DNA Detective

While introducing the "Handy Genes" chapter about using DNA to find the evolutionary history of organisms, Shubin relates genetic information to physiological features (45).

How does this type of deduction lead to variations in phylogenetic trees? What can be misleading about tracing the past of an organism solely through DNA or solely through physiological features?

Supermodel (Organisms)

Toward the end of "The Meaning of it All," Shubin provides several examples of Nobel Prize-winning studies based on model organisms (198). Pioneering researchers have used these organisms to uncover new biological insights.

What exactly are model organisms? What are the pros and cons of using them?

For procratinators who need more prompt^^:BRAINS!!!

On pg 83, Shubin discusses the head and its chaotic state with the complexity of the nerves. While head as whole provides many interesting discussions, studying brain bringings up even more possible discussions. Please discuss brain's role in the central nervous system, endocrine system, both, or any others which pertain to our study, and discuss from evolutionary perspective why the developement of the brain is more crucial in more complex organisms as opposed to early, primitive organisms.

Kevin jeon
bboybyung@gmail.com

I'm Anxious

In "Tracing Heads," Shubin briefly explains the development of nervous systems from simpler ancestral parts, like a notochord (94).
Although Shubin focuses primarily on the specific trend toward cephalization in this section, his discussion is based on the assumption that our vertebrate nervous system has evolved over time.

How exactly does this nervous system work? How has it changed from our ancestors to vertebrates? What selective pressures in our evolutionary history have favored this development?

- Vincent Fiorentini
(vincent@panatechcomputer.com)

Movement of water in our body

On page 168, while Shubin discusses the effect of alcohol, he mentions the idea of diffusion across a membrane. Refering to our past studies, explain the factors behind the movement of water such as water potentional and concentration gradients. Also, relate how these movement of water effects organisms in environments in which they live as they maintain homeostasis. (i.e. fresh water fish vs salt water fish)

Kevin Jeon
Bboybyung@gamil.com

Invertebrate Phylum

In Chapter 7, Shubin in describing the body building of the organisms and their similarty mentions the choanoflagellates in sponges. Going back to the Invertebrate unit, please discuss different phylums that exist in the unit (Porifera, Cnideria, Platyhelminthes, Nemotoda, Mollusca, Annelida, and Arthropoda) in terms of their body plan, embryonic developement and other physcial characteristics that distinguishes it from other phylums.

Kevin Jeon
Bboybyung@gmail.com

Review of pregnancies

On page 102 of Subin's book, he talks about how a fertilized egg develops into a full grown animal. Using the text book, describe the different stages the cells go through until it latches on into the uterus. Include terminology of endoderm, ectoderm, and mesoderm and describe what each layer turns into.

Nikhil Pereira (nikhil.pereira3@gmail.com)

EYES (fish vs. humans)

In Chapter 9, Shubin describes the two different kinds of eyes; one kind found in invertebrates and the other found in vertebrates (fish vs. humans). These two types of eyes work to increase the surface area where light is gathered in the eye; invertebrates do such by having many folds in the tissue, while vertebrates lots of tiny projections that extend from the tissue. What are some disadvantages and advantages of having the invertebrate type eye? The vertebrate type eye? Why is it that the vertebrate-type eye is more advantageous to humans?

Sujin Ko (sujinko93@gmail.com)

Sense of Smell

Neil Shubin indicates that a human's sense of smell can capture the scent of a "bell pepper at a concentration of less than one part per trillion". (141) How did the evolution of the acute sense of smell aid individuals in survival? Fish also have a sense of smell which they use to locate and capture food. Explain how the sense of smell evolved to accomodate life on land and how it compares to the sense of smell that a fish has. Is it possible that what we label odorless really has an odor that we can't yet detect? Why is the sense of smell of humans less refined than that of a dog?

Yekaterina Khavkhalyuk (kittykatx93x@yahoo.com)

Skin: The Plastic of Human Bodies

In chapter 4, Neil Shubin explains that skin can be modified to make various structures of an organism, such as teeth, breast, feathers, and hair. He even makes a comparison of this use to plastic, explaining how a single structure is used to make different things, much like how plastic is used to make CDs, bottles, and other products for daily use.

Recall the Reproduction and Development unit.

How does our body develop from a zygote to our full-grown body?

How are organs, such as the brain, developed from our germ layers?

Compare and contrast the embryonic development of a chicken, frog, and a human.

In what ways is our development similar? Different?

Be sure to include terms such as ectoderm, blastopore, primitive streak, etc. in your response.

