why do you think the arrangement works so well for humans and fish; that is, why would the nervous system usage of the brain stem as the “central pattern generator” be so successful? Unfortunately, the transition between fish respiration and mammal respiration was a difficult one; the air has to travel a lot farther in us mammals. What are the differences between mammals and fish when it comes to respiration? How exactly does the brain stem control our breathing? How could mammals perhaps adapt to the difficulties we inherited from the fish respiratory system?

Eugene Bulkin (doubleaw002@gmail.com)

Talking Cells

In the chapter "Adventures in Bodybuilding," Neil Shubin emphasizes the importance of how cells can "talk" to each other to cooperate in processes such as making the skin smooth and coordinating the growth of different bones, such as those in our arms and legs. What are some specific examples of how cells communicate--Shubin gives an example of how a molecule can attach to another as a signal for a process to begin, but this is a very general example. In addition, Shubin also discusses how when "the finely tuned balance among different parts of bodies breaks down, the individual creature can die" (Shubin 118). What are the specific mechanisms that are disrupted which allow these cells to "break the rules" of cell cooperation, and how can this disruption be prevented? Perhaps discuss more of how cancer can affect the body, one of the very common diseases resulting from an inability of cells to stop dividing, causing the growth of tumors, many of which are harmful to the body.

Kathy Li, kathy2132@gmail.com

Incorrect Implantation

In chapter six, "The Best-Laid (Body) Plans," Neil Shubin briefly discusses the dangers of a blastocyst implanting in sites other than the uterus, such as in the fallopian tubes, or even in the outer lining of the rectum, where the fetus can "develop to full term" (Shubin 100). Has this been a major issue for humans, and how would a doctor deal with this situation? Is it possible for the baby to grow in a site other than the uterus, and still be healthy? What are some documented cases on this, and how were they resolved? Over time, is it possible that implantation will somehow improve where it can be more accurate, and rare cases like this could be prevented?

Kathy Li, kathy2132@gmail.com

Mitochondria, Thanks Mom

On page 197, Shubin discusses mitochondrial diseases. What problems does Shubin discuss that are associated with mitochondria? What is the function of mitochondria? Explain the process of cellular respiration. Discuss the relationship between mitochondria and bacteria. Explain endosymbiosis.

(Bobby Muttilainen, rmuttilainen@gmail.com)

Jellyfishing

On page 112, Shubin discusses the similarities and differences between humans and jellyfish. Discuss these similarities and differences. What role do hox genes play into the similarities and differences between humans and jellyfish. Use pages 671-673 and 728-733 in Cambell to expand upon Shubin's points. What changes do we see as we travel down evolutionary history? Use the review diagram on page 665 of Cambell and Figure 34.2 on page 699 of Cambell for reference. In the discussion, include the major phyla we discussed in class. Also, page 183 of Your Inner Fish has a great diagram to help.

(Bobby Muttilainen, rmuttilainen@gmail.com)

The evolution of bones vs the evolution of cells

In chapter 4 of "Your inner fish," it mentions and explains the evolution of teeth to bones. Ostracoderms were the first animals found with bony structures that were made entirely from fused teeth. With the knowledge of how this occured, compare and contrast the evolution of bones with the evolution of autotrophic and heterotrophic organisms (Remember: Autotrophic organisms are believed to have formed after the heterotrophs). Include a reason for any possible similarities.

The pits of pax

In the end of chapter 10, Shubin briefly describes the presence of both Pax 6 and Pax 2 genes in box jellyfish. These genes have the effect of creating pits all over the jellyfish that function as they eyes and ears. Why would it be helpful to have more than one pit of Pax 6 and 2?

aparna.pal.1994@gmail.com

Aparna Pal

The Shark in Us All

Neil Shubin discusses the deep connection that we hold between ourselves and sharks in regards to our development. When compared, human embryos begin with four-arched gills, the same as in shark embryos. These gill arches in humans later develop into our brain and head (91). Each arch of our original gills develop into specific structures. For example, the second arch of the gills in sharks develops into two bones of the jaws and in humans, the hyoid that we use for swallowing and our middle ear bone (89-90). Evolution such as this always has a reason because of natural selection. The selective advantage of having a middle ear bone over a retractable jaw bone must have been greater. What may have been the reason for this advantage? How does a shark's ear compare to a human ear, and why have we evolved to have a significant ear bone or swallowing ability over having a retractable jaw- what is the selective advantage of this?

Sonia Doshi soniadoshi7@gmail.com

Several Ways to Get a Head

Starting in Chapter Six on page 97, Neil Shubin talks about the differences of body plans in humans and other organisms, as most mammals exhibit bilateral symmetry, with front/back, top/bottom and left/right sides. Why do the major sensory organs and nervous systems always seem to collect at the top or anterior ends of mammals' bodies? Is this merely a convenient way of categorizing anatomical sides, or is there an underlying selective advantage to placing brains/nervous organs at the end where cephalization occurs? Also, compare and contrast the spinal structure and placement of these organs in bilaterally and radially symmetrical organisms.


Christine Lin
choco_cat11@comcast.net

Odor Potency.

Shubin addresses that DNA extracting allows us to determine history of ANY part of the body, such as the inducing sense of smell. (140) Our ability to detect thousands of scents is advantageous as in attracting and repelling us towards different objectives. The tiniest molecules are detected as smells towards the brain through a lock-and-key model-type mechanism. However, odor genes vary in amount from animal to animal. Discuss genetic and evolutionary contributing factors of the potency of odor genes have in a a variety of species. For example, why is a human's sense of smell is much weaker than a dog's?



