The next step

What do you think is our next stage in our evolutionary process? what evolutionary pressures do we or might we face that could select for certain traits?

Evolution: why does it really matter?

I think it's fair to say that most scientists "believe" in evolution, but looking at the big picture, why does evolution really matter? why is it important that we argue with those that oppose evolution? why has carroll written this incredible book that provides clear evidence in support of evolution?

The Uses of the Study of Evolution

What do you believe are the modern day, common man uses from the study of Evolution. Now this is not talking about the study of DNA, but simply evolution. For example, medical research leads to cures to disease. Technological research leads to new inventions. But whats the point of studying evolution? Is the endgame to convince everyone it exsists and that its happening? In general, what are the uses of knowing about the topic of evolution and how can it affect us in our world. After all we did fine without it as a civilization for a good 12,000 years or so, how will it help us now? Post your own opinions and use examples from the book to strengthen your argument.

Biological Themes

Choose two themes of biology. In detail, define what each of these themes mean. Next, relate each theme to an example from the book Making of the Fittest, and explain exactly how each theme applies. Finally, pose a question for the next commenter relating to one of the two themes you chose (Yes that means if you reply first you get to do less work).

For obvious reasons, I will not allow you to use the biological theme of evolution.

Diversity of Life

Write about you favorite evolutionarily significant organism. Explain why it is your favorite as it pertains to being a prime example of evolution having created a highly specialized set of traits.

For example, my favorite organism is the tardigrade because evolution has selected for it the ability to live in a dehydrated state for many years (anhydrobiosis) and then being able to transition into an active state upon receiving water. Tardigrades are really interesting because they can survive 1000 times the radiation that a human can withstand. These traits make it a polyextremophile that  can survive and reproduce in almost any condition.

Why the Genetic Perspective?

As we conclude this most amazing blog, I feel we should concentrate more on big-picture ideas and themes that Carroll has emphasized throughout his book, one of which is the genetic perspective on evolution.

Why is DNA, both new and old, critical to the explanation and support of evolution? In what way is a genetic perspective effective? Also, describe TWO examples in which Carroll uses DNA evidence to bolster support for evolution. (myriad examples of this are furnished in the book...)

Making of the Fittest Reflection

As the blogging window draws to a close, I think we should have a more book focused reflective prompt for us to focus again on the book and less on the whole Humans vs. World subjects we have been getting on to.

Looking back through the book, choose your favorite example that Carroll uses to explain evolution. Briefly summarize the example and explain why this example is your favorite. Next, give your overall opinion of the book. Explain your opinion.

Finally, write at least two discussion questions that you would ask Carroll if you could have a conversation with him.

The Cambrian Explosion

By the end of the Precambrian period (4.5billion- 543 million years ago) the fossil record consisted mainly of microscopic organisms (domain archaea, domain bacteria, kingdom protista), cnidarians, and chitons ( soft-bodied mollusks). However, most of the major groups of animal phyla appear in the fossil record only 20 million years after the Ediacaran, in the early Cambrian period. This rapid diversification of animals in a short period of geologic time is called the Cambrian explosion. Use your knowledge of evolution, specifically "evo-devo", to explain the possible environmental or genetic causes of this remarkable period of diversification.

The Theory of Evolution vs. The Theory of Economics

The theory of evolution states that the organism which is most adapt to acquiring its necessary resource will survive and reproduce, allowing it to pass down its DNA to its offspring and then the offspring gets to do the same thing unless its gets out done by some one else. But for us humans, through almost all of our history the resource we most valued is currency. In a sense, "money runs the world". But this becomes a problem when money, and the greed for it, counter common sense and biophilia. For example, the marine ecosystems were destroyed in the pursuit of profit. Rain forests destroyed for wood and land, which turns into profit. The cause of Global Warming? Thousands of factories and millions of cars producing Co2, so their owners can make profit. Even in the face of a possible world wide natural catastrophe because of global warming in the next 30-50 years, big business shies away from change all because of money. No matter your opinion on it, for us humans, money is the resource we all inevitably fight over. Even subconciously, one reason you are up reading this right now is because you want to out do your fellow stevenson classmates and make more money than them later on in life (and of course biophilia).

But in a sense, won't the world greed eventually destroy it? Already nature is being taken for granted in favor of profit, and we're growing nearer and nearer to the point where our natural resources our dwindling, destroying thousands of species and habitats daily. Is there any hope for a bio diverse future with nature in it, or will humans inevetibaly mechanize and over populate the world where there is no more room for other species and nature. Could common sense eventually slow down this steady destruction of the planet earth, or will we inevitably dig our own graves out of greed. Post your opinions, and if possible any examples of people countering this phenommenon on a large scale. ( You planting a cherry tree by your house doesn't count.)

