Models and Explanations: Understanding Chemical Reaction Mechanisms

In 1997, Ross Kelly and his coworkers at Boston College reported their results from an experiment with an intriguing premise (Kelly et al., 1997; see also Kelly et al., 1998). They had synthesized the molecule shown in figure 12.1. It was designed to be a “molecular ratchet,” so named because it appeared that it should undergo internal rotation about the A—B bond more readily in one direction than the other. The reason for thinking this might occur was that the benzophenanthrene moiety—the “pawl” of the ratchet—was anticipated to be helical. Thus, in some sense, this might be an inverse ratchet where the asymmetry dictating the sense of rotation would reside in the pawl rather than in the “teeth” on the “wheel” (the triptycene unit) as it does in a normal mechanical ratchet. Kelly and coworkers designed an elegant experiment to determine whether their molecular ratchet was functioning as anticipated, and they were (presumably) disappointed to find that it was not—internal rotation about the A—B bond occurred at equal rates in each direction. In 1998 Davis pointed out that occurrence of the desired behavior of the molecular ratchet would have constituted a violation of the second law of thermodynamics (Davis, 1998). With hindsight, I think most chemists would agree that Davis’s critique is unassailable, although the appeal of the mechanical analogy was so strong that I imagine those same chemists would also understand if Kelly et al. had overlooked the thermodynamic consequences of their proposal in the original design of the experiment. But now comes the interesting question: Suppose Kelly et al. had been fully aware that their experiment, if successful, would undermine the second law of thermodynamics, should they have conducted it anyway? Davis, in his critique writes: . . .Some would argue that this experiment was misconceived. To challenge the Second Law may be seen as scientific heresy (a nice irony, considering the Jesuit origins of Boston College), and the theoretical arguments against molecular ratchets and trapdoors are well developed. . . .

Missing Elements: What Philosophers of Science Might Discover in Chemistry

In the late middle ages, chemistry was the science and technology closest to philosophy, the material realization of the method of analysis and synthesis. No longer. Contemporary philosophy is concerned with many sciences—physics, psychology, biology, linguistics, economics—but chemistry is not among them. Why not? Every discipline has particular problems with some philosophical coloring. Those in quantum theory are famous; those in psychology seem endless; those in biology and economics seem more sparse and esoteric. If, for whatever reason, one’s concern is the conceptual or theoretical problems of a particular science, there is no substitute for that science, and chemistry is just one among others. Certain sciences naturally touch on substantive areas of traditional philosophical concern: quantum theory on metaphysics, for example, psychology on the philosophy of mind, and economics and statistics on theories of rationality. In these cases, there is a special interest in particular sciences because they may reform prior philosophical theories or recast philosophical issues or, conversely, because philosophy may inform these subjects in fundamental ways. That is not true, in any obvious way, of chemistry. So what good, then, what special value, does chemistry offer contemporary philosophy of science? Typically philosophical problems, even problems in philosophy of science, are not confined to a particular science. For general problems—problems about representation, inference, discovery, explanation, realism, intertheoretic and interdisciplinary relations, and so on—what is needed are scientific illustrations that go to the heart of the matter without requiring specialized technical knowledge of the reader. The science needed for most philosophy is familiar, not esoteric, right in the middle of things, mature and diverse enough to illustrate a variety of fundamental issues. Almost uniquely, chemistry fits the description. In philosophy of science, too often an effort gains in weight and seriousness merely because it requires mastery of an intricate and arcane subject, regardless of the philosophical interest of what it says. Yet, surely, there is something contrived, even phony, in illustrating a philosophical point with a discussion of the top quark if the point could be shown as well with a discussion of the ideal gas law.