(Keigo Tanaka; tanakarus3@hotmail.com)

From advantageous to not

In chapter 11, Shubin explains how we run into physical problems due to differences in the structures of our ancestors. Can you think of any genetic diseases or inefficiencies that we suffer from due to our incompatibility with fish? Furthermore, can you think of any characteristics that we currently have that could be a hindrance in the future?

Fishy Disease

As Shubin describes on page 187, humans have many diseases that can affect our body and our lives, such as heart disease and diabetes. Why do humans develop so many diseases (such as heart disease and diabetes)? What does this have to do with our "inner fish"? Why is it that fish do not develop these diesases, whereas humans, who are a more advanced version of fish through many centuries of evolution, encounter these diseases a lot? What is different about the lifestyle of many humans at this point in time versus the lifestyle of a fish? How could these diseases be prevented? Any possibilities of using genetic engineering or other methods? Explain. Shreeraj Patel shreeraj.patel1@gmail.com

Teeth everywhere

On page 78 in Subin's book, he starts to describe the similarities in the formation of hair, feathers, breasts, and teeth. Using outside information, describe the process of each forming. Feel free to talk about the significance of all these exterior structures formed in similar ways.

Nikhil Pereira (nikhil.pereira3@gmail.com)

Embryo to organism

Shubin mentions 4 arches that compose different strictures found in creating a human on page 88. These arches represent gill like formations. In your own words, describe what each arch develops into and what the significance of the fetus taking on a 'gill' structure while developing.

Nikhil Pereira (nikhil.pereira3@gmail.com)

Vision Clarity

On page 151, Neil Shubin provides a diagram of visual clarity between a limpet, a nautilus, a scallop, and a human. As the eye structure becomes more complex, the visual perception of items achieves a new strength in clarity. Explain why certain organisms do not require as much clarity to be considered fit in their environment. Why is visual clarity more important on land than in water?
Talk about light refraction and how it effects the retina in air and in water.

Yekaterina Khavkhalyuk (kittykatx93x@yahoo.com)

The Middle Ear

The middle ear contains the incus, malleus, and stapes, all of which are instrumental in detecting timbre, loudness, and pitch. Neil Shubin mentions that these bones are instrumental to hearing through air but vaguely references that "hearing in water is different from hearing on land...". (164) Discuss the differences in hearing by comparing acoustic structures from land mammals and aquatic mammals. Use the diagram on chapter 50 of the Campbell textbook to review the role of incus, malleus, and stapes and compare specific functions of these bones to similar structures in aquatic mammals.

Yekaterina Khavkhalyuk (kittykatx93x@yahoo.com)

Smelly!

On page 145, Shubin begins the interesting discussion of how jawless fish have very small numbers of odor genes. This is very odd considering that us mammals have over a thousand genes dedicated to odor. How did this "jump" in number of odor genes occur? Also, Shubin talks of how researchers found that us humans have roughly 300 odor genes that have been rendered useless by mutations that cannot be fixed. How did this occur? Explain. Shreeraj Patel shreeraj.patel1@gmail.com

Mitochondrias.

Shubin addresses the vital role the mitochondria plays in the functioning of cells, most importantly the conversion of sugar and oxygen into energy (197). Mitochondria's processes have arose from genetic structures with a bacterial past, and gene mutations can be harmful and cause diseases. How do these genetic mutations happen? Recall the different types of distortions that can happen from the gene unit. How do scientists approach to solve diseases such as cardioencephalomyopathy? Also, incorporate mitochondria's history of endosymbiosis.

Weather

In the afterword, Tiktaalik's habitat is described in greater detail. Did Tiktaalik survive in an arctic habitat, or do the fossils of other organisms show a different past? What was the climate like 375 million years ago? Make a prediction at what could have eradicated Tiktaalik based on climate shifts nearly 400 million years ago. Use information from previous chapters and describe how the characteristics of this "fish" fit the habitat/climate it lived in.

Eryk Fundakowski

arthur2446@comcast.net

Being Bipedal Rocks!

On page 164, Neil Shubin talks about the movement of rocks in the inner ear. What would happen if a human did not have enough rocks to stimulate hair cells? Talk about the evolutionary significance of these rocks and what benefits they provide for bipedal organisms.

Yekaterina Khavkhalyuk (kittykatx93x@yahoo.com)

Light Receptors

On page 153, Shubin relates human eyes to Old World monkeys. Old World monkeys, like us, had 3 different kinds of light receptors that helped them perceive the world around. Explain how these receptors work and why an organism that has developed vision has a distinct advantage over an organism that doesn't. Shreeraj Patel shreeraj.patel1@gmail.com

Combining ears and eyes?

