Notes
1. Carol Cleland, “Historical Science, Experimental Science, and the Scientific Method,” Geological Society of America 29:987-990, 2001.
2. Peter Godfrey-Smith, 'Theory and Reality: An Introduction to the Philosophy of Science (Chicago: University of Chicago Press; 2003), pp.
57-74.3. Samir Okasha, Philosophy of Science: A Very Short Introduction (Oxford: Oxford University Press; 2002).
4. Massimo Pigliucci, Nonsense on Stilts: How to Tell Science from Bunk (Chicago: University of Chicago Press; 2010).
5. Godfrey-Smith, Theory, pp. 57-58.
6. Pigliucci, Nonsense, p. 302.
7. See, e.g., Godfrey-Smith, Theory, chapters 4 and 10.
8. Okasha, Philosophy, p. 23.
9. David J. Glass, Experimental Design for Biologists, 2nd Ed. (New York: Cold Spring Harbor: Cold Spring Harbor Press; 2014).
10. Thomas Kuhn, The Structure of Scientific Revolutions, 2nd ed. (Chicago: University of Chicago Press; 1970).
11. Godfrey-Smith, Theory, pp. 57-62: “puzzling.”
12. “Mob psychology,” Imre Lakatos, quoted in Godfrey-Smith, Theory, p. 103.
13. See Godfrey-Smith, Theory, pp. 150-154, for discussion of Quine's views and the issue of uniquely philosophical answers to questions of scientific belief.
14. Scientific consensus on human activity being the main cause of climate change; see http://iopscience.iop.org/article/10.1088/1748-9326/11/4Z048002; Naomi Oreskes and Erik Conway, The Merchants of Doubt: How a Handful of Scientists Obscured the Truth on Issues from Tobacco Smoke to Global Warming (New York: Bloomsbury Press; 2011), epilogue.
15. Kuhn, The Structure of Scientific Revolutions
16. Max Planck: “one funeral at a time.” Visit https://en.wikiquote.org/wiki/Max_Planck.
17. David A. Miller, Critical Rationalism: A Restatement and Defense (Chicago: Open Court; 1994), p. 7; see also Karl Popper, The Logic of Scientific Discovery (New York: Routledge; 2002), p.
17.18. Deborah G. Mayo, Statistical Inference as Severe Testing (Cambridge: Cambridge University Press; 2018). Mayo believes that Popper errs by not specifying exactly what he means by “severe” testing of hypotheses, which leads him to an untenable “demarcation problem” because it focuses his attention on whether or not a theory, rather than the methods of evaluating it, are “unscientific.” Her argument gives rise to a straw man about the likelihood of cluttering of science with “nutty theories.”
19. Irene Lacal and Rossella Ventura, “Epigenetic Inheritance: Concepts, Mechanisms and Perspectives,” Frontiers in Molecular Neuroscience, 11:article 292, 2018.
20. K. Laland, T. Uller, M. Feldman, K. Sterelny, G. B. Muller, A. Moczek, et al., “Does Evolutionary Theory Need a Rethink? Nature 514:161-164, 2014.
21. Miller, Critical, p. 7.
22. Ibid., pp. 38-45.
23. Malachi H. Hacohen, Karl Popper: The Formative Years, 1902-1945 (New York: Cambridge University Press; 2000).
24. Bryan Magee, Philosophy of the Real World: An Introduction to Karl Popper (La Salle, IL: Open Court; 1985), pp. 1-5.
25. Godfrey-Smith, Theory, pp. 60-61.
26. Robert M. Sapolsky, Behave: The Biology of Humans at Our Best and Worst (New York: Penguin Press; 2017).
27. Adolph Grubaum, “The Duhemian Argument,” reprinted in Can Theories Be Refuted: Essays on the Duhem-Quine Thesis, Sandra Harding (Ed.) (Boston: D. Reidel; 1976).
28. Sandra Harding (Ed.), Can Theories Be Refuted?: Essays on the Duhem-Quine Thesis (Boston: D. Reidel; 1976).
29. Thomas Edison, quoted in Frank Lewis Dyer and Thomas Commerford Martin, Edison: His Life and Inventions (New York: Harper & Brothers; 1910), volume 2 of 2, chapter 24: “Edison's Method in Inventing,” pp. 615-616. The anecdote is due to a long-time associate of Edison's named Walter S. Mallory. Cited in http:// quoteinvestigator.com/2012/07/31/edison-lot-results/.
30. Oswald Steward and Ruth Balice-Gordon, “Rigor or Mortis: Best Practices for Preclinical Research in Neuroscience,” Neuron 84:572-581, 2014.
S. C. Landis, S. G. Amara, K. Asadullah, C. P. Austin, R. Blumenstein, E. W Bradley, et al., “A Call for Transparent Reporting to Optimize the Predictive Value of Preclinical Research,” Nature 490:187-191, 2012.31. Wesley C. Salmon, “Rational Prediction,” The British Journal for the Philosophy of Science 32:115-125, 1981.
32. In some contexts, “realism” implies more than just the existence of a regular external world. Then, a scientific realist is someone who believes that the unobservable entities that scientists talk about—e.g., electrons, quarks—truly exist, whereas scientific anti-realists use concepts of unobservable entities as “convenient fictions” that enable theories to make accurate predictions. Anti-realists argue that we shouldn't worry too much about whether the unobservables actually exist or not. See Note 3, Okasha, Philosophy, pp. 58-76.
33. Karl Popper, The Logic of Scientific Discovery (London: Routledge Classics; 1959/ 2002), p. 250.
34. Salmon, “Rational Prediction,” p. 125.
35. Philosophers and physicists tend to see the problem that I'm calling “levels” of science in terms of the concept of limiting cases; see, e.g., https://plato.stanford.edu/ entries/physics-interrelate/#PhysSensRedu. Roughly speaking, when one theory, T2, subsumes another, T1, and T2 explains everything that T1 explains and goes beyond it to account for phenomena that T1 cannot explain, then T1 is said to be a limiting case of T2. So when the theory of quantum mechanics is applied to ordinary earthly masses and speeds, it predicts the same phenomena that Newton's mechanics predicts, so Newton's theory is a limiting case of quantum mechanics. Or, for a less rigorous biological example, take the Neuron Doctrine of Ramon y Cajal, which says that neurons are discrete, independent elements. Indeed, if you look at neurons through a conventional light microscope, then each one does seem to be an isolated individual.
However, if you use an electron microscope or modern, computationintensive, super- resolution optical methods you see that neurons are highly interconnected at the molecular level. I think it is fair to conclude that the Neuron Doctrine is a limiting case of the modern understanding (not yet a theory, I'm afraid) of neurons. Thus far the Neuron Doctrine provides a reliable framework for addressing problems in neuroscience, but already new higher resolution observations show that its simple framework will need to be replaced by a more powerful hypothesis.36. Karl Popper, Conjectures and Refutations (New York: Routledge; 2002), p. 152.
37. Mayo, Statistical Inference, Excursion III, Tour II note 3.
38. What is a swan? https://en.wikipedia.org/wiki/Swan. The indication that there are “six or seven” species of swan nicely makes the point here; evidently there is uncertainty about how many swan species there are.
39. Ernst Mayr, Towards a New Philosophy of Biology: Observations of an Evolutionist (Cambridge, MA: Harvard University Press; 1988).
40. Peter Godfrey-Smith, Philosophy of Biology (Princeton, NJ: Princeton University Press; 2011). Godfrey-Smith (Philosophy, p. 107) also emphasizes that, although he is uncertain as to whether the concept of “species” represents a “real unit in the natural world,” “species talk can be useful in biology.”