The Two Cultures and Systems Biology: How Philosophy Starts Where Science Ends

Abstract

The gap between Science and the Humanities becomes tangible when they both attempt to address the same problem. One such case is relationship between Life and biological molecules. Traditionally, molecular biology has attempted to explain biological processes in terms of physicochemical characteristics of individual macromolecules. The new science of systems biology largely ignores the molecular characteristics of specific molecules and endeavors to analyze biological processes through the relationship between thousands of molecules. On the face of it, the difference between the molecular and the systems approach to biological research corresponds to the tension between the reductionist and the emergentist view in the philosophy of biology. However, a closer analysis reveals that experimental science and philosophy are concerned with different aspects of the problem and therefore search for different solutions. A main reason for this is the difference in their respective concepts of “question” and “answer”, which is essentially unbridgeable.

Notes

Notes

1. Roger Kimball, “‘The Two Cultures’ Today,” The New Criterion 12.6 (1994).

2. Nicholas D. Kristof, “The Hubris of the Humanities,” New York Times (2005).

3. Tim Adams, “The New Age of Ignorance,” The Observer (2007).

4. Ibid.

5. See, for instance, the analysis and attack of the antiscience position of the “academic left” in Paul. R. Gross and Norman. Levitt, Higher Superstition: The Academic Left and Its Quarrels with Science (Baltimore, MD: Johns Hopkins University Press, 1998). The book was originally published in 1994. In the preface to the 1998 edition the authors already identified a new enemy of science in the political right.

6. Kimball, “‘The Two Cultures’ Today.”

7. Gross and Levitt, Higher Superstition. See, for example Keith M. Ashman and Philip Baringer, After the Science Wars (London: Routledge, 2001). Probably the best known battle of these wars was the Sokal Hoax, when an American physicist, Alan Sokal, wrote an article “liberally salted with nonsense” and sent it to a leading journal of cultural studies, thus exposing the scientific ignorance of the editors and their antiscientific “preconceptions.” Alan Sokal, “A Physicist Experiments with Cultural Studies,” Lingua Franca 6 (1996): 62–64.

8. For recent reviews of the debate, see Alex Rosenberg, “Reductionism (and antireductionism) in Biology,” in The Cambridge Companion to the Philosophy of Biology, ed. Michael Ruse (Cambridge: Cambridge University Press, 2007),120–139.

9. See Francisco J. Ayala and Theodosius Dobzhansky, Studies in the Philosophy of Biology: Reduction and Related Problems (Berkeley, CA: Macmillan, 1974); David L. Hull, Philosophy of Biological Science (Prentice-Hall, NJ: Prentice Hall, 1974); Ernst Mayr, Toward a New Philosophy of Biology: Observations of an Evolutionist (Cambridge, MA: Harvard University Press, 1988); Alex Rosenberg, “Reductionism Redux: Computing the Embryo,” Springer 12 (1997): 445–70; David L. Hull and M. Ruse, The Philosophy of Biology (Oxford: Oxford University Press, 1998); Elliott Sober, Philosophy of Biology (Boulder, CO: Westview Press, 2000); Paul Thompson, “The Revival of ‘Emergence’ in Biology: Autocatalysis, Self-Organisation and Mathematical Necessity,” CEEOL (2003): 217; Alex Rosenberg and David M. Kaplan, “How to Reconcile Physicalism and Antireductionism about Biology,” Philosophy of Science 72 (2005): 43–68; Alex Rosenberg and Daniel W. McShea, Philosophy of Biology: A Contemporary Introduction (London: Routledge, 2007).

10. Timothy O’Connor and Hong Yu Wong, “Emergent Properties,” in The Stanford Encyclopedia of Philosophy, ed. E. N. Zalta (Stanford, CA: Stanford University Press, 2005).

11. Jason S. Reobert, “Philosophy of Experimental Biology,” Perspectives in Biology and Medicine 50.1 (2007): 3.

12. Fred C. Boogerd, et al., Systems Biology: Philosophical Foundations (Amsterdam: Elsevier, 2007).

13. Biology can provide test cases for general questions of the philosophy of science, on the nature of theory, experiment, theory change, explanation causation and prediction. See Kim Sterelny and Paul E. Griffiths, Sex and Death: An Introduction to Philosophy of Biology (Chicago, IL: University of Chicago Press, 1999). It can also deal specifically with biological theories and findings, which is my main concern here.