In page 172 of Your Inner Fish, Neil Shubin talks about the jellyfish and how they have eyes with genes that are similar to both Pax 2 and Pax 6 which are present in modern ears and eyes respectively. After that, he also mentions that some birth defects affect both the eye and the inner ear of the infant. Give some examples to these defects, and how they affect the eyes and the ears of a baby. Then discuss how these defects relates to the Pax 2 and Pax 6 genes.

John Park (wisejsm@yahoo.com)

UV, Color, Black and White, and Infrared vision oh my

On page 152, Neil Shubin mentions color and black and white vision. What evolutionary significance does color vision have to humans and why do some animals not have the ability to see in color? Other varieties of vision exist depending on the environment of an organism. Describe how vision varies between two of the followin: deep sea chondrichthys, Arachnids, a honeybee, a dog, and a human. Explain why each type of vision is key in the survival of the respective organism.

Yekaterina Khavkhalyuk (kittykatx93x@yahoo.com)

The law of everything - except some things...

Shubin reveals the biological “law of everything” on page 175. This law states that every living thing on the planet has parents. He also mentions that this can one day be changed thanks to cloning, biological engineering, or some technology yet to be invented. Discuss the implications of artificial birth or creating an organism without parents. What are some advantages to being adjust a creature’s make-up? What are the positive and negative effects that this can have on evolutionary history since, among other reasons, it won’t have a real bloodline to any other creature?

(Alex Sapozhnikov marijio@gmail.com)

Still not blind.

Shubin mentions the advantages of vision (capturing light to process images) in Chapter 9 (148). The ability to see provides organisms such as humans with a great evolutionary advantage, as oppose to an organism without eyes, forced to use other senses by means of getting around such as sharpening their sense of smell. With eyesight, animals gain the ability to be more functional and optimize their ability as scavengers. Discuss how eyes vary among others, such as differences in invertebrates and vertebrates. How has eye structure developed differently overtime in such invertebrates, flies and worms? How is eye structure shared among different species?


Kyle Kim, piece847@gmail.com

Gene Regulation

In chapter five, Shubin mentions that the distinguished body structures of vertebrates are determined through the gene regulation going on in our gill arches through the tissues of our future brain. Describe how genes such as Otx and Hox genes map out a blueprint of our gill arches. Review Campbell of how genes are regulated and describe how specific structures such as the jaw developed and evolved from bony fishes.

Forever Diseased

Chapter 11 includes many examples of diseases that show how humans are the product of a long and unique evolutionary history. Choose a disease and explain how it shows that we are influenced by earlier evolutionary traits. Eryk Fundakowski- arthur2446@comcast.net

Examining the "Blob"

In Chapter 7, Neil Shubin remarks that sponges are an "interesting" specimen, with its body consisting of silica and collagen. Even though their body structures are relatively simple, Shubin explains that their body reveals much about our own bodybuilding apparatus. Its cells have a division of labor, the cells can communicate with one another, and the array of cells function as a single individual, much like our human body. In this way, Neil Shubin emphasizes the possibilities of discovering our past through observations on other organisms.

Recall the Invertebrate and Vertebrate Unit:

Compare and contrast Vertebrates and Invertebrates.

What greatly differentiates us(vertebrates) from invertebrates, such as sponges?

What similarities do we share with invertebrates?

Consider the theme of Evolution:

What are specific structures/mechanisms that only vertebrates have developed?

What are specific structures/mechanisms that only invertebrates have developed?

Why was the development of these structures/mechanisms necessary to survive?

(Keigo Tanaka; tanakarus3@hotmail.com)

Do We Got Time?

On page 121, Shubin describes how much time the first organisms had to evolve into different multicellular organisms which soon turned into today's organisms. Many landmark events occurred to stimulate the "production" of multicellular organisms. Using outside resources, discuss which events in the history of the Earth led to the evolution of unicellular to multicellular organisms. Why would these certain events cause this change? Did these events change living conditions? Why would the change from unicellular to multicellular organisms be an advantage in evolution after these events? Shreeraj Patel shreeraj.patel1@gmail.com