Archiving Odors

In an ode addressed to his friend Fabullus, the Roman poet Catullus speaks of a fragrance so pleasing that “when you smell it you will beg the gods to make you all nose.” Would that the recipe for such a scent had been transmitted through the ages! Even today, however, it is not possible to document chemical composition with adequate fidelity to reconstruct an odor perfectly. Catullus writes that the gods of love gave the perfume to his girlfriend. Suppose such gods existed and could list the ingredients of its aroma. The list would contain hundreds—perhaps thousands—of chemical structures and their relative proportions. Very likely, many of the structures would stand for compounds that are currently unknown, but they could be synthesized in the laboratory. Would that knowledge permit me to reproduce the odor? This chapter argues that the answer remains uncertain. The current state of chemical knowledge can neither account for why an odor smells the way it does nor what determines its intensity. The recipe for replicating a sensory experience—what is essential and what is superfluous—remains obscure. The sense of smell challenges chemical understanding. On the one hand, given the structure of a new molecule a chemist can predict its spectroscopic properties over a wide domain of electromagnetic frequencies. A mixture ordinarily displays a spectrum that superimposes the spectra of its individual components, unless they physically interact with each other. In the chemical senses, on the other hand, perceptions of mixtures often cannot be inferred from their constituents, even though the components do not interact at the molecular level. Moreover, no one can reliably predict the organoleptic properties (taste or smell) of a new molecule from its structure. Even if that were possible, the English language does not offer a vocabulary with which to describe new smells, except by analogy to odors that are already familiar. The poverty of descriptors means that, in talking about olfactory stimuli, many people allude to direct experiences. These allusions call on memories of characteristic odors of familiar objects, which represent “unitary percepts.”

Space and the Chiral Molecule

According to classical stereochemistry, the molecules of some substances have doubles, in the sense of incongruent mirror-image counterparts. This is the phenomenon of optical isomerism, first identified 150 years ago by Pasteur. In some cases, the double occurs naturally; in others, it has to be artificially synthesized. These molecules thus share a geometrical feature with such familiar objects as our hands, and, indeed, it is this connection that gives the feature its technical name: chirality (from the Greek for hand, kheir). Instances of chirality in chemistry are numerous, especially in living things: examples of chiral molecules include adrenaline, glucose, and DNA. Optical isomerism is interesting, both historically—it played a crucial role in the emergence of structural chemistry and in the attempt to link chemistry with physics— and, I believe, philosophically. I should like to take this opportunity to revisit the scene of an earlier article of mine (Le Poidevin, 1994) in which I examined the implications optical isomerism has for a philosophical debate concerning the nature of space. In that article I argued that chirality in chemistry reinforces a conclusion that Graham Nerlich (1994), in a brilliant reconstruction of a famous argument of Kant’s, had derived from more visible instances of chirality: that we should be realists about the geometrical properties of space. I did not, however, want to follow Nerlich (and Kant) in drawing a more radical conclusion: that we should be realists about the existence of space. That may sound paradoxical, but it is possible (or so I thought) to regard space as a logical construction from its contents and still think of it, qua construction, as possessing certain intrinsic properties that we do not merely impose on it by convention. Since then, I have become more sympathetic to Nerlich’s position. Chirality is best understood by thinking of space as an entity in its own right. So chemistry has some lessons for the philosophy of space. But the pedagogical relation goes the other way, too: the philosophy of space has interesting implications for chemistry.

Realism, Essentialism, and Intrinsic Properties: The Case of Molecular Shape

Figure, or shape, has long been ensconced in modern philosophy as a primary or essential quality of matter. Descartes, Malebranche, Hobbes, and Boyle all apparently endorsed the Lockean claim that shape is “in Bodies whether we perceive them or no” (Locke, [1700] 1975, p. 140). In addition, most seventeenth-century philosophers endorsed the inference that because shape is primary, it is one of the “ultimate, irreducible explanatory principles” (Dijksterhuis, 1961, p. 433; cf. Ihde, 1964, p. 28). Locke has often been read in this way, and in Origins of Forms and Qualities, Boyle claims the “sensible qualities . . . are but the effects or consequents of the . . . primary affections of matter,” one of which is figure (quoted in Harré, 1964, p. 80). Little appears to have changed. Most analytic philosophers and realist-minded philosophers of science “would endorse a distinction between primary and secondary qualities” (Smith, 1990, p. 221). Campbell (1972, p. 219) endorses the claim that “shape, size and solidity are generally held to be primary,” even though he argues that “the philosophy of primary and secondary qualities” is confused. Mackie (1976, p. 18) discounts solidity but endorses spatial properties and motion as “basic” physical features of matter. Most philosophers also endorse the inference to the explanatory character of the primary qualities. Mackie (1976, p. 25) asserts spatial properties are “starting points of explanation.” Boyd (1989, pp. 10-11) claims “realists agree” that “the factors which govern the behavior . . . of substances are the fundamental properties of the insensible corpuscles of which they are composed.” As befits our current situation, explanation purportedly flows from spatial microstructure. A body “possesses a certain potential only because it actually possesses a certain property (e.g., its molecular structure)” (Lange, 1994, pp. 109-110). Even Putnam, who argues all properties are Lockean secondaries, claims powers “have an explanation . . . in the particular microstructure” of matter (Putnam, 1981, p. 58).

