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Transcript
Lecture I. Practice Question Answers. 1. (4 pts) Questions on energy. a. Why is it necessary for organisms to obtain energy? Energy necessary for biological activity: growth, maintenance, reproduction, movement, etc.; more generally to locally reverse 2nd Law of Thermodynamics. b. How do green plants obtain energy? From the sun via photosynthesis. c. How do animals obtain energy? By eating plants or other animals (living or dead). d. What is the ultimate source of energy for all organisms? Conventional answer is “the sun”, i.e., photosynthesis at the base of the food chain. However, as we will later discuss, many microorganisms extract energy from inorganic molecules. The atoms (save hydrogen) of which these (and all other molecules) are composed 1 were produced via nucleosynthesis in ancient stars that later exploded. 2. (2 pts) The figure below shows some of the levels in the biological hierarchy discussed in introductory texts. List four additional levels that fit between genes and populations. Organelles, cells, tissues, organs, individuals, family groups. The lowest level, “genes,” would be better labeled “macromolecules.” 2 3. (1½ pts) Disorder in the Department of Entropy. List three things you could do to reduce entropy in the office. What would each reduction require? Repair the floor; re-hang the door, put the trash back in the wastepaper basket, etc. All require expenditure of energy. 3 4. (8 pts) Consider gas molecules in a box divided into two equal sized compartments by a permeable membrane. Let 𝑝1 be the fraction of molecules in compartment 1, and 𝑝2 , the fraction in compartment 2. The entropy, 𝐸, of the system is 𝐸= 𝑝1 log 𝑝1 +𝑝2 log 𝑝2 − log 2 (1) where log 𝑝1 is the common (base 10) logarithm of 𝑝1, etc. Note that by definition, 𝑝1 + 𝑝2 = 1. (2) a. What are the values of p1 and p2 in the figure? p1 = 5/15= .333… ; p2 = 10/15 = .666… . 4 b. Using Equation (1), compute E for p1 = .01, .10, .25, .5, .75, .9, and .99. p1 .01 .10 .25 .50 E .0808 .4690 .8113 1.000 p1 .75 .90 .99 E .8113 .4690 .0808 c. For what value(s) of p1 on [0, 1] is E minimal? E(0) = E(1) = 0. This one is tricky. Calculus students can use L’Hôpital’s rule to evaluate 𝐥𝐢𝐦 𝒑 𝒍𝒐𝒈 𝒑 and 𝐥𝐢𝐦(𝟏 − 𝒑)𝒍𝒐𝒈(𝟏 − 𝒑). Non𝒑→𝟎 𝒑→𝟏 calculus students can calculate E(p) for multiple p values successively closer to 0 and 1, thereby convincing themselves that 𝐥𝐢𝐦 𝒑 𝒍𝒐𝒈 𝒑 = 𝐥𝐢𝐦(𝟏 − 𝒑)𝒍𝒐𝒈(𝟏 − 𝒑) = 𝟎. 𝒑→𝟎 𝒑→𝟏 d. For what value(s) of p1 on [0, 1] is E maximal? E(0.5) = 1.0 5 5. (4 pts) Hoyle argued that the spontaneous origin of life, essentially because the time required to create biological complexity by random mutation vastly exceeds the time that was available. How might an evolutionary biologist respond? Evolution proceeds in small steps, each of which is accepted or rejected by selection when it first arises. Such a process proceeds much faster than if selection is deferred until all steps have been taken. For a whimsical analogy, go to http://www.blc.arizona.edu/courses/schaffer/182/george.htm. 6. (4 pts) Crudely, one can think of cells as “bags” of biological molecules that permit controlled molecular exchange with their environment. From the perspective of the Second Law, why should biological molecules be so packaged? According to the 2nd Law, chemicals diffuse down concentration gradients. Thus, a local concentration of biological molecules would be diluted (the biological molecules would diffuse out; water would diffuse in) absent a “bag” to separate it from the surrounding environment. 6 7. (4 pts) Why did Schrödinger imagine the information-bearing crystal to be aperiodic, i.e., why wouldn’t a “periodic” crystal such as NaCl (right) have sufficed? Table salt (NaCl) is a “periodic” crystal. A periodic crystal can only code for a limited amount of information; likewise a periodic DNA molecule. 7 8. (4 pts) Regarding cells and viruses: a. If cells from cells, whence cometh the first cell? Give two possibilities. b. Viruses lack most of the structure of even the simplest cells. Whence cometh viruses? Give two possibilities. a. 1. Originated de novo on earth after a period of chemical evolution. 2. Transported to earth by comets, meteorites, etc. (panspermia). b. 1. Descended from pre-cellular (more primitive than a bacterium) life forms. 2. Degenerate descendants of simple cells or their genetic material. 8 9. (4 pts) Regarding the evolution of multicellular organisms: a. In unicellular organisms, the cell is the organism; in multicellular organisms, cells are building blocks. How might the first multicellular organisms have evolved? b. If complete genomes are replicated when cells divide, how can one account for different cell types in multi-cellular organisms? a. Products of mitosis that failed to separate; alternatively compartmentalization of large cells with many nuclei. b. Different genes turned on or off during development. 9 10. (8 pts) Darwin and Alfred Wallace, the often neglected co-discoverer of natural selection, both imagined phyletic descent as a branching tree. By this, it is meant that any two living species have a unique common ancestor, and that, by extension, there is a universal common ancestor of all living species. Famous a. Does decent with modification necessitate a tree-like pattern of relatedness? b. Why or why not? 'branching tree” sketch from Notebook B (1837) was Darwin’s first attempt at illustrating his theory. From Shu, 2005. Guidance to Reading 'On the Origin of Species'. Peking University Press. a. By definition, Descent with Modification necessitates change, the “modification part. It does not, however, necessitate lineage splitting, i.e.., speciation. 