"Preserve the old, but know the new"

Chapter four starts out with a Chinese proverb, "Preserve the old, but know the new." Why is it important to know and study our past, and how does studying our ancestors help us attain a deeper understanding ourselves? This concept not only applies to history, but it also applies to biology! What does studying the old species reveal about the new evolved species?

DNA and Evolution

Carroll refers to DNA to show support for evolution throughout the book. He repeatedly states that "our DNA shows our evolutionary history." If that's so, why can't we easily track the evolution of a specific organ or characteristic in modern day organisms? If all the answers are in the DNA, why don't we have them yet?

The Evolution of Eyes

Starting on pg 193, Sean Carroll first describes how there are many organisms, particularly in the Great Barrier Reef, that all have very specific structures. Some examples of what I mean are "the turtle's shell, the octopus's tentacles, and the crab's claws" (194). Its very possible that one can theorize that evolution has selected these particular structures because those structures are advantageous to those organisms. However, one point of contention comes up when discussing the eyes of each of those organisms. Is it possible that evolution is the reason for so many different eye-type variations of different organisms, or do the variations of eyes stem just a repeated mixing of scratch materials? Also tie into your response how the theme of heritable information pertains to this question.

Is Gene Splicing the Answer?

Animal populations across the globe are decreasing in numbers, with many at risk of extinction. Many animals that aren't even endangered have drastically reduced populations compared to one-hundred years ago. Possibly the gravest examples are marine animals.

The krill, Euphasia superba, "may be the most abundant animal on the planet." However, densities have declined by 80% in the last 75 years. Since krill is critical to the survival of many marine species such as whales, its decline has affected the entire ocean.

A possible solution may be genetic engineering: due to overfishing, hatcheries have been made to basically farm salmon. This article: http://www.flmnh.ufl.edu/fish/InNews/calamity2004.htm  states that genes from ocean pout have been spliced into the DNA of salmon to trigger growth hormones, allowing the salmon to grow incredibly fast. 

Could genetic modifications be used to allow krill and other organisms to grow and multiply faster, and thus counteract our effect on animal population densities?

How is this counteracting natural evolution? Will this work well, and if not, what would be the negative side effects?

Consider what we learned in the ecology unit about carrying capacity.

Intelligent Design

On page 245, Carroll suggests that the idea of "intelligent design is a myth". What does the thoery of intelligent design state? What proof does Carroll use to make this conclusion that intelligent design is a myth?

Creating a Super-Human Race

Now, for a moment lets consider the possibility that even so evolution cannot be controlled, we can "push" and "nudge" it in the right direction, or whatever direction we would like it to go. For a second lets forget about past failed attempts at this, with Hitler and his Genocides, and take a more sane approach to the topic. Say the U.S. government funds an island, say, Super-Human Island, (SHI for short), where they take the people with the best traits in the U.S. and just fund their living standards and have them reproduce. This way they can pass their favorable genes down to their offspring. Now this is not so insane; we after all fund universities where only the smarter of us can get it in. You don't see many "red-necks" who do not know basic algebra hanging out Harvard, and not too many critics are yelling how horrible Harvard is for not letting in the "stupider" of us. Now back to SHI. Say on the island there were "intelligence" and "strength" requirements needed to be maintained to remain on the island, and all people who did not manage to meet these requirements were simply politely asked to leave the island and live with the rest of the "normies". In this sense, by "creating" evolutionary pressures, only the smartest and strongest would survive and pass down their genes by mating with other smart and strong people, and over time should in theory create a "super-race". By using facts from the book and your own knowledge, give an opinion on why this would or wouldn't work, and your own opinions if there is any benefeit for creating such a program.

Huxley quote

Carroll ends the book with a quote from the Huxley brothers stating that' "facts do not cease to exist because they are ignored" and that we are now "determining the future direction of evolution on this earth" '(268). What is the message that Carroll is trying to convey? What does this have to do with the book as a whole?

Why so much homology ?

Homology is a fundamental theme of evolution and is ubiquitous in nature. Explain how homology relates to taxonomy, the evolutionary tree, an Darwin's "descent with modification". Many homologous structures exist as vestigial organs, non-functional or unimportant structures. If vestigial organs are essentially useless and thus a waste of energy why don't they disappear through evolution? Essentially, why is homology maintained? (Hint: chapter 22 of the AP Bio text book.)

Does ingenuity slow down evolution?

Humans and to some degree our hominid ancestors had the remarkable ability to cope with natural selections pressures using ingenuity. Natural selection did not produce more efficient bodies for our ancestors and us because we were smart enough to evade those selection pressures using tools. In fact we still have a knee joint and spine characteristic or four legged mammals. Homo-sapiens have not evolved in the last 30 thousand years in terms of anatomy. Has our ingenuity allowed us to bypass selection to the extent that our evolution has slowed down or ceased? Or are we just evolving in different, less noticeable ways? Try to use specific characteristics to develop your argument.

Can evolution expain all traits?

