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)

Intra-molecular connectivity (that is, chemical structure) does not emerge from computations based on fundamental quantum-mechanical principles. In order to compute molecular electronic energies (of C 3 H 4 hydrocarbons, for instance) quantum chemists must insert intra-molecular connectivity “by hand.” Some take this as an indication that chemistry cannot be reduced to physics: others consider it as evidence that quantum chemistry needs new logical foundations. Such discussions are generally synchronic rather than diachronic —that is, they neglect ‘historical’ aspects. However, (...) systems of interest to chemists generally are metastable . In many cases chemical systems of a given elemental composition may exist in any one of several different metastable states depending on the history of the system. Molecular structure generally depends on contingent historical circumstances of synthesis and separation, rather than solely or mainly on relative energies of alternative stable states, those energies in turn determined by relationships among components. Chemical structure is usually ‘kinetically-determined’ rather than ‘thermodynamically-determined.’ For instance, cyclical hydrocarbon ring-systems (as in cyclopropene) are produced only in special circumstances. Adequate theoretical treatments must take account of the persistent effects of such contingent historical events whenever they are relevant—as they generally are in chemistry. (shrink)

This book examines the way in which Robert Boyle seeks to accommodate his complex chemical philosophy within the framework of a mechanistic theory of matter. More specifically, the book proposes that Boyle regards chemical qualities as properties that emerged from the mechanistic structure of chymical atoms. Within Boyle’s chemical ontology, chymical atoms are structured concretions of particles that Boyle regards as chemically elementary entities, that is, as chemical wholes that resist experimental analysis. Although this interpretation (...) of Boyle’s chemical philosophy has already been suggested by other Boyle scholars, the present book provides a sustained philosophical argument to demonstrate that, for Boyle, chemical properties are dispositional, relational, emergent, and supervenient properties. This argument is strengthened by a detailed mereological analysis of Boylean chymical atoms that establishes the kind of theory of wholes and parts that is most consistent with an emergentist conception of chemical properties. The emergentist position that is being attributed to Boyle supports his view that chemical reactions resist direct explanation in terms of the mechanistic properties of fundamental particles, as well as his position regarding the scientific autonomy of chymistry from mechanics and physics. (shrink)

Nanotechnology, as with many technologies before it, places a strain on existing legislation and poses a challenge to all administrative agencies tasked with regulating technology-based products. It is easy to see how statutory schemes become outdated, as our ability to understand and affect the world progresses. In this article, we address the regulatory problems that nanotechnology posses for the Food and Drug Administration’s (FDA) classification structure for ‘‘drugs’’ and ‘‘devices.’’ The last major modification to these terms was in 1976, (...) with the enactment of the Medical Device Amendments. There are serious practical differences for a classification as a drug or device in terms of time to market and research. Drugs are classified, primarily, as acting by ‘‘chemical action.’’ We lay out some legal, philosophic, and scientific tools that serve to provide a useful, as well as legally and scientifically faithful, distinction between drugs and devices for the purpose of regulatory classification. These issues we raise are worth the consideration of anyone who is interested in the regulation of nano-products or other novel technologies. (shrink)

There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated based (...) on their explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

