Horny Sheep

On pages 254-256, Carroll discusses the effect of evolution and mutation on the populations of big horned sheep. As humans have hunted away the largest sheep with the biggest horns, the leftovers' childrens' children have become less attractive to their kind and as a result breeding has dropped. Find another example of such a phenomena, where evolution has led to a decrease in proliferation, and actually inhibited an organism from reproducing as it should.

Testing the Evolutionary Theory

On page 247, Carroll asks the all important question, "Why does evolution matter?" This entire novel focused on providing scientific, molecular, and genetic evidence not only proving the importance of evolution but refuting creationism and all those that oppose it. So, in order to give creationists (or any others who refute evolutionary theory) a chance, is there any evidence out there that states that the genetic evolutionary theory is wrong? What evidence out there keeps certain individuals from believing in Carroll, Darwin, and all of the evolutionary scientists?

Human Survival or Quick Adaptivity?

On pages 38-39, Carroll says “Living for the moment has the dangerous disadvantage that if circumstances change more rapidly than adaptations can arise, faster than the fittest can be made, populations and species are at risk.” Is it possible with this greenhouse effect that is going on in today’s society that carbon dioxide gas will kill off humans before they adapt to have a greater affinity for oxygen? How long could such an adaptation take place? On this note, do people living in higher altitudes that are used to breathing in thinner air already have a an adaptation in their genes for a greater affinity for oxygen gas than people on sea-level ground, or are they simply used to it.

Melanin Paint

On pages 208-210, Caroll discusses his own research into the wing patterns of the fruit fly Drosophilia melanogaster. He uses the metaphor of paintbrushes and black paint to describe genes that encode for melanin-synthesizing enzymes. Explain in biological terms what exactly Caroll means by this, including a description of what the "switches" are and how this expands to a "tool kit" that allows for the many different wing patterns. Caroll also explains that the "paintbrush gene has other separate switches that control how it is used in other body parts." Explain why such complexity has arisen around the evolution of a single black spot.

Color Blind

On pages 94-98, Carroll discusses the evolution of color vision in humans and on pages 127-129 he discusses the subsequent loss of smell. Carroll states that "we no longer rely on our sense of smell to the degree that our ancestors once did" (128) because we now rely on our sight. If sight is so important to humans, evolutionarily speaking, why are there genes that code for color blindness? Is there another selective advantage in those genes that keep them around despite the negatives? Discuss also the structure of the eye and the mechanisms that allow us to see in color. Address also the genetic components of myopia and hyperopia. Why do these defects exist with such prevalence if sight is so important?

Venemous Evolution

On pages 153-154, Caroll talks about four unrelated animals -- a sea anemone, a scorpion, a marine cone shell snail, and a black mamba snake -- who all independently evolved to use venom. The protein sequences within the venoms are all structurally different, yet they have an equivalent effect on the animal's prey. Explain what factors contributed to their evolution and how essentially the same adaptation could arise in these unrelated species and give examples of other adaptations that have similarly evolved in different organisms. Also, given the venoms' different structures, address how these distinctly different genes can effectively have the same purpose and why they may be so different.

Intelligent Design vs. Carroll. cage match.

On page 243, Carroll addresses and quickly refutes a new alternative belief to Darwinian evolution, referred to as 'intelligent design.'  Explain in further detail the intelligent design concept, and examine Carroll's main points to render this belief "utter nonsense that disregards fundamentals of genetics.  Find an examples of proponents of intelligent design as well as critics of it.  Do any of them bring new information to the argument that Carroll doesn't mention?  Carroll mentions one scientist in particular, Dr. Michael Behe, who he seems to suggest is awkwardly straddling the fence between Darwinian evolution and intelligent design.  Look up Behe's arguments in detail and explain how he tries to incorporate aspects of both beliefs in his theory.  Do you agree that his reasoning is inconsistent and flawed, or is it more logically sound than Carroll says?

Genetic exceptions

One of Caroll's core arguments for evolutionary theory is the universality of genetic code, that the same sequences are used to code for proteins in every species. But as he mentions on page 75, there are a few exceptions to this rule. Find examples of those exceptions and explain why they might read genetic code differently than other cells/organisms. What clues does this give us to the nature of LUCA?

Rate of Evolution

On pages 64-65, Caroll explains how what may seem like an eternity to a human, "is barely a tick of the evolutionary clock." Throughout the book, Caroll consistently relates evolution back to three main components - variation, selection, and time. Is the amount time necessary to develop advantageous traits consistent throughout evolutionary history? What type of factors within an organism's ecosystem contribute to the rate of evolution? How can scientists determine this? (Possibly connect to neutral mutations). Humans have arguably become the dominant species on Earth. How has this affected these mutational rates in the human species and in other organisms that we have inevitably affected?

Tool Kit Genes

On pg. 206, Carroll discusses the differences in the development of pelvic spines in three spine stickleback fish. One type is "a "open-water, full spined form", while the other is a "shallow water, bottom-dwelling, reduced-spined form". The tool-kit gene responsible for spine reduction in the latter is known as Pitx1. Define what a tool-kit gene is. How does Pitxl control gene expression? What are other methods of gene expression? How is it possible that individuals of these two populations can mate when they have different features and different expressed genes?

Human genetic decay and technologies

On page 105 Carroll states that up to 8 percent of color blindness occurs in Caucasian males while only 3 of 3153 tested macaque monkeys from the wild (<.1%) were color blind. This disparity demonstrates how in many cases humans are not under the preservative forces of natural selection. Instead, humans have succumbed to comfortable living and do not struggle with daily life or death situations in nature, or at least for most humans. In addition many new technologies are allowing humans to overcome selectively disadvantageous mutations that are then passed on to successive generations and allowed to circulate populations. Under the relaxation of the pressures of natural selection, will the human genetic code begin to decay and express a excessive amount of fossilized genes similar to the Mycobacterium leprae, a microbe that has compromised its independence due to specialization of living in host cells and has 1,100 fossil genes? As well list technologies that have given humans the ability to surpass the restriction of a disadvantageous mutation as well as that specific mutation. Are these technologies benefiting or damaging the human race? Is this no longer survival of the fittest?