Kyle Kim (piece847@gmail.com)

In chapter 10 of Shubin's book, he describes the evolutionary advantages of the inner ear bones and how they affect balance as well as the creation of the mallus, incus, and stapes, or the inner ear bones. Earlier in the book (in chapter five), he had explained the evolution of certain structures including the jaw and ear bones from gill arch 1. Explain a possible way that the creation of the inner ear bones could come to be as well as their comparative location on our ancestors.

Do The Parts Make a Whole?

In Chapter Seven, starting on page 117, Shubin discusses how "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 reminded me of our Prokaryotes Unit, where we talked about different cellular types. According to Shubin, would a "complete" individual be qualified as multicellular or unicellullar? Also, use this passage as a chance to review the difference between colonial and multicellular organisms. What are some selective advantages to being multicellular or unicellular?

Why the Different Shapes and Sizes?

Even though every living creature has hands and arms which are used for functions such as grabbing and utilizing various things, their structure is completely different among animals. In the “Getting a Grip” chapter, Neil Shubin talks about how a Scottish surgeon Sir Charles Bell wrote a book about hands. On page 31, a chart is laid out with the different hand/arm structures of different animals. For the animals listed such as birds and bats, their main function is to fly. According to the research done by anatomist Sir Richard Owen about the structure and the order of the bodies, the common plan for almost all of the limbs are “one bone, followed by two bones, then little blobs, then little fingers or toes” (31). With this fact, why does a bird and a bat have different limb structures with different sized bones even though they have the same kind of bones? Or why does a pterosaur and theropod dinosaur have different arrangement with different sized bones even though the function is their limbs is the same: walking? Seals are both land and water animals. Does this have an affect on their bone size and arrangement? If so, how? All of animals listed use their limbs for major functions such as walking or waving it to swim. Should these limb structures be bigger than the human arm arrangement and size because of their constant usage? Humans wave their arms while walking or use them for minor function such as grabbing or working with various things but not for something like using them as “legs”. Why are these limbs smaller and what is the significance?

Chandrika Darbha

shiningstar0393@gmail.com

Transition of Eyes

Beginning at page 154, Neil Shubin talks about how the vertebrates and invertebrates have different kinds of eyes, and that the Polychaetes were the turning point in the differences of eyes in vertebrates and invertebrates. Explain which conditions and characteristics of the Polychaetes might have influenced the change/evolution of eyes from invertebrate eyes to vertebrate ones. John Park (wisejsm@yahoo.com)

Starting Up Fresh

In Chapter 1, Shubin talks about how paleontologists first begin to hunt for fossils, with the hardships they face. However, there are no mention of the regulations they face, such as limitation of where they can dig for fossils. Discuss what would happen if the rookie paleontologists such as Neil Shubin's gang accidentally stumble upon a fossil that was very valuable (ex. tiktaalik), but their preservation of the fossil was poor because it was on such a spot that limited them in terms of time (ex. side of the road). John Park (wisejsm@yahoo.com)

** Do not post any responses here**

Owen's Digits

On page 36, Neil Shubin mentions Owen's pattern which instigates the composition of the fin slowly separating into the bones that make up a human hand throughout evolutionary history. However, the fin that Shubin discovered had 8 finger-like bone structures instead of five. Explain why evolutionary history benefited 5 fingers over any other number of fingers. Discuss polydactyly.

Taking out the fossils

In chapter two of 'Your inner fish', Shubin talks about the removal process of of fossils. Using research from the internet/books, explain in detail the multiple ways one can take out fossils and clean them efficiently without damaging the fossils. Do you believe these are the best ways to get a fossil out? Why or why not? Would you recommend the use of explosives on hard rock?

Nikhil Pereira
nikhil.pereira3@gmail.com

Shark Blood

Shubin talks about the similarities between the cranial nerves of sharks and ours. He explains that these similarities come from the gill arches in our embryos. Knowing what we know about our similarities with sharks, and our different cardiovascular systems, talk about some ways that environmental pressures and natural selection evolved sharks' methods of cardiovascular regulation into ours. Feel free to focus on one main method, and be sure to explain how each adaptation is a benefit for our environment, and how their adaptations are suited for their environment.

Jeremy Solomon

imabum14@gmail.com

Homeoboxes and Hox Genes

When comparing human body plans to those of flies, Shubin talks about special Hox genes, segments of the genome that appear in vastly different animals. The genes present in flies which code for a specific order of body parts (anterior to posterior) also appear in the genes that code for the order of the human spine. This same pattern appears in a plethora of other animals not discussed in the book, but the same Hox genes are found across the animal kingdom and they code for similar functions. Using your knowledge of DNA and development, discuss how knowing the general functions of Hox genes, and their presence in many other animals can lead to important changes in the way we view gene expression. How can humans use this information to learn more about the diseases that afflict many?

Jeremy Solomon

imabum14@gmail.com

Genes

At the beginning of chapter three, Shubin talks about what makes one cell different from the other. He explains that the answer lies in the DNA and what genes are actually turned on. In unit 10 we learned that this is because of the DNA transcription and translation. Using prior knowledge, review the process of gene expression in both eukaryotic and prokaryotic cells and include the role of RNAi and transcription factors.

-Robbie Thomashow

diehardcubsfan93@comcast.net

Teeth: Structure vs. Function?