Bozo family and Haplogroups

The Bozo family example used by Shubin to describe the subtle process of evolution over many generations reminded me of an idea that was introduced during the genetics unit: haplogroups. I believe human haplogroups demonstrate the theme of evolution within the human species because is shows how features, such as blonde hair or black skin, eventually developed as humans migrated out of their origins in Africa and adapted to their environments across the planet. In the words of Shubin, "the key is that features--orange hair, squeaky nose, big floppy feet--enable you to recognize the groups. These features are your evidence for the different groups, or in this case generations, of clowns." (177). My question about haplogroups is how they are distinguished specfically. Obviously features across different populations are diverse, but are specific patterns of features (and genetic patterns) used to group people together? Also, can haplogroups be used to trace the origins of mutations, such as sickle-cell anemia, to explain where evolution did not work well and produced not so good results? I think my Y-DNA may be in haplogroup J due to my Sicilian and Mediterranian ancestory. Are you curious about what haplogroup you are in? Troy Glickstern cleverstar8@comcast.net

From sponge blob to Sponge Bob?

On page 132 to 133, Shubin talks about the differences between sponges, single celled organisms, and organisms with body plans. Describe how as time went on organisms were able to become more complex, becoming multicellular and even developing different types of tissues that hold the body together. Discuss the “old parts” that were used in new ways from one organism to another and give examples.

(Alex Sapozhnikov marijio@gmail.com)

The definition of a body

On page 117 in Subin's book, he goes on to define 'a body'. Explain in your own words what defines a body. In addition, explain when did bodies arise, how did they come about, and the significance of bodies. Describe the differences between a cluster of random bacteria cells and a cluster of cells creating a human.

Nikhil Pereira (nikhil.pereira3@gmail.com)

EGG

On page 98 what does Neil Shubin mean when he states, "Just as with heads and limbs, our history is written within our development from egg to adult?" On the topic of embryology, What is embryology? And list the ways fish, amphibians and chicken embryos are alike? -Eryk Fundakowski: arthur2446@comcast.net

Smelling in different environments

In Chapter 8, Neil Shubin starts to talk about the evolution of the nose and how the nose is used for smelling scents. However, there is no specific information about the difference of smelling except that the ones on ground and ones in water have different types of receptors. Go into more depth than Your Inner Fish and talk about difference in receptors and how they have to be different, with different physics of air and water for example.

John Park (wisejsm@yahoo.com)

Bones and their protector

Starting in page 126, Shubin talks about the bones and the cartilage, and how these joint tissues protect our bones from grinding against each other. He also mentions that the cartilage tissues can even withstand our entire body mass' weight. Discuss the strength of the cartilage tissues, how they are able to withstand such pressure. Also, discuss about those who have arthritis, and how those people with arthritis weakens the cartilage tissues so much that their bones start to grind against each other.

John Park (wisejsm@yahoo.com)

The Bonzo Family tree

On pg 176 of Your Inner Fish, Shubin describes the developement of clowns from humorless couples. He attributes the developement of the family full of clowns to mutation. However, a family full of clowns can develope regardless of the mutations. Describe the developement of the Bonzo family from the hereditary aspects from the humorless couple all the way to a full fledged clowns.

Kevin Jeon:bboybyung@gmail.com

Tiktaalik

Looking at Your Inner Fish as a whole, Tiktaalik was a fish that lacked an operculum; what does this tell us about the animal? Furthermore, Tiktaalik had a true neck; what did this allow it to do(advantages)? Tiktaalik was not just the "missing link" rather it was the transitional form, analyze this from an evolutionary standpoint and include outside information. -Eryk Fundakowski arthur2446@comcast.net

The Lifestyle of a Spud

On page 187, Shubin talks about how humans were built for an active lifestyle, not a couch potato lifestyle. Why were humans and other earlier creatures built this way? (include "boom/bust") Why is it detrimental to our health to eat too much fat? Include the effects of obesity on everyday functions like metabolism on a molecular level.

Operculum No More

In the afterword, on page 206, Shubin talks about how Tiktaalik lost its operculum. In what ways did this specific change in the structure of Tiktaalik effect its movement and how does this show the evolution of land animals from aquatic animals?

Different Eyes

On page 150, Shubin discusses the different types of eyes in different animals. Every creature with a skull has camera-like eyes while other animals have eyes "ranging from simple patches of cells specialized to detect light, to eyes with compound lenses..., to primordial versions of our own eye" (150). Explain the differences between these types of eyes. Give examples of animals that have each type of eye. Also, what are some advantages and disadvantages to having each type of eye? Which type of eye would be the most useful for animals? Danielle Webb (dwebb456@gmail.com)

Hox: A change we can believe in?

