Birdy

Coyne offers evidence for evolutions side against creationists that wing development would be a disadvantage rather than an advantage. He states that process would be simple, from the gliding step to the flapping of such wings to be able to fly. He offers proof in the form of the Archaeopteryx, which possesses large feathers and an opposable toe. Why would the development of feathers appear; Coyne says for insulation likely but wouldn't fur act as an equally efficient insulator and also not get in the way rather than large feathers, which would also create wind resistance to slow down the Archeopteryx from running? Also, it is necessary to have enough feathers in proportion to body weight to even glide an effective distance to escape from predators. Is it a possibility that such feather mass appeared simply through evolution for insulation? Offer evidence which provides for a stronger argument for evolution of birds and refute the claims made above.

Simplicity

When a population's traits gradually revert to a past form, some consider it to be Devolution. An example of this is mammals going back to water (47). Coyne also notes that some populations experience little/no change over long periods of time. Horseshoe crabs and gingko trees have barely changed at all (4). As we trace the fossil record, we see the appearance of increasingly complex organisms. However, we often still see the simplest organisms thriving.

What are some living organisms that have simple anatomy. Why would there be a selective advantage for simplicity? How does the organisms rudimentary make-up affect structure and function of its biological mechanisms? How does the simplicity affect the evolution of its population (past, present, future)?

Why Devolution?

On page 51, Coyne makes observations on the 'devolution' of whales; the process in which a potential land dweller returned to an aquatic habitat. At that point, however, it was highly likely that the land animals had sustained a reliable food source and was able to survive effectively. Even with the dying off of aquatic predators, why would natural selection favor the return to the water? Also, how would this 'devolution' progress? Air breathing evolved from lack of oxygen in water and mutations to be able to extract oxygen from the air. What are some adaptations that allow a land dweller that moved into the water to be able to conserve oxygen from air while underwater?

Future of Antibiotics

Monsieur Coyne has a section in his book that explains how antibiotics are losing their edge to the bacteria that they were designed to kill. For example, in 1941, penicillin was able to "wipe out every strain of staph in the world," yet now, "more than 95 percent of staph strains are resistant to penicillin (131). Tuberculosis is making a comeback, as are other types of bacteria.
What does this mean for the future of medicine? Will antibiotics become obsolete? Is it feasible to ban their use or only use them in certain situations to prolong the effectiveness they still have? What other kinds of medicines are being developed to fight bacteria while antibiotics lose their power? Research, and I implore you to post your findings in response to this post.

Evolution of Eye

Señor Coyne explains that the bacterial flagellum, "is composed of dozens of separate proteins, all of which must work in concert for the hairlike 'propellor' to move" (137). The link below is a diagram of what it looks like. This is an apparatus that demonstrates such complexity that creationists use it as a "poster-flagellum" to demonstrate the case that evolution can't produce all things. Yet evolutionists have shown that this development is "feasible". (138) Research the leading theory on how this motor evolved to the complex structure it is today, and report your findings here. Also, can you think of any other structures that ID proponents would be eager to use as "proof" of intelligent design? Examples from the book included: the human brain, eyeball, and blood-clotting chain.

http://www2.sad42.k12.me.us/teachers/lowell/7_grade_science/cell/Image5.jpg

Deadly Vestiges

Stephen Jay Gould describes vestiges as "senseless signs of history" (56). Vestigial traits demonstrate long lasting evolutionary relationships. Coyne describes many examples such as flightless birds having wings, sightless mole rats that have remnants of eyes, and whales that have leg bones. Humans also have vestiges such as the coccyx. These are all quirks that provide a solid argument for evolution. However, some of our vestiges are not just "quirky". Appendixes can rupture. Wisdom teeth can become infected. These medical issues usually become hazardous later in a person's life (after they have passed on their genes).

Can you name any other deadly vestiges in humans or in other organisms? What are the possible evolutionary histories behind them? How do they affect the organisms ability to survive and reproduce? How may it be considered an evolutionary "roadblock"?
Feel free to discus wisdom teeth or the appendix.

Palimpests in Embryos

On page 55 Coyne describes how manuscripts were made in medieval Europe. They would write on thin sheets of dried animal skin. "Because these were hard to produce, many medieval writers simply reused earlier texts by scraping off the old words and writing on the newly cleaned pages" (55). These were called palimpsests. How do these palimpsests relate to the theory of evolution and natural selection? More specifically how do palimpsests relate to embryos? See page 73, and explain how embryos are similar and different, and at what times of development these similarities and differences occur (use this to answer the question as to how palimpsests relate to embryos).

From Water to Land

On page 35 Coyne begins to describe the transition of organisms from water to land (more specifically from fish to amphibians). What adaptations, through natural selection, occurred to the organisms to better suit survival on land? What were the selective advantages to living on land instead of in the water? Neil Shubin, and his team, unveiled the discovery of the Tiktaalik roseae in 2006 in the Canadian Arctic (http://tiktaalik.uchicago.edu/index.html). How does this discovery tie into the transition from fish to amphibians?

After Reproductive Age

Jerry Coyne sadly reiterates how humans have acquired traits via evolution that encourage reproduction yet may produce a bad effect on us after reproductive age. This is why we "('senesce') as we reach old age." (120) This explains why people that are genetically prone to have heart disease, for instance, are still able to pass on their genes just as well as others. Heart diseases generally only prove fatal in the late middle ages, after reproductive age has passed. Because we have the medicine to postpone many of our diseases until after reproductive age, is it reasonable to assume that we are losing our tough, evolutionary edge? Why or why not? Also, what other traits help us "sow [our] wild oats when young" while proving to be annoyances later on, besides Coyne's examples of wrinkles and an enlarged prostate? (121)

Evolution of worker bee gang defense

On page 112, Jerry Coyne highlights the mechanisms involved with the battle between the Asian Giant Hornets and the honeybee colonies. As their only defense, the bees are able to "quickly raise the temperature inside the ball to about 117 degrees Fahrenheit," all by "vibrating their abdomens." (112) Coyne goes on to say that this behavior is encoded "in a brain smaller than a pencil point." (113) It is obvious that the hornets evolved to acquire their aggressive behavior before the bees needed their defense against that specific action, yet the bees' maneuver is so complex and genius that even an expert in evolution would have trouble decoding the steps needed in the evolution of that behavior. "Bee" the evolution expert, and put forth what you think is the most logical series of evolutionary improvements and milestones in bee behavior that all culminates in their current defensive maneuver of creating a vibrating oven.

