From the perspective of successive events, chemical reactions are expressed or thought about, in terms of the cause-effect category. In this work, I will firstly discuss some aspects of causation and interaction in chemistry, argue for the interaction, and propose an alternative or complementary representation scheme called “interaction diagram”, that allows representing chemical reactions through a geometric diagram. The understanding of this diagram facilitates the analysis of reactions in terms of the interaction, or reciprocal action, among the participating (...) entities. Secondly, I will describe the model and provide examples and finally, I will discuss the scope and limitations of the current development status of the model. (shrink)

Diagrams can serve as representational models in scientific research, yet important questions remain about how they do so. I address some of these questions with a historical case study, in which diagrams were modified extensively in order to elaborate an early hypothesis of protein synthesis. The diagrams’ modelling role relied mainly on two features: diagrams were modified according to syntactic rules, which temporarily replaced physico-chemical reasoning, and diagram-to-target inferences were based on semantic interpretations. I then (...) explore the lessons for the relative roles of syntax, semantics, external marks, and mental images, for justifying diagram-to-target inferences, and for the “artefactual approach” to scientific models. (shrink)

Summary James Watt (1736–1819) is best known as an engineer who dramatically improved the efficiency of the steam engine. What we take to be his chemical interests are conventionally seen as peripheral to his main line of work. He is usually treated as a chemist in three main contexts: his ‘practical’ chemical work relating to chlorine bleaching, varnishes, pottery, and so on; his work with Thomas Beddoes on the medicinal uses of various ‘airs’; his, much disputed, claim as (...) a chemical discoverer in the case of the composition of water. In this paper, I argue that Watt himself, and his contemporaries, saw the centrepiece of his steam engine work—the separate condenser—as a chemical invention. I also suggest more broadly that Watt understood the steam engine as a chemical device. For Watt and his Scottish friends, the study of steam and heat was a chemical enquiry. The subsequent changes in the place of heat in chemical enquiry in the early nineteenth century led to a reclassification of Watt's chemical investigations as ‘physics’. This, in turn, produced the sharp separation of his chemical and engineering activities characteristic of modern historiography. Watt's steam engine, which is usually placed in the lineage of machines understood as heat engines, and explained by the laws of thermodynamics, is better seen in context as a chemical device. Watt's ‘indicator diagram’ is reassessed in the light of this. (shrink)

This paper describes and defends the view that minimal chemical life essentially involves the chemical integration of three chemical functionalities: containment, metabolism, and program (Rasmussen et al. in Protocells: bridging nonliving and living matter, 2009a ). This view is illustrated and explained with the help of CMP and Rasmussen diagrams (Rasmussen et al. In: Rasmussen et al. (eds.) in Protocells: bridging nonliving and living matter, 71–100, 2009b ), both of which represent the key chemical functional (...) dependencies among containment, metabolism, and program. The CMP model of minimal chemical life gains some support from the broad view of life as open-ended evolution, which I have defended elsewhere (Bedau in The philosophy of artificial life, 1996 ; Bedau in Artificial Life, 4:125–140, 1998 ). Further support comes from the natural way the CMP model resolves the puzzle about whether life is a matter of degree. (shrink)

This chapter shows that the combination of mathematical and chemical thinking in particular, as evidenced by Charles Sanders Peirce’s chemical training at Harvard, formed a solid conceptual basis for his account of diagrams. The connection between the Lawrence school and the chemical tradition established by Justus von Liebig in Giessen is of crucial importance to understand the context of Peirce’s own chemistry training. A completely different picture emerges if one pays greater attention to the nature of (...) the chemistry curriculum in Harvard at the time, and in particular to the pedagogical innovations introduced by Peirce’s chemistry teacher, Josiah Parsons Cooke. Historians of science have investigated the rise of institutional scientific laboratories from a range of perspectives. The chapter concludes with some suggestions for further investigation into the role of chemistry in Peirce’s philosophical system more broadly and the potential this new avenue of inquiry might have for the direction of Peirce scholarship. (shrink)

Recent work in formal philosophy has concentrated over-whelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at (...) a certain level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used. (shrink)