10 b. Tree of Life assumes that that lineages split but do not fuse. This is often the case. But there are exceptions. For example, as we will later discuss, new species can result from hybridization. Likewise, viruses can move genes from one species to another, and at least some of the organelles in eukaryotic cells are descended from formerly free-living prokaryotes. Finally, as we also will later discus, the entire domain Eukarya may be the result of symbiogenesis. 11. (8 pts) Redraw Figure 20 under the assumption that the environment is never limiting, i.e., that reproduction and survival rates do not change with increasing population size. Do superior descendant varieties still exterminate their ancestors? If rates of reproduc11 tion and survival remain constant, both mutant and wild type grow exponentially. Therefore the mutant does not exterminate the wild type. On the other hand, wild type frequency goes to zero, as 𝒕 → ∞. 12. (8 pts) Regarding altruistic behavior, i.e., acting in a way that benefits another individual’s fitness at cost to your own: a. Why is this a problem for the theory of evolution by natural selection? b. Give three reasons why altruistic behavior might nevertheless evolve. a. Everything else being equal, selection will remove genes that reduce individual fitness. b. 1. Kin selection. Beneficiaries related to altruists. By increasing the fitness of kin, altruists promote the survival of their own genes. 2. Group selection. Altruistic behavior can enhance the probability of group 12 survival, i.e., groups with altruists may be more likely to survive than groups without, may compete less effectively In such situations, however, selection within the group will favor “cheaters” who benefit from the altruism of others, but do not themselves contribute. 3. Reciprocal altruism – I scratch your back; you scratch mine. Works in social species with individual recognition. 4. Societal rules of behavior, laws, etc. especially in man – see May (2009) for discussion. 5. Altruism may be only apparent, i.e., apparently altruistic acts, for example, helping parents at the nest instead of making your own in scrub jays, may allow young individuals to acquire parental skills that will increase reproductive success in future years. 13 13. (8 pts) As an example of unexpected relationships consequent to ecological complexity, Darwin (1859, pp. 73-74) argued that village cats can promote the abundance of red clover as shown below. Can you think of another example of complex ecological interactions that produce unexpected and/or important effects? 14 Two examples: a. “Keystone predators” promote prey species diversity by preventing one or more from out-competing the rest. Intertidal community studied by Robert Paine. The starfish, Pisaster, is the keystone predator. Without it, competition reduces prey species diversity i.e., the number of coexisting species declines. 15 b. Sea otters promote fish availability. Otter-urchin-kelp ecosystem. Protecting sea otters indirectly promotes the growth of kelp forests because otters eat sea urchins that graze kelp. Kelp forests also promote fish larva survival, and therefore indirectly make more fish available for species that eat fish. Unfortunately for fisherman, otters eat fish too. 16 14. (2 pts) What do you think Darwin and Wallace might each have had to say about the “little yappers” (below) that infest retirement communities? “Real” dogs (left) and “rodent” dogs (right), both shown in their native habitats, share a common wolf-like ancestor. Darwin would have emphasized the ability of breeder’s to produce dogs (via AS) that deviated from their presumptive wolf-like ancestor. Wallace would have emphasized that “rodent dogs” are unfit. They only survive because humans provide food, shelter, etc. 17 15. (4 pts) Regarding William Paley. a. Who was he? b. What was his iconic example? c. In what way does the existence of vestigial structures such as the human coccyx, undercut Paley’s argument? a. Wm. Paley (1743-1805) was an English minister and philosopher best known for his use of apparent design in nature as evidence for the existence of God. b. His iconic example was a watch. In Natural Theology (1809), he wrote as follows: “IN crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for any thing I knew to the contrary, it had lain there for ever: … But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer which I had before given … . [And] For this reason, … that, when we come to inspect the watch, we perceive (what we could not discover in the stone) that its several parts are framed and put together for a purpose … . 18 … the inference, we think, is inevitable, that the watch must have had a maker: that there must have existed, at some time, and at some place or other, an artificer or artificers who formed it for the purpose which we find it actually to answer; who comprehended its construction, and designed its use.” c. To the extent that vestigial structures serve no purpose, the argument of Design fails. 16. Male bighorn sheep contest with each other for mating privileges. Discuss the factors selecting for and against large horn size in this species. Favoring the evolution of large horn size is the fact that dominant males sire a disproportionate fraction of offspring. Opposing the evolution of large is the energetic cost of growing the horns and to the extent that horn growth and aggression are correlated, (both likely consequences of high testosterone), increased risk of injury. 19