In Chapter 4 starting on page 60, Neil Shubin briefly talks about the role of teeth in mastication and the importance of good teeth in fish of every size. Since teeth have evolved over time to support the function of initiating the digestive cycle in humans and other mammals, please explain this relationship of tooth structure to its function. Does the shape/type of teeth (blade-like molars, flatter teeth) directly affect what type of role that organism will play in the food web? Do different types of teeth shift food preferences of animals towards plants or other sources? Also, use this passage as a way to review the process of digestive initiation and use of enzymes to help teeth start to break down food before digestion. 

Christine Lin
choco_cat11@comcast.net

When you look me in the eyes (shout out to the JoBros)

Shubin asks the question, "how can eyes that look so different-such as those of worms, flies, and mice-be closely related?" When Mildred Hoge was recording mutations in fruit flies, she found a fly that had no eyes whatsoever. She also found that she could breed a whole line of eyeless flies, and a similar mutation was discovered in mice soon after. In humans, individuals that are missing large pieces of their eyes are said to have aniridia. Between these very different creatures, geneticists were finding similar kinds of mutants. They found that the genes responsible to eyelessness had very similar DNA structures and sequences in all three creatures, and after manipulating the normal version of the gene, Walter Gehring and his team were able to turn on the eyeless gene anywhere on the body, or even on the body of a different species, and have an extra fly eye form.
What is this "eyeless" gene called? What were some of the technologies that geneticists probably used to isolate the DNA sequence and turn the gene on anywhere they wanted on the body? How was the discovery of this particular gene important to evolution and relating the creatures that were tested? Also, explain the importance of the eye and its evolutionary history.

Hannah Kay (hgkay@aol.com)

Our Inner Shark

Shubin says that "we're all modified sharks." He compares the arches and swellings during development of sharks and humans, pointing out the 4 arches that both have in common. According to Shubin, "the richness of the story lies in what happens inside each arch."
What do these four arches develop into in humans? What do these similarities in arches tell us about humans and how we have evolved from sharks? What other similarities exist between sharks and humans? What conditions may have led to selective advantages that humans now have?

Hannah Kay (hgkay@aol.com)

What's In Your Head?

Ch. 4 of Neil Shubin's book explains the importance of the head and how it is formed from the embryo. He gives details on how all organisms' heads are similar to each other, and how evolution changed head development. What similarities does the human head share with the heads of previous organisms? How are our heads different from them? How did these differences come about and what advantages do these differences give to humans in comparison to others? Explain in detail using Shubin, Campbell, or any credible outside sources.

-Austin Lee, 2B/3
austinklee7@gmail.com

From Genes to Proteins

At the beginning of chapter three, Shubin talks about what makes one cell different from the other. He explains that the answer lies in the DNA and what genes are actually turned on. In unit 10 we learned that this is because of the DNA transcription and translation. Explain in detail how a strand of DNA is replicated and eventually ends up as a protein and why they types of proteins that are translated determine the function of the cell.

-Robbie Thomashow
diehardcubsfan93@comcast.net

What's the point of fish having lungs?

On page 32, Shubin describes the lungfish, specifically pointing out that it had a certain bone that we humans have, which is a humerus, an essential bone in the limbs. Shubin also mentions that "curiously, it is not just any fish; it is a fish that also has lungs." Since we just learned about the respiratory system and it's makeup in fish versus humans, why would a fish grow lungs? What is the biological or evolutionary advantage that lungs can give to an animal that gets oxygen to it's body in an already efficient way, specifically since it is always in the water? What other fish have this adaptation? 


Alex Sapozhnikov marijio@gmail.com

Using Old Parts in New Ways

We discussed the idea of organisms "using old parts in new ways" in class a few times, but I think the discovery of ZPA seems to contribute to the idea very nicely. At first, I thought the idea of using old parts in new ways seemed oversimplistic because there didn't seem to be enough "old parts" to use. However, ZPA was revealed to "[make] a molecule that then spread across the limb to instruct cells to make different fingers."(Shubin, 50). It is amazing how one tissue can have so much impact on the development of something as vital as fingers. What is more amazing is how similar structures as this one exist in both flies and chickens, and changes as small as an increase in vitamin A can cause enormous impacts as great as fingers being duplicated. The existence of ZPA seems to provide a basis of how animal diversity has occurred, or how the "old parts" came to be, but it does not give light to what "new ways" may exist due to the slight changes that may be not so slight.

Consider the theme of Evolution. Do random changes in the ZPA and similar genes in numerous organisms show that small changes over the course of thousands of years can create organisms as different as flies, chickens, humans, and even Tiktaalik? Also, do the differences in the common plan for animal limbs, "one bone, followed by two bones, then little blobs, then fingers or toes" (Shubin, 31), seem all that big because they may have come about as corruptions of the exact same structure? Finally, does genetics seem to have all the influence, or does the incidence of selective pressure have an even bigger role as to why some organizations of the limbs generated by ZPA exist as they do now?

Troy Glickstern
(cleverstar8@comcast.net)

A Right to Arms

In class earlier this semester, we discussed the evolutionary history of vertebrates. On page 26 of Your Inner Fish there is a diagram described as "Tracing arm bones from fish to humans." Describe the similarities of arm bones in vertebrates providing references from both Shubin, Cambell, and any outside sources. Further discuss the similarities we see among the vertebrates and describe the distinguishing features among the vertebrates. Reference the vertebrate morphological and molecular trees in your response.

