The biological sciences have become increasingly reliant on so-called 'model organisms'. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I (...) focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined. (shrink)

The biological sciences have become increasingly reliant on so-called ‘model organisms’. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I (...) focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined. (shrink)

This commentary is intended to illuminate Gold's & Stoljar 's main contentions by exploiting a favorite comparison, namely, that between biology and electronics. Roughly, and leaving out Darwinian theory and the like, biology is physics and chemistry plus natural history just as electronics is physics plus wiring diagrams. Natural history contains generalizations, not laws. Psychology and cognitive science typically give more abstract explanations, as do “block diagrams” in electronics, and are less dispensable.

in a nervous system of a given species. This chapter provides a critical perspective on the role of connectomes in neuroscientific practice and asks how the connectomic approach fits into a larger context in which network thinking permeates technology, infrastructure, social life, and the economy. In the first part of this chapter, we argue that, seen from the perspective of ongoing research, the notion of connectomes as “complete descriptions” is misguided. Our argument combines Rachel Ankeny’s analysis of neuroanatomical wiring (...) diagrams as “descriptive models” with Hans-Joerg Rheinberger’s notion of “epistemic objects,” i.e., targets of research that are still partially unknown. Combining these aspects we conclude that connectomes are constitutively epistemic objects: there just is no way to turn them into permanent and complete technical standards because the possibilities to map connection properties under different modeling assumptions are potentially inexhaustible. In the second part of the chapter, we use this understanding of connectomes as constitutively epistemic objects in order to critically assess the historical and political dimensions of current neuroscientific research. We argue that connectomics shows how the notion of the “brain as a network” has become the dominant metaphor of contemporary brain research. We further point out that this metaphor shares (potentially problematic) affinities to the form of contemporary “network societies.” We close by pointing out how the relation between connectomes and networks in society could be used in a more fruitful manner. (shrink)

Powerful ultrastructural tools are providing new insights into neuronal circuits, revealing a wealth of anatomically‐defined synaptic connections. These wiring diagrams are incomplete, however, because functional connectivity is actively shaped by neuromodulators that modify neuronal dynamics, excitability, and synaptic function. Studies of defined neural circuits in crustaceans, C. elegans, Drosophila, and the vertebrate retina have revealed the ability of modulators and sensory context to reconfigure information processing by changing the composition and activity of functional circuits. Each ultrastructural connectivity map encodes (...) multiple circuits, some of which are active and some of which are latent at any given time. (shrink)

Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) (...) used sequence searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 Gα, 2 Gβ, 2 Gγ). C. elegans encodes one ortholog of each of the four Gα classes found in metazoans and 16 new Gα genes. The orthologous genes are widely expressed, whereas 14 of the divergent Gα genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis.BioEssays 21:713–717, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Heterotrimeric G proteins, consisting of α, β, and γ subunits, couple ligand-bound seven transmembrane domain receptors to the regulation of effector proteins and production of intracellular second messengers. G protein signaling mediates the perception of environmental cues in all higher eukaryotic organisms, including yeast, Dictyostelium, plants, and animals. The nematode Caenorhabditis elegans is the first animal to have complete descriptions of its cellular anatomy, cell lineage, neuronal wiring diagram, and genomic sequence. In a recent paper, Jansen et al.(1) (...) used sequence searches of the C. elegans genome database to identify all heterotrimeric G protein genes (20 Gα, 2 Gβ, 2 Gγ). C. elegans encodes one ortholog of each of the four Gα classes found in metazoans and 16 new Gα genes. The orthologous genes are widely expressed, whereas 14 of the divergent Gα genes are almost exclusively expressed in sensory neurons where they may regulate perception and chemotaxis.BioEssays 21:713–717, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Popular culture continues fuelling public imagination with things, human and non-human, that we might beco-me or confront. Besides robots, other significant tropes in popular fiction that generated images include non-human humans and cyborgs, wired into his-torically varying sociocultural realities. Robots and artificial intelligence are re-defining the natural order and its hierar-chical structure. This is not surprising, as natural order is always in flux, shaped by new scientific discoveries, especially the reading of the genetic code, that reveal and redefine relationships between (...) life forms. However, for the first time, a new, artificial, species is being introduced into the existing diagrams, and, for the first time, it appears to hybridise the anthro-pocentric natural world order. (shrink)

It was proposed that the data from Monte Carlo statistical investigations be subjected to analysis of variance methods rather than the conventional techniques of tabling, graphing, and inspecting the data. Two examples in which analysis of variance methods were applied to published Monte Carlo studies were presented. It was suggested that balanced factorial designs should be used whenever possible in Monte Carlo studies so that analysis of variance methods would be directly applicable. Finally, three advantages of analysis of variance methods (...) over conventional techniques were described and analysis of variance methods were contrasted with a possible alternative analytical method, multiple regression analysis. (shrink)

1. 1817-1839. -- 2. 1840-1844. -- 3. 1845-1852 -- 4. 1853-1861. -- 5. 1862-1868 ; Nachträge, 1828-1861.

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.