Unmaking the fittest

On page 252 Carroll reminds us that "the 'fittest' is a conditional, if not precarious status," and that over time the ideal 'fit' changes as the climate does. He uses fossil remains of ancient palm trees in Wyoming as an example of this. What changes exactly happened in Wyoming that sparked their "unmaking?" (252) How is this mode of species decline compare to the "unnatural mode of human selection," and how has our role as the "managing director of the biggest business of all" (254) affected the shape of evolution and direction of the fittest today? (What happened with those cod fish?) Also, find another species (extinct or existing) who's evolutionary course has been changed by human intervening. Is all unnatural selection harmful in the end, or can some intervening have a positive effect?

LUCA

On page 86, Carroll states, "... there was a common ancestor of all threee domains (the last "universal" common ancestor, or LUCA) that then split into two domains, the Bacteria and Archaea, and the eukaryotes arose later from a branch of the Archaea." Explain the evidence that supports this idea, both from the book and from outside research, and discuss how the "tree of life", as Carroll calls it, grew from LUCA into what it is today. Also, discuss any information scientists may have about LUCA in terms of basic traits, how old it is, etc.

Endosymbiosis

In the beginning of the book, Carroll slightly touches on the theory of endosymbiosis (pg. 85-86). However, he doesn’t really elaborate on the specifics of the process. Describe the theory behind endosymbiosis.What are the"requirements" (i.e. shape of DNA, ribosomes, etc). What are the specific DNA sequences that have remained the same between mitochondria and plastids and prokaryote DNA. What faults are there in the logic of endosymbiosis. How have other theories branched off this original theory in order to repair these faults in logic? Carroll states that endosymbiosis “confuses the family tree” (85). Elaborate on these confusions.What microorganism's DNA is “tainting” the evolutionary tree of eukaryotes? In addition, explain how the evolution of the endomembrane system either refutes or supports the theory of endosymbiosis.

Eyes

On pages 193-195, Carroll discusses the evolution of the many eyes we see in the world. Given his previous components of evolution; chance mutation, selection, and time, discuss how all these eyes could have evolved so differently as opposed to keeping a more uniform style.

Unnatural Selection

On page 234, Carroll discusses how hunters desire for large-horned rams has caused an "unnatural selection". Briefly summarize what "unnatural selection" means and provide other examples of other species of animals that humans have impacted in a similar manner. What are some of the effects of human pressure on these species? How has human intervention resulted in disadvantages for the vitality of the species? Are there any other possible benefits to forced human selection beside the monetary rewards for humans?

On pages 231 to 232 Carroll states several methods used to discredit vaccinations. Find and describe other methods that radical scientists have used to attempt to discredit vaccines and other established medical practices. Evaluate the methods based on both their truthfulness and their effectiveness.

Tumors

On page 182, Carroll discusses the conditions necessary for tumors: chance mutations, selection, and time. Explain how these three main components of evolution apply to tumor formation and growth. Also, explain how tumors spread through the body and proliferate in other body tissue. What are some specific examples of mutations that cause tumors? Discuss the Philadelphia chromosome and its association with chronic myelogenous leukemia as well as other examples.

"Irreducible Complexity"

Carroll constantly talks about how evolution is derived from an accumulation of different mutations that singularly are only small variations through mutations that create a trait in an organism. But can Evolutionary Development explain every single happening in evolutionary history? One of the main arguments for intelligent design is the example of the motor like flagellum that developed in organisms in early earth history through the idea that the flagellum is a “irreducible complexity” and cannot be explained through Darwinian evolution. An “irreducible complexity” is defined as ". . . a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning" (Behe, M. 1996a. Darwin's Black Box. New York: The Free Press). What are some other examples of structures in organisms that are “irreducible complexities” and what are some of the explanations of these examples? Can Evo Devo be used to explain the structure of the flagellum?

Delicious Newt Death

On pages 165- 167 it talked about a man deserving one of the most honorable awards, the Darwin Awards by swollowing an extremely toxic newt. The man died within 24 hours, but the common garter snake, Thamnophis sirtalis, is able to survive, and yet experience slight side effects of eating the newt. Carroll says this sets the stage for "coevolutionary" arms race. What exactly is coevolution? What allows the snakes to survive the TTX poison? What genetic trait factors into it? Is it a chemical or physical adaptation that allows the snake to survive? Carroll also talks about a trade-off betweeen advantage of an abudnant food source nad feeling lousy for a while. How can you relate this to humans? Why do we do it? (REmember at the beginning of this class... all the way back in august, when we talked about being energy efficient and seeking food versus consuming it?) What are other examples of coevolution other than the garter snake and newt

Redundancy

On page 74, Carroll says "There are sixty-four different triplet combinations of A,C,G, and T in DNA, but just twenty amino acids". Explain the process by which DNA becomes a protein, specifically the steps where codons code for certain amino acids. What are the advantages/disadvantages for having several different combinations of codons code for the same amino acid? How can this redundancy lead to an advantageous, naturally-selected trait?

Inserted Genes

On page 99, Carroll mentions that process of finding species' relationships by the "study of...certain landmarks in specific places in species DNA", which are the result of "accidental insertions of junk DNA sequences near genes". Discuss the types of genetic point mutations, their relation to landmark DNA sequences, and their contribution to the evolution of different species.

Vaccination's bad?

Examine how, on pages 231-232, Carroll explores the applications of the themes of biology in common arguments against vaccination and provide background information backed refutations to some of the points.

Venom Varieties

On pages 153-154 Carroll discusses potassium channel blocking venoms in organisms from 4 different phyla. How can these different venoms with such different compositions have evolved into these separate phyla of organisms to serve the same purpose? In what way does this phenomenon connect the organisms and tie them together in terms of their separate evolutions? If these organisms share the same means of getting food to survive and reproduce, how can you account for the differences that separated them into their phyla?

Visual adaptations

On page 55 Sean Carroll suggests that the white rump of certain pigeons distracts predators when executing an arial dive significantly enough to escape the diving path of the falcons. What are some other visual evolutionary adaptations that have allowed organisms in danger of predation to escape. Of these adaptations, other than distraction, how do these visual adaptations facilitate escape? (ex. Batesian mimicry)

Rhodopsin

On page 107, Carroll discusses the evolution of the detection of light, based on rhodopsin in terrestrial organisms versus organisms that live deep in the ocean. In the ocean-dwelling organisms, "blue-shifted" rhodopsin were found. Explain why this would be a selective advantage based on Carroll's brief explanation and other outside research. Also, discuss the research and experiments that were done to further understand the rhodopsin of deep-living creatures. Bring in other examples of experiments that were done on this topic and results that they found. Explain the differences found in terrestrial versus marine organisms, but then also explain the difference between deep-living and shallow-living marine organisms by using specific examples.