On page 110, Shubin discusses the importance of the Hox genes and their relation to the body plan of an organism. He says specifically “if you make a fly that lacks a gene active in a middle segment, the midsection of the fly is missing or altered. Is there any way to change Hox genes that will lead to a positive outcome? Can we change the Hox genes of a person to make them grow taller or gain some sort of advantage? What are the ethical repercussions of this?

(Alex Sapozhnikov marijio@gmail.com)

Cellular Transport

Shubin's book covers a lot of important topics that we learned this year. However, one topic that is barely covered is cell transport. Without cellular transport, all of the systems in our bodies would be rendered useless. Explain the different types of transport and the importance of osmosis.

Changing Teeth

On pages 61 and 62, Shubin described the difference between mammal and reptile teeth. One of the differences is that throughout a reptile's life, their teeth are replaced continuously while for mammals, their teeth are only replaced once their whole life. Would having the same teeth one's whole life be an advantage or disadvantage? How does this relate to the fact that all of mammals teeth fit perfectly together?

Jackie James
(jackie.james@comcast.net)

Evolution of Behavior

We talk mostly about the similarities between the physical structures that make up different organisms. Scientists try to use the fossils they find to reconstruct some behaviors of their discovered organisms, but the evolution of behavior is difficult to track, because of the lack of evidence. Discuss the methods with which scientists discern behavior from bones, and some evolutionary trends that have been discovered among land animal history.

Jeremy Solomon

imabum14@gmail.com

Teeth tell all

On page 61, Shubin makes a claim that teeth can tell a lot about an organism's lifestyle. This is true for the fossils found now-a-days because back hundreds of years ago, the main goal was solely to eat and survive. Now that humans are advanced enough to go through life without worrying about finding food (for the most part), is an evaluation of our teeth enough to be able to piece together our lifestyles? If not, is there any other part of our skeletons that could tell more? Consider in your response our abilities to make our own lifestyle choices without endangering our lives, like being vegetarian or vegan for example.

Jackie James
(jackie.james@comcast.net)

Finding out an organisms past

On page 45 of Your Inner Fish, Shubin explains how the scientists use DNA to help find out the past of organisms. What are the benefits to looking at an organism's DNA over body structure? Are there anything that could be missed by just looking at DNA? Explain how this approach led to the variations in the phylogenetic trees.

Jackie James
(jackie.james@comcast.net)

Germ Layers

In chapter six, Shubin talks about developing embryos and their body plans. When Christian Pander looked at embryos he found that all organs in a chicken can be traced to one of three layers of tissue in the developing embryo -- germ layers. The endoderm, ectoderm, and mesoderm all have a specific role in embryogenesis in each animal. Use this time to review and describe what function each of the three layers plays, specifically in a human being. Also, go through each stage starting from the blastocyst stage where there is no body plan up until the embryo has completely formed. How does each layer know what to do/each cell know where to go/what to form? (Discuss the role/function of the Organizer.)

-Michelle Layvant, mlayvan2@students.d125.org

Sponges

In chapter seven, Shubin talks about body plans of animals and specifically on page 131 he talks about the body plan of a sponge. Explain the body plan of the sponge and what role does it play in how/why this organism has been successful? What environmental pressures have led the body plans of organisms to shift more into other forms like that of a jellyfish, then fish, etc? Describe the communication of cells within a sponge, expanding on Shubin's description on the beginning of page 132. 




-Michelle Layvant, mlayvan2@students.d125.org

I'll Be a Monkey's Uncle

A major theme of the book is how two seemingly different organisms are related. In most cases, Shubin takes the less-developed organism's features and explains how the organism evolved into an entirely different one. This process doesn't apply to the relationship between humans and apes (our closest relatives) with whom we co-evolved from a single common ancestor. If the "missing link" were to be found, what features would scientists use to prove its relatedness to both humans and apes? What does this say about the differences between humans and apes, in terms of which adaptations each species developed, and how the split occured?

Jeremy Solomon

imabum14@gmail.com

A Knee-Slapper!

Shubin describes the human body as a "dressed-up" fish as compared to a "hot-rod Beetle" (185). The consequences of evolution are clear in looking at our own bodies. We have the capabilities of walking on two legs, talking, and incredible dexterity in our fingers and toes, but we are still susceptible to "everything from hemorrhoids to cancer" (185). As an example, Shubin brings up the "unhappy triad" in the knee because the three structures making up the knee (medial meniscus, medial colateral ligament, and anterior cruciate ligament), are very common to injury (185). In relation to structure and function, how could the knee be better-structured in order to become less common to injury? What are the barriers that are stopping us from becoming the "perfect mammal"? Even going into our vulnerability of different diseases, what are some causes of being infected by diseases, and what are our defense mechanisms as of now?