Sea Anemones

In chapter six, Schubin discusses characterisitics of sea anemones. Schubin explains how they are very primitive in that they have a single opening to eat and expel waste and also that they have a very primitive body pattern. If sea anemones are so primitive, what is the value of studying them? While thinking about the theme of evolution, what does the discovery of multiple back-to-belly genes in sea anemones tell us about our relationship to sea anemones and other similar creatures? How might this and other similarities found (such as symmetry) contribute to our understanding of why we are able to grow body parts of frogs by injecting sea anemone genes?
Marissa Lobl marissa.lobl@gmail.com

Chapter 2 Tiktaalik

In this chapter, Shubin describes how Tiktaalik was discovered and how it had a shoulder, elbow, and wrist. He previously began by explaining why having a wrist, shoulder, and elbow is advantageous to humans. But if having limbs was used to get out of the water (to avoid predators), how were these things helpful to fish before they were able to move from water to land? What functions did a wrist, shoulder, or elbow have in fish that helped them survive from a structure/function perspective specifically focusing on why it was advantageous? (Although this is a broad topic, focus on one piece in particular and expand on how this specific structure allowed the fish to have a certain function that was more efficient than it was previously able to perform).

-Michelle Layvant, mlayvan2@students.d125.org

Animals

On page 103, Shubin provides a very nice diagram of the development of organs from three germ layers: mesoderm, ectoderm, and endoderm. On page 659 of Cambell, further discussion about these germs layers are discussed. Differentiate between diploblastic and triploblastic and the organs and tissues associated with each germ layer. Further discuss the animal kingdom and the differences we see between different phyla based on germ layer and other associated features. Discuss how the theme of evolution has affected the categorization of each of these animal phyla. Lastly, discuss the differences between the molecular tree and morphological tree. What are the similarities between these trees and what are the differences?

(Bobby Muttilainen, rmuttilainen@gmail.com)

Reproduction

Beginning on page 86, Shubin begins discussion on the formation of the zygote from sperm and egg in the section "The Essence in Embryos." For review over sperm production and the menstrual cycle, describe the path of sperm as it travels through the male reproductive parts to be ejaculated out of the urethra and the development of the egg in the female ovum. Describe the complete menstrual cycle in the discussion of egg development, and what happens when sperm does and does not fertilize the egg. Don't forget to include hormones in the discussion.

(Bobby Muttilainen, rmuttilainen@gmail.com)

Of Flies and Men

Many genes work together to lead to the development of our body. A single gene alone, such as Noggin, cannot create a fully functional body. Similarly, a gene that is missing or is malfunctioning can greatly alter the development of the embryo. In Your Inner Fish, Neil Shubin explains how mutations in the genes of a fruit fly larva had a significant impact on the development of its organs when he writes, "[t]hese 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"(Shubin, 108). Utilizing these mutants has allowed Mike Levine, bill McGinnis, and Matt Scott to recognize the presence of a homeobox.

Consider the theme of Continuity and Change.

How do mutations occur? (Refer to Unit 10: DNA, RNA, Protein Synthesis)

How are mutations essential in understanding the role of each gene sequence?

What is the significance of Hox genes that are found in various species? (Include ideas of continuity and change. What is being altered? What is kept relatively constant?)

(Keigo Tanaka; tanakarus3@hotmail.com)

sense of smell

In chapter 8, Shubin discusses how being able to smell odors is a result of external factors sending impulses to the brain. Odor molecules are sucked into our nostrils, where nerve cells will transmit the odor to the brain, and tell us about the world around us. Many animals determine what is safe or hazardous to eat for survival by noting the smell of its food. Yet, the earliest single celled organisms, or plants even, don't have a sense of smell. What environmental factors have led to the selective advantages of being able to detect odor molecules? Why was it not necessary for plants or earlier organisms to be able to smell? How come smell is beneficial when there are five other senses to depend on for survival?

Development of Hard Skeletons

In chapter 4, Shubin talks about the development of teeth and hard skeletons in animals. Shubin states that "for years, paleontologists have argued about why hard skeletons...arose in the first place" (76). He says that scientists that believe that skeletons began with "jaws, backbones, or body armor" believe that hard bones (like teeth) arose for the purpose of eating other animals. What are some other reasons that paleontologists might argue for why hard skeletons arose? Would these paleontologists also believe that skeletons began with jaws, backbones, or body armor? If not, what do you think they believed the skeleton began with?

Danielle Webb
(dwebb456@gmail.com)

From Swimming to Push-Ups

In describing his encounter with the "missing link" in evolutionary history, Neil Shubin identifies an extraordinary feature in Tiktaalik. This organism had a wrist bone in its fins, a feature seemingly useless for a fish to have. However, a close look at the structures of various joints revealed that the wrist enabled Tiktaalik to perform push-ups (Crazy!). Neil Shubin theorizes that "[f]ins capable of supporting the body would have been very helpful indeed for a fish that needed to maneuver in [various environments]", allowing them to walk on land (Shubin, 40).

Why was the transition from water to land necessary?

Consider the theme of Evolution: What were the selective advantages that terrestrial organisms (such as mammals) had over organisms that live in water?

Include in your answer terms from Unit Thirteen, Invertebrates and Vertebrates: Predation, Internal/External Fertilization, Internal/External Development, Amniotic Egg, etc.

(Keigo Tanaka; tanakarus3@hotmail.com)

Fins to Hands

In chapter 2, Shubin describes the patch of tissue called the zone of polarizing activity (ZPA) that will produce a mirror image duplication of the limb if vitamin A is injected in the right stage and concentration, as well as the Sonic hedgehog gene that "made one end of the body segment look different from the other" (52). The ZPA and Sonic hedgehog gene together form the hand of humans (making every finger look different from one another) and the fin of a shark/skate. If the Sonic hedgehog gene has the same general function in two radically different species such as humans and sharks, why do they form hands in humans and fins in sharks, two completely different appendages? Where in evolutionary history does this change occur, where the Sonic hedgehog gene goes from forming a shark fin to a human hand with a full set of moving, functional fingers? How does this change occur?

