Skip to main content
SpringerLink
Log in

Similarity and representation in chemical knowledge practices

  • Published:
Foundations of Chemistry Aims and scope Submit manuscript

Abstract

This paper argues for the theoretical and practical validity of similarity as a useful epistemological tool in scientific knowledge generation, specifically in chemistry. Classical analyses of similarity in philosophy of science do not account for the concept’s practical significance in scientific activities. We recur to examples from chemistry to counter the claim of authors like Quine or Goodman to the effect that similarity must be excluded from scientific practices (as well as their philosophical analysis). In conclusion we argue that more recent conceptualizations of the notion of similarity, particularly Giere’s one, are appropriate for a philosophical analysis that considers scientific practices on equal terms with scientific theory.

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

Similar content being viewed by others

Notes

  1. Decock and Douven (2011, p. 62) outline how the relation of similarity is represented by a metric space of similarity, as the formal model does.

  2. Actually, the first version of ‘quasi-analysis’ appears in a previous text by Carnap («Die Quasizerlegung: Ein Verfahren zur Ordnung nichthomogener Mengen mit den Mitteln der Beziehungslehre» 1923), although it is in the Aufbau that we can find the version that most philosophical literature refers to (see Mormann 2009, p. 253).

  3. We agree with Mormann (2009, p. 250) in that the Carnapian quasi-analysis of a realm S can be conceived of as a theoretical representation of S, provided that representation is understood in terms of either the representational theory of measurement or Mundy’s (1986) general theory of representation.

  4. Here Carnap follows Russell’s idea, according to which, in the realm of knowledge, logical constructions must take the place of inferred entities, especially in science (Russell 1918, p. 155).

  5. We have to remember that Goodman (1972, p. 444) denies any validity to intensional notions.

  6. Eli Hirsch calls this double condition «L» and defines it as «for any x that lacks P, there is a y that has P such that, for any z that has P, the degree of dissimilarity between x and y is greater than that between y and z» (Hirsch 1993, p. 209).

  7. We introduce the term ‘presumably’ because Mormann (2009, p. 258), Leitgeb (2007, p. 206) and Gärdenfors (2000, p. 89); see Decock and Douven (2011, p. 71) insist that there are formal solutions for the impasse identified by Goodman.

  8. Rouvray (1997) has proposed an alternative analysis of similarity in terms of fuzzy logic.

  9. That is why the analysis of similarity has attracted many advocates of the semantic view, for whom theories are not linguistic entities, but rather structures.

  10. Alongside the already mentioned advances in philosophical analysis, such as Mormann’s (2009), Gärdenfors’ (2000), or Douven and Decock’s (2011), important progress has also been made in the formal sciences with respect to the mathematization of similarity, notably leading to analyses of the concept in terms of fuzzy logic (Rouvray 1992). The latter may facilitate the identification of hitherto unrecognized or unexpected interconnections, overlaps and patterns in the scientific data that scientists use. Another approach is Schreider’s (1975) attempt of transforming the intuitive concepts of similarity and order into rigorously defined mathematical notions.

  11. Rouvray (1992) recognizes that classic set-theory could be used in chemistry for constructing models, as well as conceived of as a key structure for modeling chemical phenomena—without discounting others such as, say, topological ones—. However, according to the author, a domain C of concepts could be better represented by a fuzzy set (Zadeh 1965) than a classic one. Fuzzy sets have been applied in many cases in science. The basic idea is that none of its members is included in or excluded from a set, but rather that any member belongs to it to a certain degree. The association of each member of C is described by a function of membership—that is, a real number of [0, 1].

  12. A more accurate definition of functional group states that it «is a chemically reactive group of atoms within a molecule» and, in addition, «[e]ach functional group has its characteristic reactivity, which may be modified by its position within the molecule or by the presence of other neighbouring functional groups» (Hanson 2001, p. 1).

  13. It has to be remembered that in this process the comparisons are made between models and models, and that the ‘anchorage’ with the empirical level is usually an anchorage on the basis of some model of data. As Giere (2010, p. 272) points out, to «move from data to models of data requires models of experiments and involves statistical and other data processing techniques, empirical information from other sources, and many other things in addition».

  14. For an example of the same functional group (–OH) in the case of methanol and ethanol, see Schummer (1998, p. 152).

  15. For example, in order to determinate the amino group (–NH2) there are several methods, namely acetylation, bromination, titration in aqueous or non-aqueous media, and determination of the equivalent weight of amine by conversion to picrate and its titration in non-aqueous media (see Vidya 2009, pp. 243ff and especially chapter 10).

  16. Until about the middle of the twentieth century, scientists used to identify chemical substances—i.e., the material ontology of chemistry—by means of the analysis of the elements that formed these substances, as well as by the preparation of their derived solids (see Siggia and Hanna 1979, p. 821).