Thermus aquaticus

On page 70, Carroll writes "A heat-stable enzyme that could copy DNA at high temperatures was isolated from Thermus aquaticus. This enzyme led to the invention of a new, efficient, and very fast technique for the study of genes in any species. This technique catalyzed a vast expansion in the amount and diversity of DNA information that could be obtained from nature, as well as the creation of a multi-hundred-million-dollar market in DNA diagnostics and forensics." Discuss the impact of this enzyme and describe the technique created for the study of genes. What have we learned about DNA from this process? How is it used in DNA diagnostics and forensics? Use plenty of examples.

Neutral Theory

On page 66, Caroll introduces Mootoo Kimura's Neutral Theory, saying that "when two versions of a gene differ... the difference may be neutral, of no consequence to fitness." This may seem contradictory to the traditional view of mutations in natural selection, but it is not. Explain how a mutation could result in no change in fitness. Is it possible for a mutation that causes a change in phenotype to be neutral? And is it possible for a mutation that does not change the phenotype to affect fitness? Also, the Neutral Theory states that the majority of genetic variation within populations is due to these neutral mutations, not natural selection. Explain why this is.

Universal Code

On page 75, Carrroll writes "Much to our convenience, but also of profound evolutionary significance, this code is, with few minor exceptions, the same in every species (this is why bacteria can be used to produce human proteins for pharmaceutical use, such as insulin)." Explain in your own words, using outside sources as reference, the significance of the code for proteins being the same in every organism. Also find examples of other organisms used to produce other proteins and the significance of those manufactured proteins.

Any Means Necessary

Carrol discusses on page 186 how natural selection does not create the most efficient solution possible but rather "works with whatever materials are available." In the example of the ice fish, the loss of red blood cells was seen as an advantage in the survival of the species in their surroundings, but there was also the disadvantage of having the red blood cell gene fossilized, making the process almost irreversible. The reasoning given by Carroll is that mutations are "all a matter of the immediate benefits outweighing the immediate costs, if only by a slim margin." Give two examples of a species (at least one that was discussed in the book) that has evolved in a manner that may not be the most efficient. Discuss the advantages and disadvantages of the mutation and an alternate mutation that would have been more beneficial and explain why this was unable to occur. What caused the true mutation to occur even if there was a downfall? Discuss how if those mutations had been beneficial only by a slim margin at that time, how they are now affecting the species.

Icefish "antifreeze"

On pages 19-27, Carroll discusses the uniqueness of bloodless icefish and their invention of "antifreeze" proteins. These proteins lower the temperature at which water freezes. Using what we know of genetic engineering, specifically our class experiment in which we recombined bacterial DNA to include a jellyfish gene to cause the bacteria to glow in UV light and to be resistant to ampicillin, how might this unique icefish gene be an advantage in another organism? What adaptations does this organism have that allow it to survive without the antifreeze gene?

Making of Eukaryotic cells

On page 88 Carroll discusses the creation of eukaryotic cells. Explain how eukaryotic cells are a fussion of archaen bacteria and other prokaryotic bacteria. What are some of the traits that eukaryotes share with the ancestoral bacteria.

Smell

As Carroll points out on pgs127-129, many animals have a powerful sense of smell “used to find food, identify mates and offspring, and detect danger” (127). Describe how the different odors are detected and discriminated. Also talk about the olfactory gene and how it works, compare human’s olfactory genes to mice’s. And if possible, answer the questions of why have humans abandoned the use of such large fraction of odor receptors. In your response include the theory of evolution and relaxed selection.

Pigeons

On page 54, Carroll discusses the white rump of feathers between the base of the tail and the lower back on pigeons. The pigeons with the white rump made up 20% of the pigeon population but only 2% of the pigeons attacked by falcons. The white rump pigeons were targeted less and could escape the predators better then the normal pigeons. It is discussed that the white rump may be a distraction, and the white rump has happened through a mutation. What is another example of how a mutation has helped an organism? Is the organism going through natural selection due to this mutation such as the pigeons? Have any mutations helped humans, and can we see natural selection beginning to take place as well?

"Immortal"

What are immortal genes? What are some reasons why there may be genes that can stay the same for a long period of time? What are some functions of immortal genes? Why have these specific functions stayed the same over time? When the species differ how do the genes stay the same?

Arms race

On page 166 Carroll discusses the "evolutionary arms race," between the Oregon rough skinned newt and common garter snake. Explain what is meant by arms race, and explain how it applies to this situation. Also provide other examples of this evolutionary arms race, and can this possibly lead to changes in humans to try to match other species.

Human eyes

On page 95 Carroll talks about spectral tuning of the human eye in the retina. Explain how spectral tuning works, and the different wavelenghts it applies to. Also explain why it was a selective advantage for humans not to be able to detect UV lighting, but for other animals a selective advantage.

UV vision

On pages 110-113 Carroll talks about UV vision, especially among birds. Carroll says that “a single change may alter the function of the SWS opsin” (111). In your response explain what SWS opsin is and how it relates to UV vision. Also explain the importance of UV vision. Talk about the serine and cysteine amino acids and what will happen when they are replaced with one another. What other species use UV vision and how does it differ from the UV vision in birds?

What's in a tree of life?

On page 87, Carroll depicts a conventional tree of life. On page 89, he depicts a new tree of life. What are the fundamental differences between these two models of the history of life? How are they the same? How were these trees developed? What do "immortal genes" have to do with the classifications?

Sexual Selection

On page 109, Carroll mentions Darwin's theory of "sexual selection." Compare and contrast this theory with the theory of natural selection. Explain how the two fit together and give examples of each. Explain why "biologists view sexual selection as one of the most important... forces in the evolution of animals," (109).

If you can't take the heat...

On page 69, Carroll talks about the hot springs of Yellowstone National Park and one of its inhabitants, the Thermus aquaticus. He notes that the Thermus aquaticus's habitat is made up of water with a temperature of 163 degrees Fahrenheit! Although he does state the benefit made possible to us (think PCR), he neglects to mention the type of life forced to live by the bacterium itself. How does such a high temperature help it? How does it hurt it? If removed from its current habitat and placed into a much colder one, how would this affect the way the Thermus aquaticus is forced to live (what kind of changes in its lifestyle would it be forced to undertake)?