In this paper I tackle the question of what basic form an analytical method for articulating and ultimately assessing visual representations should take. I start from the assumption that scientific images, being less prone to interpretive complication than artworks, are ideal objects from which to engage this question. I then assess a recent application of Nelson Goodman's aesthetics to the project of parsing scientific images, Laura Perini's ‘The truth in pictures’. I argue that, although her project is an important one, (...) her Goodmanian conventionalism produces a method of analysis that is incapable of adequately parsing a certain class of pictures and her focus on truth is unnecessary. This speaks against the promise of Goodman's analytical strategy for elucidating visual content and reasoning in the sciences and elsewhere. As an alternative, I develop John Willats’ analytical method and compare it to Perini's through engaging three of her examples—a chemical diagram, a graph and an electron micrograph. Ultimately, a space remains open for a mixed system where Willats’ account provides pictorial analysis and the Goodman–Perini approach parses visual languages. (shrink)

While symbolic colour use has always played a conspicuous role in science research and education, the use of colour in historic diagrams remains a lacuna in the history of science. Investigating the colour use in diagrams often means uncovering a whole cosmology that is not otherwise explicit in the diagram itself. The periodic table is a salient and iconic example of non-mimetic colour use in science. Andreas von Antropoff's (1924) rectangular table of recurrent rainbow colours is famous, as (...) are Alcindo Flores Cabral's (1949) application of colour in his round snail form, using the RGB scheme, and Mazurs's (1967) pine tree system, consisting of warm and cold colours that he attributed to specific groups of elements—an attribution that we can relate back to humoralism and alchemy. From the first periodic tables in the 19th century, individual researchers have used different colour regimes. While standardization may play an obvious role in chemistry and its diagrams, all the more impressive is the anarchistic use of colour in the various diagrams which continue to be created. This article focuses on periodic tables in chemical journals and text books, and explores and compares the development of colour codes found in the few existing polychrome diagrams from the 1920s to the 1970s. (shrink)

" Biosemantics " was the title of a paper on mental representation originally printed in The Journal of Philosophy in 1989. It contained a much abbreviated version of the work on mental representation in Language Thought and Other Biological Categories. There I had presented a naturalist theory of intentional signs generally, including linguistic representations, graphs, charts and diagrams, road sign symbols, animal communications, the "chemical signals" that regulate the function of glands, and so forth. But the term " (...) biosemantics " has usually been applied only to the theory of mental representation. Let me first characterize a more general class of theories called "teleological theories of mental content" of which biosemantics is an example. Then I will discuss the details that distinguish biosemantics from other naturalistic teleological theories. (shrink)

Most contemporary chemists consider quantum mechanics to be the foundational theory of their discipline, although few of the calculations that a strict reduction would seem to require have ever been produced. In this essay I discuss contemporary algebraic and diagrammatic representations of molecular systems derived from quantum mechanical models, specifically configuration interaction wavefunctions for ab initio calculations and molecular orbital energy diagrams. My aim is to suggest that recent dissatisfaction with reductive accounts of chemical theory may stem from (...) both the inability of standard accounts of reduction to incorporate the diverse forms of representation found in chemical practice and our philosophical predilection to analyze all connections between theories in terms of logical reduction. (shrink)

Most contemporary chemists consider quantum mechanics to be the foundational theory of their discipline, although few of the calculations that a strict reduction would seem to require have ever been produced. In this essay I discuss contemporary algebraic and diagrammatic representations of molecular systems derived from quantum mechanical models, specifically configuration interaction wavefunctions for ab initio calculations and molecular orbital energy diagrams. My aim is to suggest that recent dissatisfaction with reductive accounts of chemical theory may stem from (...) both the inability of standard accounts of reduction to incorporate the diverse forms of representation found in chemical practice and our philosophical predilection to analyze all connections between theories in terms of logical reduction. (shrink)

This paper describes and defends the view that minimal chemical life essentially involves the chemical integration of three chemical functionalities: containment, metabolism, and program. This view is illustrated and explained with the help of CMP and Rasmussen diagrams in Protocells: bridging nonliving and living matter, 71–100, 2009b), both of which represent the key chemical functional dependencies among containment, metabolism, and program. The CMP model of minimal chemical life gains some support from the broad view (...) of life as open-ended evolution, which I have defended elsewhere. Further support comes from the natural way the CMP model resolves the puzzle about whether life is a matter of degree. (shrink)