At the heart of chemistry lies the periodic system of chemical elements. Despite being the cornerstone of modern chemistry, the overall structure of the periodic system has never been fully understood from an atomic physics point of view. Group-theoretical models have been proposed instead, but they suffer from several limitations. Among others, the identification of the correct symmetry group and its decomposition into subgroups has remained a problem to this day. In an effort to deepen our limited understanding (...) of the periodic law, we have extended the traditional Lie algebraic framework to account for the peculiar degeneracy structure of the periodic system. Starting from the four-dimensional hidden symmetry and accidental degeneracy of the hydrogen atom, as first revealed by Fock in 1935, our research has mainly focussed on the way this SO(4) symmetry of the Coulomb potential gets broken in the periodic system as a consequence of the transformation of the hydrogenic (n, l) filling order to the Madelung (n+l, n) order due to electronic repulsions, relativistic effects and spin-orbit couplings. In this PhD dissertation, a new left-step format of the periodic table is first proposed on the basis of the Madelung rule. Following the particle physics tradition, the chemical elements are then considered as various states of some 'atomic matter', which is described by a non-compact spectrum-generating dynamical Lie group. The chemical elements are shown to form a basis for a single infinite-dimensional degeneracy space of the SO(4,2) ⊗ SU(2) group. An explanation for the period doubling is then proposed in terms of a particular symmetry breaking of the SO(4,2) group to the anti de Sitter SO(3,2) group. The Madelung rule is rationalised on the basis of nonlinear Lie algebras which reflect the screening of the Coulomb hole. This opens new perspectives for a symmetry-based understanding of how the periodic law emerges from its quantum mechanical foundations, and holds the future promise of complementing our current phenomenological approach by a direct atomic physics approach. (shrink)

This paper examines the idea that there might be natural kinds of causal processes, with characteristic diachronic structure, in much the same way that various chemical elements form natural kinds, with characteristic synchronic structure. This claim -- if compatible with empirical science -- has the potential to shed light on a metaphysics of essentially dispositional properties, championed by writers such as Bird and Ellis.

Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.

Contingentism, generally contrasted with law necessitarianism, is the view that the laws of nature are contingent. It is often coupled with the claim that their contingency is knowable a priori. This paper considers Bird's (2001, 2002, 2005, 2007) arguments for the thesis that, necessarily, salt dissolves in water; and it defends his view against Beebee's (2001) and Psillos's (2002) contingentist objections. A new contingentist objection is offered and several reasons for scepticism about its success are raised. It is concluded that (...) certain higher-level laws describing the behaviours of molecular compounds may be necessary due to their dependence on underlying physical laws, and that the modal status of laws of nature cannot be determined a priori, as the structural features of the substances and properties they govern must first be investigated. (shrink)

Schröedinger’s question “what is life?” was a real challenge for the scientific community and this still remains as an opened question, because in spite of the important advances in various scientific branches like philosophy, biology, chemistry and physics,, each of them assesses life from its particular point of view to explain the life’ characteristic features, so not a coherent and well structured general model of life was reported. In this paper life is approached from informational perspective, starting from earlier Draganeacu's (...) philosophic concepts, showing that actually life is structured by matter and information. Therefore, it is analyzed carbon-matter properties on the basis of which the living structures are composed, giving rise not only of a considerable number of carbon-based compounds, but serving now beside silicon, as an useful material for micro/nanostructure applications. Such specific properties refers to the high ability of carbon to associate/dissociate in chemical reactions regulated/facilitated by informational (Bit unit) YES/NO bistable mechanisms to form macro/small molecules with complementary properties, reactive info-functional pathways of transduction, relaying, amplification, integration, spreading, modulation, activation and positive/negative feedback reactions, like in the informational microelectronic/microsystems circuits. It is argued that the negentropy invoked earlier in Schrödinger's analysis is a consequence of informational-assisted structuration/organization of the cell and human organism. From the analysis of inter/intra-communication mechanisms in the cell and comparing with the outcomes described by the Informational Model of Human Body, it is deduced that, the living organisms operate on the basis of three main streaming circuits assuring the living functions: (1) the metabolic matter-related circuit; (2) the operative informational circuit; (3) the epigenetic informational circuit for the gradual integration of information in the central informational structure – DNA. It is founded on these bases the Informational Model of the Living Structures, and the Informational System of the Living Structures (ISLS), with similar functions on the entire living scale size, from unitary to multicellular living structures, composed by seven informational systems, namely [CASI (center of acquisition and storing of information), CDC (center of decision and command), IRSS (info-reactive sentient system), MIS (maintenance info-system), GTS (genetic transmission system), IGG (info-genetic generator) and IC (info-connection)]ISLS, and are identified the specific functions of each of them. The living structures operate thus like self-“polarized" bipolar info-matter informational devices by means of the stand-by metabolic matter-related circuit, and react/respond to the external/internal informational stimuli, which modulate their functionality, returning an external reaction signal (“attitude"), for adaptation and survival. (shrink)