Gene Culture Coevolution

On page 215, Coyne explains "gene-culture coevolution." Explain the relationship between human culture and how it has come to affect our genes. Also, gene-culture coevolution has already changed our genes, sometimes for the worse. Coyne points out several examples of incidences in which we have "de-evolved." Explain this occurrence. Is gene-culture coevolution affecting natural selection and our ability to evolve? Will we continue evolving in the future, even though our culture may alter evolutionary pressures?

Homo floresienses

Coyne talks about Homo floresiensis on page 207. They were the only population of earlier hominins not suddenly replaced by H. sapiens about 300,000 years ago. The two theories used to explain this sudden replacement are the "multiregional" theory and the "out of Africa" theory (see page 206). Under the "multiregional" theory, why didn't Homo floresiensis too evolve into H. sapiens? Under the "out of Africa" theory, what conditions could of allowed Homo floresiensis to reach the island of Flores in Indonesia, but then prevented H. sapiens from reaching the same island and replacing the Homo floresiensis?
Also, Coyne mentioned that Homo floresiensis may have preyed on Komodo dragons. How could a species that is so closely related to us as to be in the same genus, eat something that is so poisonous to us now?

plant evolution

Most of the evidence Coyne uses in the book to prove evolution as true has to do with animals. For instance, evidence he uses deals with the fossils of animals, the embryos of animals, etc... to prove his point. How come Coyne didn't use more examples relating to plants in his book? On the other hand, how did he use plant examples in his book to prove evolution?
Also, Coyne says on pg 149 that features such as bright colors and ornaments in animals are molded by a type of sexual selection, mate choice. In plants, who can't choose mates, why did bright colors and ornaments evolve? Give specific examples of plants with bright colors/ornaments, and example why they adapted them.

Transitional Species, Ancestral Species, and Missing Links

Although it has been established that creationists believe in microevolution ("Minor changes in size and shape [that] occur over time" (33) ), creationists do not believe in macroevolution ("[When] one very different kind of animal or plant [comes] from another" (33) ). In proving macroevolution is true, scientists have looked to the fossil records. Compare, contrast, and provide examples of transitional species, ancestral species and missing links. How do those three terms relate to macroevolution? Which of the three terms is the hardest to find in the fossil record and why? Does a missing link have to look like an intermediate between the two species, why or why not?

The Battle of the Hominins

Fossil records give evidence that humans evolved from common ancestors with chimps. Several species of hominins arose from this common ancestor. H. erectus was the first species of hominin to leave Africa. "H. erectus was a highly successful species, not only in population size but in longevity. It was around for one and a half million years, disappearing from the fossil record about 300,000 years ago" (Coyne, 205). Also, it is thought to have left two decendents: H. heidelbergensis, and later H. neanderthalensis (around 230,000 years ago). Then, they disappeared around 28,000 years ago. Their disappearance is associated with the rise of another species: Homo sapiens. There are two theories surrounding the disappearance of the other hominins. Explain both the Multiregional theory and the Out of Africa theory. Also, describe the selective advantages of H. sapiens.

introduced species

We are always hearing about how introduced species have hurt native species, through either predation or competition. On the other hand, what are some examples of introduced species becoming victims of native species? (Hint: there is one such example in the book!). What are some examples of introduced species overall helping the native community? What are some examples of introduced species overall hurting the native community? Looking at these examples, do you think that we should continue to take it upon ourselves to introduce species, or should we be working to make sure that it stops happening? Also, could introduced species eventually be strong evidence for evolution a couple of hundred of years from now, if we start recording if and how they change to their new environments now?

why evolution is true

The back of the book says "Coyne does not aim to prove creationism wrong. Rather, by using irrefutable evidence, he sets out to prove evolution right." After reading the book, can you agree agree with that statement, or do you think that Coyne also used this book to point out holes in the creationist arguement? Remember to use examples from the book to support your opinion! Also, it's been over a year since this book has first been published (it was first published January 22, 2009). Has there been any scientific findings since then that if included in the book, would of helped Coyne's argument that evolution is true?

Convergent and Parallel Evolution

Divergent evolution is the most well known form of evolution - the evolution of one species into two distinctively different species. However, on page 91 Coyne mentions a wholly different form of evolution that caused the formation of similar body plans and physiological traits between succulents in North America and succulents in Old World deserts. This convergence to similar physical structures came as the result of similar environmental conditions and niches. Two modes of evolution that work in such a manner are Parallel Evolution and Convergent Evolution. What is the difference between these two forms of evolution? Provide examples of each.

Pass it on, or fail in life?

One of the primary reasons why an organism invests so much of their time and energy in reproducing is in order to pass on the genes to the next generations. And example experiment in explained in page 152-153 of Coyne's book. However, the question "If males with thiry-inch tails won more females, why haven't widowbirds evolved tails that long in the first place?" One of the answers to this question is longetivity. By investing energy in more survival, one many have find more partners. However, birds, such as peacocks, have many beings that go unmated to their deathbeds. Then comes the quesiton, why didn't the force of natural selection promote the elimination of organisms with such features? If organisms, such as peacocks, went unmated, shouldn't evolution have eliminated "unmating" genes? Why do such beings exist today?

Fossils, key to evidence of evolution

Coyne stated that "transitional species is not equivalent to an ancestral species; it is simply a species showing a mixture of traits from organisms that lived both before and after it." (35). Then simply, what does the transitional specie serve as? Also, why is it such a controversy when a transitional specie is found containing a features of two different species? Also what are the possible forces that drove an organism of the same specie to adapt one specific feature while giving up another feature?