Introduction

Chemistry is a substantial science by the measures of industry, economics, and politics. As an academic discipline, it underlies the vibrant growth of molecular biology, materials science, and medical technology. Although not the youngest of sciences, its frontiers continue to expand in remarkable ways. And although it shares boundaries with every other field of science, it has an autonomy, both methodologically and conceptually; this autonomy, however, continues to be unappreciated by most philosophers of science. Why is there no philosophy of chemistry? Although there have been philosophical writings on chemistry, increasingly so during recent years, curiously enough, no coherent discipline analogous to the philosophy of physics, biology, or mathematics has emerged. Indeed, some would argue that there is no subject matter here to begin with because chemistry is in the end reducible to physics and therefore without a distinct methodology or conceptual repertoire of its own worthy of philosophical consideration. One motivation for this anthology is to demonstrate that this view requires serious rethinking, particularly in the context of modern molecular science. In a 1981 review article entitled “On the Philosophy of Chemistry,” J. van Brakel and H. Vermeeren pointed out that although there is a vast amount of literature on the history of chemistry, there is precious little in the philosophy of chemistry. They observe that “even isolated articles in which the philosophy of science is applied to chemistry are extremely rare: in all cases it is clear that the published work is the outcome of a side interest of the author (most of whom are chemists who developed an interest in the philosophy of science)”. An exception to this lack of interest, cited by van Brakel and Vermeeren, is a strand of scholarly activity in Eastern Europe, particularly Russia, East Germany, and Romania, where books and articles on the philosophy of chemistry have been published since the late 1950s.

Chemical Synthesis: Complexity, Similarity, Natural Kinds, and the Evolution of a “Logic”

The goal of this chapter is to extract some of the conceptual underpinnings of the idea of synthesis and of the different aspects that constitute its practice. In so doing, we show why chemical synthesis should be of interest to metaphysicians and philosophers of science. To this end we (1) provide a provisional characterization of synthesis; (2) describe what chemists have understood to be the “logical” structure that underlies the modern practice of multistep synthesis; (3) explore the notions of molecular and synthetic complexity and the relationship between them; (4) analyze the use of similarity judgments in the categorization of compounds; and, related to this, (5) undertake a scrutiny of the notion of a natural kind in the context of the possibility of chemical synthesis. These last two, intertwined, issues having to do with categorization are of particular interest, given that some philosophers have taken chemistry to be the science that, in its theoretical workings, dispenses with such disreputable concepts as similarity and the associated idea of a natural kind which are of “dubious scientific standing.” For instance, Quine (1969) argues that the freedom from such imprecise means of categorization in chemistry is a marker of its status as a more “mature” science, one to which other domains aspire. However, by the same token, and ironically, this feature of chemistry in effect removes the discipline from the purview of philosophers, for reasons that will become clearer later on in the chapter. We argue against Quine, concluding that chemistry fails the test of maturity but becomes philosophically interesting in the process. The mid-nineteenth-century defeat of vitalism and the subsequent unification of organic and inorganic chemistry came in large measure as a result of chemical synthesis. This early indication of the powerful implications that arise for chemistry from this unique field of investigation might well suffice for its continuing philosophical scrutiny. There are at least two other reasons for undertaking a philosophical investigation of synthesis. Synthesis is, and has long been, pervasive in the practice of chemistry and is a unique, and defining, feature of this field.

