A novel non-classical mereological concept built up by blending the Metaphysics of Xavier Zubiri and the Quantum Theory of Atoms in Molecules of R. F. W. Bader is proposed. It is argued that this philosophical concept is necessary to properly account for what happens in a chemical reaction. From the topology of the gradient of the laplacian of the electronic charge density, \\) within the QTAIM framework, different “atomic graphs” are found for each atom depending on the molecular (...) context, reflecting how the whole molecule affects each atom. In this way, the whole molecular system imposes certain geometry onto each atom, and every atom exhibits different ontological modality. On the Metaphysical side, for X. Zubiri real things are system of different notes. The physical essence is the subsystem of essential notes with a coherence unity. Every note is grounded on the essence. The unity of the system is present somehow in every note-of beforehand, and every essential note-of turns towards the other. The essence determines the position of each note within the system, and hence is the grounding for modality of the notes. By conflating both “theories” and taking the atoms as essential notes, we propose the concept of “Molecule in atoms-of” or “atoms-of in Molecules”. Within the course of a chemical reaction the atoms-of modified their “of” as required by the new molecular unity being formed, and eventually change their modality. The validity to the Zubiri’s statements, is attained by evaluating necessity and possibility in a set-up of finite accessible “possible worlds”. (shrink)

It is well-known that by 1882, Peirce, influenced by Cayley’s, Clifford’s and Sylvester’s works on algebraic invariants and by the chemical analogy, had already achieved something like a diagrammatic treatment of quantificational logic of relatives. The details of that discovery and its implications to some wider issues in logical theory merit further investigation, however. This paper provides a reconstruction of the genesis of Peirce’s logical graphs from the early 1880s until 1896, covering the period of time during which (...) he already was acquainted with the works of his Johns Hopkins colleagues on the mathematical theory of graphs and was reaching the very first forms of his theory and method of... (shrink)

Graph theory is one of those subjects that is a vital part of the digital world. It is used to monitor the movement of robots on a network, to debug computer networks, to develop algorithms, and to analyze the structural properties of chemical structures, among other things. It is also useful in airplane scheduling and the study of diffusion mechanisms. The parameters computed in this article are very useful in pattern recognition and image processing. A number d f, w (...) = min d w, t, d w, s is referred as distance between f = t s an edge and w a vertex. d w, f 1 ≠ d w, f 2 implies that two edges f 1, f 2 ∈ E are resolved by node w ∈ V. A set of nodes A is referred to as an edge metric generator if every two links/edges of Γ are resolved by some nodes of A and least cardinality of such sets is termed as edge metric dimension, e dim Γ for a graph Γ. A set B of some nodes of Γ is a mixed metric generator if any two members of V ∪ E are resolved by some members of B. Such a set B with least cardinality is termed as mixed metric dimension, m dim Γ. In this paper, the metric dimension, edge metric dimension, and mixed metric dimension of dragon graph T n, m, line graph of dragon graph L T n, m, paraline graph of dragon graph L S T n, m, and line graph of line graph of dragon graph L L T n, m have been computed. It is shown that these parameters are constant, and a comparative analysis is also given for the said families of graphs. (shrink)

Let G = V G, E G be a molecular graph, where V G and E G are the sets of vertices and edges. A topological index of a molecular graph is a numerical quantity which helps to predict the chemical/physical properties of the molecules. The Wiener, Wiener polarity, and the terminal Wiener indices are the distance-based topological indices. In this paper, we described a linear time algorithm that computes the Wiener index for acyclic graphs and extended this (...) algorithm for unicyclic graphs. The same algorithms are modified to compute the terminal Wiener index and the Wiener polarity index. All these algorithms compute the indices in time O n. (shrink)

Mathematical chemistry is often thought to be a 20th-century subdiscipline of chemistry, but in this paper we discuss several early chemical ideas and some landmarks of chemistry as instances of the mathematical way of thinking; many of them before 1900. By the mathematical way of thinking, we follow Weyl's description of it in terms of functional thinking, i.e. setting up variables, symbolizing them, and seeking for functions relating them. The cases we discuss are Plato's triangles, Geoffroy's affinity table, Lavoisier's (...) classification of substances and their relationships, Mendeleev's periodic table, Cayley's enumeration of alkanes, Sylvester's association of algebra and chemistry, and Wiener's relationship between molecular structure and boiling points. These examples show that mathematical chemistry has much more than a century of history. (shrink)

The interrelation between two theories, theory of complexity and theory of systems, is analyzed by using the chemical graph-theoretical concept. The idea of complexity is systemized through three components: diachronic, synchronic, and combinatorial complexity. The relationships between entropy and complexity, as well as the problem of function are also discussed.

