I. Johnson s Darwin on Trial A. The Legal Setting (Ch. 1) Scientific Dimensions of the Debate This is mainly an introduction to the work as a whole. Note, in particular, Johnson s claim that a fact of evolution is vacuous unless it comes with a supporting theory (12). Why is it important to Johnson to undermine the distinction drawn by evolutionary biologists between the fact of evolution itself and the theory (Darwinian) marshaled to explain it? B. Natural Selection (Ch. 2) 1. Natural and Artificial Selection: the Analogy (17-20) a. Why does Johnson believe that What artificial selection actually shows is that there are definite limits to the amount of variation that event the most highly skilled breeder can achieve? (18) b. Why does Johnson believe that selective change is limited by the inherited variability of the gene pool. After a number of generations the capacity for variation runs out.? (19) c. Why does Johnson believe that Whether selection has ever accomplished speciation... is not the point? (19) 2. Natural Selection as a Tautology (20-23) 3. Natural Selection as a Deductive Argument (23-24) 4. Natural Selection as a Scientific Hypothesis (24-28) a. What is natural selection as a scientific hypothesis? (25) b. Why does Johnson believe that none of the evidence he considers for the creative effectiveness of natural selection provides any persuasive reason for believing that natural selection can produce new species, new organs, or any other major changes...? (27) 5. Natural Selection as a Philosophical Necessity (28-31) Why does Johnson believe the various adjusting devices he discusses in 9
this section (pleitropy, kinship selection, developmental constraints...) make it difficult to conceive of a way to test the claims of Darwinism empirically? (30) C. Mutations Great and Small (Ch. 3) 1. Micro and macro mutations (32-36) a. How does Johnson s respond to Dawkins suggestion regarding the gradual evolution of the eye? (34-35) b. Why does Johnson insist on the speculative character of the gradualist scenarios advanced by Dawkins and others? (36) 2. Macromutations based on micromutations (41-43) a. What is Dawkins point about mutations that although they may be large in the magnitude of their effects, turn out not to be large in terms of their complexity? (41) b. Why does Johnson not believe that a genetic engineering program which managed to alter the genetic program of a fish embryo so that it develops as an amphibian, presumably along the lines Dawkins envisions with his point about macromutations ultimately based on micromutations, would not constitute proof that amphibians could have evolved in such a fashion? How does he try to make his point with his analogy to a word processing program? (42-43) D. The Fossil Problem (Ch. 4) 1. What is the Fossil Problem and how did Darwin originally deal with it? (45-50) 2. Punctuated Equilibrium (50-54) a. What are the two characteristics of the fossil record that Gould, Eldredge, and Stanley s theory of punctuated equilibrium is meant to explain (50) 10
b. How does the theory of punctuated equilibrium attempt to explain these two characteristics of the fossil record? (52) (Note: Also see Speciational Evolution, pp. 192-193 of Mayr for another explanation of punctuated equiblibrium.) c. Johnson says that he sees no reason to doubt that punctuated equilibrium is a valid model for evolution in some cases. (53) What, then, is his problem with this evolutionary attempt to explain the fossil record? (53) 3. The Cambrian Explosion (54-56) (Also The Cambrian Explosion from Nils Eldredge s The Triumph of Evolution and the Failure of Creaionism (New York: W.H. Freeman and Co., 2000), 42-47) a. What is the Cambrian explosion and why is it a problem for Darwinian evolutionary theory? b. How does Eldredge call Johnson s conclusions regarding the lack of evidence for any intermediates into question, concluding that We now know that trilobites and other sorts of Cambrian life did not show up absolutely all at the same time all over the world; rather it apparently took a good 10 million years for the familiar faunas of the lowermost Cambrian rocks to become fully established. (Eldredge, 44-45) 4. A deception of this magnitude (58-62) Johnson claims that paleontologists have deceived the public into believing that the fossil record supports the Darwinian theory of evolution. How does he use Eldredge s account (cited on 59) to support this claim? E. The Fact of Evolution (Ch. 5) 1. How does Johnson challenge Gould s distinction between a fact and a theory of evolution? (66-68) 2. How does Johnson challenge Gould s appeal to observational evidence regarding microevolution as evidence for the fact of evolution? (68-70) 3. What is Gould s second argument for the fact of evolution which appeals to imperfections and how does Johnson respond to it? (70-72) 4. How does Johnson challenge the appeal to embryonic development as 11