On page 136. Carroll states that "the making of the fittest is not necessarily a "progressive," additive process." This can be seen in the loss of the blood cells in the icefish that its ancestors had. He also states that there is a "pattern of gain and loss" seen in species' DNA due to natural selection. How can this be seen in other organisms? Why and how is Carroll's statement true? How does the environment affect this "pattern of gain and loss"?

eyes

On page 194 Carroll examines the large differences in eyes of different species, mainly the single lens human eye, the compound eye of many arthropods, and the three eye system of scallops and clams. Explain how each eye system works and how it is beneficial to each organism. Also think about if there is any change that could happen to any organism eye including structure and placement and explain the possible changes.

Blind mole rats and senses

On page 126, Carroll discusses that the blind mole rat's lifestyle has caused evolution to create disproportional eyes that are covered with a layer of skin and fur, and the adaptations the blind mole rat has made in order to tell what time of day it is. Discuss how the mutation in the opsin gene has caused different lifestyles in animals (page 124). Also, if a human is blind (not because of evolution and their lifestyle, but by a random mutation or event) do their other senses work to tell the time of day (like the blind mole rat)? For example, is their sense of smell greater then those of a normal person? Also, Carroll mentions that our ancestors had a much greater sense of smell, what are some reasons this may be? What factors, do you believe, in our everyday lives will affect our future descendents?

Fossil Genes: Cause or Effect?

On page 133, Carroll explains that the fossilization of genes can be a "cause of evolutionary change" or an "effect." Explain what is meant by these two statements. In your response, provide examples of the fossilization of genes in both instances. Please use examples from outside of the text.

Galactose pathway

On page 130, Carroll mentions the fungus S. kudriavzevii. It is a prime example of the fossilization of genes. In this species, the galactose pathway is entirely fossilized. Please explain the role of galactose pathway in the organisms that utilize it. Include in your response an explanation of feedback mechanisms, proteins, and genes involved in the pathway. In other words, how does it work? Additionally, explain why this pathway is no longer under intense selection in S. kudriavzevii.

Opsins

On page 95, Carroll discusses opsins in humans. Humans have three opsins that are sensitive to different wavelengths of light. Birds and fish have four opsins and most mammals only have two. Why would birds and fish need more opsins compared to the three opsins humans have? What is the role of the opsin gene? Could natural selection have affected the numbers of opsins? If so, then how.

Nocturnal Species

On page 124, Carroll discusses the absense of the opsin gene in higher primates. Many times, these species evolve to become colorblind or nocturnal. Discuss Carroll's findings and do some research of your own to find examples and reasons for this. Also, research the SWS opsin gene and the mutations in the genes that may cause nocturnality. There has been a clear link between nocturnality and SWS opsin. Research this and discuss the examples that Carroll uses while bringing in your own.

Skin Color

On page 171, Carroll discusses melanin and its affect on the skin color. How does melanin interact with other hormones (feedback mechanisms)and what is its job in humans? Also, what effect does melanin have on mutations in humans? If UV radiation is so bad, why would natural selection promote our melanin pigments? Also, how does melanin affect vitamin D production in the body?

Genetics and gene expression

On page 47 of the book, Carroll shows William Castle's experiment of selection on coat color in rats. Castle states that many genes were modifying the fur patterns of the rats and creating a continuous gradation of variation. Describe the process of gene inheritance and expression that allows for this modification of fur patterns in rats in great detail. (Hint: DNA replication enzymes, promoters, meiosis, linked genes, law of independent assortment, law of segregation, DNA translation, transcription, RNA, ribosome, etc.) How can genes that are naturally selected pass on to other generations?

Senses and Fossil Genes

In Carroll’s discussion of fossil genes, he talks about the reduced reliance of humans on their sense of smell due to the evolution of trichromatic vision. The TRPC2 gene that controls the vomeronasal organ function and the V1r olfactory genes have been fossilized in the human genome. Discuss some other senses that have been relied upon less by organisms with trichromatic vision. What genes have been fossilized to lead to the reduction in reliance on the various senses? Mention the role of mutation and natural selection in gene fossilization as it relates to decreased reliance of certain senses in these organisms.

In the beginning of chapter 4, Carroll describes how colobus monkeys and chimpanzees use their sense of vision to find food and how the trichromatic vision of colobus monkeys allows them to select red leaves that are generally tender and young. What are other types of distinctions in the senses that give some organisms an advantage over others lacking this adaptation? Be sure to explain how this distinction within a sense has evolved and how it gives an organism a competitive advantage over another organism lacking this trait.

different paths to similair ends

On pages 146-147 Carroll discusses how Jianzhi Zhang had found groups of monkeys in both Africa and Asia that evolved rumination. When taking a closer look into the similarities of the different monkeys from different parts of the world, Zhang found that "the duplication of ribonuclease genes occurred at different times and produced different numbers of ribonucleases...several of the exact same changes subsequently occurred." Even after calculating the probability in which this same mutation would occur they found that it was a slim chance. Discuss how these almost identical changes occurred at two different locations a two unconnected monkey species. Include information on the probability of a certain mutation occurring(57-62) and how natural selection plays a role in allowing this all to happen. Also discuss when fossilization of a gene occurs in different species at different times and give examples. Connect both of the above to the theme of interdependence of nature and how the surrounding environment may have manipulated these changes.

Colobus Monkey's Digestion

In the very beginning of Chapter 4, Carroll explained that "bacteria in the [colobus monkey's] gut help to digest the large bolus of leaves as it travels slowly through his digestive system, and unique enzymes break down key nutrients that are released from the bacteria". Discuss whether this is an example of a symbiotic relationship. If no, explain why. If yes, explain why it is and what type of symbiotic relationship this is.
Follow up question: name and explain the different types of symbiotic relationships with a clear and understandable example of each type. Furthermore, discuss in what ways each organism is benefitting (or not benefitting) through the relationship.

Great diversity of Fruit fly wing patterns

On page 209, there are numerous pictures of Fruit fly wing patterns. Explain the uses of these patterns and how evolutionary process led to the great diversity of wing patterns. Describe how these wing patterns of Fruit fly is connected to the evolution of fruit flies.