The rigid recoil of a crystal is the accepted mechanism for the Mössbauer effect. It’s at odds with the special theory of relativity which does not allow perfectly rigid bodies. The standard model of particle physics which includes QED should not allow any signals to be transmitted faster than the speed of light. If perturbation theory can be used, then the X-ray emitted in a Mössbauer decay must come from a single nuclear decay vertex at which the 4-momentum is exactly (...) conserved in a Feynman diagram. Then the 4-momentum of the final state Mössbauer nucleus must be slightly off the mass shell. This off-shell behavior would be followed by subsequent diffusion of momentum throughout the crystal to bring the nucleus back onto the mass shell and the crystal to a final relaxed state in which it moves rigidly with the appropriate recoil velocity. This mechanism explains the Mössbauer effect at the microscopic level and reconciles it with relativity. Because off-mass-shell quantum mechanics is required, the on-mass-shell theories developed originally for the Mössbauer effect are inadequate. Another possibility is that that the recoil response involves a non-perturbative effect in the standard model which could allow for a non-local instantaneous momentum transfer between the crystal and the decay, as proposed for example by Preparata and others in super-radiance theory. The recoil time of the crystal is probably not instantaneous, and if it could be measured, one could distinguish between various theories. An experiment is proposed in this paper to measure this time. The idea is to measure the total energy radiated due to bremsstrahlung from a charged Mössbauer crystal which has experienced a recoil. Using Larmor’s formula, along with corrections to it, allows one to design an experiment. The favored idea is to use many small nano-spheres of Mössbauer-active metals, whose outer surfaces are charged. The energy radiated then varies as the charge squared divided by the recoil time. This can then be measured with the extreme sensitivity available in Mössbauer experiments. If it turns out that experiments prove the need for off-mass-shell theory, then this would have profound implications for all of condensed matter physics. It would mean that an off-mass-shell theory like those considered by Stueckelberg, Horwitz, Piron, Greenberger, and many others are required to describe nature. The inclusion of these would be a major shift in the foundations. It would mean that there are new dynamic variables—the rest masses of particles. The ability to measure the diffusion relaxation time should prove useful also in chemical analysis, and provide a new class of analytical methods for material science. This problem is also interesting because the Mössbauer effect is a phenomenon where the solid-state environment dramatically and indisputably influences the probability of a nuclear process. (shrink)

Jay Zeman one must keep a bright lookout for unintended and unexpected changes thereby brought about in the relations of different significant parts of the diagram to one another. Such operations upon diagrams, whether external or imaginary, take the place of the experiments upon real things that one performs in chemical and physical research. Chemists have ere now, I need not say, described experimentation as the putting of questions to Nature. Just so, experiments upon diagrams are questions (...) put to the Nature of the relations concerned (4.530). 1 The diagrammatic nature of mathematical reasoning suggests that as my power to create diagrams increases, so too will my capacity for fruitful mathematical reasoning. Peirce's own work involved an unending series of experiments with different diagrammatic notations, all interesting, some difficult, some extremely fruitful. And the diagrammatic notations available are not only a function of some kind of “internal mental activity.” As Dewey has noted, “Breathing is an affair of the air as truly as of the lungs; digesting an affair of food as truly as of tissues of stomach” (Dewey, 15); so analogously is mathematical reasoning an affair of the diagrams available as truly as of the “mind” (which is then not limited to something inside the head, but includes the relevant diagrams, “external” as well as “internal”); so does mathematical reasoning have its “alembics and cucurbits” just as surely as does chemistry. In doing mathematical reasoning, we make of the diagrams “instruments of thought,” and advances in the technology of diagrams can directly affect our patterns of reasoning. I can imagine Peirce spending hours (and dollars) in a modern artists' supply store. (shrink)

In this paper I contend that abduction is essentially multimodal, in that both data and hypotheses can have a full range of verbal and sensory representations, involving words, sights, images, smells, etc. but also kinesthetic experiences and other feelings such as pain, and thus all sensory modalities. The kinesthetic aspects simply explain abductive reasoning is basically manipulative, both linguistic and non linguistic signs have an internal semiotic life, as particular configurations of neural networks and chemical distributions (and in terms (...) of their transformations) at the level of human brains, and as somatic expressions, but can also be delegated to many external objects and devices, for example written texts, diagrams, artifacts, etc. Still in this case unconscious aspects takepart of the abductive procedure, which acquires the features of a kind of "thinking through doing". (shrink)

Neurons encode and transmit signals through chemical synaptic or electrical synaptic connections in the actual nervous system. Exploring the biophysical properties of coupling channels is of great significance for further understanding the rhythm transitions of neural network electrical activity patterns and preventing neurological diseases. From the perspective of biophysics, the activation of magnetic field coupling is the result of the continuous release and propagation of intracellular and extracellular ions, which is very similar to the activation of chemical synaptic (...) coupling through the continuous release of neurotransmitters. In this article, an induction coil is used to connect two HR neurons to stimulate the effect of magnetic field coupling. It is inevitable that time delays can affect the coupling process in the transmission of information, and it should be considered in the coupled model. Firstly, the firing characteristics and bifurcation modes of two coupled HR neurons are studied by using one parameter and two parameters bifurcation. With the increase of propagation delay and coupling gain, the chaotic state of neurons disappears and the high-period window decreases due to the influence of energy transfer between neurons. Then, the synchronization patterns of two HR neurons with different stimulation are analyzed by error diagrams and time series diagrams. It is confirmed that the synchronous pattern has certain regularity and is related not only to the neurons with large stimulation current but also to the time delay and coupling gain. The research conclusions of this article will provide the corresponding theoretical basis for medical experiments. (shrink)

