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This chapter reveals the discovery and different stages in the life cycle of Dictyostelium discoideum, the role of cAMP in intercellular communication, and the porphyrin photoreceptor in Escherichia coli. The significance of phototaxis and chemotaxis in the amoeba and the slug in controlling their movement is also discussed. The action spectrum of the amoeba and the slug indicates the use of different pigments to control phototaxis. Sorocarp, developed from the slug, has great adaptive value and eventually germinates and begins life anew as an amoeba.

Here are two manuscript pages from articles I’ve written. And there are the ways they appeared in print, in the Journal of the Chemical Society: Dalton Transactions and Inorganic Chemistry, two magazines you are unlikely to have read recently. The context of these images is the following: I’m a theoretical chemist. What you see is the initial draft and final printed version of fragments from two of the >500 articles I’ve written. Articles are the stock-in-trade of the professional scientist. By and large we do not write books; our achievements, such as they may be, are judged by these scholarly articles. In general they’re written in English (well, really in a jargon that has some vague relationship to English), printed in journals with limited circulation (these, among the world’s best chemistry journals, have circulations near five thousand each), glanced at only by other chemists, and read carefully by a few hundred people. On the basis of these articles my work is evaluated and I make a living. That explains circumstantially Figure 19-2, the final printed pages. What about the manuscripts, Figure 19-1? Clearly these are collages. There are samples of writing in two hands on them; one is my own, the other that of the graduate student (David Hoffman) or postdoctoral fellow (Kazuyuki Tatsumi) who has worked with me on this research. In science there is much, much collaboration. My papers typically have two or three coauthors. I pose the question, my coworkers and I discuss an approach to a solution, they do most of the tough work, we talk further, a presentation of intermediate results is made, they’re off to test various unreasonable suggestions I make, they write a draft, and I revise it into a final paper. In what you see in Figures 19-1 and 19-2, each a page of the manuscript of the final paper, I’ve pasted in photocopies of a piece of my collaborator’s draft that I decided to keep. The actual drawings that the scientific journals print are reproduced from India ink originals on tracing paper. These are masterfully done by Jane Jorgensen and Elisabeth Fields, two illustrators who worked with me for many years.

Scientific argument is supposed to be logical. But do scientists study logic? Probably not. Were they asked about the advisability of learning formal or applied logic, most would likely say, “Logic, as studied by philosophers, is just a systemization or description of what we, as scientists, do naturally. So we don’t need to study it.” The chain of reasoning that I’ve ascribed here to a straw-man scientist is, on analysis, full of the fallacies described by Aristotle in Sophistical Refutations (De sophisticis elenchis) more than 2,300 years ago. The argument suffers from circular reasoning, the fallacy of false cause, the argument ad populum (the populus here being scientists, as opposed to philosophers), and more. But actually I do not want to berate here the logically unsophisticated scientist (myself), nor to urge that scientists need study philosophy. Rather, I’d like to examine the curious role of logic in science. Good logical thinking is absolutely necessary to both everyday and revolutionary science. But I will argue that at the same time, reasoning in all science, paradigmatic or ground-breaking, on close scrutiny often turns out to be in part illogical. There is nothing new in this—we see readily the fallacies in the work of others, especially when they disagree with us, don’t we? I will try to make a case, however, that there may be a real advantage implicit in occasionally faulty reasoning, especially a mode which I will call nearly circular reasoning. Science is a curious mixture of the real and the ideal, the material and the spiritual, held together by discourse or argument. The latter is sometimes mathematical, but more often it transpires in the words of some language. The real is the material, say, a vial of a chemical, or its measured spectrum, the relative amount of light a solution of that chemical absorbs. The ideal may be a proposal on the mechanism of formation of the molecule, or a theory that interprets that spectrum as necessarily indicating the molecule contains a carbon-hydrogen bond. The discourse consists of the exposition of several arguments, several alternative models explaining the observable, and a choice between them.

Ground-state dioxygen has two unpaired electrons (·O2·), which makes it a biradical with a triplet electronic state (see Table 3-1). Its radical character is limited because the H-OO· bond is weak [-ΔGBF/ 51 kcal (Chapter 3)], and the triplet state precludes direct reaction with singlet-state substrate molecules with saturated σ bonding. Perhaps the most important (but nonproductive) reaction chemistry for 3O2 is its reversible binding by the metalloproteins: hemoglobin, myoglobin, hemerythrin, and hemocyanin. Nature developed such systems to obviate the limited solubility of O2 in water (~1 mM at 1 atm O2), which restricts the energy flux from oxidative metabolism in aerobic organisms.