This paper recommends that chemistry educators shift to a different ‘idea of nature’, an alternative ‘worldview.’ Much of contemporary science and technology deals in one way or another with dynamic coherences that display novel and important properties. The notion of how the world works that such studies and practices generate (and require) is quite different from the earlier concepts that are now integrated into science education. Eventual success in meeting contemporary technological and social challenges requires general diffusion of an overall (...) outlook that focuses on creative generation of novel and useful coherences, replacing a worldview that concentrates on analysis of pre-existing items to minimum constituents. Such a shift in emphasis would amount to general adoption of a new basic model of how nature functions. Chemistry educators can and should provide leadership for this urgently-needed development. (shrink)

It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative linguistic System 2 and unconscious automated prelinguistic (...) System 1 actions or reflexes. -/- I provide a critical survey of some of the major findings of two of the most eminent students of behavior of modern times, Ludwig Wittgenstein and John Searle, on the logical structure of intentionality (mind, language, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic problem is that one can say anything but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I analyze various writings by and about them from the modern perspective of the two systems of thought (popularized as ‘thinking fast, thinking slow’), employing a new table of intentionality and new dual systems nomenclature. I show that this is a powerful heuristic for describing behavior. -/- Thus, all behavior is intimately connected if one takes the correct viewpoint. The Phenomenological Illusion (oblivion to our automated System 1) is universal and extends not merely throughout philosophy but throughout life. I am sure that Chomsky, Obama, Zuckerberg and the Pope would be incredulous if told that they suffer from the same problem as Hegel, Husserl and Heidegger, (or that that they differ only in degree from drug and sex addicts in being motivated by stimulation of their frontal cortices by the delivery of dopamine (and over 100 other chemicals) via the ventral tegmentum and the nucleus accumbens), but it’s clearly true. While the phenomenologists only wasted a lot of people’s time, they are wasting the earth and their descendant’s future. (shrink)

It is my contention that the table of intentionality (rationality, consciousness, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative linguistic System 2 and unconscious automated (...) prelinguistic System 1 actions or reflexes. -/- I provide a critical survey of some of the major findings of two of the most eminent students of behavior of modern times, Ludwig Wittgenstein and John Searle, on the logical structure of intentionality (mind, language, consciousness, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic problem is that one can say anything but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I analyze various writings by and about them from the modern perspective of the two systems of thought (popularized as ‘thinking fast, thinking slow’), employing a new table of intentionality and new dual systems nomenclature. I show that this is a powerful heuristic for describing behavior. -/- Thus, all behavior is intimately connected if one takes the correct viewpoint. The Phenomenological Illusion (oblivion to our automated System 1) is universal and extends not merely throughout philosophy but throughout life. I am sure that Chomsky, Obama, Zuckerberg and the Pope would be incredulous if told that they suffer from the same problem as Hegel, Husserl and Heidegger, (or that that they differ only in degree from drug and sex addicts in being motivated by stimulation of their frontal cortices by the delivery of dopamine (and over 100 other chemicals) via the ventral tegmentum and the nucleus accumbens), but it’s clearly true. While the phenomenologists only wasted a lot of people’s time, they are wasting the earth and their descendant’s future. (shrink)