Adaptive changes Vs. Random changes

Coyne states that "natural selection is the cause of all adaptive evolution." (143) It is certain that most people believe that natural selection is the driving force of evolution. However, other drivers such as genetic drift, can also change the course of evolution. According to the reading and any biological thoughts, in what situations would the force of natural selection prevail? What situations would give an advantage to genetic drift? If there was a specie that can survive perfectly in any, and all environments, would genetic drift help that being in anyway or is selectively and artificially preserving genetic code the way to be?

Modern evolution in humans

On page 218, Jerry Coyne asks the question "Are we still evolving?". Many types of natural selection are no longer existent because of modern nutrition, sanitation, and medical care. Are humans moving past natural selection with the use of technology? Are humans actually getting smarter and stronger or are we on a continuous path? Also, Coyne discusses how many genes have come full circle, genes that once were helpful to us are now hurting us in our modern world. So could this possibly mean that humans are backtracking, or "de-evolving" (219)?

Evolution of Sex

There is obvious "asymmetry between males and females" (Coyne 157) in the sexually reproducing world. Compare the male and female mating strategies of various species. Include both behaviors and anatomical features in your explanation. How does the idea of parental investment explain these stark differences between males and females?

Human Evolution

Jerry Coyne states on page 193 that "all creationists draw the line at humans. The gap between us and other primates, they say, was unbridgeable by evolution, and must therefore have involved an act of special creation." There has been myriad evidence discovered linking humans to apes (with a common ancestor) and that humans have evolved from an ape-like species, yet many still deny that humans have evolved from an ancestor that was very different. What are their reasonings and are they justified? or is it just the "natural solpsism that accompanies a self-conscious brain" (192)?

Genes for everything

To what extent our genes represent the totality of our behavior? There are many sociobiologists out there stating that many genes- including homosexual genes, human universal genes, depression genes, even rape genes- are included in human's genetic make up in order to survive the crucial natural selection. Although these are not Coyne's ideas, stated on page 228, these genes seem to be logical in some way. The survival of the parental genes, the passing of the genes, is one of the strong focus of natural selection, according to some scientists. Are these gene behavior representation idea true to the six evolutionary theory points? If so, how and in what way? If not, why are these behavioral "genes" a misrepresentation of the evolutionary theory?

The Cambrian Explosion

On pages 28-29, Jerry Coyne describes the wide span of time across which evolution has occurred, using geologic eras and periods as markers. He states that from 3.5 to 1.5 billion years ago, the only life forms were prokaryotic bacteria, which were followed by the first eukaryotic single-cell organisms. However, around 600 million years ago, there was a so-called "explosion" of multicellular organisms such as worms, jellyfish, and sponges that appear at a very distinct point in the fossil record.
Why did multicellular organisms suddenly develop during this "Cambrian Explosion"? Consider a wide variety of factors in your answer, and be sure to incorporate outside information. In addition, why were bacteria and single-cell organisms able to survive after the Cambrian Explosion?

Geographic vs. Sympatric Speciation

It is widely accepted that geographically isolated populations can develop into separate species However, on page 184, Coyne mentions that Darwin believed that "new species, espectially plants, could arise from within a very small, circumscribed area." This type of speciation is called sympatric speciation. Describe geographic speciation and sympatric speciation, and why some biologists argue over the practicality of sympatric speciation.

Transitional Fossils

Transitional fossils are imperative to proving Evolutionary Theory. Name and describe several transitional fossils and explain how it proves the organism's evolution. Specifically, how does Saahelanthropus tchadensis show the divergence from chimps to humans?

OR Genes

If the ability to recognize different smells is useful to an organism, why do you think humans have about 400 hundred olfactory receptor genes that are permanently inactivated? What advantages could this have on the human race? Also, Coyne says that "we carry this genetic baggage because it was needed in our distant ancestors who relied for survival on a keen sense of smell" (71). Since evolution is driven by natural selection, wouldn't it be beneficial to stop DNA replication of this unnecessary "baggage"? What could be some reasons as to why our bodies continue to replicate 800 OR genes knowing that 400 of them are inactive?

Dog Diversity

On pages 125 to 126, Jerry Coyne discusses the large variety of breeds found in dogs today. Having stated that the dog species as a whole "comes in all shapes, sizes, colors, and temperaments," it makes sense that these numerous breeds would be considered separate species if found in fossil form at a later date, as the wide variation of traits would lend itself to that conclusion. However, it is quite clear that "dog" is still a singular species today, as shown when one breeds a purebred toy poodle with a purebred pug. Both very different in terms of traits, yet they still can make "puggles" no problem at all. Yet, it wouldn't be such a good idea to breed a toy poodle with, say, a great dane as the fetus of a great dane - poodle cross would certainly not be able to develop in such a small dog. They are still breeds of the same species, so how could they not reproduce? How could this be? The implication behind this is that not all breeds of dogs can mate with one another successfully, so some separation exists within the species. When does that line between "breed" and "species" get crossed? It would be wise to take your response beyond a simple "when they can't reproduce with each other anymore" as the line is obviously blurred in the case of dog breeds.

Island Evolution

On pages 86-88 of the book, Jerry Coyne discusses the implications of evolution on landmasses separated by the ocean. In this particular case, he cites the example of the island "Más a Tierra," where Alejandro Selkirk took refuge when he was put ashore by his ship. All of the animals there were evolving in different ways from the animals on shore on the big continents, yet the reasons behind why this particular phenomenon happens is the question in this prompt. What conditions must exist for island organisms to evolve into an "endemic" status? How would these conditions affect the traits selected in these island organisms? Also, how come these separations happen in abundance on islands yet on distant continents like Africa and South America there will be similar species found?

end of races

The widely held belief is that races began to diverge following our ancestors' exit from Africa. Coyne writes that races were formed because different populations "were genetically isolated until recent decades" (214). The last part of this quote raises some questions about races as we know them today: has modern transportation stopped the separation of races? In fact, is there any evidence that, because populations are so integrated worldwide now, races may no longer exist in the future?