Fossilization of Organs

On page 129, Carroll writes about "when an entire organ or process falls into disuse". This would include very relaxed selection and extreme fossilization in which entire processes would stop to be included in future organisms. What is an example of an organism that had an entire ORGAN fossilized? What is an example of an organisms in which an important PROCESS fell into disuse and was therefor fossilized? How is this possible? Relate this to themes of Evolution and Natural Selection.

Applications of extremophiles

Carroll discusses microbiologist Tom Brock's discovery of Thermus aquaticus in the beginning of chapter 3 and the subsequent creation of a new domain called Archaea. Thermus aquaticus live in "smoky, acidic, boiling" hot springs of Yellowstone park and have led to the scientific study of hyperthermophiles, or lovers of extremely high temperatures. What other types of extremophiles have had the same amount of practical success that Thermus aquaticus has had in the field of DNA diagnostics and forensics? Include examples and descriptions of other types of extremophiles and explain any scientific or real world applications that they may have.

Microbes exchanging genes

On page 85 of the book, Carroll states that microbes exchange genes, and some microbes live within other host species in a process called endosymbiosis. What is the advantage or benefit of exchanging genes? What are the advantages and disadvantages of living in a host species? Describe in detail how the microbes exchange genes with other organisms. Also provide specific examples of a microbe acquiring a certain gene from an outside environment or organism and the selective advantage this provides.

The Evolution of Genes that Have Simmilar Effects, but Different Amino Acid Sequences

On page 154, Carroll discuses how four different venoms, from four different animals of four different phyla, evolved to function in the same way, even though their amino acid sequences differed. Discuss other examples in which multiple animals evolved to have genes that all produced a similar result, even though the amino acid sequences differed. Also discuss the environmental stressors that led to the said gene being a selective advantage.

Diseases Causing a Selective Advantage

On page 176, Carroll talks about malaria, and how it has caused the sickle cell trait to become a selective advantage, as those with the sickle cell condition are somewhat resistant to malaria. Describe other instances in which widespread diseases have caused selective advantages in certain populations. Your discussion does not have to be limited to human examples.

FLOWERS

Carroll states on pg 133-134 that flower color is determined by both “evolutionary change brought by natural selection” and by “a by-product of natural selection for other features”. What exactly does Carroll mean by this, and what are the reasons for changes in flower color? In your response also include how flower color is determined and how different enzymes produce different colored flowers, give examples. Also explain why is the evolution of the red flower more adaptive? In your response include the theories of evolution and natural selection.

Intelligent Life

In his book, Carroll repeatedly connects environmental factors to the biological adaptations they promote. After enough time, he claims, the chance of an adaptation with a selective advantage evolving increases. It is through the build-up of these chance mutations that the diverse life on Earth that we have today arose. And then came Homo sapiens. Is it possible that the evolution of the single most dominating organism to walk the planet brought with it the downfall of evolution itself. In theory, if just being a human is a selective advantage, and physiological traits really don't factor into offspring survival rates, then won't humans have reached an end in their evolutionary road. Discuss if this is truly possible and if not, why is this not possible? Also, what were the events in our planet's history that set up the development of Homo sapiens? Under what conditions did we develop the selective traits that we have today? Finally, is it possible for another intelligent organism to develop such as ourselves independently from another origin, such as the case of the multiple developments of potassium channel blocking neurotoxins around the world?

puffer fish and humans

Carroll compares the genes in the DNA of puffer fish and humans finding 7350 genes that are similar within the two species and that the proteins that these genes code for are on average 61% identical. With this comparison it can be seen that it is not a mere coincidence but that immortal genes play a role in creating a core set that is required for survival. Discuss what these genes are and how they have survived throughout history. It also discusses that they are not prone to mutations. Discuss how the genes have adapted to mutations and the variety that now exists for certain genes. Give specific examples of immortal genes and discuss their purpose and why they are so crucial. Discuss what qualities these genes may play in survival in species that are so different and live in completely different environments [ puffer fish compared to humans].

The Evolution of Skin Color

Carroll, on page 168, brings up the question of whether skin color is a product of evolution, or just a characteristic that people in the same region share. Discuss Carroll's view on this, as well as your own by bringing in examples. Carroll also mentions the works of William Charles Wells and Charles Darwin. Using their examples, and outside research, discuss the changes in skin color over different parts of the world. Compare this to what Carroll has said about evolution and natural selection, as well as the selective advantage of different skin pigmentation.

Cancer treatments

On page 184, Carroll discusses the development of cancer treatments, specifically the evolution from broad treatments such as chemotherapy, that simply kill the cells in a target area, to more specific treatments that attempt to combat the genetic issues with cancer cells. He also discuses how these drugs can cause the selection for resistant strains of cancer cells. Give and discuss examples of the new generation of cancer drugs, as well as adaptations that scientists used to overcome the issue of resistance.

The Chain Reaction

On page 261, Carroll talks about how humans have influenced the destruction of entire ecosystems indirectly and directly. Carroll specifically talked about how overfishing has affected “complex webs of interactions (261). Can you go into more detail of how the disappearance of one species from an ecosystem can affect a complex web? Be sure to include information about trophic levels in the food chain. Also be sure to address the balance preserved by different species i.e. the lynx and the hare. Also address other ways humans have influenced the ecosystem other than overfishing.

Vaccination

Vaccinations, after application to the recipient, ostensibly remove any chance of contracting the targeted virus, such as polio, flu, etc. However, as recently last decade, the effectiveness of vaccines was questioned, as Carroll cites a 1994 survey of 171 chiropractors, who stated their belief that there was no proof as to the validity of the vaccination process and a 1998 survey of Boston chiropractors, a third of whom did not support prescribing vaccines for their patients. This brings up the questions: What are the benefits of vaccines? How do they work? What are the arguments against them not stated by Carroll? Of the ones listed by Carroll, which are valid concerns? Which aren't? Are there any potential vaccines on the horizon?