Sketching as a scientific practice goes beyond the simple act of inscribing diagrams onto paper. Scientists produce a wide range of representations through sketching, as it is tightly coupled to model-based reasoning. Chemists in particular make extensive use of sketches to reason about chemical phenomena and to communicate their ideas. However, the chemical sciences have a unique problem in that chemists deal with the unseen world of the atomic-molecular level. Using sketches, chemists strive to develop causal mechanisms (...) that emerge from the structure and behavior of molecular-level entities, to explain observations of the macroscopic visible world. Interpreting these representations and constructing sketches of molecular-level processes is a crucial component of student learning in the modern chemistry classroom. Sketches also serve as an important component of assessment in the chemistry classroom as student sketches give insight into developing mental models, which allows instructors to observe how students are thinking about a process. In this paper we discuss how sketching can be used to promote such model-based reasoning in chemistry and discuss two case studies of curricular projects, CLUE and The Connected Chemistry Curriculum, that have demonstrated a benefit of this approach. We show how sketching activities can be centrally integrated into classroom norms to promote model-based reasoning both with and without component visualizations. Importantly, each of these projects deploys sketching in support of other types of inquiry activities, such as making predictions or depicting models to support a claim; sketching is not an isolated activity but is used as a tool to support model-based reasoning in the discipline. (shrink)

The concepts developed using Upanishadic insight regarding human consciousness, mind and mental processes and their applications in information acquisition and transmission by, through and in human body will be used to model human cognitive processes. A sequential reversible process by the stepwise transformation of (i) infrasonic form of energy and transformation of information already stored in (ii) biochemical form within as memory, and retrieved as inner mental world into (iii) electrochemical and then into (iv) mechanical form while communicating and the (...) reverse of it as the (i) input stimuli from outside world as light, sound, chemical, mechanical and heat forms, into (ii) electrochemical, (iii) biochemical and finally into (iv) infra sonic form while acquiring and understanding processes is put forward and discussed. Comparisons will be made between energy transformations in electronics communication processes and these psychic energy transformations that give rise to cognitive processes. This comparison gives an insight and theory of origin, structure, function and cessation of human mental functions. A comparative diagram that describes application of infrasonic energy transformations associated with bionics as biochemical, electrochemical and mechanical forms will be given. (shrink)

This paper analyses a hitherto unknown technique of using logic diagrams to create argument maps in eristic dialectics. The method was invented in the 1810s and -20s by Arthur Schopenhauer, who is considered the originator of modern eristic. This technique of Schopenhauer could be interesting for several branches of research in the field of argumentation: Firstly, for the field of argument mapping, since here a hitherto unknown diagrammatic technique is shown in order to visualise possible situations of arguments in (...) a dialogical controversy. Secondly, the art of controversy or eristic, since the diagrams do not analyse the truth of judgements and the validity of inferences, but the persuasiveness of arguments in a dialogue. (shrink)

Reism or concretism are the labels for a position in ontology and semantics that is represented by various philosophers. As Kazimierz Ajdukiewicz and Jan Woleński have shown, there are two dimensions with which the abstract expression of reism can be made concrete: The ontological dimension of reism says that only things exist; the semantic dimension of reism says that all concepts must be reduced to concrete terms in order to be meaningful. In this paper we argue for the following two (...) theses: (1) Arthur Schopenhauer has advocated a reistic philosophy of language which says that all concepts must ultimately be based on concrete intuition in order to be meaningful. (2) In his semantics, Schopenhauer developed a theory of logic diagrams that can be interpreted by modern means in order to concretize the abstract position of reism. Thus we are not only enhancing Jan Woleński’s list of well-known reists, but we are also adding a diagrammatic dimension to concretism, represented by Schopenhauer. (shrink)