Dead Genes

On page 66, Coyne says that "when a trait is no longer used, or becomes reduced, the genes that make it don't instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA." If these genes are dead and have no purpose in an organism, what is an advantage of passing them on to the next generation? Besides consuming unnecessary energy in the DNA replication process, what other negative effects could passing on dead genes have? Also, how can dead genes help scientists trace down certain aspects of evolution?

From Green Algae to Land Plants

There is an ample amount of evidence that land plants evolved from green algae: one in particular being that both green algae and land plants have peroxisome enzymes to help minimize losses from photorespiration. What more evidence is there that land plants evolved from green algae? What challenges did land plants face as they moved away from the water? What adaptations were necessary for them to survive?

Society and Evolution

On Page 230 of his book, Jerry Coyne discusses how humans have introduced choice to how they live their lives, driven by individual perceptions that are shaped by social mores rather than only being guided by the evolutionary goals of survival and reproduction. Notably, he describes the gradual decline of social activities that may be seen as ‘barbaric’ as one aspect in which human individuals have elevated themselves beyond solely evolution. However, in class we have also discussed the existence of altruistic behavior among species that may encourage ‘kindness’ extended to other individuals even at the cost of one’s own chances of survival and reproduction. Taking these factors into account, to what extent can human society today be seen as a result of evolution? (Hint: consider the evolution of nonaggressive, communal social behavior among bonobos vs. the aggressive, individualistic behavior among the common chimp, two species closely related to humans)

Vestigial Trait

On page 57, Coyne describes how a specific body part of an ostrich is a vestigial trait. What is a vestigial trait and how does it relate to an ostrich? Do you think it was beneficial that the function of this body part has changed? Why? Relate it to our big theme- structure and function. Also, what other animals exhibit vestigial traits?

Obesity and Evolution

According to statistics, about 58 million Americans are overweight. Needless to say, this is directly caused by consuming too many calories, especially fats (fats have twice as many calories/gram). However, some research suggests that human obesity may in fact be related to evolution. Why might have being overweight have been a selective advantage in the past? Is being overweight still a selective advantage today? To what extent does research show that being overweight is genetic? What are the risks of being overweight? Do you think the risks of being overweight will eventually lead to the natural selection of those who are not overweight?

The endogenous retrovirus

Along with Coyne's explanation of "dead genes", he briefly explains a specific type of dead gene that is present in the human genome: retroviruses. "The human genome contains thousands of such viruses, nearly all of them rendered harmless by mutations. They are the remnants of ancient infections." (69) However, as we know, there is one major retrovirus that has greatly affected some humans today: HIV. Does this mean HIV was present in our ancestors even though, according to Campbell, HIV is referred to as an emerging virus because it was just discovered in the 1980s? Can you find any specific retroviruses that are still around today that were also found in the DNA of our ancestors? What makes retroviruses different from other viruses?

Evolution in the Future

Throughout the book, Coyne provides great evidence that the theory of evolution is credible. Evolution can never be proved to be the ultimate truth because there will always a lack of evidence in certain areas. How do you see the acceptance of evolution in society changing in the future? Is there any evidence that if found would help to make evolution more credible? Is there any evidence that limits the acceptance of evolution in society? Connect to the book and outside sources in your response.

To be vestigial, or not to be vestigial. That is the question.

Throughout the first chapter in the book, Jerry Coyne explains the premise behind vestigial organs: that is, organs that are no longer of use to animals and are just evolutionary leftovers which have not been completely phased out of the body plan. The most prominent of such examples would obviously be the human appendix, which, simply, is thought to do nothing in the human colon. However, when reading an article on Wikipedia about the "Vermiform Appendix," it becomes clear that the appendix may actually serve a useful function. That function, at the risk of sounding gross, is thought to be the "safehouse" for healthy bacteria which help clean the colon after an episode of diarrhea. This begs the question, are all vestigial organs really useless in their current forms? Do they possibly serve some use that is insignificant yet still there? Also, when in the many phases of evolution would one finally call an organ vestigial? That is, when is something finally considered useless?

how neanderthals disappeared

Coyne writes that "what really happened to [neanderthals] is arguably the biggest unknown about human evolution" (206). The two main theories are that neanderthals simply evolved into other species in all the areas it had inhabited, or that homo sapiens had migrated out of Africa and out-competed neanderthals into extinction world-wide. Based on the traces that evolution leaves and speciation in geographically separated areas, which theory on the extinction of neanderthals is more likely to have occurred? Could it have been a combination of both theories?

The Basis of Race

On page 212, Coyne briefly discusses races as "populations of a species that are both geographically seperated and differ genetically in one or more traits". If this is true, what led to the evolution of difference races that we see today around the world ? How has sexual selection also driven the evolution of races? If races merely represent species living in different areas of the globe, should the characterisitics of different races be varied? Connect to natural seleciton and selective advantage in your response.

The Ever-Changing Embryo

Jerry Coyne states on pg. 75-79 that the development of the human embryo is powerful evidence for evolution. All vertebrate embryos begin as the same thing, with evolutionary changes occurring as the embryo develops. As the embryo changes, it mirrors the pattern of evolutionary history: first it looks like a fish embryo, then a reptile embryo, and so on. Eventually, all of the previous characteristics have disappeared, and the result is a human.
How does the development of the human embryo relate to gene regulation and expression? Explain the connection between the obsolete DNA in humans and the various stages through which an embryo passes. What examples are there of organs from other types of animals that disappear during embryonic development?