(Sujin Ko, sujinko93@gmail.com)

Digging Ourselves

In chapter 1, Shubin details the process which field paleontologists like himself narrow down a long list of possible excavation sites to very reliable ones. Using his "everythings" analogies, he explains that a single column or rocks can hold billions of years of evolutionary history. However he also explains that due to the ever expanding nature of our society, it has become increasingly difficult to find and properly excavate good dig sites. In detail, explain the system he uses to find reliable dig sites as well as the type of terrains that produce the best results. Furthermore, explain how we as a culture are making it increasingly difficult to find good dig sites.

-Robbie Thomashow
diehardcubsfan93@comcast.net

why bodies?

In Chapter 7, Shubin talks about building bodies with different types of cells and division of labour, and relates it to the early experiments of H.P.V.Wilson on sponges and their reassembly after being passed through a sieve. He also deals with why there are bodies, noting that for the first 3.5 billion years of evolution there were only microbes and then suddenly bodies appeared.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.

-Adnan Jahan

(adnanjahan@gmail.com)

Limbs Chapter 2

This chapter was all about how limbs and hands in particular can be a big help in following the path of evolution. Shubin starts off by talking about cadavers, and how it wasn’t until he saw the hands that he realized he was dealing with what was once a live human being. He goes on to describe how important hands are, and that they can create a greater emotional response, than one might expect. Following that, he goes onto explain how anatomist Richard Owen made the theory that all limbs, hands and feet are quite similar to each other in structure. They each follow a certain pattern that can be found in animals world wide. 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 this idea of exceptional similarities and to Shubin's discovery.

-Adnan Jahan

(adnanjahan@gmail.com)

Beyond the Tooth

In chapter 4, "Teeth Everywhere," Shubin extensively discusses the evolution of specialized teeth. He describes how teeth over time became evolved to meet the changing diet of evolving organisms. The teeth of humans and other organisms are "extra hard," Shubin concludes, because "teeth have to be harder than the bits of food they break down," (Shubin 74). Human teeth are capable of handling the varied diet that we consume today, but what other body systems/parts have adapted to meet the demands of human nutrition? What aspects of the human diet caused changes in the digestive system of humans? How do those changes give humans a selective advantage?

A Walk Through the Zoo (SPOILER: It's a Metaphor)

In the last chapter of the book, "The Meaning of It All," Shubin presents a simplified tree of life from unicellular organisms to humans. He notes several key features in the development of humans, including multicellularity, bilateral symmetry, skulls, hands and feet, a three-boned middle ear, and a bipedal gait with large brains (p. 183).

This list of features, of course, does not include all the important and defining characteristics of humans.

Select what you think are the most important traits humans have that were not covered by Shubin. These traits can be shared with human ancestors, or they can be entirely unique to human beings.
Then, explain how these features may have been selected for over evolutionary history, drawing connections to at least one theme of biology in addition to evolution.

- Vincent Fiorentini
(vincent@panatechcomputer.com)

Structure and Function of Heads

A key trait that defines Tiktaalik in many ways is its possession of shoulder bones, showing it to be a transitional species from fish with fixed heads to amphibians that could move their head independently of their body.

From an ecological perspective - particularly focusing on interspecies interactions - explain how the structural development of this type of head may have aided the survival and reproduction of this type of organism, explaining the functional value of this structural development.

- Vincent Fiorentini

(vincent@panatechcomputer.com)

DNA is not the Same in Every Cell?

On page 45, Shubin writes, “there is a deep similarity among every cell inside our bodies: all of them contain EXACTLY the same DNA”. There are new studies out that are now contradicting this most basic assumption that almost all people make. Explain why this assumption is wrong and what differences are being brought to light in these new studies.

Matt Micucci (coochqbk@sbcglobal.net)

Bodies

In chapter seven, Shubin discusses several theories about the appearance of bodies on earth. One theory is that the increased amount of oxygen contributed to the rise of bodies, and another theory is that predation contributed to microbes getting big and forming bodies. Thinking about the theme of evolution, how could the rising level of oxygen have contributed to the rise of bodies? What else happened as result of rising oxygen levels on earth that supports this theory? Why might predation have caused the formation of bodies? What specific adaptions to predation supports this?

Marissa Lobl , marissa.lobl@gmail.com

Similiar Genes

In chapter seven it is mentioned that sponges have many important properties of bodies. Furthermore, Choanoflagellates, which look like the goblet-shaped cells inside a sponge, have genes that are active in both animals and single-celled microbes. How do Choanoflagellates give us a road map for comparing our bodybuilding apparatus to that of other microbes? List and explain specific properties that both have in common. What do these similiarities tell us about the history of these microbes?

Bones

In chapter 7, Shubin talks about the different types of cells that make up bones. He says that cartilage is "a perfect pad for our joints. The role of Cartilage cells is to secrete these molecules when the animal is growing and maintain them when the animal is not" (127). Why is it that people get osteoporosis and arthritis if these cells are supposed to be maintained? Is it possible for children to get these diseases, even though the cartilage is supposed to be maintained while animals are still growing? Under what conditions does the cartilage stop/start secreting these molecules?

