Wednesday, December 7, 2011

Other questions that the class had trouble with, and their explanations

I wanted to go through a bunch of the final exam questions to broadly address topics I wanted you to understand. Below are questions that less than 50% of the class got correct. If you have any questions, comments or concerns, please post a comment.

7. The remarkably high frequency of sexual reproduction in most taxonomic groups is paradoxical given what facts?
a. In sexual populations, females contribute to population growth
b. In sexual populations, individuals contribute only half of their genetic material to their offspring
c. In asexual populations, recombination is more frequent
d. A and B are correct
e. All of the above

The correct answer is D, this is the two-fold cost of sex. However, I gave full credit for all answers but C and E. Unfortunately, I think it would have been clearer if I had put "In sexual populations, ONLY females contribute to population growth".

8.  You find a species of bird with a ridiculously long tail in males that is clearly maladaptive for the organism's niche. You can conclude conclusively that:
a. The tail is a honest indicator of the males genetic quality
b. The tail catches the attention of the females because of sensory bias
c. Females prefer the costly trait because it means that their sons will be sexy
d. All of the above
e. None of the above

The correct answer is E. The key word here is "conclusively". In fact, A, B and C all could be true, but none of them are conclusively true. All three are mechanisms for the evolution of secondary sexual ornaments that may be maladaptive from a viability perspective.

9. Which of the following can result in a decrease in mean fitness in the population?
a. Stabilizing selection
b. Disruptive selection
c. Frequency-dependent selection
d. Balancing selection
e. Adaptive evolution

The correct answer is C, as in the Hawk-Dove game. I sense that most of you chose B because it "sounds bad". Don't fall into that trap, rely on what you know. Disruptive selection increases mean fitness, it just means that the extremes of the population survive the best.

11. The figure above is taken from Hanifin et al. (2009) with regard to prey toxicity of Rough-skinned newts and garter snakes resistance to those newts. Which of the following can you conclude from this figure?
a. Garter snakes are so resistant to TTX that there are rarely any fitness consequences to consuming them.
b. TTX is so high in most newts that the coevolutionary arms race with garter snakes could not be an explanation.
c. The coevolutionary arms race between newts and garter snakes generally ends with garter snakes winning.
d. Stabilizing selection favors an optimum ratio between TTX toxicity and resistance to be about 50%
e. none of the above

The correct answer is C. Not much to say about this one other than it was covered in the worksheet you did in-class, and reading the paper. Answer D was popular, but is gibberish. Stabilizing selection cannot select for a ratio between two different species' phenotypes. Both would have fluctuating or directional selection being applied on them during coevolutionary arms races, not selection to stay the same.

21. A Darwinian demon cannot exist because of the existence of:
a. Semelparity
b. Trade-offs
c. Senescence
d. Unstable equilibria
e. B and D are correct

B is correct. I suspect many of you chose E because of test-taking beliefs rather than because you thought unstable equilibria limit Darwinian Demons. Fundamentally, answer D doesn't actually mean anything in this context.

25. This modeling approach is especially useful for studying frequency-dependent selection
a. Game theory
b. Optimality theory
c. Quantitative genetic theory
d. Neutral theory
e. None of the above

The correct answer is A. Seemingly, every question that involved frequency-dependent selection was a struggle. Suggestions on how I could have made this concept clearer would be appreciated.

41. Helacyton gartleri, or HeLa cells, is a species under all of the following species concepts EXCEPT:
a. Biological species concept
b. Morphological species concept
c. Evolutionary species concept
d. Phylogenetic species concept
e. None of the above

The correct answer was D. Many chose A. However, unless you believe a human will mate with HeLa cells and produce viable offspring, you are wrong. B is wrong because HeLa cells on a petri dish look morphologically different than Homo sapiens. C is wrong because A is wrong, these species are distinct evolutionary species and will never interbreed again. D is the only one in which HeLa cells fail to be a distinct species. While HeLa cells are monophyletic, naming them their own species would make humans paraphyletic.