Evo Devo

Evolutionary development is a very important field of biology because it is now beginning to answer some of the main questions about the diversity of organisms and how such complex organisms such as humans have developed. Many people can comprehend how an organism might make its sight better to meet certain circumstances, but then they might wonder, “How does an organism, through a random mutation, end up with a complete eye? Or a brain?” Afterall, haven’t we been constantly taught in this book that natural selection acts on very small differences to create changes in one trait at a time in an organism? Use the development of the eye as an example of how a single mutation doesn’t account for a complex structure, but rather the accumulation of such mutations. Explain the complete development and differentiation of the eye in different organism. Second, we have also learned that beneficial mutations are rare in occurring, but with enough time they will most likely occur. If we need a whole series of mutations to occur, then the chances that the same complex structures develop from scratch independently among different species is very rare. What actually does happen that accounts for multiple species having similar complex structures? Once again, use the development of the eye to answer the question.

Pax-6 gene

On page 194, Carroll talks about how different eye structures did not independently evolve multiple times, but rather they all stem from the same eye-building gene, known as the Pax-6 gene. A common ancestor of animals with the Pax-6 gene used the gene in the development of a primitive eye, and its descendents' eyes became different as time progressed. According to Carroll, this Pax-6 gene is responsible for eye development in a humongous amount of animals, including humans, fruit flies, mice, squids, planarians, and ribbon worms. Besides animals without eyes, do some animals NOT have the Pax-6 gene? Is there another gene in the animal kingdom that is responsible for eye development? If there is, how do the eyes of those animals differ than the eyes of animals with the Pax-6 gene?

Old vs. New

One aspect of the book that I never really figured out was the difference between Old World and New World monkeys. They were mentioned a couple of times throughout the book. In the beginning of Chapter 4, Carroll mentions that Old World monkeys were African and Asian (p 92). Go into more detail about the difference between the Old and New World monkeys - where are they from, how are the classified, why are they called this, what do the eat, look like, etc. Use examples both from the book and outside sources.

Vaccination - Does It Really Work?

In Chapter 9, there is a section titled, “Spinal Crackers” (Carroll 228). The section concentrates on chiropractors and their various beliefs on medicine. Carroll specifically focuses on the fact that chiropractors do not believe in vaccination. “A 1994 survey of 171 chiropractors reported that one-third believed there was no scientific proof that immunization prevents disease.” (Carroll 230). My question is is this actually true? With so much emphasis on the importance of vaccination and vaccination requirements in schools it would appear that they are successful otherwise why would they be a requirement? Find evidence that vaccinations do, in fact, work or find evidence in support of the chiropractors that shows that vaccinations may not be as effective as commonly thought.

Cancer

On pages 182-185 it talks about evolution in nature that causes mutations like cancer. How is cancer formed and what is metastasis and how does it connect to evolution? Include some of the drugs that treat cancer, and give a specific example from the book and discuss how the drug works. In your discussion talk about the resistance patients evolve to these drugs and what can be done to limit the resistance. You may want to include some of the biological themes like evolution and emergent properties and talk about how the current research will lead to future medicines and therapy dealing with cancer.

Climate Changes

On pages 251-252, Carroll talks about the great diversity of flora/fauna and other animal species that inhabited the area known today as Wyoming approximately 40 million to 50 million years ago, as he tells us of Ferdinand Hayden's correct conclusions that "what is now a semiarid desert of flat-topped buttes and badlands was once a lush tropical forest, with a climate and flora much like the southeastern United States today. " (251) He states that this dramatic change was a result of severe climate changes. What kind of climate change is he talking about? Why did this not affect he southeastern United States? With the current situtation regarding global warming, is it possible that we could view dramatic changes like this again? What kind of changes?

environemntal effects

Selective advantage is one of the major reasons of evolution and adaptations in allowing for survival. In accordance to the ecosystem of a species, adaptations occur in correlation to certain threats that may be present. The surrounding environment or other species that are present in the ecosystem may both play roles in selective advantage. Give examples from the text of both the effects of environment and other species of the ecosystem. Also discuss how selective advantage and survival of the fittest play roles in certain characteristics that each organism portrays. Discuss the effects that humans may play on the survival of each of these animals.

Nocturnal Monkeys

On pages 124-127 Carroll talks about how the opsin gene, in owl monkeys, seemed to have "accumulated mutations that render it nonfunctional" (124) and render the monkey color blind. This is due to a lifestyle that the owl monkeys have adapted? What other types of monkeys or similar creatures, who are closely related, also adapted this nonfunctional opsin gene? What kind of interaction with its environment caused this to occur? How exactly can this gene be deemed fossilized and nonfunctional (what kind of a change in genetic code)? Furthermore all these point that a relaxation of a certain gene will lead to its decay. How is this related to us human? What gene or organ, might I say, has become almost nonessential because of our loss of use for it and what was its previous purpose and why dont we need it anymore?

Regulatory DNA

On page 206, Sean Carroll discusses the various parts of genes. “In addition to the coding part of a gene, every gene also contains noncoding DNA sequences that are regulatory,” (Carroll 206). Discuss how these regulatory sections of DNA work – where they are located, how they are formed, how are they turned on and off, etc. In the book, Carroll talks about these regulatory genes in relation to the pelvic spines in stickleback fish. What other examples of organisms can you find in which regulatory genes play a role?

Genealogical Trees?

Why is it so important from a scientific standpoint to have genealogical trees? Scientists have spent hundreds of years slaving over newer and better methods to categorize all organisms into groups. Why is it so important? Examine the different attempts over the years to create trees. How are they different and similar? How are the organisms categorized in each tree, and why is it significant? Discuss terms like kingdom, domain, etc and discuss what they mean.

The Source Of All Variety Is Mutation

On page 57, Carroll starts his discussion of how traits are worked into genes because of their selective advantage to the species. According to Carroll, selective advantages become dominant because of mutations that occur sometimes one in a billion in one organism's DNA. This mutation can lead to a successful trait that gave the organism an advantage over others. Therefore, over time, the gene became dominant in the species. Explain this process. How does one single mutation turn into a dominant trait that every member of the species has? How long does it take for these traits to spread? How many mutations must occur before the gene is seen regularly? Finally, discuss the spread of different traits and the varying ways they can spread. For example, is there a difference between the way hair color (for hiding from predators) versus immunity (to a deathly disease) spreads? Does one take longer to catch on than the other? Do they become regular traits in different ways?

