Genealogical Trees?

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

The Source Of All Variety Is Mutation

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

Independent Convergence

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

Return to Bouvet Island

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

Fitting into the World

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

The Evolutionary Arms Race

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

Complexity in Fruit Fly Wing Patterns

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

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

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

Wisdom Teeth

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

Overfishing and the Domino Effect

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

DNA Record

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

Ruminating Monkeys :D

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

Common ancestor

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

Speed of evolution

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

Sudden change in the sticklebacks

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

Fossil Genes

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

Are we evolving yet?

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

YES we are all mutants...

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

The relation between primates and humans

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

The organization of life and mutations

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

Ultraviolet Rays

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

Bighorn Sheep and Unnatural Selection

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

Melanic Moths

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

Selective Advantage

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

Gleevecs

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

Senses

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

Ice Fish and Hemoglobin

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

Heart Size and Metabolism

On page 24, Carroll says that icefish have "larger hearts and blood volumes than those of their red-blooded relatives." If icefish are ectotherms and therefore, by definition, have a lesser need for a large and complex heart than endotherms do due to their comparative lack of metabolic activity, what is the selective advantage of having such a large heart?

Malaria and CF

On page 179-181, Carroll speaks of how Malaria and the Typhoid fever bacterium greatly effected the abundance of both sickle cell disease and cystic fibrosis. The presence of these diseases, "shaped the evolutions of humans and may be responsible for the high incidence of particular genetic diseases" (180). In order to prevent these genetic mutations, drugs were administered to stop them at their source (by curing malaria or cf). My question is, is there any globally spread disease that has caused a beneficial mutation amongst the specimens it has infected? Are there any benefits to having an increased affinity to genetic mutations through disease? 

Endosymbiosis

On page 88, Carroll attributes our eukaryotic origins to the "fusion of genomes between an endosymbiont and its host". How is this possible? What key mechanisms would need to be involved for this fusion to occur? Is this fusion possible in an endosymbiotic relationship between eukaryotes?

SINES and LINES

On page 99, Carroll talks about how lots of our DNA is made up of short interspersed elements (SINES) and long interspersed elements (LINES). These elements are noncoding "chunks of junk DNA" that are created by accidental insertions. Carroll states that these rare DNA elements are important as landmarks to trace genealogy and to prove that two species of organisms came from a single common ancestor. Besides helping scientists track evolutionary relationships, why is long noncoding "junk DNA" such as SINES and LINES beneficial to organisms? Is it necessary for organisms to have noncoding DNA interspersed in their genome?

Timeline of Icefish Evolution

On page 28, there is a timeline of icefish evolution, along with events happening in their habitat. Discuss each adaptation and relate it to what happened in the habitat. Discuss why each adaptation occurred, and why it would be a selective advantage to the icefish.

Ultraviolet Vision of Birds

On pages 110-112, Carroll talks about how "many birds have tuned an opsin to detect ultraviolet light, and have evolved body markings that reflect light in the ultraviolet part of the spectrum." Carroll also states that "ultraviolet vision has evolved at least four separate times in birds." Why do you think ultraviolet vision and body markings that reflect ultraviolet light are so important to birds? Why has ultraviolet vision evolved in some bird species but not in others? Is it because these birds have a differet habitat or lifestyle than other birds? Also, why has ultraviolet vision evolved more in birds than in other vertebrate?

Fossilization of Human Olfactory Genes

On page 128, Carroll talks about how "about half of all our olfactory receptor genes are fossilized and incapable of making functional receptors." Also, Carroll states that there was "a striking correlation between the proportion of fossilized olfactory receptor genes and the evolution of full color vision." Which do you think came first in our ancestors: the fossilization of olfactory genes or the evolution of full color vision? In other words, do you believe that the evolution of full color vision reduced the necessity for many of our olfactory genes (relaxed evolution), or did the fossilization of these genes promote natural selection for full color vision in order for many of our ancestors to survive? Also, does full color vision give animals a better relative fitness than having more functional olfactory genes?

The Coelacanth

On page 118, it states that the ceolacanth was "a member of a group of fish with paired fins thought to be closely related to the first four-legged vertebrates and believed to be extinct since the end of the Cretaceous period 65 million years ago."  Therefore how was it discovered in 1938, about 70 years ago in the Cape Province of South Africa when it hasn't been seen for 65 million years?  Carroll describes it as a "living fossil," but how can a creature go extinct for so long and then appear so recently?  Can fossils preserve the DNA that is needed for it to reproduce again, or was this simply a lucky day when they found this fish?  Are there any other organisms that have been said to be extinct, but have recently been discovered again?  Why does this occur?

Hungry Ghosts

On page 228, Carroll discusses the educated people of communist society, and outlines how the Chairman Mao Zedong of Communist China destroyed his nation's agriculture by ordering close planting of crops, deep plowing, refraining from fertilizers, and extreme pest control. Explain how the Chinese's failure to learn from the Russians caused their crops to fail, why exactly their crops failed (or how each one of these things can cause plants to die), and how these things could have been avoided if simple Mendelian genetics could've been taught in school.

Color Vision

On page 95 it states that "Color vision begins when light of a particular wavelength strikes the visual pigments in our retina. These visual pigments are made up of a protein, called an opsin, and a small molecule called a chromophore."  So what happens when a decrease in vision or blindness occurs? Does opsin and chromophores decrease? Have these proteins always been in eyes of all species, or have they evolved through evolution? Are they a natural selection? Does opsin and chromophore play a role in the shape of the retina?