It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative linguistic System 2 and unconscious automated prelinguistic (...) System 1 actions or reflexes. -/- I provide a critical survey of some of the major findings of two of the most eminent students of behavior of modern times, Ludwig Wittgenstein and John Searle, on the logical structure of intentionality (mind, language, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic problem is that one can say anything, but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I analyze various writings by and about them from the modern perspective of the two systems of thought (popularized as ‘thinking fast, thinking slow’), employing a new table of intentionality and new dual systems nomenclature. I show that this is a powerful heuristic for describing behavior. -/- Thus, all behavior is intimately connected if one takes the correct viewpoint. The Phenomenological Illusion (oblivion to our automated System 1) is universal and extends not merely throughout philosophy but throughout life. I am sure that Chomsky, Obama, Zuckerberg and the Pope would be incredulous if told that they suffer from the same problem as Hegel, Husserl and Heidegger, (or that that they differ only in degree from drug and sex addicts in being motivated by stimulation of their frontal cortices by the delivery of dopamine (and over 100 other chemicals) via the ventral tegmentum and the nucleus accumbens), but it’s clearly true. While the phenomenologists only wasted a lot of people’s time, they are wasting the earth and their descendant’s future. -/- . (shrink)

Usual narratives among prehistoric archaeologists consider typological approaches as part of a past and outdated episode in the history of research, subsequently replaced by technological, functional, chemical, and cognitive approaches. From a historical and conceptual perspective, this paper addresses several limits of these narratives, which (1) assume a linear, exclusive, and additive conception of scientific change, neglecting the persistence of typological problems; (2) reduce collective developments to personal work (e.g. the “Bordes’” and “Laplace’s” methods in France); and (3) presuppose (...) the coherence and identity of these “methods” over time. It explores the case of the “Structural and analytical typology” method, developed in France, Spain, and Italy from the 1950s to the 2000s by Georges Laplace and his collaborators for lithic implements. This paper (1) provides a detailed historical account of the evolving content of this collective endeavour over five decades; (2) it addresses the epistemological question of what makes the identity and unity of a scientific method, demonstrating that the core component of the “analytical typology” lies in its particular way to represent real-world phenomena through its notation system; and (3) it reveals how this little known but significant episode of advances in the methods and theory of archaeology, contemporary but independent of the “New Archaeology” trend in English-speaking archaeology, was instrumental in the continuation of evolutionary perspectives in France and in the development of quantitative and formal methods in archaeology in southwestern Europe, foreseeing crucial knowledge representation issues raised today by digital methods in archaeology and data curation. (shrink)

The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget’s central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is supported by formal inference methods of Bayesian statistics, and is based on Heinz von Foerster’s fundamental metaphor of objects as tokens for eigen-solutions. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the definition (...) or identification of chemical elements. Some of von Foerster’s epistemological imperatives provide general guidelines of development and argumentation. (shrink)

Origin of a dissipative structure in a chemical dynamic system: occurs under the following constraints: 1) Affinity must be high. (The system must be far from equilibrium.); 2) There must be an auto-catalytic process; 3) A process that reduces the concentration of the auto-catalyst must operate; 4) The relevant parameters (rate constants, etc.) must lie in a range corresponding to a limit cycle trajectory. That is, there must be closure of the network of reaction such that a state (...) sufficiently close to the prior condition is achieved at the corresponding part of each oscillation. If these constraints continue to be met interactions of the system with the rest of the world are quite different in the presence of the dissipative structure than they would be in the absence of that self-organized coherence. Closure of a network of relationships which gives rise to a dissipative structure is a 'unit-determining' feature. The effects of the structure as a whole are the resultants of the effects of the components, but the concentrations of the components at any instant are effects of the closure of the limit cycle. This is an influence on components arising from what those components constitute --- downward causation. (shrink)

This contribution demonstrates that the development and growth of plants depends on the success of complex communication processes. These communication processes are primarily sign-mediated interactions and are not simply an mechanical exchange of ‘information’, as that term has come to be understood (or misunderstood) in science. Rather, such interactions as I will be describing here involve the active coordination and organisation of a great variety of different behavioural patterns — all of which must be mediated by signs. Thus proposed, a (...) biosemiotics of plant communication investigates communicationprocesses both within and among the cells, tissues, and organs of plants as sign-mediated interactions which follow (1) combinatorial (syntactic), (2) context-sensitive (pragmatic) and (3) content-specific (semantic) levels of rules. As will be seen in the cases under investigation, the context of interactionsin which a plant organism is interwoven determines the content arrangement of its response behaviour. And as exemplified by the multiply semiotic roles playedby the plant hormone auxin that I will discuss below, this means that a molecule type of identical chemical structure may function in the instantiation of differentmeanings (semantics) that are determined by the different contexts (pragmatics) in which this sign is used. (shrink)