Independent Convergence

Carroll believes that the strongest evidence for the process of natural selection is the idea behind independent convergence. On pages 155-163, Carroll describes more of the mathematics of mutations and why it is very credible that species can independently produce the exact same mutations. What is independent convergence and why does it happen? What is the difference between two species that have independently evolved a trait and two species that both received it from the same ancestor. What are two methods that scientists can use to determine which of these two cases happened between different species? Provide an example from the text. Finally, and most importantly, why is independent convergence among species the most convincing evidence for natural selection? (In other words, why is it more convincing to show that two species found the same solution to the same problem rather than showing one species found a solution to its problem). To answer the last part, it's necessary to explain the three recurring "ingredients" of evolution. Explaining the two independent convergences as two trials of an experiment might make it much easier to explain your argument.

Return to Bouvet Island

From page 264-266, Carroll discuses the potential causes of dwindling numbers of krill, which is used as an important source of food and feed. Among these reasons the most prominent are overfishing and temperature increase in the arctic. Explain how each of these reasons affect the krill population. Also how may these factors play in the population of icefish that were discussed in pages 19-27. Discuss how temperature rise may be catastrophic for these fish and their hemoglobin free blood.

Fitting into the World

Humans are a diverse bunch. In the section Man Against the Sun, Carroll discusses skin color in the genetic sense. Why did skin color and hair color adapt the way it did to help Europeans, Africans, Indians, Asians, and Hispanics in their respective climates? Explain what helps absorb light rays, relating back to hormones and the endocrine system. What other features could be explained by adaption to the climate? Do these also have a genetic backing? Explain.

The Evolutionary Arms Race

At the beginning of Chapter 7, Carroll discusses the Oregon rough-skinned newt, an animal which has developed the ability to produce the TTX poison. Carroll also mentions that this happens in the puffer fish as well. Why do animals such as these develop poison instead of adapting other techniques? Where else have we seen the development of poison inside a species outside of that mentioned? Where has the predator of these animals developed resistance to the poison, and what was the next step those animals took? What are some other techniques used for survial that we've learned about?

Complexity in Fruit Fly Wing Patterns

On page 208, Carroll notes that the “fruit fly Drosophila melanogastor has pale wings but its many cousins in the large family to which it belongs display a great variety of black pigment patterns”. Explain the pigment pattern and the purpose it serves. Additionally, explain how the diversity in fruit fly wing patterns are created using Figure 8.8 on page 211.

Even though Allison is his last name I keep thinking its a girl!

On Page 174 it talks about Allison's adventures in Africa experimenting with Sickle Cell Disease. So the question is... How does the shape of sickled cell affect its ability to resisit Malaria? So Basically how does the structure relate to its function? How does the passage of Malaria through the generations affect evolution? Are humans battling evolution for humans when they attempt to interfere with natural selection through pesticides and DDT, or are they catlayzing the evolution chain for mosquitos to become this super mosquito that is immune to everything but time? Is our interaction with the environment solely affecting mosquitos and humans or are they affecting other things too? What are the environmental casualties that were just caught in the cross fire between mosquitos and humans such as crops and plants? How are we affecting them and changing their evolutionary pace?

Wisdom Teeth

Humans have wisdom teeth, but it is clear that in today’s age there is no benefit of having these wisdom teeth come in, because our normal teeth do the job well enough. In fact, wisdom teeth coming in can actually be detrimental to other teeth. If this is true, why do we still have these teeth come up? Will humans lose these wisdom teeth over time? Discuss the loss of smell in humans and primates and how wisdom teeth might follow the same pathway. Also, is it possible that human actions are interfering with the process of natural selection to rid the human race from this harmful trait?

Overfishing and the Domino Effect

On page 261, the domino effect is mentioned. Explain what it is and how it connects to kelp deforestation. Also, mention overfishing and how it can affect the marine ecosystem. Why do/did people believe that the oceans were inexhaustible? Are there any specific examples of overfishing mentioned by Carroll?

DNA Record

On page 66, Carroll talks about how by examining DNA we can study the evolution changes in different species. Explain the details of this technology and discuss the science knowledge needed to do this type of experiment. Furthermore, explain the techniques used to determine how a species has evolved over time. Finally, discuss how technological advancement may or may not better the accuracy of DNA studies.

Ruminating Monkeys :D

On page 113, Sean Carroll talks about special digestive system of Colubus monkey. Compare and contrast the digestive tract of colubus monkey and human. Describe different digestive enzymes of Colubus monkey and explain how digestion is regulated in both human and the Monkey. Also, what is the selective advantage of Colobus monkeys as leaf-eaters?

Common ancestor

In chapter 3, Sean Carroll talks about Immortal genes that can be found in various organsims from different Kingdoms. What are some of examples of Immortal genes? Why are they so important that it never changes? From these immortal genes from different organsims, what can we conclude about LUCA( last universal common ancestor)?

Speed of evolution

Mr. Carroll makes it clear that natural selection happens gradually. Mutations occur randomly, and when they do occur it takes many generations to spread over the entire population. However, it is also clear that some mutations work their way into the population relatively quick. On page 56, he wrote that the development of armor plating in stickleback fish was "rapid". What determines the quickness of a mutation? Does the species it is occurring in matter? Does the mutation itself matter? Discuss generation times, different species, effectiveness of mutations, etc.

Sudden change in the sticklebacks

On pages 56-57, Carroll discusses the evolution of the stickleback fish. The original ocean form of the fish, he explains, usually has a "continuous row of more than 30 armor plate running from head to tail" and this long armor plate may not be as good for maneuvering in water in contrast to shorter armor plates. He latter explains that in a short span of 11 years (1990-2001), the long armored sticklebacks in Loberg Lake, Alaska, are declining at a rapid rate while the other form, ones with shorter armor plates, are rising in surprising numbers. My question is, why would it be advantageous to have short armor plates in lake water because I would assume that there are more dangerous predators in the ocean, thus the sticklebacks would be expected to have short armor plates in the ocean and long armor plates in lakes. Furthermore, explain how such a rapid evolution is possible and the possibility that this observation isn't really an evolution, but rather a raise in one species and a decline in another.

Fossil Genes

On page 134, Rebecca Zufall and Mark Rausher showed that I. quamoclit has degenerated its pathway for making blue and purple. Why is this? Compare I. quamoclit to M. leprae (132) and discuss what happened to each. How does M. leprae relate to the “use it or lose it” rule (pg. 132)?

Are we evolving yet?