Body Plans

In chapter 6, Shubin describes the importance of the Hox gene in being the "organizer" of the body plan. One type of Hox gene called Noggin determines the body axis of an organism. While humans display bilateral symmetry, other organisms such as sea anemone or jellyfish show radial symmetry. What has caused the differences between organisms to survive better with either form of body axis? How does the locomotion of each organism relate to the symmetry of the organism or the body plan in general? What is the purpose of the Hox genes to create a dorsal and ventral side on humans when these features aren't present on Cnidarians?

(Claire Yao, claire.yao521@gmail.com)

Hand structure

In chapter 2, Shubin describes Sir Richard Owen as a great anatomist that discovered many of the patterns that links the similarities between the species of animals as they have evolved over time. Owen discovered that "All creatures with limbs, whether those limbs are wings, flippers, or hands, have a common design. One bone, the humerus in the arm or the femur in the leg, articulates with two bones, which attach to a series of small blobs, which connect with the fingers or toes" (30). Wings, flippers, and hands all perform different functions that benefit the specific species, yet they all develop from the same basic foundation. What are some of the environmental factors that have caused this evolution of the fin to hand? How come humans have more use for hands with five fingers rather than wings for flying? What are some specific examples of how the variations on bone structure found in the human hand benefits the survival of various species?

(Claire Yao, claire.yao521@gmail.com)

Sonic [the] Hedgehog

In chapter three, Shubin talks about the function of Sonic hedgehog, which acts in the ZPA to control how the digits formed, and what they would look like (for example, look at your hand--the formation of the pinky and thumb, their length and distance from each other, is controlled mainly by the ZPA). Shubin also briefly discusses how if "things go wrong with Sonic hedgehog, the hand ends up looking like a broad paddle with as many as twelve fingers that all look alike" (53). What are some of these possible errors that would throw off the formation of digits, and how does this happen? Have there been past experiments on how we can prevent this from happening? Explain with specific examples.

Kathy Li, kathy2132@gmail.com

Smell and Vision

In chapters 8 and 9, Schubin discusses how, over time, a strong sense of smell has been replaced with advanced vision. Why did this change occur? What does this tell us about the changes happening to the earth during this time? What does this tell us about the lifestyles of these animals? How does this show the theme of evolution?

Marissa Lobl marissa.lobl@gmail.com

Colors Colors Everywhere

The Earth was once not nearly as colorful as it is today. Monochromatic forests dominated the landscape WAY before the first colorful flower did, and this forever changed the way animals actually see! Color seems like such a minuscule factor in the evolution of animals, but Shubin believes it was the primary factor that led to the formation of the modern-day human eye. On page 151, Shubin displays four different eye structures that allow an animal to see objects at different levels of clarity. In order to understand how and why eyes have evolved the way they have, we must "understand the relationship between the structures that make our camera-eye and those that make other kinds of eyes". Primitive eyes contain molecules that allows the animal the see in black and white, which displays a very blurred image. But modern eyes contain molecules that can see colors, which create images that are crystal-clear. How could color be a primary reason why eyes have evolved the way they do? How does this relate to the Relationship between Structure and Function? (pg. 154 gives a hint)

Mikey Ling
(mikeyling@ymail.com)

The Hox Box

In chapter six, Shubin explains how bodies are built. He explains that Hox genes control mutations by "establishing proportions of our bodies...changes in them bring about changes in the ways our bodies are put together" (110). Hox genes are common among all animals, but the number of genes present differ from species to species. Why do you suppose this is? Is it of any benefit to have more or less Hox genes? Clearly, such genes play a vital role in assembling our body plan, but how much will a mutation involving the Hox gene impact an organism's ability to survive and reproduce? What would happen if the gene did not impact an organism's ability to survive?

Anna Leng (annaissbananas@gmail.com)

Orderly Change

In chapter seven, Shubin describes the bodies of animals as being very orderly. He explains that "each of our organ 'knows' its size and place in the body. We grow in the correct proportions because the growth of the bones in our arms is coordinated with the bones in our fingers and skulls" (118). Animals are continually changing, yet they are still very organized organisms. Has this always been the case for animals, even early in evolution or was this something that evolved as an adaptation over time? Is this function entirely necessary to survival, or could we do without it? Use examples of living/extinct/mutated animals and incorporate gastrulation and cell development to help explain why or why not.

Anna Leng (annaissbananas@gmail.com)

Why do we feel?

In chapters 8, 9, 10, and quite frankly throughout the entire novel, Shubin describes the evolutionary process that took place to give us the organs that we humans possess today. He goes in depth to describe the pressures put on organisms by the environment, forcing some selective advantages to be present in certain members of the species.

An aspect of evolutionary development that Shubin does not address in depth, probably due to the lack of evidence in fossils for these traits, is the advent of emotions in organisms. Logically, there must have existed some selective advantage for humans to become capable of expressing significant emotion, ranging from sadness to anger to happiness. What selective advantages do emotions provide? What environmental pressures might have caused the development of these emotions and feelings? Is it possible that other species of mammals possess the same emotional capacity?

(Vickram Pradhan vickram.pradhan@yahoo.com)

Ears and Jaws

In chapter ten titled, "Ears", Shubin discusses how ears have evolved from being part of the jaw in reptiles to becoming a complex three bone ear in mammals. Shubin explains how the different bones in the reptiles jaw changed to become part of the ear as mammals evolved. Using the theme of evolution, explain why this may have happened. Does it have anything to do with the lifestyle of the animal? The feeding mechanisms? What does this change of function in jaw bones tell us about the connection between reptiles and mammals?