A chemical compound in the form of graph terminology is known as a chemical graph. Molecules are usually represented as vertices, while their bonding or interaction is shown by edges in a molecular graph. In this paper, we computed various connectivity indices based on degrees of vertices of a chemical graph of indium phosphide. Afterward, we found the physical measures like entropy and heat of formation of InP. Then, we fitted curves between different indices and the thermodynamical (...) properties, namely, heat of formation and entropy. Curve fitting was done in MATLAB through different methods based on linearity and nonlinearity. Furthermore, we depicted our results numerically and graphically. These numerical systems may give an approach to concentrate on the thermodynamical properties of the compound design of InP at an exceptional level that will help understand the connection between framework measurement and these actions. (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)

An accessible yet rigorous introduction to the field, Environmental Ethics: Theory in Practice helps students develop the analytical skills to effectively identify and evaluate the social and ethical dimensions of environmental issues. Covering a wide variety of theories and critical perspectives, author Ronald Sandler considers their strengths and weaknesses, emphasizes their practical importance, and grounds the discussions in a multitude of both classic and contemporary cases and examples. FEATURES * Discusses a wide range of theories of environmental ethics, representing their (...) strengths and weaknesses as charitably as possible without advocating for any particular theory, thereby encouraging students to think critically about which views are well justified and which are not * Extensive use of cases and examples links theoretical and practical issues and shows how environmental issues have both social and ecological components; issues covered include climate change, species conservation, ecological economics, consumption, environmental justice, intergenerational justice, genetically modified crops, animal agriculture, population, environmental rights, and food security, among many others * Incorporates both classic and cutting-edge cases and examples; iconic cases include the spotted owl, Bhopal chemical link, and Hetch Hetchy controversies, while contemporary cases include lead contamination of Flint, Michigan's water supply and innovations is conservation genetics, including conservation cloning, deextinction, and gene drives * Covers food ethics--addressing such topics as genetic engineering, food systems, food waste, and eating animals--and technology ethics, reflecting on technological power and the role of technology in creating and responding to environmental issues * Emphasizes the social justice dimensions of environmental problems with chapters on environmental justice, food security, ecofeminism, and more * Includes text boxes that provide extended discussions of cases; thought experiments; additional coverage of theoretical issues discussed in the main text; and exercises that ask students to apply theories or reflect on how theoretical issues intersect with practical problems * Provides numerous pedagogical aids including review questions, discussion questions, key terms and additional reading lists at the end of each chapter, extensive internal cross-referencing, a glossary of key terms and concepts, and more than thirty images, illustrations, tables, and graphs. (shrink)

A topological index can be focused on uprising of a chemical structure into a real number. The degree-based topological indices have an active place among all topological indices. These topological descriptors intentionally associate certain physicochemical assets of the corresponding chemical compounds. Graph theory plays a very useful role in such type of research directions. The hex-derived networks have vast applications in computer science, physical sciences, and medical science, and these networks are constructed by hexagonal mesh networks. In this (...) paper, we determined the exact values of vertex-edge-degree-based topological descriptors for hex-derived networks HDN 1 p and HDN 2 p, which are generated by the hexagonal network of dimension p. (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)

Climate change, pollution, and deforestation have a negative impact on global mental health. There is an environmental justice dimension to this challenge as wealthy people and high-income countries are major contributors to climate change and pollution, while poor people and low-income countries are heavily affected by the consequences. Using state-of-the art data mining, we analyzed and visualized the global research landscape on mental health, climate change, pollution and deforestation over a 15-year period. Metadata of papers were exported from PubMed®, and (...) both relevance and relatedness of terms in different time frames were computed using VOSviewer. Co-occurrence graphs were used to visualize results. The development of exemplary terms over time was plotted separately. The number of research papers on mental health and environmental challenges is growing in a linear fashion. Major topics are climate change, chemical pollution, including psychiatric medication in wastewater, and neurobiological effects. Research on specific psychiatric syndromes and diseases, particularly on their ethical and social aspects is less prominent. There is a growing body of research literature on links between mental health, climate change, pollution, and deforestation. This research provides a graphic overview to mental healthcare professionals and political stakeholders. Social and ethical aspects of the climate change-mental health link have been neglected, and more research is needed. (shrink)