Carroll frequently uses the concepts of "compound interest" and Evo Devo to prove evolution developed all traits we see in nature. However some traits like the flagellum have generated waves of controversy among the scientific community. The flagellum is an irreducibly complex structure such that if any components of the structure were to not have developed the flagellum would not function. However, Darwinian evolution acts on only working traits because traits evolve only in response to previous selection pressures. How would you resolve the issue of irreducibly complex structures using the knowledge gained from Carroll's work?

Detrimental Diseases helping Life pg. 174

According to the book we are currently reading, the sickle cell trait was first discovered in 1910. Later on, an expedition was put under way along the Kenyan cost to try and understand why tribes along the cost had a "20 percent" higher rate of sickle cell anemia then tribes more towards the interior of the land. What Anthony Allison, the scientist working in this expedition, found was that sickle cell anemia actually helps to combat malaria, which was also prevalent at the time. Please provide one example of how such a detrimental disease to humans can actually have some preventative properties. Also, tie into your response the evolutionary outlook that the disease creates for humans.

Treating Cancer

Tumors are the result of mutations in cells: these chance mutations are errors in DNA replication that end up allowing a cell to "proliferate unchecked" (183). The human body is made of trillions of cells, many of which are constantly replaced through life. Since so many cells are regularly being replenished, an occasional mistake should be expected. However, we have many ways of preventing and treating cancer. Besides the use of the ABL-kinase in treating CML tumors, in what other ways do we humans alleviate cancer?

Think not only of technological methods. What does the body itself do that makes it so effective at preventing tumor cells from occurring and proliferating in the first place? (Refer to chapters 16 and 43 on DNA and the Immune System) Keep the theme of regulation in mind as you answer.

Censoring Science

In the "The Commissar of Soviet Biology" section of the book starting on page 219, Carroll describes how the Soviet scientist and political manipulator T. D. Lysenko. This section shows how Lysenko used propaganda and sensationalism to promote scientific discoveries (or falsely represented discoveries) that supported Soviet ideology and needs (such as saying a certain pea crop could survive the winter, but only tested it during one winter which was surprisingly mild).

Expound on this idea of censorship of science by finding a historical example of the stifling or the "editing" science in the United States for ideological or political purposes. Give a summary of what occurred and give your opinion on the events that transpired.

Next, find a historical example where ideological and political forces aided scientific research in the United States. Give a summary of what occurred and give your opinion on the event.

Finally, say whether or not you believe that ideological and political concerns should have an impact on science, along with whether or not the government should be involved with science. Why do you believe this?

Humans Changing Selective Conditions

With the Industrial Revolution in England and North America, the coloration and lichen growth on trees where the peppered moth rests was altered. (Directly from page 52) There was a huge increase in the dark, melanic forms of the moth in these industrial areas and a decrease in the light form. After only 50 years, the frequency of dark form moths increased to 98% in some areas, but after the enactment of clear air laws, the percent of dark melanic moths quickly decreased. This is one example of how humans directly affect the process of natural selection of other species. What effect do humans have on their environment, and how does human involvment change the proccess of evolution and natural selection? Give a couple examples. Do humans have a positive or negative effect on the rest of the environment. Explain.

Coral Reefs

Coral reefs are amazing places with a colorful variety of species. Discuss the formation of coral reefs and what it is about the coral reefs that allows myriad species to thrive. Describe at least two invertebrates of different phylums and at least one vertebrate that live off of coral reefs. In your description, talk about the specific physical traits of the species and what the species may provide to the coral reefs. ---- see chapter 8 pg. 191

Quotes

Besides introducing the chapter, what is the purpose of using quotations at the beginnings of chapters? What do the quotes tell us? Consider who says the quote and what he/she has done for their field of study. Choose two distinct quotes from the beginnings of chapters to answer the aforementioned questions. Note: as more people reply to this prompt, it will be harder to find an unused quotation.

Fossilizing Genes in Humans?

Chapter five (begins p.117) focuses on fossil genes. In coelacanths and dolphins, the opsin gene fossilized due to mutations. Due to a drop in selective pressure, the gene lost its usefulness, so mutations that inactivated the gene didn't harm the organisms. 

For humans, life is obviously not a life and death struggle (at least for us). Besides diseases, we live with very little selective pressure. Carroll mentioned the fossilized MYH16 gene in humans on page 134. This gene contributes to large fibers in muscles, which explains why human "muscle fibers are much smaller than those in our relatives." 

We can't say for certain that this gene fossilized because of declining selective pressure. However, as we are becoming less and less dependent on our own bodies for day-to-day activities, is it possible that many of our own genes will eventually fossilize and lead to the decay of the human body? Could this occur for domesticated/captive zoo animals as well? What might result of this?