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. (...) The thesis comprises four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science. (shrink)

Mucilage are bio-substances derived from plants or microorganisms that have positive effects on health, including boosting the immune system, calming the gastrointestinal tract, and decreasing blood pressure. Overall, recent developments in mucilage research have shown the materials’ potential for usage in variety of other fields, including adhesion or binding, textiles, papers, etc. However, there is limited widespread knowledge on the characteristics and use of mucilage in adhesion, textile, and paper industries. Therefore, this review navigates through the mucilage's chemical (...) class='Hi'>structure, and thermal, mechanical, physiochemical, and phytochemical features, weaving together their advanced applications. As the scientific community continues to unravel the advantages of mucilage extracts and harness their untapped potential, this review serves as both a testament to past achievements and a beacon guiding researchers towards a future enriched by the possibilities they hold. (shrink)

Note: Many types of nanosensors are designed using CP nanomaterials for nanobiological applications. (Conductive surface) The oxidation of conductive polymeric materials is easily altered by redox mechanisms, and the charge transfer properties of these materials are affected by structural parameters, such as diameter and dimensions. CP materials are able to provide sensitive and rapid responses to specific biological and chemical species. Techniques such as chemical polymerization are often used to make CP nanomaterials. Manufacturing strategies can be divided into (...) three categories: hard mold synthesis, soft mold synthesis, and mold-free synthesis. The most widely used conductive polymers in nanosensors are nanomaterials made from CP due to their unique chemical and electrical properties resulting from the properties of their pie-electron nanosystem. Many modeling and functionalization technologies are being developed to control the location, distribution, amount, or structure and orientation of biological nanomolecules at the nanomaterial level. Therefore, our level of contact between biological nanomolecules and nanomaterials is of particular importance in countless applications. Covalent and non-covalent modifications are two general methods for coupling biological molecules and CP nanomaterials. Covalent functionalization is a chemical process in which a strong bond or relationship between nanomaterials and biological molecules is formed. In many cases, surface chemical modifications are required to create active groups that can bind to biomolecules. Unlike covalent functionalization, in the non-covalent method, nanomolecules can be removed without destroying the geometric and electronic structure on the surface. Nanomaterials are formed. Conclusion : The large surface-to-volume ratio in nanostructures and the high potential for signal amplification provide ideal conditions for marking and detecting biological elements in the structure of nanosensors. (shrink)

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

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)

The nature and structure of time and time-intervals in physical, chemical and biological systems will be elucidated. The relation and dependence among time, energy and taking place of natural processes will be critically analyzed. The bio-processes taking place in nano-time intervals will be identified. Their relevance to nano-bio-science and nano-bio-technology will be developed and nano-time interval-aspect of nano-sciences and nano-technology will be advanced. -/- .

Natural kind essentialism is a specification of the intuitive idea that there are some mind-independent or objective categories in nature. These categories are thought to be characterised by a shared essence, which may involve intrinsic or extrinsic properties, mechanisms, or causal history. While the ontological basis of natural kinds has its roots in antiquity and especially Aristotle, the contemporary notion of a “natural kind” in philosophical discussion is often traced to William Whewell’s and John Stuart Mill’s work in the 1800s. (...) In its more modern form, natural kind essentialism was popularised in the 1970s mainly by Saul Kripke and Hilary Putnam. Traditionally, natural kind essentialism has been associated with intrinsic and microstructural properties, but contemporary work has made it clear that more refined versions of natural kind essentialism may have to accept extrinsic or relational essences. (shrink)

