Andrew Reynolds

This study in the history and philosophy of science is concerned with the role of metaphors in the creation of scientific concepts, theories, and explanations. It treats the history of key metaphors that have informed cell theory and the experimental, philosophical and social circumstances under which they have emerged, risen in popularity, and in some cases faded from view. How we think of cells, as organisms or as machines, for instance, makes a difference to scientific practice. Consequently an accurate picture of how scientific knowledge is made requires us to understand how the metaphors scientists use—and the social values that often surreptitiously attend them—influence our understanding of the world, and ultimately of ourselves. Moreover, by illustrating how scientific language originally intended as metaphor can become quite literal, the book explores the implications of this for the issue of scientific realism.

Peirce's Scientific Metaphysics is the first book devoted to understanding Charles Sanders Peirce's (1839-1914) metaphysics from the perspective of the scientific questions that motivated his thinking. Deftly situating Peirce's often original and pathbreaking ideas within their appropriate historical and scientific contexts, Reynolds traces his reliance upon the law of large numbers, which illustrated for Peirce the emergence of a stable order and regularity from a multitude of chance events, throughout his writings on late nineteenth-century physics, chemistry, biology, psychology, and cosmology. Along the way, Peirce's vision of an indeterministic and evolutionary cosmology is contrasted with the thought of other important late nineteenth-century scientists and philosophers, such as James Clerk Maxwell, Ludwig Boltzmann, William Thomson (Lord Kelvin), Herbert Spencer, Charles Darwin, and Ernst Haeckel. While offering a detailed account of the scientific ideas and theories essential for understanding Peirce's metaphysical system (e.g., the irreversibility of time and the reversibility of physical laws, the statistical law of large numbers), this book is written in a manner accessible to the non-specialist. This will make it especially attractive to students of Peirce's philosophy who lack familiarity with the scientific and mathematical ideas that are so central to his thought. Those with an interest in the history and philosophy of science, especially concerning the application of statistical and probabilistic thinking to physics, chemistry, biology, psychology, and cosmology, will find this discussion of Peirce's philosophy invaluable. "Andrew Reynolds has written exactly the book we need, a clear, well-argued, scientifically informed study of Peirce's metaphysics. I wish it had been available well before now!"--Christopher Hookway, author of Peirce

This chapter looks at the incorporation of cell theory into evolutionary theory in the 19th century with special discussion of Darwin's remarks on cell theory in relation to his theory of pangenesis, and Haeckel's gastraea theory of animal development and evolution.

Peirce is often credited with having formulated a pragmatic theory of truth. This can be misleading, if it is assumed that Peirce was chiefly interested in providing a metaphysical analysis of the immediate conditions under which a belief or proposition is true, or the conditions under which a proposition or belief is said to be madetrue. Cheryl Misak has exposed the subtleties in Peirce's discussion of truth, especially showing the difficulties faced by any ascription to him of an analytic definition of truth. In this paper I follow Misak in urging that Peirce's contribution to the philosophical discussion about the nature of truth was not of that kind. What makes his pragmatic approach distinctive is that rather than attempting to state the nature of truth per se, it attempts to uncover the beliefs and expectations we commit ourselves to when we make specific claims that such and such is true or is the case.

Reaction to Darwin’s theory of evolution within the community of natural history enthusiasts in 19th century Nova Scotia focused on his use of hypothesis to account for a diversity of facts about organic species and their historical origins. Critics here as elsewhere often faulted his reasoning as straying from proper Baconian inductive method. Those locally engaged in natural history were inclined to stick closely to a descriptive inventory of the colony’s (and as of 1867 province’s) natural resources. But more fundamentally, Darwin’s approach challenged the mission of natural theology to support a providential reading of the natural world and humanity’s place within it. A review of publications in the Proceedings and Transactions of the Nova Scotian Institute for Natural Science and a private diary account of a discussion emerging from a Mechanics Institute lecture during the 1860s and ‘70s reveals how generally their members reacted critically to Darwin’s science while insisting on the compatibility of science and religion.

This chapter looks at the incorporation of cell theory into evolutionary theory in the 19th century with special discussion of Darwin's remarks on cell theory in relation to his theory of pangenesis, and Haeckel's gastraea theory of animal development and evolution.