The "Superbug"

On page 130, Jerry Coyne shares one side of evolution that may be harming humans: antibiotic resistance. Explain how antibiotic resistance relates to evolution. Fossils suggest that species take millions of years to evolve, so how is it that penicillin, which was produced in 1940, could have already evolved? If bacteria continue to evolve, what will happen if the medical world is unable to keep up with these "superbugs"? What else can we potentially use to fight infection if we have no antibiotics? (Hint: think viruses) What effect does the use of antibacterial hand sanitizers and soaps have on this phenomenon?

Evolution Redux

Coyne claims that evolution is not theory, it is fact. He also asserts that to opponents, "evolution raises such profound questions of purpose, morality, and meaning that they just can't accept it" (224). Explain why many feel the acceptance of evolution would lead to a decrease in morality. Do you agree? Or are morality and evolution actually intertwined?

Transitional Forms

According to scientists, the Archaeopteryx lithographica (page 40) is the earliest and most primitive bird known. Certain features allow scientists to think that it is a transitional fossil between modern birds and reptiles, more specifically dinosaurs. What are these specific features that connect theropod dinosaurs with birds? Does the Archaeopteryx fossil resemble one of these animals more than the other? Also, have scientists found any other transitional forms between dinosaurs and birds that prove this relationship of evolution is true?

reptiles to birds

Coyne states, "If evolution is true, then we should expect to see the reptile-bird transition in rocks between 70 and 200 million years old" (39). This has been one major challenge toward evolution: the transition from reptile to bird. Site and explain how examples including fossil transitions, behavior similarities, and the role of feathers/wings in the transitional stages proves this evolutionary transition.

Atavisms

Coyne explains what atavisms are from pages 64-66 and why they are strong evidence for evolution. "True atavisms must recapitulate an ancestral trait, and in a fairly exact way" (64). These are different from vestigial traits since their occurrence is not seen in every organism of a species, but every once in a while. What are some examples that are provided in the book and how are scientists able to use this as evidence for proving that evolution is true? Also, with all the studies that have been done on birds in the past showing that they can produce teeth, what other organisms may be the target to new experiments and why? On the other hand, if you do not believe scientists will try to bring back past traits from organisms, please explain why. (Hint: think about the definition of evolution and adaptations to the gradually changing environment of present time).

Different Mating Strategies Among The Two Sexes

From pages 155-159, Coyne explains how males and females have developed different mating strategies. "A male can produce large quantities of sperm, and so can potentially father a huge number of offspring, limited only by the number of females he can attract and the competitive ability of his sperm." On the other hand, females have the bigger investment (pregnancy) of child development and therefore are unlike males in the sense that if they mate many times, it still would not increase their number of offspring. Coyne then goes into details from the Guinness Book of World Records and describes although the record number of children one mother gave birth to was 69, Mulai Ismail, a male- emperor of Morocco, was to have fathered "at least 342 daughters and 525 sons...".

What has natural selection favored in the male populations and female populations (think investment)? Also, how does this scenario affect whether an organism evolves to be monogamous (2 percent) or polygamous? Can these strategies provide answers to questions related to the phylogeny of organisms? Use information from the text and outside resources to explain.

Embryology

On page 80, Jerry Coyne describes one case of embryological evidence supporting evolution. As embryos, human fetuses have a fine, downy coat of hair called "lanugo," which is usually shed about a month before birth when it's replaced by the more sparsely distributed hair with which we're born. There is no need for humans to have a coat of hair in the womb because the temperature inside the womb is warm enough, and thus, it's explained as a remnant of our primate ancestry, given that fetal monkeys also develop a coat of hair at about the same stage of development which they actually keep. Coyne goes on to say that "while embryology provides such a gold mine of evidence for evolution, textbooks often fail to point this out." Why do you suppose this is? Are there certain flaws in the reasoning that embryology supports the theory of evolution? Provide other examples of how embryology supports evolution, and try to identify any flaws in those examples.

Stunting Natural Selection

Coyne says that the idea of natural selection is when "species differ genetically from one another, and some of those differences affect an individual's ability to survive and reproduce in its environment, then in the next generation the 'good' genes that lead to higher survival and reproduction will have relatively more copies than the 'not so good' genes" (11). Explain how today's society has stunted the process of natural selection in humans.

Genetic Drift

"Random change in the frequency of genes over time is called genetic drift," (Coyne, 123). The line between genetic drift evolution and natural selection evolution to me seems very blurred. How can gene interactions be labeled random when the people mixing their genes to create a child may still exist because they have traits that helped them in natural selection? How can genes become "fixed" in a population to the point where there is 100 percent frequency of the gene, isn't there too much variation in the world to make that happen? What information can be found that verifies that genetic drift is a random process; that there is no possible reason that it happens? Also, genetic drift is said that it cannot cause adaptations then why is it considered evolution if evolution is a process that leads to adaptation? The book says that "What drift can do is cause the evolution of features that are neither useful or harmful to the organism," (Coyne, 123). This is saying that genetic drift does not help or hurt the organism but on the next page it contradicts itself by saying that it can "Raise the frequency of harmful genes even though selection is working in the opposite direction," (Coyne, 124). If genetic drift can raise the frequency of harmful genes than it is hurting the organism correct? Overall, what is the point of genetic drift and where is the line between genetic drift and natural selection? 

evolution stopping

Coyne writes that "every species is pretty well adapted, which means that selection has already brought it into sync with its environment" (133). Since species of animals are becoming so well adapted to the environment, will there eventually not be any more selective advantages in animals, leading to the end of evolution?

Why Choose?

Charles Darwin believed mate selection in sexually dimorphic species of animals was based on "pure aesthetics" (161). On the next few pages (162-167), Jerry Coyne gives several reasons for which animals may prefer the appearance of certain mates to others, but never completely disregards Darwin's hypothesis. Do you believe there is any reason that humans are attracted to certain mates besides aesthetics, as Darwin believes?