  17. Although not from a point of view related to functional groups, Scerri (2008, pp. 45ff) claims that the nature of hafnium, the element 72, was predicted by means of purely chemical arguments and not from Bohr’s theory of the periodic system.

  18. For a view of regulatory science as a disciplinary realm, see Jasanoff (1990).

  19. For a review of the use by regulatory agencies of (quantitative) structure–activity relationships for predicting environmental effects and interactions of chemicals, see Cronin et al. (2003).

  20. Several methodologies are used in chemistry for making classifications of this kind, among which we can find similarity analyses in chemotopological studies in quantum chemistry or cluster analyses (Restrepo and Pachón 2007, p. 197). In all these cases, mathematical tools are used in order to study chemical elements and properties with the aim of defining the latter. By and large, these tend to be purely phenomenological studies that make use exclusively of experimental information (chemical information) about elements (see Restrepo et al. 2006).

  21. A typical case of two molecules that are very similar in structural terms, but show clearly differentiated biological behavior is the one of phenyl acetate and nytrophenyl acetate. The two molecules are differentiated by a single NO2 group but show very different potential for carcinogenity (Martin et al. 2002, p. 4356; Walker 2003).

  22. In his analysis of the study of scientific practices, Rouse (2002) argues that articulating a theory consists of, on one hand, designing experiments that give account of a consistent realm of phenomena and, on the other, generating concepts that scientists may use in a flexible manner in order to support and extend the relations between experimental practices and phenomena. He concludes that not taking sufficient account of experimental practices has been one of the most significant limitations of the ‘classic’ or analytic philosophy of science of the twentieth century.

  23. Similarity is conceived of as a local concept, as can be seen in processes as diverse as the discovery of new medicines or the identification of the constituents of jet propellant, in both of which similarity is crucially relevant (see Gute et al. 2002, p. 376).

  24. For a similar notion of a conceptual tool, although applied to the case of models, see Klein (1999, pp. 154–158).

References

  • Balzer, W., Moulines, C.U., Sneed, J.: An Architectonic for Science: The Structuralist Program. Reidel, Dordrecht (1987)

    Book  Google Scholar 

  • Brown, T.L., LeMay, H.E., Bursten, B.E., Murphy, C.J., Woodward, P.M.: Chemistry: The Central Science, 12th edn. Prentice Hall, New Jersey (2012)

    Google Scholar 

  • Bueno, O.: Empirical adequacy: a partial structures approach. Stud. History Philos. Sci. 28, 585–610 (1997)

    Article  Google Scholar 

  • Carnap, R.: The Logical Structure of the World: Pseudoproblems in Philosophy, p. 1967. University of California Press, Berkeley (1928)

    Google Scholar 

  • Cartwright, N.: How the Laws of Physics Lie. Clarendon Press, Oxford (1983)

    Book  Google Scholar 

  • Contessa, G.: Scientific representation, interpretation and surrogative reasoning. Philos. Sci. 74, 48–68 (2007)

    Article  Google Scholar 

  • Corey, E.J., Chelg, X.-M.: The Logic of Chemical Synthesis. John Miley & Sons, New York (1995)

    Google Scholar 

  • Cronin, M., Walker, J.D., Jaworska, J.S., Comber, M., Watts, C.D., Worth, A.P.: Use of QSARs in international decision-making frameworks to predict ecologic effects and environmental fate of chemical substances. Environ. Health Perspect. 111, 1376–1390 (2003)

    Article  Google Scholar 

  • da Costa, N.C.A., French, S.: Science and Partial Truth. Oxford University Press, Oxford (2003)

    Book  Google Scholar 

  • Decock, L., Douven, I.: Similarity after Goodman. Revue Philos. Psychol. 2, 61–75 (2011)

    Article  Google Scholar 

  • Gärdenfors, P.: Conceptual Revolutions: The Geometry of Thought. The MIT Press, Cambridge, Mass. (2000)

    Google Scholar 

  • Giere, R.N.: Explaining Science: A Cognitive Approach. University of Chicago Press, Chicago (1988)

    Book  Google Scholar 

  • Giere, R.N.: How models are used to represent reality. Philos. Sci. 71, 742–752 (2004)

    Article  Google Scholar 

  • Giere, R.N.: Scientific Perspectivism. The University of Chicago Press, Chicago (2006)

    Book  Google Scholar 

  • Giere, R.N.: An agent-based conception of models and scientific representation. Synthese 172, 269–281 (2010)

    Article  Google Scholar 

  • Godfrey-Smith, P.: The strategy of model-based science. Biol. Philos. 21, 725–740 (2006)

    Article  Google Scholar 

  • Goodman, N.: The Structure of Appearance, 3rd edn, p. 1977. Reidel, Dordrecht (1951)

    Google Scholar 

  • Goodman, N.: Languages of Art: An Approach to a Theory of Symbols. The Bobbs-Merrill Company, Indianapolis (1968)