Sonia Doshi soniadoshi7@gmail.com

Great Balls of Cells!

As you may already know, the origins of many of the features on the human head, such as the jaws, ears, larynx, and throat, can be traced to the gill arches from an embryo to an adult in a human. If look back to the Handy Genes chapter, a similar phenomenon occurs when the origin of the wing of a chicken can be trace to a wing bud and areas close to the ZPA, where high concentration of ZPA molecule exist, develop the wing in the exact way they are supposed to. I noticed a pattern. Almost all the features that organisms develop originate from a tiny region of cells, much like the entire embryo originates from a single ball of cells called the morula. My question is whether this is significant to understanding evolution, and whether this phenomenon occurs across multiple species (and kingdoms) to explain the source of changes that brought about speciation and diversity.

Consider the theme of evolution. Almost all organisms originate as tiny cells and develop from such minute beginnings into the organisms they are destined to become, but why is that so? Could this be a weak spot for earth dwelling organisms because “if anything interferes with normal development during the embryonic phase, the effects can be devastating.” (Weiten, 427). Is this important period of development the very period during which diversity comes to be?

Weiten, W., & Halpern, D. (2004). Motivation and Emotion. Psychology: Themes and Variation 6th Edition, 10, 427

Troy Glickstern

cleverstar8@comcast.net

Shubin, I think we have a problem

If you look at the flowchart on page 176, a very interesting explanation for evolution over the course of many generations is provided. The key principle emphasized in this schematic is that “descent with modification can build a family tree, or lineage, that we can identify by characters.” (Shubin, 176). This is an easy way to justify how all organisms branched out from one common ancestor, but the one question that the flow chart does not answer is how divergence occurred in the first place? If an original humorless couple is the origin of the entire generation of full bozos, how did the bozos inherit such incredible diversity if the tools for such were not in their original genetic code? Did they intermarry? Obviously that is not possible in the animal kingdom because organisms of different species cannot interbreed.

Consider the theme of evolution and maybe the theme of structure and function. If descent with modification occurs, what causes the modification? Mutations in DNA do occur, which does explain why proteins do not function in the way they are intended, but it doesn’t seem possible that they occur so often that they result in the divergence of species so far over millions of years that jellyfish and humans could possibly be related. Prove me wrong?

Troy Glickstern

cleverstar8@comcast.net

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 which served as a defense from predators. Explain why it would be beneficial for bones to occur after teeth. Include at least one other example in which a similar evolutionary pathway occurs.

Old parts in new ways

Throughout the book, Shubin has described different ways organisms have evolved by using pre-existing parts in a different way. Find at least three examples throughout the book and explain how they helped the organism gain an advantage. Describe any setbacks that were later seen as an evolutionary byproduct

Aparna Pal

aparna.pal.1994@gmail.com

my genes, your genes, their genes, more genes!

In Chapter 6, Neil Shubin discusses Hox genes and their role in determining anterior/posterior/ventral/dorsal sections of organisms. Humans have Hoxa, Hoxb, Hoxc, and Hoxd when organisms such as jellyfish and fruit flies have less Hox genes. What determines the number of Hox genes in an organism in terms of complexity and symmetry? Would a bilateral or a radial symmetry organism have more complex Hox genes? Provide and example of both.

Fossil Finding

On page 9 of your inner fish, there is a great diagram titled "pattern at the zoo." Furthermore, Shubin says that "every rock sitting on the ground has a story to tell" (11). Discuss the evolutionary changes we see from fish like animals to humans using the diagram, campbell, and any outside resources. Further explain how this evolution affects the fossils we see and where we find these fossils. How did Shubin use this background knowledge when looking for fossils that showed evidence of the change from water to land animals. What challenges do scientists face when searching for these fossils?

Matt Kim

(matthewkim0803@gmail.com)

Rocks can Explain the Past and Predict the Future

On page 11, Shubin mentions 2 very interesting things. The first is how the summit of Mount Everest (nearly 5 miles above sea level) contains rocks from an ancient sea floor. The second is how fossils of Amazon-like plants have been found in rock layers north of the Arctic Circle. Explain how both of these phenomena occur and what they could tell us about the Earth’s past and future.

Matt Micucci (coochqbk@sbcglobal.net)

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