Marissa Lobl marissa.lobl@gmail.com

Nom Nom Nom

In the chapter entitled “Teeth Everywhere”, Neil Shubin discusses the importance of teeth to the study of fossils and the study of evolution, overall. In our last unit of AP Biology regarding animal diversity, we had discussed that the factor that would determine if a fossil was a mammal versus another classification would be teeth. Shubin describes the “major patterns of chewing” over time as they had aided paleontology and evolutionary research (73). The mouth became more specialized as we evolved to have incisors to cut food, canines to puncture food, and molars to shear or mash food (73). He discusses that this “new tooth row” first appeared in small mammals about 150 million years ago (73).

This change in jaw structure clearly became a quick identifier to the developmental stage of fossils discovered for paleontologists. What factors caused teeth to become a popular identifier in fossils for paleontology? And if, hypothetically, this evolutionary change did not occur within the jaw, then what may be another structure-identifier to determine the evolutionary status of the organism due to its evident and obvious increased specialization over time?

Sonia Doshi soniadoshi7@gmail.com

Bones, bones, bones

On page 30, Shubin tells of a discovery that Owen had made on the number of bones in limbs. He tells us that a common pattern in all limbs is that it starts off with one bone then the number of bones increases. For example, in a human arm there is "one bone in the upper arm, two bones in the forearm, a bunch of nine little bones in the wrist, then a series of five rods that make the fingers". Using the theme of structure and function and evolution, why is it that all limbs follow this common pattern?

Benny Jeong, bennyjeong218@gmail.com

We Aren't Humans, We're Cake!

All the animals on the Earth are different. Some have two legs while some have four. Some have two eyes, and others have over ten! Sometimes it's very hard to compare one animal to another. For example, try comparing a human to a jellyfish and you'll find yourself stumped! It seems as if the two have nothing in common! Shubin, however, believes "all animals are the same...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" (115). In a nutshell, Shubin says that humans are a small sliver in the "recipe of animals". We are simply modified versions of animals that weren't as environmentally fit as us. But what exactly modifies us? What makes changes to the "recipe" we are part of? How could our "recipe" possibly have originated from a recipe that called for a jellyfish? The answer is Evolution. Explain the concept of Evolution. Then use the terms natural selection, ecological fitness, variation, selective advantage, and adaption to describe how our "recipe" was modified to cook-up the animals we are today.

Mikey Ling
(mikeyling@ymail.com)

Extreme Reproduction

Shubin ponders "What if you could do an experiment in which you treated the embryo of a fish with various chemicals and actually changed its body, making part of its fin look like a hand? What if you could show that the genes that build a fish's fin are virtually the same as those that build our hands?" on pg. 45. And later (on pg. 56) he states that the Sonic the Hedgehog gene in skates, chickens, and humans are virtually identical. This reminds me of he idea of putting different genes with specific traits into another species. (Like when we inserted jellyfish glow genes into E. Coli!) So, if the genetic code is compatible across the boards, at what point, how much of one's organisms genes has to be inserted another for the two different species to be able to reproduce with one another? Or would it always be impossible (based on the number of chromosomes in one species vs. another? And would this be considered convergent evolution?

(Jackie Edelson, jedelson92@gmail.com)

Mutants

On page 56, Shubin highlights a major part of our development/hormone unit: "Whole batteries of genes are turned on and off during fly development, and this pattern of gene activity serves to demarcate the different regions of the fly." Evolution has been dictating the regulation and expression of genes since the beginning of life on Earth; however, it appears that human research is making strides in being able to dictate certain gene expressions. Using your knowledge of regulation and development, would it be possible to arrest, say, brain development to create organims with bigger brains? Or move certain genes/molecules to create many armed creatures? And if this is possible, is it ethical? (Feel free to consult our ethical values on pg. 16 of the course outline book.)

(Jackie Edelson, jedelson92@gmail.com)

Future Medicine?

Shubin begins describing what he later names at ZRA on pg. 49 when he says "A strip of tissue at the extreme end of the limb bud is essential for all limb development. Remove it, and development stops. Remove it early, and we are left with only an upper arm, or a piece of an arm." I'm curious as to what further research has been done with this molecule. (Anyone up for looking for journal articles?) I suppose I would label this question a futuristic 'continuity and change' one, because what I'm curious about specifically, is the possibility of use for ZRA past the process of development. For example, if a person lost a finger or two (or an arm, or a leg, for that matter) in some sort of accident or war, would it be plausible to to somehow smear some ZRA on the spot to re-grow the digit/limb? Is this the future of biomedical engineering or just an idea for a cheesy science fiction movie? Would our genes even respond to this molecule or an undifferentiated stem cell past development?

(Jackie Edelson; jedelson92@gmail.com)

Get Big, Get Armor, Or Get out of the Water

On page 41 of the novel, Shubin gives an in-depth description on what life probably was like in the time of Tiktaalik. He says "the most common fish species we find alongside Tiktaalik is seven feet long and has a head as wide as a basketball" (p. 41), in addition to mentioning sixteen-foot-long predators. Although Tiktaalik was probably 'jacked' (seeing as he was the only creature around with the ability to perform push-ups), this fish was definitely 'the prey' in these predator-prey relationship. (See Campbell p. 1201 for more information on predation.)

This interdependence of predator-prey in nature eventually caused some creatures to avoid the hunt and, as according to Shubin, "get out of the water" (p. 41). What other examples can you think of a prey developing special skills/features to avoid being hunted? Additionally, if fish like Tiktaalik had not been in danger of predators, would limbs ever have arisen?