Modern-Day Advantages with Technology

Jerry Coyne describes the importance of the studies conducted by John Wells of Cornell University though pages 24-25. His "ingenious study" of fossil corals increased the popularity of radiometric dating, which involves the idea that "the length of a day increases by about two seconds every 100,000 years." Knowing that they existed during the Devonian Period, about 380 million years ago, he claimed each year during the period would be about 31 days longer than a modern year (396 days). This also meant that each day was shorter by two hours. By comparing the "tidal" age against the "radiometric" age, he was able to determine there must have been around 400 days per year, which meant everyday was around 21.9 hours. In the time Darwin was studying the idea of evolution, no such methods and technology existed, so formulating promising ideas was very tedious and difficult. Today scientists have many more opportunities and accumulated knowledge and are able to make more advancements in this "theory."

Discuss the importance of technology to scientists and how it will affect their findings of the future. What are other methods have helped scientists so far? In fifty years, will everyone believe the idea of evolution...? Use evidence from the text to relate the conception of microevolution and present-day adaptations to a world dominated by humans and how these interactions will help support the theme of evolution in times to come.

Macro v Micro Evolution

On page 32, Coyne says that creationists will admit that minor changes in size and shape might occur over time-a process called microevolution-but yet they reject the idea of macroevolution. What do you think is the reason that they will believe in one type of evolution, but not in the other? Theoretically, doesn't microevolution lead to macroevolution?

Battle Against Viruses

On pages 130-132, Coyne discusses how the the quick evolution of viruses has changed the options humans have to battle deadly diseases. How do these viruses evolve so quickly? What process do viruses show at work? What potential effect could this have on society and how we treat viruses in the future?

Whale and Hippopotamus Prove Duane Gish Wrong

"Duane Gish, an American creationalist, is renowned for his lively and popular (if wildly misguided) lectures attacking evolution" (pg. 47). Gish made fun of evolutionists that thought that whales descended from land animals related to cows. He did not believe that it was possible for an animal that could live in both an aquatic and terrestrial environment to have evolved. Explain how it is possible for an animal to have been naturally selected to live in both an aquatic and terrestrial environment and how the transition between aquatic and terrestrial environments proves that evolution is possible. Use the example of the hippopotamus to support your explanation. Use outside resources to provide other examples of transitional species that prove the existence of species that evolved and had the ability to live in both aquatic and terrestrial environments.

Evolution in the Test Tube

On page 129, Jerry Coyne describes an experiment performed by Barry Hall and his colleagues at the University of Rochester, in which they removed a gene from E. coli that would have produced an enzyme that would have allowed the bacteria to break down lactose into subunits that could be used for food. After a few chance mutations, the bacteria evolved so that it could still take up lactose despite not having the special enzyme necessary - another enzyme took over the process, and ultimately, a different gene allowed the bacteria to take up lactose in the environment more easily. If we were to repeat this experiment, would we obtain the same results that Hall and his colleagues did? Did these mutations occur simply by chance, or were they somehow influenced by the environment that the bacteria was in? Provide outside research on Hall's experimental design and discuss situations in which we wouldn't get the same results that Hall got after performing this experiment.

Written in the Rocks

Even with all this proof and fossil evidence about evolution, creationists still adhere to their religious beliefs about the origin of life on Earth. What is it that keeps them so constant with their views? What holes are there in the evolutionary theory that allow them to do so?

Written in the Rocks

On page 49, Jerry Coyne suggests the theory that whales descended from terrestrial animals. He says that the transitional form between the terrestrial and aquatic mammal could possibly be a hippopotamus. Supposedly, this evolutionary sequence occurred after land mammals had evolved from fish, particularly a group of "lobe-finned fishes" as described on page 36. So if humans potentially evolved from aquatic animals (fish), then wouldn't it be contradictory to say that aquatic whales evolved from terrestrial animals? What evidence is there that proves that one event happened before the other or that it was possible to move from water to land and then back to land again?

Technology and "Natural" Selection

Jerry Coyne describes the human appendix as a vestigial organ which no longer has any use in our bodies (pg. 61). The appendix can become clogged and infected easily, a process which can cause it to rupture and kill a person. However, with the advent of appendectomy, we have reduced the chances of dying of appendicitis from over twenty percent to about one percent.

What effect does the relatively safe surgical removal of an infected appendix have on the process of natural selection as it pertains to humans and the appendix? Think of how the survival of affected individuals that would otherwise have died impacts future generations. What other examples of medical technology alter patterns of human survival, and how does the increased survival rate affect traits of future generations of humans? (Hint: think vaccines)

Land Mammals Migrating to the Water

On pages 51-52, Jerry Coyne talks about the evolution of whales from land mammals such as Indohyus, Pakicetus, Rodhocetus, and Dorudon, with each new species spending more and more of its lifetime in the water. He discusses one possible reason for why these animals went back to the water in the first place, which was the lack of competition for food from dinosaurs. This way, they could live in an environment that had abundant food and was predator-free. What other explanations are there for why land mammals moved back to the water? Provide examples and use external sources as evidence.

The Evolution of Birds

From page 39 to 47, Jerry Coyne talks about the evolution of birds from animals that live on land to animals that slowly adapted to the birds we know today. The evolution of birds shows the slow process of evolution at work to create a new species of organisms.

Question: How do the multiple "transition animals" from land animal to flightless bird show the adaptive process of evolution? What other adaptions besides wings do the birds evolve over time and how were they adpative? Provide examples of transition animals that exist today.

"Dead" Genes

Coyne explains that there is evidence of evolution in every organism's genome. "Dead" genes are genes that "once were useful but are no longer intact or expressed" (Coyne 67). These "dead" genes are not the only non-coding portion of DNA. Introns are sections of DNA that are transcribed to pre-mRNA and then spliced out during RNA editing. However, recent research suggests introns may actually serve an integral part of transcribing RNAi. How does this act as further evidence of evolution within DNA?

Apes & Human Evolution

Humans and apes share a common ancestor. We are both in the order Primates, superfamily Hominoidea, family Hominidae.
What traits do we humans have that allow us to be classified with Primates? What traits set us apart?