Humans Outwitting Natural Selection

Throughout most of his comparisons and case studies of natural selection in his book, Carroll avoids using humans as examples. He usually tends to focus on simpler organisms, but it seems slightly curious since his readers can much more easily identify with humans. However, the problem with using humans as examples to explain natural selection is our vast problem-solving abilities that we use to “outwit” evolution.
For example, lactose intolerance should be a grave selective disadvantage that would surely mean death for a toddler The toddler would have no way to obtain nutrition in the breast feeding stage of infancy from the mother due to the inability to digest lactose. However, through using formula and immunity boosting drugs this selective disadvantage has been circumvented, thus allowing what normally would have been a fatal mutation in the lactase gene to survive and be passed on into the human gene pool. This presents the ultimate irony in that human use of tools and resources to avoid selective pressures can be seen as “weakening” the human genome in the long run.
In a very detailed manner, explain at least 2 other cases in which humans have used technology or reasoning to avoid selective pressures from the environment. Also, give your opinion on whether you believe that human use of technology to circumvent natural selection is beneficial or damaging to the human species

Deja Vu

In Ch. 6, Carroll begins talking about how different species evolve similarly or differently to achieve the same end result. One method he talks about is how “different means” lead to “similar ends” . What were the different means that led to the similar ends of the Arctic and Antarctic fish antifreeze? Why do you think different means were needed to get to the same end result?

Evolution Designed?

A couple days ago during class Ms I mentioned something about the blog responses being poor, because some of us were saying things that implied evolution occurs on a needs basis. For example, "birds needed to be able to find prey more quickly, so they evolved with better eyesight." According to natural selection, this is clearly wrong, but evolution is still only a theory, right? Through studying biology, it almost seems that organisms are perfectly designed to be the most suitable for their environment. Chapter 6 talks about evolutionary convergence among species that are genetically and geographically unrelated. Although this is used as evidence for evolution, could this also point to a designer? How could this evidence be used to support theory of intelligent design? Is there other biological evidence that could imply a design, thus a designer?

Ultimate Arms Race

Who will win in an "evolutionary 'arms race'"? The Oregon rough-skinned newt (Taricha granulosa) or the common garter snake (Thamnophis sirtalis)? (pg. 166). Will there be some form of "compromise" in the end? Why? Explain your reasoning. Relate back to ecology unit. It's up to you to decide....dun dun dun....

"Different Means to Similar Ends"- pg. 151

Explain how similar adaptations have occured in completely different populations of organisms. Especially note chapter 6, for it has myriad examples.

Coloring of Organisms

Throughout the novel there have been many examples of species that differ in terms of coloring. Give an example of a species where the colorings of the organisms differ. How did the differences evolve and what is the selective advantage to the organism of having that specific coloring?

Taxonomy

Contrast how the new modern genetic-based method of species classification and ancestry differs from the older version of taxonomy. Explain how genetic biologists are able to use "junk" DNA (use specific terms, hint: p.99) to establish new hierarchies and discover ancestry and relationships between different species. Also, give at least 2 examples of genetic-based discoveries that have led to the reorganization of taxonomic branches. Finally, explain your opinion on whether or not genetic based organization over classical body plan organization will affect your biophilia (in essence, will it increase or decrease your respect for the diversity of life, specifically in regards to our closest ancestors).

Number of Opsins

What is the evolutionary significance of humans having three opsin genes while the majority of other mammals have only two opsin genes while birds and fish have four opsin genes? (pg. 97)Discuss the role of the opsin gene in animals and why more opsin genes could be necessary in birds and fish while fewer opsin genes could be necessary in most mammals.

Climates of the World

On pgs 51-52, Carroll discusses the climate of Wyoming and how it has changed from a lush tropical climate to a semi-arid desert climate over the course of 40-50 million years. Let us discuss climates...
Name ONE climate, it's temperature ranges, amount of rainfall, where the climate is found on Earth today, as well as specific flora and fauna found in areas with such a climate.

Plutarch's quote

Carroll cites a beautiful quote by Plutarch, on page 139. What significance does this quote have in biological terms? Also, if you could find another awesome quote feel free to post it here.

Eww...Pathogens...

According to the beginning of Chapter 9, what is germ theory?
Provide an example of a pathogen. What has the pathogen developed to be particularly harmful to other organisms and more beneficial to itself? Explain how these "developments" came about. (Hint: The organisms didn't attain a selective advantage because it wanted it!) What is the bodily response against the pathogen? (elaborate on this...) Is it effective? Are there medical treatments against the pathogen? Why do they work? Are there preventative measures against the pathogen? (Ex. vaccines) Why do they work?

Vision and Hearing abilities

Caroll discussed how as full color vision developed many olfactory receptor genes were fossilized. So as sight became a better tool for organisms their sense of smell decreased.(128). How does this idea hold true for humans who have lost their ability of sight or hearing. Can a blind person hear better than an average person? If so, is it better in terms of decibels?Hertz? Can a deaf person see better than an average person? How can this idea be proved or disproved by the ideas of evolution and natural selection?