Social metaphors have long been a part of the cell theory. In the nineteenth century plants and animals were described as ‘cell-states’ (ZellenStaaten) composed of cell ‘citizens’ functionally arranged into specialized tissue ‘classes’ or ‘professions.’ This conception of the organism as a ‘society of cells’ was conceptually grounded by the principle of the division of (physiological) labour, an idea transferred from political economy to help explain the functional organization of a coherent system of semi-autonomous parts. More recently however cell biology has been reshaped by the idea of inter-cellular communication. This paper details how the science of cell communication provides a new explanatory account of how multicellular organisms and other ‘cell societies’ with their division of labour are created and maintained through the bonds of communication. The idea of ‘cell sociology’ is discussed as a particular reflection of this new communicative model of multicellular organization and function.
Keywords:  Cell-cell communication, multicellularity, metaphors in science, cell sociology, group effect

Multicellular development and tissue maintenance involve the regular elimination of damaged and healthy cells. The science of this genetically regulated cell death is particularly rich in metaphors: ‘programmed cell death’ or ‘cell suicide’ is considered an ‘altruistic’ act on the part of a cell for the benefit of the organism as a whole. It is also considered a form of ‘social control’ exerted by the body/organism over its component cells. This paper analyzes the various functions of these metaphors and critical discussion about them within the scientific community. Bodies such as the Nomenclature Committee on Cell Death (NCCD) have been charged with bringing order to the language of cell death to facilitate scientific progress. While the NCCD recommends adopting more objective biochemical terminology to describe the mechanisms of cell death, the metaphors in question retain an important function by highlighting the broader context within which cell death occurs. Scientific metaphors act as conceptual ‘tools’ which fulfill various roles, from highlighting a phenomenon as of particular interest, situating it in a particular context, or suggesting explanatory causal mechanisms.

The cell theory – the thesis that all life is made up of one or more cells, the fundamental structural and physiological unit – is one of the most celebrated achievements of modern biological science. And yet from its very inception in the nineteenth century it has faced repeated criticism from some biologists. Why do some continue to criticize the cell theory, and how has it managed nevertheless to keep burying its undertakers? The answers to these questions reveal the complex nature of the cell theory and the cell concept on which it is based. Like other scientific laws, the assertion that all living things are made of cells purchases its universality at the expense of abstraction. If, however, it is regarded as a mere widely applicable empirical generalization with notable exceptions, it still remains too important to discard. Debate about whether the cell or the organism standpoint provides the more correct account of anatomical, physiological, and developmental facts illustrates the tension between our attempts to express the truth about reality in conceptual terms conducive to a unified human understanding.

In the nineteenth century protozoology and early cell biology intersected through the nexus of Darwin’s theory of evolution. As single-celled organisms, amoebae offered an attractive focus of study for researchers seeking evolutionary relationships between the cells of humans and other animals, and their primitive appearance made them a favourite model for the ancient ancestor of all living things. Their resemblance to human and other metazoan cells made them popular objects of study among morphologists, physiologists, and even those investigating animal behaviour. The amoeba became the exemplar of the new protoplasmic cell concept of mid-century and because its apparent simplicity made it widely generalizable it became a popular subject in a breadth of experimental investigations and theoretical speculations. It was able to do this because “the amoeba” denotes not a particular organism, but a general type of behaviour common to the cells of a range of protozoa, simple plants and higher animals. Its status as an exemplary cell also rested upon auxiliary philosophical assumptions about what constitutes a primitive characteristic and the thesis that evolution is a progressive development of order from chaos.

The concept of the cell has been based on metaphor since its inception, and the history of cell theory has continued to rely on metaphor and analogy. In the nineteenth century, cells were most popularly conceived either as building stones or elementary autonomous organisms from which larger organisms are composed. With advances in physiology and the rise of modern biochemistry in the early twentieth century, the chemical factory or laboratory became the dominant metaphor for this biological unit. Today in the twenty-first century, the metaphorical imagery has become a reality, with cells acting as chemical factories for the synthesis of commercially valuable bio-products. The history of the cell shows how metaphors act as conceptual tools, with particular strengths for facilitating different sorts of questions and experimental techniques.