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)

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 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)

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 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)

This paper examines the explanatory distinctness of wiring optimization models in neuroscience. Wiring optimization models aim to represent the organizational features of neural and brain systems as optimal (or near-optimal) solutions to wiring optimization problems. My claim is that that wiring optimization models provide design explanations. In particular, they support ideal interventions on the decision variables of the relevant design problem and assess the impact of such interventions on the viability of the target system.

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)

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 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)

The connectivity patterns of many neural circuits are highly ordered and often impressively complex. The intricate order and complexity of neuronal wiring remain not only a challenge for questions related to circuit functions but also for our understanding of how they develop with such an apparent precision. The chemotropic guidance of the growing axon by target‐derived cues represents a central paradigm for how neurons get connected with the correct target cells. However, many studies reveal a remarkable variety of important (...) target‐independent wiring mechanisms. These mechanisms include axonal sorting, axonal tiling, growth cone polarization, as well as cell‐intrinsic mechanisms underlying growth cone sprouting, and neurite branching. Our review focuses on target independent wiring mechanisms and in particular on recent progress emerging from studies on three different sensory systems: olfactory, visual, and somatosensory. We discuss molecular mechanisms that operate during axon‐axon interactions or constitute axon‐intrinsic functions and outline how they complement the well‐known target‐dependent wiring mechanisms. (shrink)

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)

Combinatorial network optimization appears to fit well as a model of brain structure: connections in the brain are a critically constrained resource, hence their deployment in a wide range of cases is finely optimized to “‘save wire". This review focuses on minimization of large-scale costs, such as total volume for mammal dendrite and axon arbors and total wirelength for positioning of connected neural components such as roundworm ganglia (and also mammal cortex areas). Phenomena of good optimization raise questions about mechanisms (...) for their achievement: the examples of optimized neuroanatomy here turn out to include candidates for some of the most complex biological structures known to be derivable purely from simple physical energy minimization processes. Part of the functional role of such fine-tuned wiring optimization may be as a compact strategy for generating self-organizing complex neuroanatomical.. (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)

The meta-problem of consciousness is framed as a route into investigating why there are problems in understanding consciousness by describing the mechanisms underpinning our tendency to describe consciousness as problematic, and the evolutionary origins of these mechanisms. This is framed as a means of uniting illusionists and realists toward a common goal, but this supposes that the only viable form of illusionism is what I call 'hard-wired' illusionism, under which phenomenal judgments are a direct product of natural selection. I argue (...) that, instead, 'soft-wired' illusionism is more plausible, where phenomenal judgments are seen to be cultural phenomena. Since the problem of consciousness arises from a flawed theory of consciousness, pointing out the mechanisms underlying expression of the theory and the historical origins of the theory will not suffice to tell us why the theory is problematic. As such, the meta-problem is exclusionary toward soft-wired illusionism. (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)

There is substantial evidence from many domains that visual representations aid various forms of cognition. We aimed to determine whether visual representations of argument structure enhanced the acquisition and development of critical thinking skills within the context of an introductory philosophy course. We found a significant effect of the use of argument diagrams, and this effect was stable even when multiple plausible correlates were controlled for. These results suggest that natural⎯and relatively minor⎯modifications to standard critical thinking courses could provide substantial (...) increases in student learning and performance. (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)

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)

Suppose that the following describes an intelligible scenario. A subject is wired up to another's body in such a way that she has bodily experiences ‘as from the inside’ caused by states and events in the other body, that are subjectively indistinguishable from ordinary somatosensory perception of her own body. The supposed intelligibility of such so-called crossed wire cases constitutes a significant challenge to the claim that our somatosensory judgements are immune to error through misidentification relative to uses of the (...) first person pronoun. After all, the subject in this case is liable to commit precisely the sort of error ruled out by such a claim. In this paper I argue that the proponent of this challenge must establish at least two things: that the subject is committing an error of misidentification, and that her judgement shares its epistemic grounds with our ordinary somatosensory judgements. Neither condition, I argue, can be reached from the stipulations permitted into the starting descriptions of the cases. (shrink)

Throughout the history of the philosophy of science, theories have been linked to formulas as a privileged representational format. In this paper, following, I defend a semantic-representational conception of theories, where theories are identified with sets of scientific re-presentations by virtue of their epistemic potential and independently of their format. To show the potential of this proposal, I analyze as a case study the use of phase diagrams in statistical mechanics to convey in a semantically consistent and syntactically correct way (...) theoretical principles such as Liouville’s theorem. I conclude by defending this philosophical position as a tool to show the enormous representational richness underlying scientific practices. (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)

Although depression is characterized as a mood disorder it turns out that, like moods in general, it cannot be explained independently of a theory of emotion. In this paper I outline one promising theory of emotion and show how it deals with the phenomenon of depressive mood. An important aspect of MAT is the role it assigns to peripheral information processing systems in setting up emotional responses. The operations of these systems are automatic and opaque to consciousness, but they represent (...) information about the significance of the environment for the subject, bias cognition and behaviour, and have a characteristic phenomenology. I show how understanding the nature of peripheral appraisal provides a principled way to link neurochemistry and mood via an information processing theory of the circuitry targeted by antidepressant treatment. The discussion is organized around Matthew Ratcliffe's distinction between pre-intentional and intentional feelings and suggests that the MAT might provide a way to link phenomenological and mechanistic accounts of feeling states characteristic of depression. (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)