Owl monkey

When mammals were developed they were originally nocturnal color vision was not necessary. However, most developed mammals currently use color vision and are not nocturnal. Color vision is possible with the presences of a functional SWS opsin gene. This gene is present in mammals including most primates. However, it has been found that in the owl monkey the SWS opsin gene is not functional because a triplet of “TGG” was changed to “TGA”(124). The change in the triplet causes there to be a stop codon that causes the rest of the gene to be unread. Is it feasible that the owl monkey became nocturnal and then the SWS opsin gene became a fossil gene? Why or why not? If so what could have caused the owl monkey to become nocturnal(think in terms of ecology)?

Nonbelievers

According to many anti-evolution people, Charles Darwin did not believe that natural selection could account for the evolution of complex organisms, such as humans. These people argue that Darwin only thought evolution could occur in small populations with relatively simple organisms. What evidence does Carroll give to convince these people that evolution can account for complex organisms? Also, give an example/examples of evolution in a large population with complex organisms.

Anthropology

Human origin is one of the most debated topics in anthropology. Currently there are two major propositions for the origin of anatomically modern Humans: the multiregional hypothesis and the “out of Africa”/ replacement hypothesis. Yet, these theories fail to explain the variations in skin color among human populations. What is the explanation Sean Carroll provides in chapter 7?  Does Dr. Carroll’s theory on skin color weakens or strenghtens both hypotheses’ claim that our hominid ancestors originated from a small population in Africa? How So? Do you think that skin color simply reflects relatedness among humans or that people of different origins can develop the same skin tone once they migrate to a certain area due to selection pressure?

Pax-6 and Eye Structure

Different eyes have developed in different species. The Pax-6 gene plays a role in the eye development of many organisms such as the mouse, human, squid, and ribbon worm. What is Pax-6 and what is its function? What would occur if there was a disruption in the Pax-6 gene of a human? Why would a mouse Pax-6 gene be able to also "induce fly eye tissue" (196)?

The structure of the eye differs in complexity even if we just examine the phylum of mollusks. What factors would induce such a difference? One could address the information we learned about mollusks in the invertebrate unit. 

Yeast and Pathogens

M. leprae is a microbe that is responsible for the disease leprosy. The microbe is "closely related to M. tuberculosis, the species responsible for pulmonary tuberculosis" (131). M. leprae contains a vast number of fossil genes: almost 1100 fossil genes out of 1600 functional genes. However, M. tuberculosis only has 4000 intact genes and only 6 fossil genes. Why is there such a difference in fossil genes between the two closely related species?

Compare and contrast M. leprae with S. kudriavzevii, the only yeast that cannot utilize glucose. What does the pattern of the genes of the S. kudriavzevii reveal about natural selection? One could relate their response to fermentation. How would fermentation (if fermentation changes) differ in the S. kudriavzevii when compared to other yeasts that can utilize galactose? (What would happen if the glucose supply ran out?)

What do the accumulation of fossil genes in both of the organisms reveal about the environment of the organisms? One should remember to address the themes of biology: for example, heritable information and evolution. 

LINES and SINES and other fun things

Explain what LINES and SINES are. Why do LINES and SINES survive from generation to generation? How can we use LINES and SINES to determine ancestral relationships between species, and why does a similarity in LINES and SINES indicate a relationship between species? Use an example of a relationship between a human and another species found using LINES and SINES. Have a nice last day of Spring Break!

Natural Selection: Change Is Not Necessarily Progess

"Natural selection cannot preserve what is not being used, and it cannot plan for the future." -Carroll pg. 136. Both in "Making of the Fittest" and in AP Biology class, it is always reinforced that evolution doesn't think ahead, or really think at all; natural selection only acts to select what is best for whatever the present situation of a species may be. Using a specific species example, show an instance in shich natural selection has caused a species to move in a direction that could be considered "unprogressive."

Technology's effect Nature

Today's technology allows for scientists to sequence a child's DNA before he/she is even born. This knowledge allows the scientists to find any mutations that exist in the unborn child’s DNA. The existence of these mutations can give parents a look into how “normal” their child will be. However, scientists are unaware of how all these mutations will effect the child since the outcome of all the different mutations are unknown. This information can cause the termination of a pregnancy. How does this process affect nature and what are the positive and negative effects of it? In your explanation use Carroll’s ideas about natural selection and immortal genes.

Sexual Selection and Ultraviolet Light

In many cases, the forces of evolution have been shaped by sexual selection. In the book, Carroll mentions that "many birds have tuned an opsin to detect ultraviolet light" (110). What mutation(s) occur in birds for the birds to see in the ultraviolet range? How does this ability to detect ultraviolet light connect to how the females select mates? How would the different characteristics (relating to ultraviolet light) of the male be a measure of his fitness? One could relate this phenomenon to the courtship behavior we have learned about in the ecology unit (Campbell 1141). Please examine how sexual selection pertains to the themes of evolution or heritable information. 