Chemical visualizations and models are special kinds of situated, inductive arguments. In this paper, I examine several historical case studies—an archive of images from museums, special collections, and popular magazines—as examples of emergent practices of physical modeling as theoretical play which became the basis for molecular biology and structural chemistry. Specifically, I trace a legacy of visualization tools that starts with Archibald Scott Cooper and Friedrich Kekulé in the late 1800s, crystallizes as material manipulatives in Kekulé’s student Jacobus Henricus (...) Van’t Hoff and his folded paper “toys,” is legitimized in the California lab of Linus Pauling, and is glorified in the popular imaginary with James Watson and Francis Crick’s model of DNA. My tracing then follows several threads into contemporary modeling practices. I ultimately argue that modeling play, originally outside of the boundary of deductive, positivist science, is now an accepted mode of inductive reasoning in these related chemical fields. (shrink)

In this paper it is analyzed from the informational perspective the relation between mind and body, an ancient philosophic issue defined as a problem, which still did not receive up to date an adequate solution. By introducing/using the concept of information, it is shown that this concept includes two facets, one of them referring to the common communications and another one referring to a hidden/structuring matter-related information, effectively acting in the human body and in the living systems, which determines the (...) dynamic inter-change of information between specific structures of the organism by electric/electronic/chemical agents and genetic/epigenetic processes. It is shown that the maintenance of body, permanently and obligatory depending on the external matter (foods, air, water) resources, needed to provide both the structuring/restructuring basic material and energy, determines the necessary existence of an info-managing system, administrating the internal mechano-chemical/physical processes. As a natural consequence, such a system should organize and assure own survival by an effective informational operability to detect the external food resources, to select the appropriate interest information and to decide as a function of circumstances. One important component in such an informational system is memory, allowing to dispose of the reference informational data for analysis/comparison and the selection between good and bad binary possible decisions. The memory receives and stores therefore signals from external reality and from the body itself, referring to the emotional reaction, digestion status, creation, and inherited predilections, within specific info-neural communication circuits between the brain and body execution/sensitive organs, the human body appearing as an integrated info-matter self-managed dynamic system. The specific body components memorize information with different degrees of info-integration: short/long-term integration, emotive/action reaction, info-abilities, culminating with the integration in the chromosomal structures by epigenetic processes. The new acquired information is transgenerationally transmissible, and is manifested as new traits, showing the adaptation capability of the human and close relation between mind and body. Analyzing the results of such a mind-body informational model in comparison with the earlier assumed/proposed/asserted archaic, Greek and Occidental philosophies, which represent only partial aspects of this relation, it is shown that this informational model, elaborated in terms of information on the basis of scientific reasons and arguments, constitutes a general, realist, and coherent model of the mind-body relation, able to integrate and/or explain most of the others. (shrink)

This article aims to clarify how aspects of current chemical understanding relate to some important contemporary problems of philosophy. The first section points out that the long-running philosophical debates concerning how properties stay together in substances have neglected the important topic of structure-determining closure. The second part describes several chemically-important types of closure and the third part shows how such closures ground the properties of chemical substances. The fourth section introduces current discussions of structural realism (SR) and (...) contextual emergence: the final sections reconsider the coherence of the properties of substances and concludes that recognition that structures qualify as determinants of specific outcomes—as ‘causes’ as that designation is used in Standard English—clarifies how properties stay together in chemical entities, and by analogy, how characteristics cohere in ordinary items. (shrink)

Many mechanisms, functions and structures of life have been unraveled. However, the fundamental driving force that propelled chemical evolution and led to life has remained obscure. The second law of thermodynamics, written as an equation of motion, reveals that elemental abiotic matter evolves from the equilibrium via chemical reactions that couple to external energy towards complex biotic non-equilibrium systems. Each time a new mechanism of energy transduction emerges, e.g., by random variation in syntheses, evolution prompts by punctuation and (...) settles to a stasis when the accessed free energy has been consumed. The evolutionary course towards an increasingly larger energy transduction system accumulates a diversity of energy transduction mechanisms, i.e. species. The rate of entropy increase is identified as the fitness criterion among the diverse mechanisms, which places the theory of evolution by natural selection on the fundamental thermodynamic principle with no demarcation line between inanimate and animate. (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and (...) how the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