The comparison of growth, whether it is between different strains or under different growth conditions, is a classic microbiological technique that can provide genetic, epigenetic, cell biological, and chemical biological information depending on how the assay is used. When employing solid growth media, this technique is limited by being largely qualitative and low throughput. Collecting data in the form of growth curves, especially automated data collection in multi‐well plates, circumvents these issues. However, the growth curves themselves are subject to (...) stochastic variation in several variables, most notably the length of the lag phase, the doubling rate, and the maximum expansion of the culture. Thus, growth curves are indicative of trends but cannot always be conveniently averaged and statistically compared. Here, we summarize a simple method to compile growth curve data into a quantitative format that is amenable to statistical comparisons and easy to graph and display. (shrink)

Molecular models are typical topics of chemical research depending on the technical standards of observation, computation, and representation. Mathematically, molecular structures have been represented by means of graph theory, topology, differential equations, and numerical procedures. With the increasing capabilities of computer networks, computational models and computer-assisted visualization become an essential part of chemical research. Object-oriented programming languages create a virtual reality of chemical structures opening new avenues of exploration and collaboration in chemistry. From an epistemic point of (...) view, virtual reality is a new computer-assisted tool of human imagination and recognition. (shrink)

Domination is a structural complexity of chemical molecular graphs. A dominating set in a graphG=V,Eis a subsetS⊆Vsuch that each vertex inV\Sis adjacent to at least one vertex inS. The domination numberγGof a graphGis the minimum size of a dominating set inG. In this paper, computer-aided approaches for obtaining bounds for domination number on torus graphs are here considered, and many new exact values and bounds are obtained.

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of these (...) variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles. (shrink)

A personal account is presented for the present status of mathematical chemistry, with emphasis on non-numerical applications. These use mainly graph-theoretical concepts. Most computational chemical applications involve quantum chemistry and are therefore largely reducible to physics, while discrete mathematical applications often do not. A survey is provided for opinions and definitions of mathematical chemistry, and then for journals, books and book series, as well as symposia of mathematical chemistry.

The search for a systems‐level picture of metabolism as a web of molecular interactions provides a paradigmatic example of how the methods used to characterize a system can bias the interpretation of its functional meaning. Metabolic maps have been analyzed using novel techniques from network theory, revealing some non‐trivial, functionally relevant properties. These include a small‐world structure and hierarchical modularity. However, as discussed here, some of these properties might actually result from an inappropriate way of defining network interactions. Starting from (...) the so‐called bipartite organization of metabolism, where the two meaningful subsets (reactions and metabolites) are considered, most current works use only one of the subsets by means of so‐called graph projections. Unfortunately, projected graphs often ignore relevant biological and chemical constraints, thus leading to statistical artifacts. Some of these drawbacks and alternative approaches need to be properly addressed. (shrink)

Theory of networks serves as a mathematical foundation for the construction and modeling of chemical structures and complicated networks. In particular, chemical networking theory has a wide range of utilizations in the study of chemical structures, where examination and manipulation of chemical structural information are made feasible by utilizing the numerical graph invariants. A network invariant or a topological index is a numerical measure of a chemical compound which is capable to describe the chemical (...) structural properties such as melting point, freezing point, density, pressure, tension, and temperature of chemical compounds. Wiener initiated the first distance-based TI which is considered to be the most important TI to preserve the chemical and physical properties of chemical structures. Later on, degree-based TI was introduced to find the π -electron energy of molecules. Recently, connection number-based TIs are studied which are more efficient than degree and distance-based TIs. In this paper, we compute the connection number-based TIs of the structure of crystal cubic carbons which are one of the most significant and interesting composites in modern resources of science due to the involvement of carbon atoms. (shrink)

The mathematical field of graph theory has recently been used to provide counterexamples to the Principle of the Identity of Indiscernibles. In response to this, it has been argued that appeal to relations between graphs allows the Principle to survive the counterexamples. In this paper, I aim to show why that proposal does not succeed.