42. Which of the following is an ultimate explanation for why organisms senesce and die?
a. Antagonistic pleiotropy
b. Shortening telomeres
c. Oxidative stress
d. The failure of cellular repair mechanisms
e. All of the above

Answers B, C and D are proximate explanations. Only A provides an evolutionary explanation for aging.

44. SAT analogy time! Humans : Sexual reproduction
a. Viruses : coinfection
b. Viruses : infection
c. Viruses : Mutation
d. Viruses : Red Queen
e. Viruses : Virulence

I was going for A, but I realized that B is also potentially a correct answer and have given full credit to that question. I was hoping to draw a parallel between both being processes that allow for genetic recombination, but both also are processes that replicate the species.

51. Life history traits (which are usually complex, polygenic traits with many inputs) are characterized by:
a. Low heritability, but high genetic variance.
b. Low genetic variance due to constant directional selection
c. High heritability and low genetic variance
d. High phenotypic variance and high genetic variance
e. Low phenotypic plasticity and high heritability

It turns out that both A and D are correct, and have been given full credit.  B is wrong because life history traits actually have abundant genetic variance. C is impossible given the equation for heritability. E is false on both counts.

57. In general, if genetic drift were the only force acting on populations (there was no natural selection), we would expect to observe:
a. More morphological diversity than we observe today
b. Less morphological diversity than we observe today
c. About the same amount of morphological diversity that we observe today
d. Genetic drift is not strong enough to result in evolutionary change.

A is the correct answer. Many chose B. One student commented on their exam that we have not covered this in class. However, we did cover the example of human cranial capacity, and showed that even this extreme case of rapid evolution was easily explained by genetic drift. In problem set III we showed that genetic drift would change human body size far more than it has. Stabilizing selection and stasis are the dominant patterns we observe in nature, genetic drift would result in far more variability and variance than we observe today.

62. Consider a population with two alleles at a locus and an effective population size of 100. Assuming neutrality, what is the probability that the population will become fixed for only one allele at that locus?
a. 0
b. 1/100
c. 1/200
d. 1
e. It's stochastic so we can't know

Only 11% of you got the right answer. The correct answer is D. This looks similar to a question on the last exam, but you need to read the questions carefully. I don't mean to be asking trick questions here, just testing your understanding. The question on the last exam was "what is the probability of a new mutation drifting to fixation?", which would be in this case, 1/200. However, this question asks "What is the probability that ANY allele drifts to fixation?", which is 1. It's like asking "What is the probability that you become president?" vs. "What is the probability that SOMEONE becomes president?".

    What went wrong?


    One of the questions on the final exam I was a little dismayed to see that only 36% of the class got correct.

    Here is the question:
    49. Humans probably evolved directly from which of the following:
    a. Chimpanzees
    b. Gorillas
    c. Tiktaalik
    d. An ancient unicellular eukaryote
    e. Darwinius masillae (an early primate fossil)

    Across the board, even among the top students in the class, folks chose A. Why? What was confusing about this question? Humans did not evolve directly from chimpanzees, chimpanzees are an existing species. We share a common ancestor with chimpanzees. We did however, necessarily evolve from an ancient unicellular eukaryote (i.e. an ancient unicellular eukaryote is everybody's great ^ 500,000,000 grandparent, no chimpanzee that has ever existed is any sort of grandparent of any human being). As you leave this class, make sure that you understand the common fallacies that are made about evolution. Make sure you directly confront your misconceptions. We did not evolve from any species that exists today!! A less important concept this question was trying to address was that almost all fossils we find are probably not direct ancestors, but side branches close to direct ancestors.

    Tuesday, November 29, 2011

    Charles Darwin

    "Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science."

    -Charles Darwin

    Charles Darwin is thought to be the father of evolution. His most famous book is the Origin of Species by Means of Natural Selection published in 1859 and his most well-known theory is the idea of natural selection or survival of the fittest (Nale, 2010). Shrewsbury, UK is the birthplace of this naturalist. He was born into an educated family, with a father that was a doctor, and was one of three children. His older brother studied literature and the arts (Darwin, 2008). However, Charles did not always intend to become the scientist that we know him as. He was originally a student studying medicine, but he was not cut out to follow in his father’s footsteps. He then transferred to Cambridge to become a minister. While at Cambridge, his interest in zoology and geography lead him to relationships with professors in both the biology and geology department. After a trip to Wales with the geology professor, he went to survey South America on the Beagle (Landry, 2011). This is when Darwin started to become the scientist that we know him to be.