In the last few decades there has been a revival of interest in diagrams in mathematics. But the revival, at least at its origin, has been motivated by adherence to the view that the method of mathematics is the axiomatic method, and specifically by the attempt to fit diagrams into the axiomatic method, translating particular diagrams into statements and inference rules of a formal system. This approach does not deal with diagrams qua diagrams, and is (...) incapable of accounting for the role diagrams play as means of discovery and understanding. Alternatively, this paper purports to show that the view that the method of mathematics is the analytic method is capable of dealing with diagrams qua diagrams, and of accounting for such role. (shrink)

This book investigates a number of central problems in the philosophy of Charles Peirce grouped around the realism of his semiotics: the issue of how sign systems are developed and used in the investigation of reality. Thus, it deals with the precise character of Peirce's realism; with Peirce's special notion of propositions as signs which, at the same time, denote and describe the same object. It deals with diagrams as signs which depict more or less abstract states-of-affairs, facilitating reasoning (...) about them; with assertions as public claims about the truth of propositions. It deals with iconicity in logic, the issue of self-control in reasoning, dependences between phenomena in their realist descriptions. A number of chapters deal with applied semiotics: with biosemiotic sign use among pre-human organisms: the multimedia combination of pictorial and linguistic information in human semiotic genres like cartoons, posters, poetry, monuments. All in all, the book makes a strong case for the actual relevance of Peirce's realist semiotics. (shrink)

In this paper, we present a survey of the development of the technique of argument diagramming covering not only the fields in which it originated - informal logic, argumentation theory, evidence law and legal reasoning – but also more recent work in applying and developing it in computer science and artificial intelligence. Beginning with a simple example of an everyday argument, we present an analysis of it visualised as an argument diagram constructed using a software tool. In the context of (...) a brief history of the development of diagramming, it is then shown how argument diagrams have been used to analyze and work with argumentation in law, philosophy and artificial intelligence. (shrink)

Diagrams are ubiquitous in mathematics. From the most elementary class to the most advanced seminar, in both introductory textbooks and professional journals, diagrams are present, to introduce concepts, increase understanding, and prove results. They thus fulfill a variety of important roles in mathematical practice. Long overlooked by philosophers focused on foundational and ontological issues, these roles have come to receive attention in the past two decades, a trend in line with the growing philosophical interest in actual mathematical practice.

We contend that diagrams are tools not only for communication but also for supporting the reasoning of biologists. In the mechanistic research that is characteristic of biology, diagrams delineate the phenomenon to be explained, display explanatory relations, and show the organized parts and operations of the mechanism proposed as responsible for the phenomenon. Both phenomenon diagrams and explanatory relations diagrams, employing graphs or other formats, facilitate applying visual processing to the detection of relevant patterns. Mechanism (...) class='Hi'>diagrams guide reasoning about how the parts and operations work together to produce the phenomenon and what experiments need to be done to improve on the existing account. We examine how these functions are served by diagrams in circadian rhythm research. (shrink)

In a multi-study naturalistic quasi-experiment involving 269 students in a semester-long introductory philosophy course, we investigated the effect of teaching argument diagramming on students’ scores on argument analysis tasks. An argument diagram is a visual representation of the content and structure of an argument. In each study, all of the students completed pre- and posttests containing argument analysis tasks. During the semester, the treatment group was taught AD, while the control group was not. The results were that among the different (...) pretest achievement levels, the scores of low-achieving students who were taught AD increased significantly more than the scores of low-achieving students who were not taught AD, while the scores of the intermediate- and high-achieving students did not differ significantly between the treatment and control groups. The implication of these studies is that learning AD significantly improves low-achieving students’ ability to analyze arguments. (shrink)

From his earliest student days through the writing of his last book, Charles Darwin drew diagrams. In developing his evolutionary ideas, his preferred form of diagram was the tree. An examination of several of Darwin’s trees—from sketches in a private notebook from the late 1830s through the diagram published in the Origin—opens a window onto the role of diagramming in Darwin’s scientific practice. In his diagrams, Darwin simultaneously represented both observable patterns in nature and conjectural narratives of evolutionary (...) history. He then brought these natural patterns and narratives into dialogue, allowing him to explore whether the narratives could explain the patterns. But Darwin’s diagrams did not reveal their meaning directly to passive readers; they required readers to engage dynamically with them in order to understand the connections they disclosed between patterns and narratives. Moreover, the narratives Darwin depicted in his diagrams did not represent past sequences of events that he claimed had actually occurred; the narratives were conjectural, schematic, and probabilistic. Instead of depicting actual histories in all their particularity, Darwin depicted narratives in his diagrams in order to make general claims about how nature works. The conjunction of these features of Darwin’s diagrams is central to how they do their epistemic work. (shrink)

