REVIEW QUESTIONS FOR THE FINAL EXAM1) If Watson and Crick hadn't published their DNA structure (or if they hadn't been born) then who else would have come up with the correct idea about how amino acid sequences are coded by nucleotide base sequences? (And please explain why).
2) In what sense did Watson and Crick invent hypotheses, compare predictions of their theories with observations, modify their theories to make the fit the data better, etc. with the difference that their "experiments" consisted of looking in books, talking to other scientists, and borrowing other people's research?
3) What are some specific examples in which Kuhn's ideas were most accurate? That can include progress being blocked by the dominance of a given paradigm.
4) Alternatively, please describe examples where scientific progress was most different from Kuhn's ideas.
5) What about Karl Popper's key concept of disprovability? Please either criticize or praise several biological theories, as regards their potential susceptibility to disproof. For example, to what degree did they "stick their necks out"?
6) Osteoclasts need to have a large area in order to seal off broad enough areas of bone surfaces to accumulate acid and enzymes between bone and osteoclast (analogous to fumigating a house or a tree with insecticide). Based on this need of osteoclasts, please invent one or more new strategies for curing or preventing osteoporosis in people.
8) In your opinion, what specific advances in knowledge would be most helpful in finding cures for autoimmune diseases? To discover a real cure, what you most need to find out IS WHAT? Please explain your main reasons for this opinion.
9) What is most misleading about the idea that the immune system can detect special properties of cells that are possessed only by "self". Do bullets work by detecting special properties of "targets"? When a bullet hits something you didn't aim at, is that because the bullet mistakenly detected "target-ness"at the wrong locations? Does the accuracy of a rifle depend how correctly it detects target-ness? Please think of a better analogy than my joke about detecting target-ness.
11) Why are macrophages so interesting? List their differences from most cell types. How could improved understanding and ability to control macrophages lead to treatments and cures for atherosclerosis? Ditto for osteoporosis? What other diseases might result from misbehavior of macrophages?
12) Invent possible reasons why macrophages respond in the opposite way than other cells to electric fields, hydrophilic surfaces, roughened surfaces, proteolytic enzymes and calcium ion concentrations. Suggest experimental tests for your hypothesis.
13) What are bioassays, and what do researchers use them for? Explain why.
14) Please explain the false assumption in the underlined part of the following quote from an encyclopedia:
15) Do antibodies "latch onto" antigens ...Because the shape of the binding site fits (is complementary in shape an charge distribution) to the shape of the antigen?
16) Argue pro or con: Frequent use of the words "recognize", "self" and "non-self" traps people's thinking in an outdated paradigm about the mechanisms of immunity and the causes of autoimmune diseases. Explain the paradigm, why it is out of date, and whether (and how) it holds back discoveries of cures for autoimmune diseases.
17) Would/could autoimmune diseases exist if the paradigm in the previous question were really how the immune system works? Your answer might include a description of an imaginary alternative cause of autoimmune diseases.
18) On what subject has your own opinion changed the most as a result of the content of this course? (and explain why).
19) What if Watson had never received a post-doctoral fellowship for study in Europe? Do you think that he or Crick would have made such a discovery? Discuss why, or why not.
20) Was Watson justified in spending money donated by the public for polio research for his attempts to understand DNA structure? (In your opinion, pro and/or con)
21) Suppose that life was discovered on another planet, and you were assigned the task of figuring out whether they had the equivalent of genes, and (if so) how those genes encode information and also copy themselves. Please include some mention of whether you would expect to find some equivalent of Chargaff's Rules.
23) Why could electro-osmosis of skeletal tissues be misinterpreted as piezoelecricity? What functions could these phenomena serve in the body? How could you distinguish between them? Please include explanations of the mechanisms of both.
24) To achieve replacement of missing body cells, which of the following do you need? (a) cells that have never differentiated, (b) cells that have reverted back to being undifferentiated, or (c) a method that can cause cells to switch from one differentiated cell type to another?