    The idea of Natural Selection had been around from before Darwin was born, but it was Darwin’s use of real life observations and data that allowed this concept to become accepted (Landry, 2011). Darwin contributed to the scientific world with many of this other works, including The Descent of Man. Published in 1871, this novel compares lower and more basic species with the construction and behaviors of humans (Landry, 2011). Each chapter moves to a higher level of understanding, starting with similar body construction, and ending with sexual characteristics and behaviors (Darwin, 2008). One thing most people don’t know about is his contribution to the marine sciences. Darwin was first person to document the origin of corals. While sailing on the Beagle, he made many evolutionary discovers about organisms in general, but he also research small coral polyps with geologists aboard the ship (Rainbow, 2011). Darwin also showed a special interest in barnacle species. He studied their adaptive reproductive abilities and the differences between multiple barnacle species. These observations along with many others gave more evidence to his works, specifically The Origin of Species (Rainbow, 2011).

    Some of Darwin’s other works include Coral Reefs, Effects of Cross and Self Fertilization on the Vegetable Kingdom, Geological Observations on South America, The Autobiography of Charles Darwin, The different Forms of Flowers on Plants of the Same Species, The Expression of the Emotion in Man and Animals, The Formation of Vegetable Mould Through the Action of Worms, The Voyage of the Beagle, and Volcanic Islands (Darwin, 2008). While alive, he received the Royal Medal, the Wallaston Medal, and the Copley Medal (Landry, 2011). Charles Darwin passed away April 19th 1882. Even though Darwin had died, he continued to receive many awards for his work and four of his seven children became respected scientists (Darwin, 2008).

    "The fact of evolution is the backbone of biology, and biology is thus in the peculiar position of being a science founded on an improved theory, is it then a science or faith?"

    - Charles Darwin

    Works Cited

    2008. Charles Darwin Biography. Received at

    2008. Charles Darwin: The Descent of Man Overview. Received at

    Darwin, C. (2008). Charles Darwin Quotes. Received at

    Landry, P. (2011). Charles Darwin. Received at

    Nale, J. (2010). Biotic Competition and Progress in the Works of Charles Darwin. Southern Journal Of Philosophy, 4836-42. doi:10.1111/j.2041-6962.2010.00019.x

    Rainbow, P. S. (2011). Charles Darwin and marine biology. Marine Ecology, 32130-134. doi:10.1111/j.1439-0485.2010.00421.x

    Evolution in Schools: 2 Landmark Trials

    Note: I do not know why the background changes to white half way through my post. I've tried editing several times to correct the problem, but blogger continues to publish the wonky colors. If you highlight the text you will be able to read it. Anyone who can tell me how to fix this problem, please leave a comment on the post.


    The saga of evolution and education should not be news to anyone. Individuals and groups opposed to evolution being taught in schools raise the battle cry at the drop of a hat, and their persistence is bordering on sociopathiological. Some simply want evolution to be banned from the science curriculum, but others have decided to push for the inclusion of religion (dressed in the sheep’s clothing of “Intelligent Design”) in the science classrooms of public schools. I’d like to take some time to acquaint you with two landmark cases that made it to court trial.

    The first of these trials is the State [or Tennessee] v. John Scopes, also known as “The Monkey Trial.” William Jennings Bryan sought to banish the teaching of evolution in schools as part of his bid for presidency. At the time, teaching evolution in a public school was against the law in Tennessee, but John Scopes, a high school biology teacher, assigned readings on evolution because he believed that biology cannot be taught without evolution. He even got these readings from the state approved biology text, Hunter’s Civic Biology. Scopes, in league with George Rappalyea, agreed to stand for trial in defense of teaching evolution. The defense team was extensive, and included Herbert and Sue Hicks, John Neal, Clarence Darrow, Arthur Hays, and Dudley Malone. The prosecution team consisted of A.T. Stewart, Ben McKenzie, and William Bryan Jr. The goal of the trial was to overturn the law prohibiting the teaching of evolution in schools. The turnout for the trial was so impressive that it had to be held outdoors on the courthouse lawn. Scopes was found guilty and fined $100, which please the defense because it allowed them the opportunity to appeal to the state Supreme Court. Sadly, this case ends in a rather anti-climactic manner. The original court decision was reversed on a sentencing technicality, and then dismissed from further action. It is counted historically, as a win for the pro-evolution movement, however. This case took place in 1925. More information on this trial can be found here, and there are several books published on “The Monkey Trial.”