    Google Scholar 

  • Goodman, N.: Problems and projects. The Bobbs-Merrill Company, Indianapolis (1972)

    Google Scholar 

  • Groutas, W.C.: Organic Reaction Mechanisms: Selected Problems and Solutions. Wiley, Hoboken, NJ (1999)

    Google Scholar 

  • Gute, B.D., Basak, S.C., Mills, D., Hawkins, D.M.: Tailored similarity spaces for the prediction of physicochemical properties. Intern. Electron. J. Mol. Design 1(8), 374–387 (2002)

    Google Scholar 

  • Hanson, J.R.: Functional Group Chemistry. Royal Society of Chemistry, Cambridge, UK (2001)

    Google Scholar 

  • Hirsch, E.: Dividing Reality. Oxford University Press, Oxford (1993)

    Google Scholar 

  • Hughes, R.I.G.: Models and representation. Philos. Sci. 64(Proceedings), S325–S336 (1997)

  • Jasanoff, S.: The Fifth Branch: Science Advisers as Policy Makers. Harvard University Press, Cambridge, Mass. (1990)

    Google Scholar 

  • Klein, U.: Techniques of modelling and paper-tools in classical chemistry. In: Morgan, M.S., Morrison, M. (eds.) Models as Mediators: Perspectives on Natural and Social Science, pp. 146–167. Cambridge University Press, Cambridge, Mass. (1999)

    Chapter  Google Scholar 

  • Kubinyi, H.: Similarity and Dissimilarity-a Medicinal Chemists View. Perspect. Drug Discov. Des. 11, 225–252 (1998)

    Article  Google Scholar 

  • Kuriki, T., Imanaka, T.: The concept of the a-amylase family: structural similarity and common catalytic mechanism. J. Biosci. Bioeng. 87, 557–565 (1999)

    Article  Google Scholar 

  • Leitgeb, H.: A new analysis of quasianalysis. J. Philos. Logic 36(2), 181–226 (2007)

    Article  Google Scholar 

  • Lloyd, E.A.: A semantic approach to the structure of population genetics. Philos. Sci. 51, 242–264 (1984)

    Article  Google Scholar 

  • Martin, Y.C., Kofron, J.L., Traphagen, L.M.: Do structurally similar molecules have similar biological activity? J. Med. Chem. 45, 4350–4358 (2002)

    Article  Google Scholar 

  • Medin, D.L.: Concepts and conceptual structure. Am. Psychol. 44, 1469–1481 (1989)

    Article  Google Scholar 

  • Medin, D.L., Goldstone, R.L., Gentner, D.: Respects for similarity. Psychol. Rev. 100, 254–278 (1993)

    Article  Google Scholar 

  • Miller, J.H., Page, S.E.: Complex Adaptive Systems: An Introduction to Computational Models of Social Life. Princeton University Press, Princeton (2007)

    Google Scholar 

  • Monev, V.: Introduction to similarity searching in chemistry. Match Commun. Math. Comput. Chem. 51, 7–38 (2004)

    Google Scholar 

  • Mormann, T.: New work for carnap’s quasi-analysis. J. Philos. Logic 38, 249–282 (2009)

    Article  Google Scholar 

  • Mundy, B.: On the general theory of meaningful representation. Synthese 67, 391–437 (1986)

    Article  Google Scholar 

  • Nikolova, N., Jaworska, J.: Approaches to measure chemical similarity-a review’. QSAR Comb. Sci. 22, 1006–1026 (2003)

    Article  Google Scholar 

  • O’Boyle, N.M., Holliday, G.L., Almonacid, D.E., Mitchell, J.B.: Using reaction mechanism to measure enzyme similarity. J. Mol. Biol. 368, 1484–1499 (2007)

    Article  Google Scholar 

  • Quine, W.V.O.: Ontological Relativity and Other Essays. Columbia University Press, New York (1969)

    Google Scholar 

  • Restrepo, G., Pachón, L.: Mathematical aspects of the periodic law. Found. Chem. 9, 189–214 (2007)

    Article  Google Scholar 

  • Restrepo, G., Llanos, E.J., Mesa, H.: Topological space of the chemical elements and properties. J. Math. Chem. 39, 401–416 (2006)

    Article  Google Scholar 

  • Rouse, J.: How Scientific Practices Matter: Reclaiming Philosophical Naturalism. The University of Chicago Press, Chicago (2002)

    Google Scholar 

  • Rouvray, D.H.: Definition and role of similarity concepts in the chemical and physical sciences. J. Chem. Inf. Comput. Sci. 32, 580–586 (1992)

    Article  Google Scholar 

  • Rouvray, D.H. (ed.): Fuzzy logic in chemistry. Academia Press, San Diego, CA (1997)