“Laws” and “Theories” in Chemistry Do Not Obey the Rules

Most philosophers’ discussions of issues relating to “laws of nature” and “scientific theories” have concentrated heavily on examples from classical physics. Newton’s laws of motion and of gravitation and the various conservation laws are often discussed. This area of science provides very clear examples of the type of universal generalization that constitutes the widely accepted view of what a law of nature or a scientific theory “ought to be.” But classical physics is just one very small branch of science. Many other areas of science do not seem to throw up generalizations of nearly the same breadth or clarity. The question of whether there are any laws of nature in biology, or of why there are not, has often been raised (e.g., Ghiselin, 1989; Ruse, 1989). In the grand scheme of science, chemistry stands next to physics in any supposed reductive hierarchy, and chemistry does produce many alleged laws of nature and scientific theories. An examination of the characters of these laws and theories, and a comparison with those that arise in classical physics, might provide a broader and more balanced view of the nature of laws and theories and of their role in science. From the outset, we should very carefully define the terms of our discourse. The notion of laws of nature has medieval origin as the edicts of an all-powerful deity to his angelic servants about how the functioning of the world should be arranged and directed. It may be helpful to distinguish three quite different senses in which laws of nature are considered in modern discussions. On occasion, the discussion has become sidetracked and obscure because of conflation and confusion of two or more of these senses. In the first, or ontological, sense, laws of nature may be considered as a simply expressed generalization about the way an external world does operate. Laws of nature are often seen as principles of the way the world works. They are an objective part of the external world, waiting to be discovered. The laws that we have and use may be only approximations of the deeper, true laws of nature.

How Symbolic and Iconic Languages Bridge the Two Worlds of the Chemist: A Case Study From Contemporary Bioorganic Chemistry

Chemists move habitually and with credible success—if sometimes unreflectively—between two worlds. One is the laboratory, with its macroscopic powders, crystals, solutions, and intractable sludge, as well as the things that are smelly or odorless, toxic or beneficial, pure or impure, colored, or white. The other is the invisible world of molecules, each with its characteristic composition and structure, its internal dynamics and its ways of reacting with the other molecules around it. Perhaps because they are so used to it, chemists rarely explain how they are able to hold two seemingly disparate worlds together in thought and practice. And contemporary philosophy of science has had little to say about how chemists are able to pose and solve problems, and, in particular, to posit and construct molecules, while simultaneously entertaining two apparently incompatible strata of reality. Yet chemistry continues to generate highly reliable knowledge, and indeed to add to the furniture of the universe, with a registry of over ten million well-characterized new compounds. The philosophy of science has long been dominated by logical positivism, and the assumptions attendant on its use of predicate logic to examine science, as well as its choice of physics as the archetype of a science. Positivism thus tends to think of science in terms of an axiomatized theory describing an already given reality and cast in a uniform symbolic language, the language of predicate logic. (See especially the locus classicus of this position, Carnap, 1937.) We here wish to question certain positivist assumptions about scientific rationality, based on an alternative view brought into focus by the reflective examination of a case study drawn from contemporary chemistry. Our reflections owe something to Leibniz (1686, 1695, 1714), Husserl (1922), Kuhn (1970), and Polanyi (1960, 1966), and draw on the earlier writings of both of us—Hoffmann (1995; Hoffmann & Laszlo, 1991) and Grosholz (1991; Grosholz & Yakira, 1998). We will offer a nonreductionist account of methods of analysis and synthesis in chemistry.

The Nature of Chemical Substances

Professor Hare, delivering the presidential address to the Aristotelian Society in Oxford in 1984, said: “It is commonly said that the property of being water supervenes on the chemical (or ultimately on the physical) property of being H2O. As it stands this view seems to me to be obviously false.” In terminology, that will become clearer as we proceed, Hare defended the manifest image—in this case, ordinary liquid water against elimination by the scientific image (which reduces “being water” to “being H2O”). Hare used the verb to supervene instead of to be reducible, but the difference between the two is slight (as we shall see in a later section). A more common view among philosophers and scientists is expressed in the following citation from Kim (1990, p. 14): “Chemical kinds and their microphysical compositions (at least, at one level of description) seem to strongly covary with each other, and yet it is true, presumably, that natural kinds are asymmetrically dependent on microphysical structures.” Kim takes the view that manifest objects are “appearances” of a reality constituted by systems of imperceptible particles. Such a view takes for granted that the macroscopic, manifest world is dependent on the microstructure of the world in such a way that it is underlying things that are more real and determine appearances. In crude jargon: science uncovers the Dinge-an-sich that explain the phenomena we see. I chose the quotations of Hare and Kim because both point to, though fail to address, the philosophical issue I discuss in this chapter, viz. the tension between manifest and scientific image, focusing on chemistry. “Manifest” versus “scientific” imagery talk stems from Sellars. The manifest image refers to things like water, milk-lapping cats, injustice-angry people, as well as sophisticated interpretations of “people in the world.” The scientific image is concerned with things like neurons, DNA, quarks, and the Schrödinger equation, again including sophisticated reflection and a promise of more to come. I use “manifest image” with a different inflection from Sellars, avoiding associations with sense data (which was an important part of his concern), associating it rather with forms of life.