Early discussion of a genetic code inscribed in DNA suggested a close resemblance between the sequence of nucleotide triplets ('codons') arranged along the length of the DNA molecule and codes written in computer or natural languages. Human codes are typically arranged as two-dimensional scripts. But because the nucleotides making up the ‘genetic code’ of DNA are normally packaged in densely coiled chromatin structures wound around histone proteins, the cell machinery responsible for ‘reading’ (copying, transcribing, and translating) the genetic ‘information’ does not always have direct access to the relevant nucleotide segments. Accessibility to coding segments and tagging of nucleotide sequences with epigenetic markers (e.g. methylation) have significant effects on which genes are active and when. Determining therefore how chromatin is organized, located, and modified within the environment of the cell nucleus has become a vital research topic. Since the 1980s researchers have increasingly spoken of chromatin landscape and nuclear architecture to highlight these three-dimensional topographical features of the nuclear genome. This talk 1) provides a preliminary history of the employment of these phrases in the literature from the 1980s to the present, detailing how an apparently implicit consensus formed around them, 2) discusses the significance of these metaphors for scientific understanding of chromatin biology and genetics, and 3) considers how these quite distinct perspectives (the linear genetic code and the topological chromatin landscape-nuclear architecture frameworks) are integrated into a coherent account of cell structure and function.

Throughout the 1960s and 70s scientists began to uncover the details of how cells communicate by means of electrical and chemical signals. The process by which an extracellular signal is received at a membrane-bound receptor and transmitted into the inner cell environment where it can trigger changes in cell behaviour was dubbed ‘signal transduction.’ The complete chain of events and molecular components describing this signal transmission was called a ‘signaling pathway.’ Metaphors and analogies from electronic engineering and cybernetic theory have strongly informed understanding of these processes. The cell is regarded as consisting of circuits and programs, which scientists have been busy trying to map in their efforts to understand development, health, and disease in humans and other organisms. The 1980s and 90s saw recognition of the widespread occurrence of ‘cross-talk’ between signalling pathways, and as a result the metaphor of signaling ‘networks’ began to appear more frequently. Increasingly one now sees criticisms that the signal pathway concept is misleadingly simplistic and impedes further progress in understanding cell behaviour and biomedical intervention to treat diseases arising from altered cell communication and intracellular signaling. Signaling networks are highly dynamic processes which belie the implication of a static and deterministic entity suggested by the pathway and circuit metaphors. For this reason alternative metaphors have also been suggested of a more social or sociological nature highlighting the ‘cooperativity’ of signaling molecules like semi-autonomous agents interacting within an intracellular ‘ecology’. Rather than the strictly hierarchical and deterministic logic of an electronic circuit board these alternatives stress that there is no dominant molecule or agent controlling the entire intracellular signaling network – the intracellular organization is ‘anarcho-syndicalist’(Gibson 2009). Greater emphasis is now placed on the context of the ‘informational signal’, seeing as how the same ligand can have very different consequences in different cell types or even in the same type of cell at different times depending upon cell context and history.  There is no ‘signal’ with a stable semantic meaning as the metaphor of an electronic circuit may suggest; there is rather a shifting and dynamic ‘social network’ of molecules that collectively constructs the ‘meaning’ of a signal in the sense of an ultimate effect on cell behaviour or morphology. This has interesting implications for philosophical theories of mechanism and explanation, not to mention biomedical research into drug development and therapy.  And yet the importance of spatial organization within the cell by means of scaffolding and adaptor proteins suggests electronic circuit or wiring models of intracellular signaling may not be entirely inaccurate, as do recent successes by synthetic biologists in the construction of artificial logic gates and switches in bacterial cells.
This talk will describe some of the history of this shift in language and perspective, and the implications for the philosophy of science’s account of mechanism as an explanatory scheme, and for understanding the roles of metaphor in science. For example, metaphors do more than just describe things (like cells and their behaviour). Metaphors are also prescriptive, they encourage and facilitate particular approaches to the object under study. So if we use electronic and computer metaphors to talk and think about cells, it should not be surprising that we try to reengineer, redesign and rewire them. Synthetic biology and its project of creating patentable commodities from living cells and bio-molecules is facilitated by the description of cells as electronic gadgets and devices. But as useful as those metaphors may be for these sorts of interventionist and commercial ventures, they may not be as adequate for other projects, for instance understanding how cells and organisms naturally develop into differentiated cells and organisms. For this social metaphors may be more useful, and with them different prescriptive stances towards cells may be in the making.