Fossil Genes

On page 118, Carroll starts talking about a unique fish, Latimeria chalumnae, that was found many years ago but was preserved for the years to come. This fish has been labeled as a "living fossil" because the chances of finding and studying another one like it is very slim. Carroll compares this "living fossil" to the idea of "fossil genes". Why are fossil genes so important and how can they help us understand the behaviors and lifestyles of the species that are present in our world today?

Genealogic Trees

Explain the various genealogic trees that have been made, focusing on the more recent trees that have been approved by the scientific community. In doing so, explain the major differences between the trees and note the scientific reasoning behind the changes. Is there one tree that is more accurate than another? Why or why not? Why bother spending times on creating genealogic trees, especially when it will most likely be made obsolete in a few years? And of course, as this is AP Bio, use scientific terms and reasoning in your responses.

Cancer and Cancer Treatment

Cancer is a leading cause of death worldwide, predicted to become the number one cause of death in the year 2010. Certain types of cancers are always associated with specific gene mutations, such as the chronic myelogenous leukemia (CML). According to Carroll, CML is caused by the fusion of genes that "[disrupt] the normal control of a potent regulatory protein called the ABL kinase" (183). The ABL kinase signals the induction of apoptosis. How would the disruption of the ABL kinase promote cancer? How does the disruption relate to the cellular checkpoints that regulate the cell cycle? Please relate your response to the theme of regulation. 

The drug Gleevec targets the ABL kinase in the CML tumors. How do the CML cells become resistant to Gleevec? Also, how does the change in the ABL protein relate to the concept of the substrate-enzyme model? Please relate the response to the theme of structure vs. function. What methods should be pursued to avoid and/or treat resistant CML cells?

On the subject of ABL kinase, this online journal suggests that the kinase induces apoptosis: 

http://www.pnas.org/content/94/4/1437.full

Junk DNA

In chapter three, Sean Carroll discusses the structure and layout of DNA, noting the sequences known as introns, or non-coding segments. He refers to these sequences as "junk" DNA, saying that this DNA is merely an accumulation of informationless sequences; as such, he chooses mostly to ignore introns. However, many would protest such an abjection. Having thouroughly studied the mechanisms of DNA in Campbell chapter 17, do you agree with Carroll's assertation? Or, as some scientists now feel, do you believe there is a purpose to these seemingly useless sequences? Explain your opinion.

Archaea vs. Bacteria

Tom Brock found what he thought to be another kind of bacteria living in the hot springs of Yellowstone National Park. However, further analysis revealed that these oragnisms were actually as different from bacteria as eukaryotes. We now call these organisms Archaea. Using your understanding of the diversity of life, compare and contrast the two traits of bacteria and archaea (preferably one compare, one contrast), how these are selective advantages, and how these difference might have arisen.

The Age Old Question of Race

"Because Europeans are so variable, and lighter-skinned, we might also ask whether this is due to selection for light skin or the relaxation of selection in melanin production...it is possible that lighter skin is an adaptation to lower levels of sunlight. No matter which is the case, the evolution of human skin color and the MC1R gene demonstrates that as humans spread out across the globe, the conditions of selection varied in different regions, the amount and quality of sunlight being just one obvious variable," (Carroll 173).

Human skin color has always been a battle of debate. As evolutionary theorists and biologists come to explain the idea of natural selection as the perceived driving force upon skin color, new findings are beginning to occur. How have mutations and natural selection acted upon the specific gene MC1R? Weigh and consider the benefits/costs to each race. Is the MC1R gene the only contributing factor to variation within skin color? What other conditions of selection affect the evolution of human skin color? Finally, what do you think is the cause of the evolution of skin color: Natural Selection, Relaxation of Natural Selection, or Both? Please delineate the reasons for your though process. Again, as always, I urge responders to connect to the various themes of Biology: Structure/Function, Heritable Information, Interaction with the Environment, and Evolution. Please discuss the relationship(s) with mutations and natural selection.

The Great Compromise

"'Bad' mutations such as the sickle cell and G6PD mutations and the irreversible fossilization of genes can be favored in meeting the imperatives imposed by conditions of selection. It is all a matter of the immediate benefits outweighing the immediate costs, if only by a slim margin," (Carroll 186).

Of the many examples Carroll provides, one which is most intriguing is that of the sickle-cell disease that can provide greater protection from malaria. Malaria has had a great effect as a driving force upon the genetics of human populations. Carroll cites the evolution of the sickle cell gene as "the classic textbook example of natural selection in humans," (176). Although the sickle-cell gene may provide an advantage in protection from malaria, it provides a disadvantage as to the amount of oxygen a red blood cell (RBC) can carry (on the hemoglobin molecule). With such a disease, humans who carry/suffer from the disease have chronic pain and fatigue*. With such inadvertent effects, are the benefits with the development of the disease worth the costs (protection from malaria)? Applying this ideology to other diseases that could possibly develop or changes in the genome, are the benefits greater, or are the costs greater? If natural selection favors humans who carry the sickle-cell gene, could natural selection at one point favor the return of normal hemoglobin and RBCs? Under what conditions would this occur? Relate all answers to mutations and themes of genetic disorders, evolution/natural selection, mutations, and inheritance.