The way in which one understands information and concepts, and the way a student works to develop this, is an individual aspect of learning that cannot be universally defined as (at least manifested) the same for everyone. ‘Understanding’ is a broad term, and the way one achieves understanding is dependent on the way that material is presented. In this article, we argue that the philosophy of science can be important to nursing education—in particular, by showing that the way we imbue (...) understanding might depend on the meaning of ‘understanding’. Diagrams and concept maps are meant to guide newly formed knowledge and connections to develop proper thinking (e.g., the order in which nursing students must prioritize data) that a student requires in the field. We argue that whether or not an image/diagram/concept map confers understanding will depend on both what the object is and what we mean by ‘understanding’. (shrink)

This book is about the relationship between necessary reasoning and visual experience in Charles S. Peirce’s mathematical philosophy. It presents mathematics as a science that presupposes a special imaginative connection between our responsiveness to reasons and our most fundamental perceptual intuitions about space and time. Central to this view on the nature of mathematics is Peirce’s idea of diagrammatic reasoning. In practicing this kind of reasoning, one treats diagrams not simply as external auxiliary tools, but rather as immediate visualizations (...) of the very process of the reasoning itself. Thus conceived, one's capacity to diagram their thought reveals a set of characteristics common to ordinary language, visual perception, and necessary mathematical reasoning. The book offers an original synthetic approach that allows tracing the roots of Peirce’s conception of a diagram in certain patterns of interrelation between his semiotics, his pragmaticist philosophy, his logical and mathematical ideas, bits and pieces of his biography, his personal intellectual predispositions, and his scientific practice as an applied mathematician. (shrink)

There is a persisting debate about what chemical bonds are and whether they exist. I argue that chemical bonds are real patterns of interactions between subatomic particles. This proposal resolves the problems raised in the context of existing understandings of the chemical bond and provides a novel way to defend the reality of chemical bonds.

This article presents diagrams developed from the insights of three middle school children with limited mobility about their experiences navigating social and spatial relations in their home, school and neighbourhoods. The paper explores the concept of assemblage as well as operationalising the Deleuzian idea of the diagram. The diagrams we produce are developed in connection with dominant idealisations of neighbourhood and home range that function in North America to choreograph children's progression from infancy through adolescence. We undertake this (...) diagramming in order to immediately and affectively illustrate the limits and possibilities of the challenges these young people face. (shrink)

This chapter provides a survey of issues about diagrams in traditional geometrical reasoning. After briefly refuting several common philosophical objections, and giving a sketch of diagram-based reasoning practice in Euclidean plane geometry, discussion focuses first on problems of diagram sensitivity, and then on the relationship between uniform treatment and geometrical generality. Here, one finds a balance between representationally enforced unresponsiveness (to differences among diagrams) and the intellectual agent's contribution to such unresponsiveness that is somewhat different from what one (...) has come to expect in modern logic. Finally, challenges and opportunities for further work are indicated. (shrink)

Biologists depend on visual representations, and their use of diagrams has drawn the attention of philosophers, historians, and sociologists interested in understanding how these images are involved in biological reasoning. These studies, however, proceed from identification of diagrams on the basis of their spare visual appearance, and do not draw on a foundational theory of the nature of diagrams as representations. This approach has limited the extent to which we under- stand how these diagrams are involved (...) in biological reasoning. In this paper, I characterize three different kinds of figures among those previously identified as diagrams. The features that make these figures distinctive as representational types, furthermore, illuminate the ways in which they are involved in biological reasoning. (shrink)

In this paper I investigate the relationship between vernacular kind terms and specialist scientific vocabularies. Elsewhere I have developed a defence of realism about the chemical elements as natural kinds. This defence depends on identifying the epistemic interests and theoretical conception of the elements that have suffused chemistry since the mid-eighteenth century. Because of this dependence, it is a discipline-specific defence, and would seem to entail important concessions to pluralism about natural kinds. I argue that making this kind of (...) concession does not imply that vernacular kind terms have independent application conditions. Nor does it preclude us saying that chemists, with their particular epistemic interests, have discovered the underlying nature of water, the stuff that is named and thought about in accordance with the practical interests of everyday life. There are limits to pluralism. (shrink)