(Jackie Edelson; jedelson92@gmail.com)

From Teeth to Organs

Some of the earliest teeth were first discovered in lamprey fish in what has become known as conodont fossils. Through the study of teeth, it has been determined that they develop as the result of an interaction between two tissue layers from which cell division, shape change, and protein production within the two layers brings the formation of a tooth. This process of formation by two layers of tissue was modified to build other organs including hair, feathers, and mammary glands. Using the themes of evolution and relationship between structure and function, explain how the different purposes of each of these organs relate to their similar structure.

Sami Kopinsky
sami_kopinsky@yahoo.com

Tiktaalik: the Holden Caulfield of Biology

Tiktaalik: Part Fish, Part Land-Animal In 2004, Neil Shubin and his team discovered a new creature which they named Tiktaalik, or “large freshwater fish”. Tiktaalik exhibited traits of both a fish and a land animal. With scales and webbed fins, this new animal also had a flat head, neck, and the beginning of limbs and joints. While Tiktaalik was not a land-animal himself, his adaptations allow us to better understand the traits needed for animals to transition to life on land. Explain how exhibiting all of these traits could give Tiktaalik a competitive advantage in both his natural habitat and a land environment. Explain how these characteristics could give Tiktaalik a disadvantage. Be sure to consider Tiktaalik’s relationship with his environment or habitat, as well as other animals that may have been living at that time.

Growing Limbs

Shubin explains how a molecule organizes limbs in chickens. He explains how the Sonic hedgehog gene affects limb development, which is by diffusing from pinky to thumb. Are there any other factors that play a role in the development of limbs not only at the ZPA, but also at the apical ectodermal ridge (AER)? What is a possible experiment to demonstrate the universality of the Sonic hedgehog gene? From an evolutionary standpoint, what conclusion can be drawn from the fact that sharks have an AER in their median fins? Explain why or why not the genes for growing a limb from a chicken can be used on a shark using the answers from the previous questions.

Teeth Teeth Teeth Teeth Teeth Teeth Teeth

Throughout the year, we have discussed the Relationship Between Structure and Function in regards to proteins. Proteins are the epitome of this Biological Theme as they follow either the Lock and Key relationship with their specific substrates. Proteins are the first things that come to mind when the theme "Structure and Function" is ever mentioned, yet Shubin thinks differently. As opposed to any typical AP Bio student, he thinks about teeth. In chapter four, "Teeth Everywhere", Shubin describes how the structure and shape of a tooth can reveal the history of how animals processed their food. Using the Biological Theme of The Relationship Between Structure and Function, answer the following question: What is the relationship between the different types of teeth present in an animals mouth and the overall complexity of that animal?

Mikey Ling
(mikeyling@ymail.com)

Inner Organisms

Throughout the book, Shubin brings up our "inner fish" and other inner organisms, like how humans, fish, and other organisms (such as bats and lizards) all share a similar limb structure (31), or how ZPA and Sonic hedgehog have similar effects in flies, skates, chickens and humans (54). He uses the term to describe how modern-day animals, especially humans, show traces of previous organisms in their structure and genetic expression.

How did humans develop such traits that are similar to predecessors but still different? More importantly, how do humans and such wildly different organisms as fish and reptiles all have similar adaptations even after long periods of diverging evolution? Explain how continuity and change affected evolutionary patterns in such a way that humans could have similar genetic features as other, completely different animals, and give examples of more connections among very different animals.

Eugene Bulkin

(doubleaw002@gmail.com)

Reliability of Evidence

Throughout the book, Neil Shubin focuses on a variety of different types of evidence that reveal important aspects of humans that can be traced back to previous species in evolutionary history.
These types of evidence include: fossil records, embryonic development, DNA comparison, and behavioral similarities.
Although Shubin provides specific evidence for the role of each of these types of support as they relate to Tiktaalik, no one alone can be completely reliable to draw a full conclusion. Some, however, are more revealing than others.

Of the types of evidence Shubin provides for the connections between humans and previous animal species, which do you think are the most reliable? Which do you think are the least reliable? Explain, using outside information to validate your claim.

-Vincent Fiorentini

vincent@panatechcomputer.com

A Pattern Among Limbs

In the mid-1800s, anatomist Sir Richard Owen discovered that "our arms and legs, our hands and feet, fit into a larger scheme" (30). He noticed a pattern in the bone structure of the human arm and leg: one big bone followed by two bones, a bunch of little bones, then digits. He focused the rest of his research on the similarities between skeletons of different organsism instead of how skeletons vary between different organisms (as many anatomists did at that time). He found "exceptional similarities" between animals that seemed to have nothing in common, like a whale and a frog. It appeared that all animals with limbs followed the one bone-two bones-lots of blobs-digits pattern. This discovery gave birth to an interesting question: How can modern-day animals be so different yet be so similar? What kind of environmental pressures could have caused a Common Ancestor with the one bone-two bones-blobs-digits pattern evolve into the animals that inhabit the Earth today? Use the Biological Theme of Evolution to support your answer.

Mikey Ling
(mikeyling@ymail.com)

Formation of Fossils

Considering the following information, do you think that the corpses of humans these days will be fossilized for later years? Explain.

1.       Fossils are only kept intact in places that have few human disturbances, even though now a day we live in highly populated areas and are highly disrespectful to the environment.

2.       Bodies are buried in wood caskets which are in cement boxes.

3.       We have removed a whole bunch of sedimentary rock for our own personal use, therefore unable to preserve our corpses.

4.       Cemeteries are built where there is dirt instead of rock which will decompose the dead bodies.

(Jackie James
jackie.james@comcast.net)