25) What additional functions, that nobody has discovered yet, might be accomplished by resting potentials or action potentials? Remember how much ATP gets constantly used up by all the more than two-hundreds differentiated cell types of the body. Surely so much energy can't be serving no function, can it? For nerves, muscles and oocytes, we know what functions are served by voltage depolarizations. It would be a major breakthrough to discover even just one additional function.
26) Some introductory textbooks claim that sizes of animal cells are limited by difficulties of getting enough oxygen and/or glucose to the cells. As far as I know, there is no evidence in favor of this idea, and quite a bit of evidence against it. Please suggest either experiments or other observations that support or disprove this theory. Also suggest what mistaken assumptions have caused this fallacy.
27) Regarding leg regeneration of salamander legs, cell marking studies show that regenerated muscles and cartilages develop from cells that had previously been parts of muscles and cartilages in the stump. Assuming that all differentiated cell types of regenerated legs likewise regenerate from cells their same cell type, argue pro or con that regeneration works by rearrangement of differentiated cells.
28) It is still not known whether or not leg regeneration in salamanders has the same basic mechanism as their original embryonic development. Please argue pro or con (or both?), displaying as much knowledge as you can, including knowledge indirectly related to regeneration.
29) H. V. Wilson believed that dissociated sponge cells either redifferentiate according to their random locations, or possibly that undifferentiated archeocytes (= stem cells) differentiate into whichever cell type is needed at their random location. What is a third possibility? How might Wilson's assumptions about cell sorting be related to the first sentence of question number two?
30) In the game "20 Questions", you try to identify an unknown something based on asking 20 "yes or no" questions about it. Please invent 10 such questions, the answers to which would be most useful in finding a cure for cancer, or a cure for autoimmune diseases, or a cure for the COVID-19 coronavirus. The questions must be "yes or no", and not something like "what causes spontaneous remissions." For each of your questions, explain why you expect the answer would be, or might be, so useful. What would you conclude if the answer to that question were "yes"? What would you conclude if the answer to that question were "no"?
31) Argue pro or con: so far, knowledge of the molecular cause of cancer (or multiple sclerosis) has been little or no help in treating or curing these diseases.
32) How might treatment of cancer and MS be helped by finding differences in the DNA base sequences (i.e. differences between people with one of these diseases, as compared with normal people)? [Question edited, November 13]
33) Please discuss what relevance the following has for cancer and autoimmune diseases: The first billion dollar drug was a stomach ulcer treatment, with temporary effects, which patients had to keep taking permanently. Meanwhile, during those same years, the medical mainstream strongly resisted use of an easily-testable, long lasting and cheap cure for ulcers (consisting of a combination of antibiotics and bismuth), and stomach ulcers killed six thousand Americans per year.
34) Without at least one hypothesis, you can't design an experiment. Nobody can interpret the meaning of the results of an experiment, except in terms of some theory. Explain why or why not, using examples from research topics studied in this course.
35) Popper has been criticized on the basis that what seems like a disproof in terms of one paradigm will usually make perfect sense in terms of some other paradigm. Discuss whether a phenomenon that disproves a theory depends on some other theory. Discuss examples in biology? Or argue that there aren't any examples.
36) Does it (should it?) help research scientists to learn about the Philosophy of Science? It what ways might it help? In what ways might it hinder?
37) Guess some particular scientific phenomenon, that is currently taught as fact, that you think is most likely to be disproven. Discuss your reasons, such as evidence against the current paradigm, lack of sufficient evidence in its favor, logical flaws, etc.
38) Predict (and explain your reasoning) two or three major breakthroughs that seem to you very likely to occur soon. Will these (probably?) be new facts, new interpretations of old facts, or new connections between "old" facts (that had already been discovered)?
39) For several years, Popper claimed that Darwinian Evolution wasn't truly "scientific" (because he believed that there were no experiments that could possibly disprove it, in the sense that its supporters could always invent a plausible explanation). Do you agree? What arguments can you make against such an opinion?