    Fast forward to 2004, and we’re still fighting the same battle over evolution being taught in schools. This time the battle ground is in Dover, Pennsylvania and started when the school board passed a policy requiring science teachers to read the following disclaimer before teaching evolution:

    “The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part.

    Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

    Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.

    With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.”

    Science teachers and parents alike pushed back, with teachers sending in a formal response and refusing to read the statement, and parents filing case in court for the violation of the separation of church and state. An excerpt of the response from teachers:

    “Central to the teaching act and our ethical obligation is the solemn responsibility to teach the truth. Section 235.10 (2) guides our relationships with students and provides that "The professional educator may not Knowingly and intentionally misrepresent subject matter or curriculum."


    I believe that if I as the classroom teacher read the required statement, my students will inevitably (and understandably) believe that Intelligent Design is a valid scientific theory, perhaps on par with the theory of evolution. That is not true. To refer the students to "Of Pandas and People" as if it is a scientific resource breaches my ethical obligation to provide them with scientific knowledge that is supported by recognized scientific proof or theory.”

    The full text of the response can be read here.

    In contrast with the Stokes trial, which simply sought to ban evolution from being taught, the Dover trial (formally known as Kitzmiller v. Dover) was focused on the inclusion of “Intelligent Design” (ID) in the science classroom. Jerry Coyne, in his book Why Evolution is True (2009) mentions that the Dover trial was “billed as the ‘Scopes Trial of our century’,” and the trial is nicknamed “The Panda Trial” after the name of the ID book that was being offered up as the scientific counter to evolution, Of Pandas and People.

    This trial attracted as much attention as its predecessor, and the pro-evolution group was worried, since the judge for the trial, Judge John Jones III, was appointed by G.W. Bush and a conservative Republican. However, these fears proved to be unfounded as the following verdict was read:

    “It is our view that a reasonable, objective observer would, after reviewing both the voluminous record in this case, and our narrative, reach the inescapable conclusion that ID is an interesting theological argument, but that it is not science…In summary, the [school board’s] disclaimer singles out the theory of evolution for special treatment, misrepresents its status in the scientific community, causes students to doubt its validity without scientific justification, presents students with a religious alternative masquerading as a scientific theory, directs them to consult a creationist text [Of Pandas and People] as though it were a science resource, and instructs student to forego scientific inquiry in the public school classroom and instead seek out religious instruction elsewhere” (Coyne, 2009).

    The Panda Trial is an unambiguous win for the pro-evolution group, and its importance in school policy is ongoing as the battle for evolution education continues. More information on the Dover trial can be found here, and is based on the excellent NOVA documentary of the trial (in recreation) called Judgment Day: Intelligent Design on Trial.

    J B S Haldane: The Life of a Scientific Beast

    “I have no doubt that in reality the future will be vastly more surprising than anything I can imagine. Now my own suspicion is that the Universe is not only queerer than we suppose, but queerer than we can suppose.”

    -Possible Worlds and Other Papers

    John Burdon Sanders Haldane is well known for many achievements. Of his numerous achievements, his contribution to the founding of population genetics is most recognized, but to limit Haldane’s brilliance to so small a subject does him great injustice. Even attempting to summarize his life into words is somewhat of a fruitless act. From the time he was born in 1892 until his death in 1964, he dedicated his life and body to science.
    "My body has been used for both purposes during my lifetime and after my death, whether I continue to exist or not, I shall have no further use for it, and desire that it shall be used by others. Its refrigeration, if this is possible, should be a first charge on my estate."