*Please take time to review this website as to inform yourself of sickle-cell anemia: http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html

Fishing in Hot Springs

If you were to go "fishing" (see pg. 70) at Yellowstone National Park hot springs (assuming it was legal), what species might you find- list at least two species examples? What characteristics would those species have? What domain of species would you have found? What are the different types (those that live in hot water, in salt, etc.) and name a specific species of each type. Discuss the conditions of the Earth that would lead to these types of species and their characteristics. How have the conditions of the Earth changed so that other species are born and relate to the theme of evolution. Finally, how have these species helped us discover new information?

Immortal genes

What are 'immortal' genes? Why have these genes been able to stay the same through a large amount of time without being altered by mutations? Name two functions of immortal genes, and explain why the genes serving those functions have survived in many different species.

Mutations

Describe the difference between synonymous and nonsynonymous mutations. Mathematically, which type of mutation is more common? In nature, which type of mutation do we see more often, and why is this so?

Selective Pressures

For every organism in every ecosystem, there are selective pressures that influence what traits are passed on and what traits die out based on selective advantages/disadvantages. Sometimes this selective pressure is simply due to competition for resources; one trait gives an individual an advantage in collecting food or water, for example. More often, the selective pressure is applied by "agents of natural selection," organisms that act to literally determine which trait is the fittest for survival; these agents are usually predators that consume less well adapted prey.
Cite an instance of selective pressure; state the nature of the pressures; discuss the effects of this pressure in the context of the fifth theme of biology, interaction with the environment, or the sixth theme of biology, regulation.

Natural Selection based from Mutations

The pigeon example mentioned through pages 53-54 helps to show how a mutation can actually help the selection of a certain species over another. The example illustrated is that some pigeons have a white rump that helps in maneuvering so as to evade falcons. What are two other examples through the book where a mutation has actually helped an organism's chance at survival? Also, Sean Carroll states that natural selection picks out the winners and losers of mutated organisms, please add in your response how a mutation, or lack thereof, has determined the status, whether a winner or loser, of that organism.

Prompt 2: "Unnatural Selection"(see page 254)

Prompt 2: "Unnatural Selection"(see page 254)

How has human behavior and actions caused certain traits to be selected for in a given population of organisms? Are these traits necesarily a selective advantage in a natural, non-disturbed environment? (Use the Bighorn ram and the Atlantic cod as examples)

Fossil Genes Versus Immortal Genes

Carroll classifies fossil genes as those that have evolved "as a consequence of the continuing action of mutation, over time, in the absence of natural selection," (123). Mutations and sexual recombination create variation within the genetic pool of a population. New alleles originate only by mutation and these can be either synonymous or non-synonymous. As a result, some mutations can cause redundancy and others have no significant impact. However, mutations that cause the erosion of genes contribute to fossil genes. With such fossil genes being left behind with the relaxation of natural selection, many "injurious variations," as Darwin would have stated, will become rampant. Are such "junk" fossil genes truly "injurious" if they (can) create new alleles over time? Are fossil genes only eroding away just as Carroll states? Is it possible to have a once functional gene become a fossil gene, and then the same fossil gene becomes new gene that has either an injurious or a beneficial effect? What if immortal genes became fossil genes-why or why can't it happen? Could fossil genes contribute to the creation, through mutations, of "new" immortal genes to last through future generations? Carroll uses the phrase "Use it or lose it." How does this affect immortal versus fossil genes as well as your response(s) to the previous questions? I urge responders to read Carroll 123 carefully as well as Campbell 454.

Color Blindness A Fossil Gene?

"Color blindness is common in humans-up to 8 percent of Caucasian males are color-blind due to abnormalities in their X-linked red/green opsin genes. However, in the wild, color blindness is very rare. A study of 3153 macaque monkeys revealed only 3 color-blind individuals (less than 0.1 percent). Given the high frequency of color blindness in humans (where color vision is certainly under less intense selection now, if at all) and the low frequency of color blindness in the wild macaque, this suggests that selection is maintaining color vision in these monkeys and other trichromatic species," (Carroll 105). To review and understand why a male is more likely to receive the mild disorder (color-blindness), please read Campbell page 278.

If color blindness is increasing, albeit a rare disorder inherited as a sex-linked trait, why has natural selection relaxed (Carroll 123) upon these genes (opsins MWS and LWS) that lead to the development of color vision? How could natural selection contribute to creating these genes into fossil genes? Could natural selection be relaxed more upon sex-linked genes causing greater disruptions through evolutionary history because males receiving one copy of their X-chromosome from their mother could receive disorders much more easily?

