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.