    Haldane was born into a family of aristocrats and scientists. He inherited a knack for scientific self-experimenting from his father, John Scott Haldane, a Scottish physiologist known for his extensive research on the dangers of natural gases to the human body. During his early education, Haldane excelled at mathematics, and after graduating from Eton, received a mathematics scholarship to New College at Oxford. After being wounded during the First World War, Haldane was taken to India to recover, a place to which he would return in 1957.
    At Oxford, in order to relax from mathematical studies, Haldane attended E S Goodrich’s course in Zoology which led to his eventual study of genetics. In addition to his studies of genetics, Haldane took up the study of the classics and writing, allowing him to become one of the, still, few skilled scientific writers. A few of Haldane’s most well known publications include Daedalus (1924), Enzymes (1930­), Animal Biology (1929), The Causes of Evolution (1932), On Being the Right Size (1926), and perhaps the most influential of all his publications, A Mathematical Theory of Natural and Artificial Selection (1924). Haldane’s skill in writing stayed in him until his death. Even in India, his pupils noted that he was not only an extremely good writer, but spent a good part of the day writing letters and answering mail. “He believed that a written communication gave the writer time to think carefully before expressing his thoughts and was then less likely to be influenced by emotions. Also he felt that a statement in writing eliminated possible disputes in what had been said or not said….he was known to use certain abbreviations involving numbers and letters, for example, best wishes 2 U” (Dronamraju).

    Having a strong knowledge of mathematics allowed Haldane to become a leading contributor to the study of population genetics. He was a major contributor to the Modern Evolutionary Synthesis. In A Mathematical Theory of Natural and Artificial Selection, Haldane analyzed the processes of natural selection from a mathematical point of view. During his occupation at University College, London from 1937 to 1957, Haldane was able to devise methods to calculate human mutation rates, prepare linkage maps for human chromosomes, better understand different modes of inheritance, measure the degree or intensity of natural selection operating in human populations, study the effects of close inbreeding, and even developed a better understanding of nature and nurture and the genetic basis of psychological and other behavioral characteristics.

    Although much of Haldane’s work was theoretical, he was as much of a keen experimenter has his father. Early on in his scientific career, Haldane subjected his body to many rigorous and dangerous scientific experiments. He stated “An experimental animal is not capable of describing the physiological reactions of pain, smell and so on….and make no serious attempt to cooperate with the scientists” (Dronamraju). In one experiment to test the theory that carbon dioxide in the human blood enabled the regulation of breathing under different conditions, he ingested large quantities of bicarbonate of soda to raise the alkalinity in h is blood stream and drank ammonium chloride to raise the acidity. In another he tested the effects of carbon monoxide poisoning in mines, a subject his father rigorously studied.

    Haldane left University College, London in 1957 and moved to India where he stayed until his death in 1964. In the 1950’s, Haldane grew dissatisfied with his life in England, finding the political situation intolerable. Although many colleagues in England considered his move scientific suicide, Haldane quickly embraced the new customs. He became an Indian citizen and grew interested in Hinduism. To his pupils in India, Haldane’s life in India was a sort of second life to the one he had in England. In 1962, Haldane moved to Bhubaneswar, India to carry out his last projects before succumbing to cancer in 1964.

    Clark, Ronald. J. B. S.: The Life and Work of J.B.S. Haldane. 1st. Oxford University Press, 1984. Print.

    Dronamraju, Krishna. Haldane: The life and work of JBS Haldane with special reference to India. 1st. Aberdeen: Aberdeen Univeristy Press, 1985. Print.

    Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck: A Man with Too Many Names

    By: Lauren Wolf

    On August 1, 1744 Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck was born in a small village in the north of France called Bazentin (University of). He was born into a noble but un-wealthy family with a background rich in military service and was the youngest of eleven children. When Lamarck was eleven he enrolled in the Jesuit seminary at Amiens as his father expected his youngest son to become a priest (Bookrags). In 1760, after the death of his father, Lamarck purchased a horse and rode off to join the French Army who was campaigning in Germany at the time (Clifford). At the age of 17, while fighting in the Seven Years War, Lamarck distinguished himself and as acknowledgment of his actions on the battlefield was rewarded with a commission for bravery (Macroevolution). His given name, Jean-Baptiste Pierre Antoine de Monet was changed because of this and he became the Chevalier de Lamarck and was know as Jean-Baptiste Lamarck from then on (Macroevolution). After the war ended Lamarck continued to serve in the military until 1768 when he left because of an injury (Bookrags). After the military Lamarck worked as a bank clerk in Paris, during which time he began study medicine and botany.

    In 1778 he published a three volume book on French plant life which was known as Flore Française, in which he used a dichotomous key to identify each plant (Macroevolution). The book was highly praised. Afterwards he acquired a position at the Jardin des Plantes. In 1793 the Jardin des Plantes was converted to the Musée National d'Histoire Naturelle (Bookrag). The newly converted museum was run by twelve professors in different fields and Lamarck was appointed to the professor of zoology (Bookrag). He was also in charge of organizing the collection of animals and fossils without backbones, which he called invertebrates (Bookrag).
    In 1809 Lamarck published Philosophie zoologique, including his theory of transmutation about which he wrote "Nature, in producing in succession every species of animal, and beginning with the least perfect or simplest to end her work with the most perfect, has gradually complicated their structure” (University of). Lamarck did not believe in extinction. He thought that the disappearance of species was due to their evolution into new species and that continued progression of this process meant that “less perfect” organisms vanished (University of). Although Lamarck had to claim that organisms such as protists that were simple were under continuous generation (University of).

    In 1815 he published his first volume of Histoire Naturelle des Animaux sans Vertèbres and in 1822 he published his second volume (University of). This work included his evolutionary theory founded on four laws. The first law was the idea that organic matter had a natural inclination to increase in complexity and defended the notion that evolution advanced to create plants and animals that became more complicated over time (Hannaby). The second law described the influence of the environment and the continual needs of animals to use new movements resulting in the development of new organs (Hannaby). The third law sums up the principle of use and disuse. This says that reoccurring actions or lack of actions caused modifications to the size and strength of an animal’s body (Hannaby). The fourth law talked about Lamarck’s theory of acquired characteristics or “Lamarckism,” stating that characteristics acquired by animals in their life span could be passed on to future generations and that inheritance was essential to account for the continuing accumulation of traits over time (Hannaby).

    For most of his life, Lamarck and his theories were ignored by the scientific community. George Cuvier valued Lamarck’s work with invertebrates but discredited his theories of evolution as they opposed his own. Though Lamarck was married three times and had a total of eight children, most of his life was a constant battle with poverty (Scoville). To make matters worse, Lamarck lost his eyesight at age 65 but continued his work with the aid of his daughter (Bookrags). Lamarck died on December 18, 1829 and because his family was so poor, his books and works were auctioned in order to pay for his funeral in which he only received a rented grave that he was removed from five years later (Clifford). The location of his remains is unknown to this day. While many of Lamarck’s theories were proved incorrect, he is one of the first scientists to publish the concept of adaption and to acknowledge the idea that adaption occurred in order to help species better survive in their given environment.

    Works Cited:

    Clifford, David. "Lamarck (1744 - 1829)." The Victorian Web: An Overview. 14 Sept. 2004. Web. 28 Nov. 2011.

    "Jean-Baptiste Lamarck – Biography." Web. 27 Nov. 2011.

    "Jean-Baptiste Lamarck Biography |" | Study Guides, Lesson Plans, Book Summaries and More. Web. 27 Nov. 2011.

    "Jean-Baptiste Lamarck Biography – French Naturalist «" Web. 26 Nov. 2011.

    "Jean-Baptiste Lamarck." University of California Berkeley, 2006. Web. 26 Nov. 2011.

    Scoville, Heather. "Jean Baptiste Lamarck." Evolution - Natural Selection, History of Life on Earth, Darwinism, Lesson Plans and More! Web. 26 Nov. 2011. .

    *note: because most of the references begin with “Jean-Baptiste Lamarck…” I used the website or sponsor as internal references.