Skip to main content
SpringerLink
Log in

Explaining features of fine-grained phenomena using abstract analyses of phenomena and mechanisms: two examples from chronobiology

  • S.I. : Abstraction and Idealization in Scientific Modelling
  • Published:
Synthese Aims and scope Submit manuscript

Abstract

Explanations of biological phenomena such as cell division, protein synthesis or circadian rhythms commonly take the form of models of the responsible mechanisms. Recently philosophers of science have attempted to analyze this practice, presenting mechanisms as organized collections of parts performing operations that together produce the phenomenon. But in some cases what researchers seek to explain is not a general phenomenon, but a specific feature of a more fine-grained phenomenon. In some of these cases, it is not the model of the mechanism that performs the explanatory work. I consider a case in which the investigator offered an abstract representation of a fine-grained phenomenon to show why in had the feature in question. I consider a second case in which a researcher abstracted from the mechanism to identify a design principle that explains why the functioning mechanism exhibits a specific feature.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Notes

  1. In Levy and Bechtel (2013) we explore how abstracting from details of a mechanism can reveal the organization of the mechanism that is responsible for certain phenomena. In this paper I extend the focus on abstraction as a tool for developing explanations further.

  2. Although the clock metaphor was actually introduced by Brown, who was one of the last holdouts for the view that circadian rhythms depended on environmental cues, Pittendrigh soon adopted it to characterize the endogenous mechanism he took to be responsible.

  3. There has been substantial disagreement over whether computational models explain. Focusing on the mathematical model of the action potential advanced by Hodgkin and Huxley (1952), Weber (2008) defended it as explanatory while Craver (2008) argued that it did not explain since it did not describe the mechanism. Subsequently, Levy (2013) argued that Hodgkin and Huxley offered a deliberately abstract account but one that does explain the action potential in terms of component currents. The computational accounts discussed by Bechtel and Abrahamsen, Brigandt, and Baetu, in contrast, are tightly linked to mechanistic accounts—the differential equations in these models are drawn from the operations thought to constitute the mechanism. Although invoking mathematical derivations, these models are in the service of showing how mechanisms work and arguably in many cases one cannot show that the mechanism can produce the phenomenon except by using such models. At least in these cases, computational models seem to be critical to mechanistic explanation. Other mathematical models, such as those discussed by Chemero and Silberstein (2008), are models of phenomena, not mechanisms. The example from Winfree discussed below suggest a relatively clear way in which these models are explanatory as long as one is clear about what is being explained.

  4. With the discovery that it was the concentrations of proteins such as PER that oscillated, the clock stopping can be understood as the concentration of these proteins reaching a constant level and no longer oscillating.

  5. Abrahamsen and I (Bechtel and Abrahamsen 2010, 2011) refer to mechanistic explanations that rely on computational modeling to establish that they exhibit specific dynamical behavior as dynamic mechanistic explanations.

References

  • Alon, U. (2007a). An introduction to systems biology: Design principles of biological circuits. Boca Raton, FL: Chapman & Hall/CRC.

  • Alon, U. (2007b). Network motifs: Theory and experimental approaches. Nature Reviews Genetics, 8, 450–461.

  • Baetu, T. (2015). From mechanisms to mathematical models and back to mechanisms: Quantitative mechanistic explanations. In P.-A. Braillard & C. Malaterre (Eds.), Explanation in biology. An enquiry into the diversity of explanatory patterns in the life sciences. Dordrecht: Springer.

    Google Scholar 

  • Baggs, J. E., Price, T. S., DiTacchio, L., Panda, S., FitzGerald, G. A., & Hogenesch, J. B. (2009). Network features of the mammalian circadian clock. PLoS Biology, 7, e1000052.

    Google Scholar 

  • Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36, 421–441.

    Google Scholar 

  • Bechtel, W., & Abrahamsen, A. (2010). Dynamic mechanistic explanation: Computational modeling of circadian rhythms as an exemplar for cognitive science. Studies in History and Philosophy of Science Part A, 41, 321–333.

    Google Scholar 

  • Bechtel, W., & Abrahamsen, A. (2011). Complex biological mechanisms: Cyclic, oscillatory, and autonomous. In C. A. Hooker (Ed.), Philosophy of complex systems. Handbook of the philosophy of science (Vol. 10, pp. 257–285). New York: Elsevier.

    Google Scholar 

  • Bechtel, W., & Richardson, R. C. (1993/2010). Discovering complexity: Decomposition and localization as strategies in scientific research. Cambridge, MA: MIT Press. 1993 edition published by Princeton University Press.