    Google Scholar 

  • Russell, B.: Mysticism and Logic and Other Essays. George Allen & Unwin Ltd, London (1918)

    Google Scholar 

  • Russell, B.: Vagueness. In: Keefe, R., Smith, P. (eds.) Vagueness: A Reader, pp. 61–68. The MIT Press, Cambridge, Mass. (1923)

  • Scerri, E.C.: Collected Papers on Philosophy of Chemistry. Imperial College Press, London (2008)

    Book  Google Scholar 

  • Schaafsma, G., Kroese, E.D., Tielemenas, E.L.J.P., Van de Sandt, J.J.M., Van Leeuwen, C.J.: REACH, non-testing approaches and the urgent need for a change in mind set. Regul. Toxicol. Pharmacol. 53, 70–80 (2009)

    Article  Google Scholar 

  • Schreider, Ju.A.: Equality, Resemblance and Order. Mir Publishers, Moscow (1975)

    Google Scholar 

  • Schummer, J.: The chemical core of chemistry I: a conceptual approach. HYLE-Int. J. Philos. Chem. 4(2), 129–162 (1998)

    Google Scholar 

  • Siggia, S., Hanna, J.G.: Quantitative Organic Analysis via Functional Groups. Wiley, New York (1979)

    Google Scholar 

  • Sneed, J.: The Logical Structure of Mathematical Physics. Reidel, Dordrecht (1971)

    Book  Google Scholar 

  • Stegmüller, W.: The Structuralist View of Theories: A Possible Analogue of the Bourbaki Programme in Physical Science. Springer, Berlin (1979)

  • Suárez, M.: An inferential conception of scientific representation. Philos. Sci. 71, 767–779 (2004)

    Article  Google Scholar 

  • Suárez, M.: Scientific representation. Philos. Compass 5(1), 91–101 (2010)

    Article  Google Scholar 

  • Suppe, F.: The Semantic Conception of Theories and Scientific Realism. University of Illinois Press, Chicago (1989)

    Google Scholar 

  • Suppes, P.: A comparison of the meaning and use of models in mathematics and the empirical sciences. Synthese 12, 287–300 (1960)

    Article  Google Scholar 

  • Swoyer, C.: Structural representation and surrogative reasoning. Synthese 87, 449–508 (1991)

    Article  Google Scholar 

  • Toon, A.: The ontology of theoretical modelling: models as make-believe. Synthese 172, 301–315 (2010)

    Article  Google Scholar 

  • Toon, A.: Similarity and scientific representation. Int. Stud. Philos. Sci. 26, 241–257 (2012)

    Article  Google Scholar 

  • Van Fraassen, B.: The Scientific Image. Oxford University Pres, Oxford (1980)

    Book  Google Scholar 

  • Vemulapalli, G.K.: Nature of chemical substances: Microscopic and macroscopic views. In: Ruthenberg, K., van Brakel, J. (eds.) Stuff: The Nature of Chemical Substances, pp. 123–142. Königshausen & Neumann, Würzburg (2008)

  • Vidya, G.: Basics of Drug Analysis. Pharmamed Press, Hyderabad (2009)

    Google Scholar 

  • Vihalemm, R.: Natural kinds, explanation, and essentialism in chemistry. In: Earley Sr, J.E. (ed.) Chemical Explanation: Characteristics, Development, Autonomy, pp. 59–70. Annals of the New York Academy of Sciences, New York (2003)

    Google Scholar 

  • Walker, J.: QSARs for pollution prevention: Toxicity screening, risk assessment and web applications. SETAC Press, Brussels (2003)

    Google Scholar 

  • Weisberg, M.: Simulation and Similarity: Using Models to Understand the World. Oxford University Press, Oxford (2013)

    Book  Google Scholar 

  • Zadeh, L.A.: Fuzzy sets. Inf. Control 8, 338–353 (1965)

    Article  Google Scholar 

Download references

Acknowledgments

The authors would like to thank the Spanish Government’s State Secretary of Research, Development and Innovation (research projects La explicación basada en mecanismos en la evaluación de riesgos, FFI2010-20227/FISO, and La evaluación de beneficios como ciencia reguladora, FFI2013-42154), as well as the European Commission’s European Regional Development Fund (FEDER) program, for their support.

Author information

Authors and Affiliations

  1. University of the Balearic Islands, Palma, Balearic Islands, Spain

    Juan Bautista Bengoetxea, Oliver Todt & José Luis Luján

Authors
  1. Juan Bautista Bengoetxea
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Oliver Todt
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. José Luis Luján
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Juan Bautista Bengoetxea.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bengoetxea, J.B., Todt, O. & Luján, J.L. Similarity and representation in chemical knowledge practices. Found Chem 16, 215–233 (2014). https://doi.org/10.1007/s10698-014-9203-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10698-014-9203-y

Keywords

Search

Navigation