Brain size, teeth, and locomotion (bipedalism) have been used to differentiate species of hominin fossils that have been found. On page 199, Coyne tells us that "bipedal walking was one of the first evolutionary innovations to distinguish us from other apes", and on page 202 that "our upright posture evolved long before our big brain".

Theorize about the order in which our bipedalism, big brains, and teeth evolved. Include why each trait would have been and important advantage and why it came before and after other traits. Include other hominin species and their advantages (for example, we know that H. erectus could use tools and control fire, and had a brain size "nearly equal to that of modern humans" (Coyne 205)).

Also consider the further evolution of humans. Are we done evolving? Are we just too good at fighting disease and other things that would wipe out those without selective advantages? Or are we part of a continuous arc of evolution that will keep producing humans better suited for life on Earth?

Convergent Evolution

One of the most interesting points Coyne makes is that similar environments will cause similar traits in species that aren't related very closely. He does this on pgs. 92-94. This is called convergent evolution. The idea is that natural selection will make animals on two different sides of the world but in similar environments acquire similar traits. Examples he uses include similarities between many animals that have marsupial equivalents in Australia. What other examples are there of convergent evolution around the world? This could be similarities between any two organisms. What environmental pressures are theorized to have caused the similar traits?

Genetic Drift

Coyne brings up another way that species evolve, without natural selection, on pgs. 122-24. This is called genetic drift. Genetic drift happens when a relatively small population of organisms reproduces with each other. Eventually, because of how the small population breeds together, variation is lost and it is possible to get alleles in weird ratios or even completely loose alleles. The allele that gets expressed more often is random and environmental pressures do not affect it. Coyne uses the example of weird blood type frequencies in the Amish and Dunker religious communities. What other traits in populations of plants and animals might arise from genetic drift? Are these traits beneficial or hurtful? If they are harmful, what can we do to help populations get rid of the harmful gene (or can we do anything at all)?

The Geography of Life: Oceanic Islands

Oceanic islands prove to be strong evidence for evolution versus creationism from pages 100-109. Although these islands are suitable for mammals, amphibians, reptiles, and fishes, there is an obvious pattern that unless introduced by man, many of these organisms have not evolved in these areas. Coyne defines oceanic islands as islands that were "never connected to a continent... [and having] unbalanced biotas" since the organisms usually found to inhabit these islands belong to similar species such as the Gálapagos finches. How do these places differ from continental islands and support the theme of evolution? Think about the different adaptive radiations and why life on these islands is unbalanced. Also, site specific examples of these adaptive radiations and explain evolution in terms of adaptations, which allow an organism to gain selective advantages in a specific environment.

Evolution Today

Many ID proponents refute the evidence for evolution by saying that its not readily observable. While evolution is the gradual divergence of a species from its previous form due to adaptive advantages from genetic variation among individuals, Jerry Coyne mentions an example of the production of lactase (an enzyme used to digest milk) in humans beyond infancy is due to the rise of "pastoral" farmers. Another example of modern evolution mentioned by Jerry Coyne--is the increased presence of allele CCR5-Δ32 in humans, which provides significantly increased resistance to AIDS virus. (pg. 217-9) Why is this information important? How can small adaptations today turn into a bigger evolutionary change in the future (give examples of how this could happen)? Where is evolution still occurring today--not just in humans? (Hint: Why did we discuss the need for vaccinations and seasonal flu shots in biology class?)

The Engine of Evolution

In Coyne's book Why Evolution is True, he describes the evolution of one parasitic species (Central American roundworm) to prey on native ants and changes not only their physical traits (change color of abdomen)--but also their behavior (crawl up tree to be more visible for birds). (pg. 112-3) In our behavior unit we learned how deeply ingrained, and even instinctive, animal behaviors can be. So how is it possible for a parasite to slowly evolve the multiple tools required to successfully control these ants (How did this process begin? Was each adaptation simultaneous?)? Doesn't this go against the very things we learned about in evolution? Provide another example of advanced symbiotic relationship between two species (parasitism, mutualism, or commensalism) between species and how it could have evolved/why it would be advantageous to survival of the species/'s.

Artificial Selection

The domestic dog is an example of a species that has been "sculpted" into many different breeds. The difference between artificial selection and natural selection is that "it is the breeder rather than nature who sorts out which variants are 'good' and 'bad'" (Coyne, 127). Breeders can mate dogs with desirable traits to create just about any variation they would like. This selection extends to Coyne's examples of the wild cabbage and of the svelte wild turkey.

How come domestic dogs can exhibit such variation but still remain just one species?
How is artificial selection evidence for natural selection?
Give some examples of organisms that have been bred for a desirable variant and state their purpose(s).
In your opinion, is there anything wrong with humans imposing their will on the characteristics of other organisms? Why or why not?

Vertebrate Evolution

On page 8, Coyne breaks down how the common ancestor of vertebrates evolved into the organisms we see today. Describe how the different traits developed in these organisms and how these traits were passed on through mutations in genes from the common ancestor to the organisms we see today in the vertebrate phylogeny. Use key words such as vertebrate, jaws, digits, amniotic egg, hair, placenta, and opposable thumbs. What were the names of the different species that arose from the splitting of species from the common ancestor due to these traits? How are these species similar and dissimilar? Explain how these traits lead to a "natural" classification of these species and how "natural" classification is strong evidence for evolution.

Gene Alteration

Evolution has a lot to do with gene alteration among different individuals in a species and how those traits get passed on to their offspring over thousands of generations and how eventually this leads to the evolution of a completely different species that cannot interbreed with the previous. From our molecular genetics and DNA & protein synthesis units, how do genes alter? What are the different ways that they can be altered? How do these alterations affect what proteins are made and what genes are turned on and off? Explain the differences between changes in the genome and epigenome. Explain how all these genetic alterations lead to the process of evolution.