  • Bogen, J., & Woodward, J. (1988). Saving the phenomena. Philosophical Review, 97, 303–352.

    Google Scholar 

  • Brigandt, I. (2013). Systems biology and the integration of mechanistic explanation and mathematical explanation. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 477–492.

    Google Scholar 

  • Bromberger, S. (1966). Why-questions. In R. C. Colodny (Ed.), Mind and cosmos: Essays in contemporary science and philosophy (Vol. 68-111). Pittsburgh, PA: University of Pittsburgh Press.

    Google Scholar 

  • Bromberger, S. (1968). An approach to explanation. Paper presented at the In R. J. Butler, ed., Analytic philosophy: Second series (pp. 72–105). Oxford: Blackwell.

  • Burnston, D. C. (2016). Data graphs and mechanistic explanation. Studies in History and Philosophy of Biological and Biomedical Sciences, 57, 1–12.

    Google Scholar 

  • Burnston, D. C., Sheredos, B., Abrahamsen, A., & Bechtel, W. (2014). Scientists’ use of diagrams in developing mechanistic explanations: A case study from chronobiology. Pragmatics and Cognition, 22, 224–243.

    Google Scholar 

  • Chemero, A., & Silberstein, M. (2008). After the philosophy of mind: Replacing scholasticism with science. Philosophy of Science, 75, 1–27.

    Google Scholar 

  • Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. New York: Oxford University Press.

    Google Scholar 

  • Craver, C. F. (2008). Physical law and mechanistic explanation in the Hodgkin and Huxley model of the action potential. Philosophy of Science, 75, 1022–1033.

    Google Scholar 

  • Craver, C. F., & Darden, L. (2013). In search of mechanisms: Discoveries across the life sciences. Chicago: University of Chicago Press.

    Google Scholar 

  • De Mairan, J.-J. (1729). Observation botanique. Histoire de l’Academie Royale Sciences, 35, 36.

    Google Scholar 

  • DeCoursey, P. J. (1960). Daily light sensitivity rhythm in a rodent. Science, 131, 33–35.

    Google Scholar 

  • Edmunds, L. N. (1988). Cellular and molecular bases of biological clocks: Models and mechanisms for circadian timekeeping. New York: Springer-Verlag.

    Google Scholar 

  • Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335–338.

    Google Scholar 

  • Goldbeter, A. (1995). A model for circadian oscillations in the Drosophila period protein (PER). In Proceedings of the Royal Society of London. B: Biological Sciences, 261, pp. 319–324.

  • Gonze, D. (2011). Modeling circadian clocks: From equations to oscillations. Central European Journal of Biology, 6, 699–711.

    Google Scholar 

  • Green, S. (2015). Revisiting generality in biology: Systems biology and the quest for design principles. Biology and Philosophy, 30, 629–652.

    Google Scholar 

  • Halberg, F. (1959). Physiologic 24-hour periodicity: General and procedural considerations with reference to the adrenal cycle. Zeitschrift für Vitamin-, Hormon- und Fermentforschung, 10, 225–296.

    Google Scholar 

  • Hardin, P. E., Hall, J. C., & Rosbash, M. (1990). Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature, 343, 536–540.

    Google Scholar 

  • Hastings, J. W., & Sweeney, B. M. (1958). A persistent diurnal rhythm of luminescence in Gonyaulax polyedra. Biological Bulletin, 115, 440–458.

    Google Scholar 

  • Hempel, C. G. (1965). Aspects of scientific explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation and other essays in the philosophy of science (pp. 331–496). New York: Macmillan.

    Google Scholar 

  • Hempel, C. G. (1966). Philosophy of natural science. Englewood Cliffs, NJ: Prentice-Hall.

    Google Scholar 

  • Hodgkin, A. L., & Huxley, A. F. (1952). A quantitative description of membrane current and its application to the conduction and excitation of nerve. Journal of Physiology, 117, 500–544.

    Google Scholar 

  • Hogenesch, J. B., & Ueda, H. R. (2011). Understanding systems-level properties: Timely stories from the study of clocks. Nature Reviews Genetics, 12, 407–416.

    Google Scholar 

  • Konopka, R. J., & Benzer, S. (1971). Clock mutants of Drosophila melanogaster. Proceedings of the National Academy of Sciences (USA), 89, 2112–2116.