14. Many textbooks on the philosophy of biology focus on evolution and evolutionary theory. See, for instance, Sober, Philosophy of Biology; Mayr, Toward a New Philosophy of Biology, where the first chapter deals with “cause and effect in biology” and the subsequent eight chapters discuss evolutionary theory. Others devote chapters both to evolution and to the question of the physical basis of biological phenomena: Hull, Philosophy of Biological Science; Hull and Ruse, The Philosophy of Biology, Rosenberg and McShea, Philosophy of Biology.

15. Arguably, most philosophers of biology are preoccupied with problems that are as remote from the bench as philosophy of time is remote from experimental particle physics. However there are cases in which the philosopher and the experimental biologist deal with the same problems. For instance, the definition of “gene” preoccupies both philosophers and computational biologists who design algorithms for identifying genes in genomic sequences; epigenetic inheritance is the research subject of both philosophers and experimental biologists. Systems biology provides a good test case where biologists introduce a new way of analysis that seems to address the concerns of many philosophers, and still, as we shall see, scientists and philosophers see in systems biology very different things.

16. Erwin Schrodinger, What Is Life: The Physical Aspect of the Living Cell; With, Mind and Matter;  & Autobiographical Sketches (Cambridge: Cambridge University Press, 1992).

17. Mayr, Toward a New Philosophy of Biology.

18. Ibid.

19. Rosenberg, “Reductionism Redux: Computing the Embryo,” 446.

20. Théodora Niault, Khaled Hached, et al., “Changing mad2 Levels Affects Chromosome Segregation and Spindle Assembly Checkpoint Control in Female Mouse Meiosis I,” Public Library of Science ONE 2.11 (2007): e1165.

21. See, for example, Ayala and Dobzhansky, Studies in the Philosophy of Biology.

22. Richard C. G. Langton, Artificial Life: An Overview (Cambridge, MA: MIT Press, 1995).

23. Sunny Y. Auyang, Foundations of Complex-system Theories: In Economics, Evolutionary Biology, and Statistical Physics (Cambridge: Cambridge University Press, 1998).

24. Most philosophers also did not preach for changes in scientific method to accommodate their antireductionist approach.

25. Nigel Williams, “Biologists Cut Reductionist Approach Down to Size,” Science 277 no. 5325 (1997): 476–77.

26. Sandra Blakeslee, “Some Biologists Ask ‘Are Genes Everything?’” New York Times (1997).

27. As mentioned, there are cases that fall within the blurry boundaries between Science and the Humanities. Formal logic, for example, which lies somewhere between math, philosophy, and computer science, also attempts to provide quantitative predictions. Arguably, though, the philosophical studies in logic focus less on developing the formalisms required for such predictions, and more on their implication and on the definition of terms.

28. Reka Albert, Hawoong Jeong, et al., “Error and Attack Tolerance of Complex Networks,” Nature 406 n. 6794 (2000): 378–82.

29. R. Milo, S. Shen-Orr, et al., “Network Motifs: Simple Building Blocks of Complex Networks,” Science 298 no.5594 (2002): 824–27.

30. Hans V. Westerhoff and Bernard O. Palsson, “The Evolution of Molecular Biology into Systems Biology,” Nature Biotechnology 22.10 (2004): 1249–52.

31. See D. P. Dubhashi, “Systems Biology: A Paradigm Shift?” (Sweden: Chalmers University, 2007); Westerhoff and Palsson, “The Evolution of Molecular Biology into Systems Biology”; M. Bentele and R. Eils, Systems Biology of Apoptosis, Springer (2005); J. H. F. Bothwell, “The Long Past of Systems Biology,” Blackwell Synergy 170 (2006): 6–10. Although not much has been written on this point by philosophers, it is safe to bet that most philosophers of biology would agree that systems biology does not constitute a paradigm shift.

32. Andrew Brown, In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite (New York: Columbia University Press, 2003).

33. Ibid.

34. For instance, evolution is studied both by scientists and by philosophers and historians. A good way to distinguish between them is to check whether the study can provide predictions, where “prediction” does not necessarily mean saying something about the future. Rather, it means providing a quantitative assessment of something that was not observed, based on an observation. To do this, one typically needs to identify rules that are fewer in number than the observations.