A Classification Conundrum

Jerry Coyne, during much of the first chapter, cites examples such as the Tiktaalik roseae and Archeopteryx as "transitory" species in the fossil record that show the change from one specific classification of organism to another distinct classification. For example, the Tiktaalik roseae links the change from reptile into fish by possessing hinged limbs and a neck, distinctly reptilian features, yet also has gills and other fishlike features! However, this presents a problem: the present means of classifying animals does not provide a place for such organisms to "fit in." Are organisms like the Tiktaalik roseae and Archeopteryx able to be considered both animal and reptile? Neither? More or less one than the other? Can you find a way to determine how they can fit into a presently available classification? Cite examples from the text to support your claim, and it may be helpful to include an explanation of what a "mosiac" is in terms of transitory organisms as evidence.

The Enigmatic Appendix

Among the vestigial organs in the human body, Jerry Coyne focuses most on the appendix. Apparently, the appendix was once of use in digesting cellulose, but since humans do not eat cellulose, the appendix has been reduced to almost nothing. Yet it is still large enough to become infected and lethal. Thus, what effects does the practice of appendectomy have on the presence of the appendix in humans? Would it be beneficial to the human race to cease operations on infected appendices? Why or why not?

Missing Links

The fossil record has given scientists many clues as whether or not evolution is true and how new species have come about. There are many gaps in the fossil record, however, that cause some people to be skeptical about whether or not evolution is really true. Define transitional forms, macroevolution, and microevolution, and explain how they contribute to "missing links" in the fossil record. Explain why these are important to the theory of evolution and how these missing links have both benefited and harmed scientists trying to prove this theory. (Hint: Coyne explains missing links in the fossil record on pg. 32)

Bad Design

In pages 81 - 85, Coyne shows us that bad design is a mark of evolution. One example of bad design is the "small gap between the human ovary and Fallopian tube, so that an egg must cross this gap before it can travel through the tube and implant in the uterus". The design is "maladaptive" because it evolved from fish without consideration of the Fallopian tube until much later.

Why does bad design support evolution? What arguments could a Creationist make about bad design to support himself?
Name an organism with a feature that could have been better placed/designed. Explain the bad placement by tracing the evolution of the feature.

How Sex Drives Evolution

In our behavior unit, we learned about how animals had different types of courtship rituals to attract a mate. Are there other ways in which organisms attract mates of the opposite sex? Jerry Coyne mentions in page 144 of Why Evolution is True that sometimes species have adaptations that seem pointless in survival. For example, the male peacock, which has an extravagant display of tail plumage--which is detrimental in its ability to camouflage from predators as well as flight--is an example of a trait that clearly hurts the individuals survival. Despite this, creatures like peacocks and stag beetles continue to develop these disadvantageous traits. Give examples of organisms who exhibit sexual dimorphisms (differences between males and females of a species) and explain how these differences can give an evolutionary advantage. How does evolution explain how these seemingly disabling and detrimental traits actually help in survival of the species as a whole?

Geography and Evolution

As we all learned from our ecology unit, evolution involves species variation, adaptation, and eventually evolution. However, whenever we think of evolution, we often think of it as a predator vs. prey adaption. In Jerry Coyne's book Why Evolution is True, he talks about how different geographical factors could also play in evolutionary change--especially in terms of convergent evolution (pg 92). Give examples of two different species that show similar traits despite developing in separate yet similar environments, and how this could have occurred.

Components of Evolution

Coyne's book is obviously about him proving why he believes evolution is true. Before stating whether or not evolution is true, he must first define what he believes evolution is. He first mentions his definition of evolution on page 3 and says that evolution consists of 6 main components. What are the six main components of evolution? Define each component as well as how they relate to one another (Hint: Coyne refers to two of the components as "flip sides of the same coin," on page 4).

Drift v. Natural Selection

On pages 122-124, Coyne discusses the difference between evolution by genetic drift and evolution by natural selection. He says that certain features, like blood type, "especially in small populations...can change over time entirely by chance".
Think of a neutral ("neither useful nor injurious") trait, such as an animal's external feature, that seems to have evolved by genetic drift, and argue that it has a selective advantage. Suggest features for other responders to argue for.
Are there any features that are known to have evolved by genetic drift that are obviously helpful, (or that used to be injurious or neutral but are now helpful under different circumstances)? Why is it hard to tell whether helpful features evolved by natural selection or genetic drift?
We also know that "genetic drift is...powerless to create adaptations, but can actually overpower natural selection". Are there any small populations that seem to have unhelpful features that evolved by genetic drift? Name the population, the feature they have, and what makes the feature unhelpful.

Neanderthals

I find human evolution to be one of the most interesting parts of evolutionary biology because it affects us directly. On pgs. 205-06, Coyne mentions the famous Neanderthals, whose fossils are found around Europe. He says that "when I was a student, I was taught they simply evolved into modern humans." Now, evidence suggests that Neanderthals were a evolutionary dead end. What theories revolve around Neanderthals? How did they evolve? How did they go extinct? Talk about them possibly encountering modern man H. sapiens. Also, how close were Neanderthals to modern man? There is evidence of them having burial rituals, which might suggest a religion. Some debate that they had a sort of culture with art and music. Who were H. neanderthalensis?

Vestigial Organs

From pgs. 56-64, Coyne has a whole section about vestigial organs: organs that animals have but don't really need. Some examples of vestigial organs that Coyne gave were the human appendix and the wings of flightless birds. What other examples of vestigial organs are there? Theorize what purpose they could've served in ancestors of today's animals and plants.

Smooth v. Erratic Evolution

On pages 29-30, Jerry Coyne uses the example of the marine organism Globorotalia conoidea to explain how tracing a single fossil species can help geologists to see how that species evolved. In this particular example, the number of chambers in the final whorl of the plankton shell decreases gradually and smoothly over time. However, Coyne goes on to say that "evolution, though gradual, need not always proceed smoothly, or at an even pace." What factors determine how smoothly or erratically evolution occurs in a particular species? Provide examples and compare and contrast the environmental conditions in which a certain species can undergo smooth evolution and erratic evolution.