Most mammals are nocturnal and thus the need for color vision is not truly a selective advantage as opposed to having rhodopsin (Caroll 123-124). If humans are diurnal, why is there a greater loss of color vision as it may provide a selective advantage?

Gene transfer from Fish to Chimp

According to Sean Carroll, "The three opsin genes of humans (SWS, MWS, and LWS) are also present in chimpanzees and other apes. However, most other mammals have just two opsins and genes, while birds and fish have four or more."
Amy the Mad Scientist has the embryo of a chimpanzee (in G0 state) and a fish with 4 opsins. Amy knows the DNA sequence for the genes that code for all 4 fish opsins, as well as the 3 opsins in the chimpanzee, but she doesn't know where these genes are found in the respective genomes. Amy wants to substitute the 3 opsin genes in the chimpanzee with the 4 opsin genes in the fish, so that she can observe the mutant chimp for further studying. How will she get about this?
Please be very thorough in your response. Subsequent responses following the first should build upon the pervious response, so that in the end, we have a very detailed process of how Amy should do this...

Symbiotic Relationships...

At the beginning of Chapter 4, Sean Carroll describes the colobus monkey and its digestion. "Bacteria in the colobus'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". What type of symbiotic relationship is this? Why?
In addition, identify and explain each type of symbiotic relationship, with an example for each. For each example, explain how the relationship is selectively advantageous for at least one organism involved.

Prompt 1: Form and Function

Discuss how the form (protein structure) of an opsin affects the function of the opsin, specifically referrencing various opsin proteins. Then, evaluate the functions of the various opsins as a selective advantage for a given organism.

Transposon

In the course of 525 million years of vertebrate evolution, the opsin gene has gone from 5 opsins in lampreys to 4 opsins in fish, reptiles, and birds to 2 opsins in non-primate mammals and finally to 3 opsins in primates. Does the high frequency of the opsin gene’s deletion and duplication during vertebrate evolution indicate that the opsin gene is a transposon? Discuss other incidents where the duplication and/or modification genes contributed to an organism’s success.

Color Vision - Good or Bad?

The presence of five opsin genes in primitive lampreys and four opsin genes in birds, reptiles, and fishes indicates that color vision evolved early on in vertebrate evolution. Non-primate mammals, higher up on the evolution tree than fish or reptiles, only have two opsins. Thus fishes, reptiles, and birds have full color, trichromatic vision while non-primate mammals have dichromatic vision and can only see the visible spectrum from blue to yellow (no red or green). Sean Carroll postulates that the loss of color vision in non-primate mammals was due to the nocturnal lifestyle of early mammals. Color vision might have been unnecessary but was it so detrimental that natural selection would eliminate it from the early mammalian branch? Wouldn’t it have been more advantageous for mammals to fine tune their three or four opsins to fit their nocturnal needs rather than eliminate opsins?  

Block Mutations vs. Single Letter Mutations

Throughout chapter one of the book, Sean Carroll mentions two distinct ways in which mutations can arise (specifically p 33). A simple manner is single-letter mutations, where letter by letter genes are changed, creating different genes, creating different proteins, creating different phenotypes, creating selective advantages. Another mode by which genetic mutation can occur is by entire segments of genetic material relocating themselves within the genome, through transposition (in other words, these genes are transposons). We see this latter type in the development of the antifreeze gene, coding for proteins that prevent the icefishes' blood from freezing.
Given your knowledge of the various effects of different types of genetic mutations, discuss the possibilities and implications that follow with each type of mutation.

Traits from Common Ancestors

Sean Carroll says that there exists a "descent of all living species from common ancestors," implying that different groups of living things share certain traits which came from a common ancestor between the groups. Using your knowledge from previous units we have studied, choose EITHER two phyla of animals OR two kingdoms and note at least three similarities derived from a common ancestor between the two groups, and three differences between the two groups.

Prompt III

Genetic diseases are found in all human populations. Some diseases such as Tay-Sachs disease and sickle-cell disease occur more frequently in certain populations such as Ashkenazi Jews and African Americans respectively. Does this phenomenon indicates that the genetic mutations for these particular diseases occurred in our hominid ancestor or that the mutation arose independently after the human race had diversified?   

Huxley vs. Darwin - Natural Selection

Biologist Thomas Huxley believed that natural selection took place on a bloc-by-bloc basis, essentially that evolution took place involving large discontinuous differences among individuals. How does this differ with natural selection proposed by Darwin? Which type of selection is correct? Why?

Antarctic Icefish

Describe the major anatomical developments that occured to certain species of fish during the time that the oceans cooled significantly. What anatomical developments specifically occured during the evolution of the Antarctic Icefish? How did the environment affect these changes?