We are immersed within an odorous sea of chemical currents that we parse into individual odors with complex structures. Odors have been posited as determined by the structural relation between the molecules that compose the chemical compounds and their interactions with the receptor site. But, naturally occurring smells are parsed from gaseous odor plumes. To give a comprehensive account of the nature of odors the chemosciences must account for these large distributed entities as well. We offer a focused (...) review of what is known about the perception of odor plumes for olfactory navigation and tracking, which we then connect to what is known about the role odorants play as properties of the plume in determining odor identity with respect to odor quality. We end by motivating our central claim that more research needs to be conducted on the role that odorants play within the odor plume in determining odor identity. (shrink)

Modeling mechanisms is central to the biological sciences – for purposes of explanation, prediction, extrapolation, and manipulation. A closer look at the philosophical literature reveals that mechanisms are predominantly modeled in a purely qualitative way. That is, mechanistic models are conceived of as representing how certain entities and activities are spatially and temporally organized so that they bring about the behavior of the mechanism in question. Although this adequately characterizes how mechanisms are represented in biology textbooks, contemporary biological research practice (...) shows the need for quantitative, probabilistic models of mechanisms, too. In this paper we argue that the formal framework of causal graph theory is well-suited to provide us with models of biological mechanisms that incorporate quantitative and probabilistic information. On the ba-sis of an example from contemporary biological practice, namely feedback regulation of fatty acid biosynthesis in Brassica napus, we show that causal graph theoretical models can account for feedback as well as for the multi-level character of mechanisms. However, we do not claim that causal graph theoretical representations of mechanisms are advantageous in all respects and should replace common qualitative models. Rather, we endorse the more balanced view that causal graph theoretical models of mechanisms are useful for some purposes, while being insufficient for others. (shrink)

We introduce a framework for a graph-theoretic analysis of the semantic paradoxes. Similar frameworks have been recently developed for infinitary propositional languages by Cook and Rabern, Rabern, and Macauley. Our focus, however, will be on the language of first-order arithmetic augmented with a primitive truth predicate. Using Leitgeb’s notion of semantic dependence, we assign reference graphs (rfgs) to the sentences of this language and define a notion of paradoxicality in terms of acceptable decorations of rfgs with truth values. It (...) is shown that this notion of paradoxicality coincides with that of Kripke. In order to track down the structural components of an rfg that are responsible for paradoxicality, we show that any decoration can be obtained in a three-stage process: first, the rfg is unfolded into a tree, second, the tree is decorated with truth values (yielding a dependence tree in the sense of Yablo), and third, the decorated tree is re-collapsed onto the rfg. We show that paradoxicality enters the picture only at stage three. Due to this we can isolate two basic patterns necessary for paradoxicality. Moreover, we conjecture a solution to the characterization problem for dangerous rfgs that amounts to the claim that basically the Liar- and the Yablo graph are the only paradoxical rfgs. Furthermore, we develop signed rfgs that allow us to distinguish between ‘positive’ and ‘negative’ reference and obtain more fine-grained versions of our results for unsigned rfgs. (shrink)

In this paper, we analyze and discuss Schopenhauer’s n-term diagrams for eristic dialectics from a graph-theoretical perspective. Unlike logic, eristic dialectics does not examine the validity of an isolated argument, but the progression and persuasiveness of an argument in the context of a dialogue or even controversy. To represent these dialogue situations, Schopenhauer created large maps with concepts and Euler-type diagrams, which from today’s perspective are a specific form of graphs. We first present the original method with Euler-type diagrams, (...) then give the most important graph-theoretical definitions, then discuss Schopenhauer’s diagrams graph-theoretically and finally give an example of how the graphs or diagrams can be used to analyze dialogues. (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.

We define a model for computing probabilities of right-nested conditionals in terms of graphs representing Markov chains. This is an extension of the model for simple conditionals from Wójtowicz and Wójtowicz. The model makes it possible to give a formal yet simple description of different interpretations of right-nested conditionals and to compute their probabilities in a mathematically rigorous way. In this study we focus on the problem of the probabilities of conditionals; we do not discuss questions concerning logical and (...) metalogical issues such as setting up an axiomatic framework, inference rules, defining semantics, proving completeness, soundness etc. Our theory is motivated by the possible-worlds approach ; however, our model is generally more flexible. In the paper we focus on right-nested conditionals, discussing them in detail. The graph model makes it possible to account in a unified way for both shallow and deep interpretations of right-nested conditionals. In particular, we discuss the status of the Import-Export Principle and PCCP. We briefly discuss some methodological constraints on admissible models and analyze our model with respect to them. The study also illustrates the general problem of finding formal explications of philosophically important notions and applying mathematical methods in analyzing philosophical issues. (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)

This modern, advanced textbook reviews modal logic, a field which caught the attention of computer scientists in the late 1970's.