This paper explores the question of what makes diagrammatic representations effective for human logical reasoning, focusing on how Euler diagrams support syllogistic reasoning. It is widely held that diagrammatic representations aid intuitive understanding of logical reasoning. In the psychological literature, however, it is still controversial whether and how Euler diagrams can aid untrained people to successfully conduct logical reasoning such as set-theoretic and syllogistic reasoning. To challenge the negative view, we build on the findings of modern diagrammatic logic (...) and introduce an Euler-style diagrammatic representation system that is designed to avoid problems inherent to a traditional version of Euler diagrams. It is hypothesized that Euler diagrams are effective not only in interpreting sentential premises but also in reasoning about semantic structures implicit in given sentences. To test the hypothesis, we compared Euler diagrams with other types of diagrams having different syntactic or semantic properties. Experiment compared the difference in performance between syllogistic reasoning with Euler diagrams and Venn diagrams. Additional analysis examined the case of a linear variant of Euler diagrams, in which set-relationships are represented by one-dimensional lines. The experimental results provide evidence supporting our hypothesis. It is argued that the efficacy of diagrams in supporting syllogistic reasoning crucially depends on the way they represent the relational information contained in categorical sentences. (shrink)

Diagrams have played an important role throughout the entire history of differential equations. Geometrical intuition, visual thinking, experimentation on diagrams, conceptions of algorithms and instruments to construct these diagrams, heuristic proofs based on diagrams, have interacted with the development of analytical abstract theories. We aim to analyze these interactions during the two centuries the classical theory of differential equations was developed. They are intimately connected to the difficulties faced in defining what the solution of a differential (...) equation is and in describing the global behavior of such a solution. (shrink)

In his Berlin Lectures of the 1820s, the German philosopher Arthur Schopenhauer (1788–1860) used spatial logic diagrams for philosophy of language. These logic diagrams were applied to many areas of semantics and pragmatics, such as theories of concept formation, concept development, translation theory, clarification of conceptual disputes, etc. In this paper we first introduce the basic principles of Schopenhauer’s philosophy of language and his diagrammatic method. Since Schopenhauer often gives little information about how the individual diagrams are (...) to be understood, we then make the attempt to reconstruct, specify and further develop one diagram type for the field of conceptual analysis. (shrink)

In his Berlin Lectures of the 1820s, the German philosopher Arthur Schopenhauer (1788–1860) used spatial logic diagrams for philosophy of language. These logic diagrams were applied to many areas of semantics and pragmatics, such as theories of concept formation, concept development, translation theory, clarification of conceptual disputes, etc. In this paper we first introduce the basic principles of Schopenhauer’s philosophy of language and his diagrammatic method. Since Schopenhauer often gives little information about how the individual diagrams are (...) to be understood, we then make the attempt to reconstruct, specify and further develop one diagram type for the field of conceptual analysis. (shrink)

Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of (...) the cell cycle and facilitate the construction of mathematical models of the cell cycle. But, extending beyond those analyses, we show how diagrams facilitate the construction of mathematical models, and we argue that the diagrams permit nomological explanations of the cell cycle. We further argue that what makes diagrams integral and indispensible for explanation and model construction is their nature as locality aids: they group together information that is to be used together in a way that sentential representations do not. (shrink)

In his 1903 Syllabus, Charles S. Peirce makes a distinction between icons and iconic signs, or hypoicons, and briefly introduces a division of the latter into images, diagrams, and metaphors. Peirce scholars have tried to make better sense of those concepts by understanding iconic signs in the context of the ten classes of signs described in the same Syllabus. We will argue, however, that the three kinds of hypoicons can better be understood in the context of Peirce's sixty-six classes (...) of signs. We analyze examples of hypoicons taken from the field of information design, describing them in the framework of the sixty-six classes, and discuss the consequences of those descriptions to the debate about the order of determination of the 10 trichotomies that form those classes. (shrink)

Six characteristics of effective representational systems for conceptual learning in complex domains have been identified. Such representations should: (1) integrate levels of abstraction; (2) combine globally homogeneous with locally heterogeneous representation of concepts; (3) integrate alternative perspectives of the domain; (4) support malleable manipulation of expressions; (5) possess compact procedures; and (6) have uniform procedures. The characteristics were discovered by analysing and evaluating a novel diagrammatic representation that has been invented to support students' comprehension of electricity—AVOW diagrams (Amps, Volts, (...) Ohms, Watts). A task analysis is presented that demonstrates that problem solving using a conventional algebraic approach demands more effort than AVOW diagrams. In an experiment comparing two groups of learners using the alternative approaches, the group using AVOW diagrams learned more than the group using equations and were better able to solve complex transfer problems and questions involving multiple constraints. Analysis of verbal protocols and work scratchings showed that the AVOW diagram group, in contrast to the equations group, acquired a coherently organised network of concepts, learnt effective problem solving procedures, and experienced more positive learning events. The six principles of effective representations were proposed on the basis of these findings. AVOW diagrams are Law Encoding Diagrams, a general class of representations that have been shown to support learning in other scientific domains. (shrink)

Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be (...) made more complicated in order to accommodate such challenges; and finally, at what this increasingly complicated picture implies for our standard assessment of chemical kindhood—primarily, for the widespread assumption that chemical kinds in general are more neat and tidy than those messy biological ones. _1_ The Received View _2_ A Taxonomy of Chemical Kinds _3_ Atomic Number _4_ H2O, H3O+, OH−, and More _5_ Complicating the Microstructuralist Picture _6_ Concrete and Other Mixtures _7_ Macromolecules, Especially Proteins _8_ Abandoning Sameness of Elemental Composition _9_ Not So Different after All. (shrink)

Although traditionally neglected, mathematical diagrams have recently begun to attract attention from philosophers of mathematics. By now, the literature includes several case studies investigating the role of diagrams both in discovery and justification. Certain preliminary questions have, however, been mostly bypassed. What are diagrams exactly? Are there different types of diagrams? In the scholarly literature, the term “mathematical diagram” is used in diverse ways. I propose a working definition that carves out the phenomena that are of (...) most importance for a taxonomy of diagrams in the context of a practice-based philosophy of mathematics, privileging examples from contemporary mathematics. In doing so, I move away from vague, ordinary notions. I define mathematical diagrams as forming notational systems and as being geometric/topological representations or two-dimensional representations. I also examine the relationship between mathematical diagrams and spatiotemporal intuition. By proposing an explication of diagrams, I explain certain controversies in the existing literature. Moreover, I shed light on why mathematical diagrams are so effective in certain instances, and, at other times, dangerously misleading. (shrink)

This article puts forward the notion of “evolving diagram” as an important case of mathematical diagram. An evolving diagram combines, through a dynamic graphical enrichment, the representation of an object and the representation of a piece of reasoning based on the representation of that object. Evolving diagrams can be illustrated in particular with category-theoretic diagrams (hereafter “diagrams*”) in the context of “sketch theory,” a branch of modern category theory. It is argued that sketch theory provides a diagrammatic* (...) theory of diagrams*, that it helps to overcome the rivalry between set theory and category theory as a general semantical framework, and that it suggests a more flexible understanding of the opposition between formal proofs and diagrammatic reasoning. Thus, the aim of the paper is twofold. First, it claims that diagrams* provide a clear example of evolving diagrams, and shed light on them as a general phenomenon. Second, in return, it uses sketches, understood as evolving diagrams, to show how diagrams* in general should be re-evaluated positively. (shrink)

Long-standing neglect of the chemical senses in the philosophy of perception is due, mostly, to their being regarded as ‘lower’ senses. Smell, taste, and chemically irritated touch are thought to produce mere bodily sensations. However, empirically informed theories of perception can show how these senses lead to perception of objective properties, and why they cannot be treated as special cases of perception modelled on vision. The senses of taste, touch, and smell also combine to create unified perceptions of flavour. (...) The nature of these multimodal experiences and the character of our awareness of them puts pressure on the traditional idea that each episode of perception goes one or other of the five senses. Thus, the chemical senses, far from being peripheral to the concerns of the philosophy of perception, may hold important clues to the multisensory nature of perception in general. (shrink)

In his well-known paper on Euclid’s geometry, Ken Manders sketches an argument against conceiving the diagrams of the Elements in ‘semantic’ terms, that is, against treating them as representations—resting his case on Euclid’s striking use of ‘impossible’ diagrams in some proofs by contradiction. This paper spells out, clarifies and assesses Manders’s argument, showing that it only succeeds against a particular semantic view of diagrams and can be evaded by adopting others, but arguing that Manders nevertheless makes a (...) compelling case that semantic analyses ought to be relegated to a secondary role for the study of mathematical practices. (shrink)

Historians occasionally use timelines, but many seem to regard such signs merely as ways of visually summarizing results that are presumably better expressed in prose. Challenging this language-centered view, I suggest that timelines might assist the generation of novel historical insights. To show this, I begin by looking at studies confirming the cognitive benefits of diagrams like timelines. I then try to survey the remarkable diversity of timelines by analyzing actual examples. Finally, having conveyed this (mostly untapped) potential, I (...) argue that neglecting timelines might mean neglecting significant aspects of reality that are revealed only by those signs. My overall message is that once we accept that relations are as important for the mind as what they relate, we have to pay closer attention to any semiotic device that enables or facilitates the discernment of new relations. (shrink)

We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)