40) What have you been taught and/or learned in this course that is most directly contrary to something that you were taught in some other course? Please make lists of arguments and evidence on both sides of this difference of belief.
41) List examples of paradigm shifts from your own education, where you once accepted one set of related assumptions, but then switched to another set, and perhaps a third or a fourth. For example, what different sets of assumptions have you held regarding how people with type A blood manage not to attack it with antibodies? (In high school, I assumed this was somehow because of genetic linkage; what about you?)
42)What is misleading about the idea that the immune system can detect special properties of cells that are possessed only by "self"? Suggest why so many scientists believe this mistaken idea.
43) What evidence would prove that a given autoimmune disease is partly caused by genetic differences? What would prove that susceptibility to this disease results from differences in one particular gene? Explain your reasoning.
44) Hypothesize what event or environmental difference might affect the probability of a person getting multiple sclerosis.
46) What evidence proves that either bone formation or bone destruction, or both, are either stimulated or inhibited by physical forces imposed on living bone?
47) Compare the effects of stimulating formation of bone by osteocytes versus inhibiting the dissolving of bone by osteoclasts? By what combinations of experiments and molecular labeling could you find out which of these stimulations or inhibitions is the mechanism of a drug for treating osteoporosis.
48) Discuss, pro or con, or whatever mixture of both pro and con: Medical science tends to regard diseases as external to the body's structures and normal activities, ignoring the extent to which medical problems result from over-activities and other abnormalities of the body's own cells.
50) Are there any explanations for particular biological phenomena that you believe you, yourself, could have discovered significantly sooner than they actually were discovered if only you had realized one particular fact or principle?
51) What are needed most: New ideas or new observations? Discuss specific examples from current biology, and from the history of Biology.
52) Sometimes the vocabulary used in an area of biology is biased in favor of some theories and biased against other theories, sometimes making the alternatives seem illogical or improbable. Please discuss as many examples as you can think of, starting with immunology and the word "antigen".
53) Pro or con: The reason that many diseases cannot be cured is because we don't have enough knowledge about them. Or is it more because we don't figure out how to use the knowledge we have?
54) Describe Professor Harris' concept of shape homeostasis, and give examples of some of the phenomena that it is meant to explain. (Good arguments against the concept will earn more credit.)
55) Limb buds respond to being grafted back to the body in reversed orientation by branching into two or three distal ends. Try to explain how such branching can be interpreted as resulting from tissues "trying" to restore their normal neighbors.
56) Explain how gradients of chemical concentrations can be generated even without diffusion through cell membranes from the cytoplasm of each cell to the cytoplasm of adjacent cells.
57) Explain the true cause of the "zipper" adhesions apparently caused by long stiff filopodia poking out from some kinds of cells toward each other until they eventually contact other filopodia that have been poked outward from the sides of each cell's closest neighboring cells. Suggest experiments by which you could prove the true cause of these cytoplasmic protrusions.
58) What are some specific examples of properties that are scalars, and others that are second order tensors? What are the important differences between tensors of different orders?
59) Describe and explain why D'Arcy Thompson reached misguided conclusions as a result of treating second order tensor properties as if they were scalars.
60) Contrast Wikipedia's idea of the meaning of a "bioassay" in comparison with this course's description of using bioassays to discover which chemical causes some important biological effect.
61) Imagine that a combination of two chemicals with very different properties are needed to produce some important biological effect. Why would this prevent you from using a bioassay to identify either one of the two chemicals?
62) Invent methods to circumvent this problem, in the sense of becoming able to identify both chemicals.
63) Scientists use the word "chemotaxis" to refer to several (at least two) fundamentally different methods. Please explain the differences, including examples of cells that use each different category of chemotaxis.
Final question: Please invent and answer some question about a topic covered in the course, but which especially interests you and about which none of the questions on this list gave you a chance to demonstrate the excellence of your understanding or the depth of your insight (= that you wish I had asked)