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)

A graph-theoretic account of logics is explored based on the general notion of m-graph (that is, a graph where each edge can have a finite sequence of nodes as source). Signatures, interpretation structures and deduction systems are seen as m-graphs. After defining a category freely generated by a m-graph, formulas and expressions in general can be seen as morphisms. Moreover, derivations involving rule instantiation are also morphisms. Soundness and completeness theorems are proved. As a consequence of the generality of (...) the approach our results apply to very different logics encompassing, among others, substructural logics as well as logics with nondeterministic semantics, and subsume all logics endowed with an algebraic semantics. (shrink)

A graph-theoretic account of fibring of logics is developed, capitalizing on the interleaving characteristics of fibring at the linguistic, semantic and proof levels. Fibring of two signatures is seen as a multi-graph (m-graph) where the nodes and the m-edges include the sorts and the constructors of the signatures at hand. Fibring of two models is a multi-graph (m-graph) where the nodes and the m-edges are the values and the operations in the models, respectively. Fibring of two deductive systems is an (...) m-graph whose nodes are language expressions and the m-edges represent the inference rules of the two original systems. The sobriety of the approach is confirmed by proving that all the fibring notions are universal constructions. This graph-theoretic view is general enough to accommodate very different fibrings of propositional based logics encompassing logics with non-deterministic semantics, logics with an algebraic semantics, logics with partial semantics and substructural logics, among others. Soundness and weak completeness are proved to be preserved under very general conditions. Strong completeness is also shown to be preserved under tighter conditions. In this setting, the collapsing problem appearing in several combinations of logic systems can be avoided. (shrink)

Can you find an xy-equation that, when graphed, writes itself on the plane? This idea became internet-famous when a Wikipedia article on Tupper’s self-referential formula went viral in 2012. Under scrutiny, the question has two flaws: it is meaningless (it depends on fonts) and it is trivial. We fix these flaws by formalizing the problem.

Improving a theorem of Gasarch and Hirst, we prove that if 2 ≤ k ≤ m < ω, then the following is equivalent to WKL0 over RCA0 Every locally k-colorable graph is m-colorable.

This paper examines the contemporary philosophical and cognitive relevance of Charles Peirce's diagrammatic logic of existential graphs (EGs), the ‘moving pictures of thought’. The first part brings to the fore some hitherto unknown details about the reception of EGs in the early 1900s that took place amidst the emergence of modern conceptions of symbolic logic. In the second part, philosophical aspects of EGs and their contributions to contemporary logical theory are pointed out, including the relationship between iconic logic and (...) images, the problem of the meaning of logical constants, the cognitive economy of iconic logic, the failure of the Frege–Russell thesis, and the failure of the Language of Thought hypothesis. (shrink)

Given the rich diversity of research fields usually ascribed to chemistry in a broad sense, the present paper tries to dig our characteristic parts of chemistry that can be conceptually distinguished from interdisciplinary, applied, and specialized subfields of chemistry, and that may be called chemistry in a very narrow sense, or 'the chemical core of chemistry'. Unlike historical, ontological, and 'anti-reductive' approaches, I use a conceptual approach together with some methodological implications that allow to develop step by step a (...) kind of cognitive architecture for chemistry, which basically contains: (1) systematic chemical knowledge on the experimental level; (2) clarification of chemical species; (3) chemical classification systems; (4) theoretical foundation through the chemical theory of structural formulas. In a succeeding paper the results will be checked for resisting physicalistic reduction. (shrink)

The problem of when a recursive graph has a recursive k-coloring has been extensively studied by Bean, Schmerl, Kierstead, Remmel, and others. In this paper, we study the polynomial time analogue of that problem. We develop a number of negative and positive results about colorings of polynomial time graphs. For example, we show that for any recursive graph G and for any k, there is a polynomial time graph G′ whose vertex set is {0,1}* such that there is an (...) effective degree preserving correspondence between the set of k-colorings of G and the set of k-colorings of G′ and hence there are many examples of k-colorable polynomial time graphs with no recursive k-colorings. Moreover, even though every connected 2-colorable recursive graph is recursively 2-colorable, there are connected 2-colorable polynomial time graphs which have no primitive recursive 2-coloring. We also give some sufficient conditions which will guarantee that a polynomial time graph has a polynomial time or exponential time coloring. (shrink)

I argue that Frege Problems in thought are best modeled using graph-theoretic machinery; and that these problems can arise even when subjects associate all the same qualitative properties to the object they’re thinking of twice. I compare the proposed treatment to similar ideas by Heck, Ninan, Recanati, Kamp and Asher, Fodor, and others.

