Sample Final Examination Questions for Unsolved Problems, 2010

The final exam will be "Open Book", which includes free use of your own class notes,

{I solemnly promise to be fair in grading conclusions that I disagree with at least as favorably as I grade answers that happen to match my current opinions. In other words, please don't try to guess what I believe, and argue in favor of it. Strategically, you could be better off to present well-argued opinions that are different from mine. Please believe me about this. A. H.}

As these sample questions suggest, you will be very wise to review the summaries about Popper and Kuhn; But I do not suggest rushing to read the original books by either of these philosophers of science.

IT IS OK TO DISCUSS THESE SAMPLE EXAM QUESTIONS WITH ANY OTHER MEMBERS OF THE CLASS. (But please don't ask faculty members, graduate students or others, until after the exam.)

And please don't ask me to tell you the answers. I am willing to make hints or suggestions, or to clarify the questions, but not simply to answer them.

1) Compare and/or contrast Thomas Kuhn's opinions with what you have learned in this course about specific scientific questions, phenomena or experiments. For example, do beliefs about the causes of atherosclerosis correspond to Kuhn's ideas; Or do they fit elementary ideas of "The Scientific Method"? (From High School, or Intro. Biology)

2) What about Karl Popper's opinions, as compared with actual subjects (about atherosclerosis, multiple sclerosis, the mechanism of gene control, or any other combination of research subjects)?

3) What is the smallest number of alternative hypotheses that you would need to have, in order to design good experiments? Two? One? None? Can you design an experiment without at least one theory? ...That the experiment is designed to DIS-prove? ...That the experiment is designed to confirm? Your answer should include as many specific examples as you can think of.

4) Suggest examples from the past or current history (of one or more specific research subjects) in which a newly discovered phenomenon did NOT replace and disprove an earlier theory that had until then been confidently believed to have been proven true.

5) Make a list of as many examples as you can (perhaps starting with ulcers) in which there has been a major scientific breakthrough ("paradigm shift"), including for each example:

a) What is now believed.
b) What was previously believed.
b) The major change that has occurred (in how scientists explain each particular phenomenon)
c) The main evidence or experiment that caused the breakthrough.

6) If you had to make a bet about what major current biological belief will turn out to have been wrong, misleading or deeply misguided (including medical beliefs and treatments) which would you predict is wrong? The following are some possible examples: Gene therapy? "Adult stem cells"? Anti-cholesterol drugs? Self-tolerance by clonal selection? Hox genes as fundamental control phenomena in embryos? But you can choose any example that you want.

7) In your opinion, are Physics and/or Chemistry more advanced than Biology? In what respects? For what reasons? What changes would cause Biology to catch up?

8) Make a list of specific "Yes or No?" questions, the answers to which would advance medical science the most. (List these in descending order of importance, starting with those that would help cure the most people.)

9) Contrast what Kuhn says actual scientists spend most of their time doing, versus what Popper says good scientists should try hardest to do. (Include as many specific examples as you can from current and past scientific research.

10) Explain how cells' responses to each other's properties could produce spatial patterns that look exactly as if they were responses to diffusion gradients. (I explained this in class, with an example running on a computer; please don't ask me to repeat that explanation, unless you were sick those days. But you can ask other students to explain it to you; prior to the exam, of course).

11) What surprised you most, among the facts and principles that you learned about in this course?

12) Imagine that you now had to choose a topic, and plan experiments, to earn a Masters Degree or a PhD. What topic would you pick? Describe the experiments that you would plan to carry out, and what conclusions you would expect them to lead to.

13) Consider the following aphorism: "The more surprised you are by an observation, the more information it is trying to tell you! But the more difficult it will to interpret." Think of examples in which this is NOT true. As many as possible.

14) List as many surprising facts as you can about multiple sclerosis.

15) What good are computer simulations? For the purpose of experimental design? Is it possible to invent or interpret experimental results about complicated phenomena without the use of mathematical models? Please give examples pro and/or con.

16) What various different advantages did Watson and Crick have over Rosalind Franklin? Were there any of these advantages of which they did not take selfish advantage?

17) Imagine that Watson had been an ordinarily generous person: Write a page-length autobiographical description of how he synthesized facts and ideas that he learned from Franklin, Crick, Pauling, Delbruck, Bragg and others, leading to a Nobel Prize, shared between himself, Franklin and...who? Chargaff?

18) Why would Chargaff have been wise to invent hypotheses about how genes encode information?

19) Imagine another planet, on which life evolved so as to use proteins as the genetic material - with no DNA or RNA, just protein. Invent details as to how this could work. Would it be more practical to have life with just nucleic acids (and no proteins? Or the reverse? Why?).

20) Two bright-colored diagrams are on the course web site, illustrating how Eratosthenes actually did "measure" the diameter of the earth based on the lengths of shadows on a certain day at a certain place. Please explain the logical basis of Eratosthenes' measurements and calculations; and also explain how he could have misinterpreted these same observations as a measure of how far the sun is from the earth. Please relate this difference to Kuhn's ideas about paradigms, and how they channel our interpretation of data. (Feel completely free to discuss this question with other students before the exam. It's OK just to flat out ask another student to explain it to you; and likewise OK for you to explain it to them. Assuming you get the point, yourself! No fair giving them deliberately misleading explanations.)

21) a) To what extent were embryonic stem cells a discovery? (That something existed that had not previously been realized to exist.)

b) Or to what extent was stem cells' "discovery" more of an invention? (That damaged or lost cells of the body could be replaced from undifferentiated cells - equivalent to how blood cells are continually replaced by stem cells in the bone marrow?)

22) Invent different ways to produce antibody molecules that specifically fit the shapes of germs, while avoiding autoimmune diseases? (In addition to clonal deletion of lymphocytes that randomly created genes for binding sites that fit some "self" molecule.) For example, before you learned about clonal selection and the generator of diversity, how did you think people with type A blood avoided making anti-A antibodies?

23) Suppose that somebody took DNA from mouse B-lymphocytes that were being used to synthesize monoclonal antibodies, and "transformed" this DNA into mouse embryos at the one-cell stage, explain why it would be expected that some mice developed from these transformed embryos would only be able to make antibodies specific for the same antigen as the monoclonal antibodies were specific for. (In other words, make antibodies against that one antigen, but no others.)

a) What combination of phenomena would explain this result? (Explain your reasoning.)

b) If you mated such a mouse with a normal mouse, what would be the pattern of inheritance of this strange property of making antibodies against that same, specific antigen, but not making antibodies against any other antigen? (Explain your reasoning.)/

c) Suppose the monoclonal antibodies had been specific for binding to some "self" antigen of the strain of mice into which the DNA was "transformed". Why might some of the mice not be able to produce any antibodies at all.