Preventing Mutations

On page 59 Carol lists 4 facts about mutations, that they either "(1) occur in regions of our D?Na that are empty of any meaningful information (2) fall in or near a gene and do not change how that gene works, (3) are compensated for by our carrying two seperate copies of most genes, or, (4) affect the gene in such a way that produces an effect within a tolerable range of variation." My question is, don't almost all of these facts mean that our bodies are designed to prevnt or prolong mutations? If so, what prime conditions, threats, or situations does it truely take for a mutation to "stick", to be benificial? If the "odds of adaptively useful mutations arising are very much on the side of nature," should we create more mutations that could lead to advantages later on in the evolutionary scale?!

DNA decay

Throughout this novel, Carroll talks about nucleotides decaying from the genome, and how this process is a result of the specific nucleotides losing importance in the genome as a whole. However, Carroll neglects to go into detail about this "DNA decay". Describe the process of "DNA decay" in depth and explain how this can attribute to mutations in the genes of that organism.

Armor Plates of Stickleback Fish

On page 56, Carroll discusses stickleback fish and their evolution pertaining to armor plates. The oceanic sticklebacks typically have 30 armor plates or more as a part of their body skeleton. However, in freshwater environments, "this number has been reduced to a range of from 0 to 9 plates". According to Carroll, "the selective advantage of plate reduction in lakes and streams may be due to greater body flexibility and maneuverability while swimming".
My question is why would freshwater fish need greater body flexibility and maneuverability as compared to the marine fish? Do the stickleback fish occupy a different niche in the ocean than fresh water? Also, the armor plates provide protection for the fish against predators. Why does flexibility and maneuverability outweigh the advantage of protection in the case of the freshwater sticklebacks?

Immortal Genes

On page 79 it says that "The genes these organisms all share have withstood more than 2 billion years of the steady bombardment of mutation and stand out as threads of text whose sequence and meaning have not changed significantly despite the bast differences among the species that carry them."  How can genes stay the same while the species differ so drastically?  The genes are immortal, as it says in the text, but what are some examples of such an organism that has many different species, but have many of the same strands of DNA?  How does an organism diverge so far that it doesn't appear to be part of the same species, yet it contains the same DNA?  What parts are therefore the same between those species if what we see is so different?

Original Triplet

On page 82 it says that "bases may be changing but their translated meaning is not."  So because the triplet pairs can be mutated but still code for the same protein then are the triplets that we know and study today different then those that existed a million or more years ago?  For example, on page 82 it says that TTA codes for leucine but also TTG, CTA, CTT, CTC, and CTG code for leucine, so my question is did the code for leucine used to be something very different than the TTA code that we recognize today?  If so, why has this dramatic change happened, in the future will TTA no longer code for leucine but a whole new and different triplet base code for leucine?

Bacteria "mix up"

On page 70, Carroll talks about how "Brock lumped all of his new species into the classification 'bacteria'" concerning his discovery of the hyperthermophiles. What characteristics do archaea exhibit that can be mistaken for bacteria? Also, how are bacteria and archaea different? Specifically describe some tests that can be done on these hyperthermophiles that would prove that they do not belong in the kingdom Bacteria. When creating tests, concentrate on how archaea are structurally different from bacteria (and all the other kingdoms for that matter).

Preservative force of Natural Selection

"The survival of individual genes over vast geological periods provides more than unimpeachable evidence of the preservative force of natural selection" (72)
What is the significance or the importance of the preservative force of natural selection? Why would it be important for different evolving species?

Reproducible Evolution

"Evolution is remarkably reproducible." (154) Why would it be important to different species for evolution to be reproducible? What would be some pros and some cons of the reproducibility of evolution? Why would it be important for genes to be able to change to code for a specific important characteristic for species in a certain area? Basically, what Carroll is saying is that species in a certain environment have the ability to evolve the same types of genes that code for a specific feature that allows those species to survive. Why would this be an important aspect of evolution of different species?

Cold Resistant Microtubules

"In mammals, microtubules are unstable at temperatures below 50 degrees F" (25). Although Carrol states that icefish DNA have evolved to code for proteins that construct microtubules capable of thriving at temperatures much lower than this, he does not explain how a micrtubule can funtion at these lower temperatures. What about the microtubule proteins in icefish are different from the microtubule proteins in all other mammals? Also, how does the new microtubule structure affect cell shape and function? Finally, are there any current applications for microtubules that can survive low temperatures in fields such as medicine or technology?

Fossil Records

Refer to page 72. "...two key elements of the evolutionary process -- the power of natural selection to preserve the DNA record and the descent of life from common ancestors."
Why is it important to maintain a fossil record of DNA? Why is fossil DNA present? Is it biologically important, aside from the fact that it's helpful for biologists to see what genes we have had and scientifically deduce the importance of these genes and the reason for their presence beforehand? Basically, is it biologically important when you don't think about people actually researching it? How is it important for our bodies?

Brains

Refer to page 65. "Our ancestors' brains doubled in size in 1 million years." Was it evolutionarily necessary for our brain size to increase? Why would it be evolutionarily necessary?