The study of graph structure has advanced in recent years with great strides: finite graphs can be described algebraically, enabling them to be constructed out of more basic elements. Separately the properties of graphs can be studied in a logical language called monadic second-order logic. In this book, these two features of graph structure are brought together for the first time in a presentation that unifies and synthesizes research over the last 25 years. The author not only provides (...) a thorough description of the theory, but also details its applications, on the one hand to the construction of graph algorithms, and, on the other to the extension of formal language theory to finite graphs. Consequently the book will be of interest to graduate students and researchers in graph theory, finite model theory, formal language theory, and complexity theory. (shrink)

We examine possible causal structures of experiments with entangled quantum objects. Previously, these structures have been obscured by assuming a misleading probabilistic analysis of quantum non locality as 'Outcome Dependence or Parameter Dependence' and by directly associating these correlations with influences. Here we try to overcome these shortcomings: we proceed from a recent stronger Bell argument, which provides an appropriate probabilistic description, and apply the rigorous methods of causal graph theory. Against the standard view that there is only an influence (...) between the measurement outcomes, we show that there must be an influence from one setting to its distant outcome: EPR correlations can only come about if one of the outcomes is a common effect of both settings. Our discussion makes explicit under which assumptions similar conclusions from information theoretic considerations can be interpreted causally. (shrink)

This paper introduces a class of graphical independence models that is closed under marginalization and conditioning but that contains all DAG independence models. This class of graphs, called maximal ancestral graphs, has two attractive features: there is at most one edge between each pair of vertices; every missing edge corresponds to an independence relation. These features lead to a simple parameterization of the corresponding set of distributions in the Gaussian case.

We investigate dependence of recursively enumerable graphs on the equality relation given by a specific r.e. equivalence relation on ω. In particular we compare r.e. equivalence relations in terms of graphs they permit to represent. This defines partially ordered sets that depend on classes of graphs under consideration. We investigate some algebraic properties of these partially ordered sets. For instance, we show that some of these partial ordered sets possess atoms, minimal and maximal elements. We also fully (...) describe the isomorphism types of some of these partial orders. (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)

We describe Peirce’s 1903 system of modal gamma graphs, its transformation rules of inference, and the interpretation of the broken-cut modal operator. We show that Peirce proposed the normality rule in his gamma system. We then show how various normal modal logics arise from Peirce’s assumptions concerning the broken-cut notation. By developing an algebraic semantics we establish the completeness of fifteen modal logics of gamma graphs. We show that, besides logical necessity and possibility, Peirce proposed an epistemic interpretation (...) of the broken-cut modality, and that he was led to analyze constructions of knowledge in the style of epistemic logic. (shrink)

Graphs are employed to define a variety of distance-based binary merging operators. We provide logical characterization results for each class of merging operators introduced and discuss the extension of this approach to the merging of sequences and multisets.

Studies to neutrosophic graphs happens to be not only innovative and interesting, but gives a new dimension to graph theory. The classic coloring of edge problem happens to give various results. Neutrosophic tree will certainly find lots of applications in data mining when certain levels of indeterminacy is involved in the problem. Several open problems are suggested.

Nicholas Shackel (2011) has proposed a number of arguments to save the Dipert–Bird model of physical reality from the sorts of unpalatable consequence I identified in Oderberg 2011. Some consequences, he thinks, are only apparent; others are real but palatable. In neither case does he seem to me to have deflected the concerns I raised, leaving graph structuralism on Dipert–Bird lines as problematic as ever.

The lattice operations of join and meet were defined for set partitions in the nineteenth century, but no new logical operations on partitions were defined and studied during the twentieth century. Yet there is a simple and natural graph-theoretic method presented here to define any n-ary Boolean operation on partitions. An equivalent closure-theoretic method is also defined. In closing, the question is addressed of why it took so long for all Boolean operations to be defined for partitions.

The paper is concerned with the existence of a universal graph at the successor of a strong limit singular μ of cofinality ℵ0. Starting from the assumption of the existence of a supercompact cardinal, a model is built in which for some such μ there are $\mu^{++}$ graphs on μ+ that taken jointly are universal for the graphs on μ+, while $2^{\mu^+} \gg \mu^{++}$ . The paper also addresses the general problem of obtaining a framework for consistency results (...) at the successor of a singular strong limit starting from the assumption that a supercompact cardinal κ exists. The result on the existence of universal graphs is obtained as a specific application of a more general method. (shrink)