In page 58, Sean Carroll says " the rate of mutation has been carefully studied in many species, In humans, there are an estimated 175 new mutations among the 7 billion DNA letters in every individual" (58) It seems like DNA of humans are changing every seconds. Human population is keep rising and there are 6.7 billion of us right now. However, we hardly notice any changes. It seems like evolution has stopped for humans. We can easily see the process of evolution in rats or birds (ex)pg.55). Discuss promoting factors and limiting factors for evolution and explain why humans have stopped evolving. Surely, mutations are keep occuring, but why aren't we getting picked on by natural selection? You may need to explain carrying capacity and factors that maintain carrying capacity. Expalin how carrying capacity of humans differ from other animals and compare factors that maintain carrying capacity with factors that promotes evolution. On the other hand, you may prove that humans are keep evloving and that there are no organisms that completely stopped evolving. Use specific examples to support your arguments.

YES we are all mutants...

On page 57, Sean Carroll explains the importance of mutations in evolution. Discuss differences between mutaion and natural selections and how they affect the process of evolution. Give some examples of each process ( not from the book) Discuss how mutation and natural selection occurs and explain why we have misconseptions about mutation that all mutaions are bad. You may need to discuss the process of making DNA, RNA and proteins and the relationship between structure and function and fianlly, explain how this relates to survival and evolution.

The relation between primates and humans

A common misconception of people who gloss over the fundamentals of evolution is that humans are descendants of primates. Although we are not direct descendants of primates, according to the evolutionary tree of hominoids (figure 4.4 pg. 101), which solidifies what should be common knowledge, both primates and humans are descendants of a shared ancestor. Using figure 4.4 and the statistics provided regarding “DNA typing and hominoid evolution” (figure 4.3 pg. 100), analyze the ultimate causes of divergence presented by the tree. What is the correlation between the divergent structures of, for example, a human and chimp, and how do these disparities serve their function of improving fitness (in addition to the example provided regarding trichromatic/dichromatic vision). Is there a particular region of DNA that has been continually modified to give rise to these adaptations, or is it dispersed? Is there some sort of pattern to proportionally how far away the genetic information is from the centromere that organizes the divisions of the tree? If not, what seems like a proper estimate of how far the genetic code should be from the centromere on a chromosome to facilitate the changes seen? What characteristics would make-up the genetic code of the shared ancestor of both the primate and humans? Is there a key redundancy in the genetic code that unifies the branches of the tree while still providing the “wiggle room” for evolution of structure and function?

The organization of life and mutations

One of the major themes of biology is that the properties of life emerge from the hierarchical organization of life: progress is a consequence of more complex organization. However, chapter 2 of the book , which focuses on the “holy trinity” of evolution (chance, selection, and time), makes it seem as though natural selection contradicts this theme because it is based on random mutations to further development. Carroll attempts to reject this contradiction by stating that “Mutation generates random variation, selection sorts out the winners and losers” (57). Explain how the coupling between mutation and selection reinforces the first theme of biology rather than rejects the first theme of biology. What examples does Carroll provide to help expand and explain the correlation presented in his statement on pg. 57? How do LINES and SINES represent the organization of randomness? How does the interplay, or exclusiveness, of fossil and immortal genes reflect organization? How do introns/exons, tandem repeats, and redundancy in the genetic code represent that natural selection harnesses the randomness of mutations to fuel the organization of life?

Ultraviolet Rays

On page 91, Carroll states that humans cannot see the ultraviolet range of colors. Why is this? Why is it a selective advantage for us humans to not be able to see in that range of colors? Why can birds and insects see it? Discuss the properties of ultraviolet light and how it helps birds and insects, as well as why it wouldn't help for humans.

Bighorn Sheep and Unnatural Selection

On page 254, Sean Carroll talks about the bighorn ram. Female bighorn sheep desire male bighorn sheep with the largest horns; bighorn sheep grow their horns usually between the ages of two and four years old. However, “rams at on locale in the Canadian Rockies have shown a marked downward trend in their “breeding value”” (255). Why is this happening? How would this be a selective advantage to the bighorn ram? Are there any other examples in the book or otherwise that is similar to this (where an outside factor/group affects a species)?

Melanic Moths

On page 52, Carroll gave a brief discussion of the melanic moths and how the lighter populations were slowly declining due to air pollution. At the same time, "there was a dramatic, rapid increase in the frequency of dark, melonic forms of the moth in industrial areas" (Carroll 52). Discuss why it would be advantageous for the moths to appear darker in polluted, industrial areas. Furthermore, discuss the probable changes in the local environment (populations of other species, not necessarily moths but birds or other animals) and possible dangers of this sudden change in nature. If possible, relate to biological themes and outside resources.

Selective Advantage

The Antarctic icefish have gone through various adaptations that allow them to survive in freezing temperature such as the modification of proteins that develop microtubules stable in freezing temperature. What would happen if the icefish was removed from its environment and placed in a warmer environment? What effects would occur to the icefish's distinct cardiovascular system? How would the advantages that allowed them to survive in the Antarctic environment become a disadvantage in the warmer environment?

Gleevecs

On p. 183, Carroll describes Gleevec or Imatinib, a drug that inhibits the ABL kinase protein by binding to it, like a toxin. Describe what happened to the effectiveness of the drug, why this happened, how and where we've seen this before, both in the book and in class, and then describe some future treatments that are possible for cancer, and explain how they would overcome the problems described.

Senses

On page 128 Carroll speaks of the relationship between sense of smell and sight, stating that there is a "striking correlation between the proportion of fossilized olfactory receptor genes and the evolution of full color vision" and that " the evolution of trichromatic vision has reduced their reliance on the sense of smell". My question is whether or not there are any other correlations between other senses and their intensity, perhaps a reason for the differences in hearing amongst species?

Ice Fish and Hemoglobin

On page 24, Carroll says that ice fish “[eliminated] red blood cells altogether”. This means that there is no hemoglobin because erythrocytes contain about 250 million molecules of hemoglobin each. What key roles do red blood cells have that ice fish now lost or have to make up for? Also, if there is no hemoglobin, oxygen cannot attach and be carried throughout the body. How does the ice fish make up for this substantial lack of oxygen? How does it get enough oxygen to the tail and other parts for cellular respiration to occur? How is the ice fish’s environment advantageous for obtaining oxygen?