    Google Scholar 

  • Lange, M. (2012). What makes a scientific explanation distinctively mathematical? The British Journal for the Philosophy of Science, 64, 485–511.

    Google Scholar 

  • Leloup, J.-C., & Goldbeter, A. (2003). Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences, 100, 7051–7056.

    Google Scholar 

  • Leloup, J.-C., & Goldbeter, A. (2008). Modeling the circadian clock: From molecular mechanism to physiological disorders. BioEssays, 30, 590–600.

    Google Scholar 

  • Levy, A. (2013). What was Hodgkin and Huxley’s Achievement? The British Journal for the Philosophy of Science, 65, 469–492.

  • Levy, A., & Bechtel, W. (2013). Abstraction and the organization of mechanisms. Philosophy of Science, 80, 241–261.

    Google Scholar 

  • Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1–25.

    Google Scholar 

  • Mayr, O. (1970). The origins of feedback control. Cambridge, MA: MIT Press.

    Google Scholar 

  • Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002). Network motifs: Simple building blocks of complex networks. Science, 298, 824–827.

    Google Scholar 

  • Peterson, E. L. (1980). Phase-resetting a mosquito circadian oscillator. Journal of Comparative Physiology, 138, 201–211.

    Google Scholar 

  • Pittendrigh, C. S. (1966). The circadian oscillation in Drosophila pseudoobscura pupae: A model for the photoperiodic clock. Zeitschrift für Pflanzenphysiologie, 54, 275–307.

    Google Scholar 

  • Relógio, A., Westermark, P. O., Wallach, T., Schellenberg, K., Kramer, A., & Herzel, H. (2011). Tuning the mammalian circadian clock: Robust synergy of two loops. PLoS Computational Biology, 7, e1002309.

    Google Scholar 

  • Salmon, W. C. (1984). Scientific explanation and the causal structure of the world. Princeton, NJ: Princeton University Press.

    Google Scholar 

  • Salmon, W. C. (1998). Causality and explanation. Oxford: Oxford University Press.

    Google Scholar 

  • Smolen, P., Baxter, D. A., & Byrne, J. H. (2002). A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophysical Journal, 83, 2349–2359.

    Google Scholar 

  • Ukai-Tadenuma, M., Kasukawa, T., & Ueda, H. R. (2008). Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks. Nature Cell Biology, 10, 1154–1163.

    Google Scholar 

  • Ukai-Tadenuma, M., Yamada, R. G., Xu, H., Ripperger, J. A., Liu, A. C., & Ueda, H. R. (2011). Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell, 144, 268–281.

    Google Scholar 

  • van der Pol, B. (1920). A theory of the amplitude of free and forced triode vibrations. Radio Review, 1(701–710), 754–762.

    Google Scholar 

  • van Fraassen, B. C. (1980). The scientific image. Oxford: Clarendon Press.

    Google Scholar 

  • Weber, M. (2008). Causes without mechanisms: Experimental regularities, physical laws, and neuroscientific explanation. Philosophy of Science, 75, 995–1007.

    Google Scholar 

  • Wiener, N. (1948). Cybernetics: Or, control and communication in the animal and the machine. New York: Wiley.

    Google Scholar 

  • Winfree, A. T. (1970). Integrated view of resetting a circadian clock. Journal of Theoretical Biology, 28, 327–374.

    Google Scholar 

  • Winfree, A. T. (1980). The geometry of biological time. New York: Springer Verlag.

    Google Scholar 

  • Winfree, A. T. (1987). The timing of biological clocks. New York: W.H. Freeman.

    Google Scholar 

Download references

Acknowledgements

I thank two anonymous referees for this journal for their very helpful comments and suggestions. I also thank John Norton and visiting fellows at the Center for Philosophy of Science at the University of Pittsburgh in 2014–15 for their spirited discussion of an earlier draft of this paper. Likewise, I thank members of the audience at a workshop on Describing the Abstract and Representing the Real at the University of Cyprus, Nicosia, Cyprus in June, 2015.

Author information

Authors and Affiliations

  1. Department of Philosophy and Center for Circadian Biology, University of California, San Diego, CA, USA

    William Bechtel

Authors
  1. William Bechtel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to William Bechtel.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bechtel, W. Explaining features of fine-grained phenomena using abstract analyses of phenomena and mechanisms: two examples from chronobiology. Synthese 198 (Suppl 24), 1–23 (2021). https://doi.org/10.1007/s11229-017-1469-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11229-017-1469-x

Keywords

Search

Navigation