evidence for the fact of evolution? (72-73) F. The Vertebrate Sequence (Ch. 6) 1. Fish to Reptiles (76-77) Johnson makes quick business of the transitions from fish to amphibian and amphibian to reptile. Note his objections, but we will focus in class on the other transitions he devotes more analysis to in the chapter. 2. Reptiles to Mammals (77-80) a. Why does Johnson consider the skull bone structure of the therapsids, which he accepts as intermediate between reptile and mammal, as insufficient evidence for claiming them to be evolutionary intermediaries between reptiles and mammals? (78) b. Why does Johnson consider the abundant documentation of the transition from reptiles to mammals which Futuyma refers to (78) as itself a problem for the Darwinian claim of the descent of mammals from reptiles? 3. Reptile to Bird (80-81) How does Johnson answer the question he poses on p.81: Archeopteryx is on the whole a point for the Darwinists, but how important is it? 4. From Apes to Humans (81-87) (for more background on the evidence regarding human evolution from apes, see Mayr, Ch. 11, How did Mankind Evolve?, in particular, 233-252) a. How does Johnson call into question the professional competence of physical anthropologists who document the fossil evidence for transitional intermediaries between apes and humans? (82-84) b. How does Johnson suggest the abundance of evidence regarding the evolutionary transition from ape to human is itself cause for suspicion regarding the validity of the evidence? (85) G. Science and Pseudoscience (Ch. 12) 1. Popper and the Falsifiability of Scientific Theories (147-151) 12
2. How does Popper propose to distinguish science from pseudoscience? What do we mean in speaking of the falsfiability criterion? 3. Darwinism as Pseudoscience (151-156) a. Why does Johnson believe Darwinism is a form of pseudoscience, that Evolutionary science became the search for confirming evidence, and the explaining away of negative evidence? b. What sorts of risky predictions does Johnson believe Darwinism would have to make before it could become a legitimate scientific hypothesis? II. Behe s Molecular Machines (Ch. 10) A. The Problem of the Eye and Beyond (242-247) 1. Note that Behe sees the problem he will raise for Darwinism as a continuation and deepening of the same sort of problem raised in the time of Darwin (indeed, raised by Darwin himself) of how a complex organ like the eye could have evolved gradually. 2. How are proteins necessary for life and the structure of amino acids necessary for proteins? (245) B. Irreducible complexity (247-252) 1. What does Behe mean by irreducible complexity? (247) 2. Why does Behe believe that An irreducibly complex system cannot be produced directly by slight, successive modification of a precursor system... (247)? Why does this entail that an irreducibly complex system could not have evolved through natural selection? 3. How do cilia provide an example of an irreducibly complex molecular machine? Note: There s no reason to develop a detailed knowledge of the biochemical working of cilia here. All we need is just enough to see how it exemplifies Behe s concept of an irreducibly complex system. (249-251) C. Intelligent Design (252-256) 1. Behe does not merely want to argue that there are many biochemical 13
processes at the molecular level that could not have evolved gradually through natural selection, but that they are they product of intelligent design? Why does he believe that the conclusion follows from the data itself - not from sacred books or sectarian beliefs? (254) 2. Why does Behe believe his conclusion that many biochemical processes are the product of intelligent design is consistent with is consistent with the operation of many of the factors cited by evolutionary biologists in their attempts to explain the development of life (though not, of course, consistent with their denial that intelligent design is one important factor)? (254-255) 3. Why does Behe believe that we are not drawing the conclusion that many biochemical processes are the product of intelligent design from what we do not know, but from what we do know? (256) III. Kitcher s Born Again Creationism (Ch. 1, 257-281) A. Why Literalism Failed (258-261) Note: this section reviews Kitcher s assessment of the failings of earlier creationists, based more in Biblical literalism than the new creationists. Read it for background, but we will focus in class on his criticisms of Behe and Johnson. B. Behe s Big Idea (262-268) 1. How does Kitcher try to answer Behe s claim that irreducibly complex biochemical processes couldn t have evolved through natural selection