#1) Which fact or principle surprised you most, among those that you learned about in this course?
Explain and analyze the reasons for your surprise. In particular, was it because new information directly contradicted something that you had been taught, or that you previously assumed? Perhaps your surprise resulted from a new perspective about new directions that research might take.

#2) Has this course changed your belief about future cures for cancer? In particular, do you now believe that a new cure for cancer is closer than you had previously thought? Or do you think a cure is farther away, than you thought before? And do you think the best chance of a cure is in a different "direction" (in the sense of the kinds of knowledge most needed.) as compared with your previous beliefs? Alternatively, if your new knowledge confirmed your previous beliefs, please explain in what ways, and for what reasons.

#3) 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.

#4) List as many surprising facts as you can about multiple sclerosis. For as many as possible of these surprising facts, suggest at least one way in which that fact might be useful for developing a new cure, or for improving treatments now in use. (And the more, the better.)

#5) Imagine that Watson had been an ordinarily generous person: Write an imagined page-length autobiographical description of how he synthesized facts and ideas that he learned from Franklin, Crick, Pauling, Delbrück, Bragg and others, leading to a Nobel Prize, shared between himself, Franklin and Chargaff. Your answer could be phrased as if it were his acceptance speech for his share of that Nobel Prize.

#6) Conversely, imagine a parallel alternative history in which the Brits stick together, freeze out Watson (despite him being co-author on the first Nature paper, with Crick), and the Nobel Prize had gotten equally divided between Bragg, Franklin and Crick. Write the first 3 or 4 pages of an imaginary autobiography by Watson, written 20 years later, describing how this could have happened, and what Watson's life would then have been like

#7) Watson and Crick had many advantages over Rosalind Franklin. List as many as you can.
Were there any of these advantages of which they did not take selfish advantage?

#8) 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?)

#9) Please read the Wikipedia articles on "War On Cancer" and on the meaning of the word "Druggable"; also see "Undruggable". A quote from the "War..." article:

"Though there has been significant progress in the understanding of cancer biology, risk factors, treatments, and prognosis of some types of cancer (such as childhood leukemia) since the inception of the National Cancer Act of 1971, progress in reducing the overall cancer mortality rate has been disappointing. Many types of cancer remain incurable (such as pancreatic cancer) and the overall death rate from cancer has not decreased appreciably since the 1970s."

Would I be unfair to claim that that the "war" was a political campaign to accomplish two related goals?
a) To convince the public that cancer research was soon going to be increased and/or improved?
b) To re-channel NIH research money more narrowly toward virology, and genetic abnormalities of cancer cells? Please explain your conclusions and opinions.

#10) Many people are infected by Helicobacter, but for some reason don't get ulcers. Suppose that everybody was infected by these bacteria, but that they only produced ulcers in people who worried a lot (which is actually NOT true, but suppose it were), then would you say, or would most people say, that worry really is the cause of ulcers? You can argue both pro and con, in the sense of explaining logical reasons why people might reach one conclusion, and then also explaining logical support for the opposite conclusion. Or you could frame your answers in terms of people's beliefs about causes of particular other diseases.

#11) Suppose that Helicobacter hadn't been curable by any antibiotics then available, so that curing ulcers had required discovery and development of an entirely new kind of antibiotic,

    (A) then explain how living Helicobacter could have been used in a bioassay for discovering these new antibiotics.

    B) Explain why pharmaceutical companies would have helped, encouraged and financially supported the research of those two Australian blighters (and more people would have been cured 5 or 10 years earlier)

#12) 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.

#13) Suggest examples from the past or current science breakthroughs in which a newly discovered phenomenon replaced and/or disproved an earlier theory that had until then been confidently believed to have been proven true.

#14) In contrast to the preceding question, make a list of scientific breakthroughs in which the discovery filled in a blank spot on the map, in the sense that scientists had realized there was some major phenomenon that they just didn't understand at all. For example, heat shock proteins had been known for decades before it was realized that their function was to catalyze renaturation of denatured proteins. (Scientists knew that they didn't know what function these proteins served).

#15) Speculate about why so many people are intuitively attracted by the idea that the immune system works by distinguishing whether molecules are self or non-self, and selectively attacking any molecules that are non-self. For some reason, a huge percentage of the public believes this. Even the majority of biologists believe it, although it has never been one of the "Kuhnian" paradigms that were at any time believed by immunologists. In other words, it is not even out of date; it is a product of the "parallel universe" of introductory biology textbooks, with their many junior college fallacies, that textbook authors faithfully copy from each other. One explanation somebody suggested to me is that "It's easier to understand that way."

#16) 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.

#17) 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?

#18) 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.)

#19) 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).

#20) 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.

#21) A classic scientific discovery of ancient times was Eratosthenes' very accurate measurement of the diameter of the earth, based on the distance from Alexandria to what is now the site of the Aswan Dam, combined with the angular position of the sun in the sky on a certain day.

Based on the two diagrams in the link below, of a round earth and a flat earth, explain how and why a person who believed the earth was flat, instead of round, would have interpreted the same observations of angular position of the sun as proof that the height of the sun above the earth is about 4,000 miles, and as supporting the theory that the earth was flat.

Eratosthenes diagrams


More questions have been added December 3: second set

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