with his appeal to the common theme of evolutionary biology that constituents of a cell, a tissue, or an organism, are put to new uses because of some modification of the genotype? (263-264) 2. Why does Kitcher believe he simply has to illustrate the possibility of how a complex biochemical system could have evolved in order to answer Behe s objection? How does Kitcher believe that this is sufficient to show that the problem Behe is dealing with is simply an open problem of the kind that spurs scientists in any field to engage in research? (264) 3. Why does Kitcher believe that lacking the details of how the flagellum (the example he s using) is actually assembled... it s quite likely that any efforts to describe precursors to intermediates (to any fully developed complex biochemical system) will be whistling in the dark? (264-265) 14
4. How does this last point (#3) suggest that Behe s conclusion regarding biochemical structures as the product of intelligent design is, despite Behe s insistence to the contrary, an argument based on what we do not know? 5. Calculating Probabilities of Blood-Clotting Mechanisms (265-267) Kitcher s rebuttal of Behe s assessment of the high improbability of the evolution of a blood clotting mechanism is interesting, but as we have not read Behe s argument itself, we won t consider Kitcher s rebuttal in class. C. Contra Johnson (268-281) 1. The fact of evolution. (268-272) a. Are facts vacuous unless they come with supporting theories? (269) b. Can evolution be a fact without being something we directly observe? (270-271) c. How does Kitcher call into question what he describes as a typical kind of criticism Johnson levels against the evidence for the fact of evolution: his criticism of Basilosaurus as evidence an evolutionary transition from land dwelling mammals to whales? (271-272) 2. Burden of Proof and Standards of Evidence (272-277) a. Do we know for certain that evolution has taken place? (272-273) b. Is Archaeopteryx a confirmation of common descent or a lonely exception in the fossil record? (273-274) c. How does Kitcher respond to the two points Johnson makes in dismissal of the evidence for an evolutionary transition from reptiles to mammals: his demand to see evidence of a transition in the reproductive system and his charge that the evidence does not establish a single line of ancestral descent? (274-277) 3. Are evolutionary claims falsifiable? (277-281) 15
a. How does Kitcher challenge Johnson s Popperian view of science that what makes a scientific theory genuinely scientific is its vulnerability to refutation by single decisive experiments? (277-278) b. Is the fact of evolution protected from empirical testing? (278-279) c. How does Kitcher respond to Johnson s claim that Darwin made no risky predictions about the fossil record that might disconfirm it? (280-281) 4. Where s the Beef? (281-287) In the last section of his article, Kitcher turns the tables on Johnson and Behe, arguing that the possible creationist scenarios they might propose create more problems than Johnson and Behe believe they solve. It s worth reading, but given considerations of time we won t consider these critical remarks in class. IV. Murphy s Phillip Johnson on Trial (Ch. 18, 451-462) A. Basic Scientific Reasoning (452-453) 1. What is hypothetico-deductive reasoning? 2. Why does science often make use of models? What is a model? 3. Can hypothetical reasoning in support of a scientific theory ever amount to proof? B. Johnson on Natural Selection (454-457) 1. Why is artificial selection (selective breeding) needed as a model of the hypothesis that natural selection is capable of producing radically different new species? (455) What observations are needed to confirm the hypothesis, according to Murphy? Do they obtain? Does Johnson admit they obtain? 2. How does Johnson s dismissal of the importance of observations confirming the hypothesis of speciation through natural selection lead Murphy to claim that Johnson consistently fails to distinguish between evidence confirmatory of a hypothesis and a set of observations that 16
together are equivalent to a hypothesis? (457) C. Science and Auxiliary Hypotheses (457-462) 1. What does it mean to say that Theories (hypotheses) rarely or never face the test of experience standing alone and why does this make the falsification of a theory very difficult? (458) 2. How does Lakatos distinguish (according to Murphy) progressive from degenerative or ad hoc auxiliary hypotheses? (459) 3. Are the auxiliary hypotheses of Darwinian theory that Johnson points out progressive or degenerative? (460-461) 4. Why does Murphy believe that Johnson s reliance on Popper s criterion of falsifiability displays an inadequate understanding of the philosophy of science? (462-463) 17