A compelling idea holds that reality has a layered structure. We often disagree about what inhabits the bottom layer, but we agree that higher up we find chemical, biological, geological, psychological, sociological, economic, /etc./, entities: molecules, human beings, diamonds, mental states, cities, interest rates, and so on. How is this intuitive talk of a layered structure of entities to be understood? Traditionally, philosophers have proposed to understand layered structure in terms of either reduction or supervenience. But (...) these traditional views face well-known problems. A plausible alternative is that layered structure is to be explicated by appeal to explanations of a certain sort, termed / grounding explanations/. Grounding explanations tell us what obtains in virtue of what. Unfortunately, the use of grounding explanations to articulate the layered conception faces a problem, which I call /the collapse/. The collapse turns on the question of how to ground the facts stated by the explanations themselves. In this paper I make a suggestion about how to ground explanations that avoids the collapse. Briefly, the suggestion is that the fact stated by a grounding explanation is grounded in its /explanans/. (shrink)

In scientific and analytical research, Ultraviolet-visible spectroscopy, Fourier Transform Infrared spectroscopy, and Nuclear Magnetic Resonance spectroscopy have widely been used to analyze and characterize various substances. Ultraviolet, infrared, and Nuclear Magnetic Resonance spectroscopy were studied for diastereoisotopic protons of dorzolamide, which is used to treat glaucoma and ocular hypertension. Methanol was used as a solvent in Ultraviolet and we obtained three wavelengths: 203 nm, 253 nm, and 257 nm, where Ultraviolet spectroscopy was employed for stability testing of pharmaceuticals. By analyzing (...) the Fourier Transform Infrared spectrum, we also can determine the presence or absence of specific functional groups in a compound, helping to identify the compound or confirm its structure in analyzing the Nuclear Magnetic Resonance spectrum. It can determine the types and numbers of hydrogen (proton) and carbon atoms in a molecule and their chemical environment, which helps elucidate the molecular structure. (shrink)

The question of ontological foundation has undergone a noteworthy revival in recent years: metaphysicians today quarrel about how exactly to understand the asymmetrical and hyperintensional relationship of grounding. One of the reasons for this revival is that the old quantificationalist meta-ontology inherited from Quine has been effectively criticised by leading philosophers favourable to a meta-ontology, the aim of which is to come to know “which facts/items ground (constitute the base of) which other facts/items”, thus to examine the relation of ontological (...) dependence between beings (e.g. chemical properties depend on physical properties, the economic situation on the behaviour of individuals etc.), i.e. to explore the hierarchical structure of reality. I shall not discuss here the relationship of grounding in itself, but make some historical-formal remarks on the properties of the ultimate ontological foundational item itself and its aporetic nature. To do so I explore various more or less exotic philosophical ecosystems in the following order: Heidegger (Seyn), Plato (ἕν), Wáng Bi (道, dào). On the way I shall propose a new interpretation both of certain hypotheses in the Parmenides and of the nature of the opposition between Wáng Bì and Guō Xiàng in regard to the logical grammar of the expression “nothing (無, wú)” (transl. J. Dudley). (shrink)

The second volume of “Advancing Uncertain Combinatorics through Graphization, Hyperization, and Uncertainization: Fuzzy, Neutrosophic, Soft, Rough, and Beyond” presents a deep exploration of the progress in uncertain combinatorics through innovative methodologies like graphization, hyperization, and uncertainization. This volume integrates foundational concepts from fuzzy, neutrosophic, soft, and rough set theory, among others, to further advance the field. Combinatorics and set theory, two central pillars of mathematics, focus on counting, arrangement, and the study of collections under defined rules. Combinatorics excels in handling (...) uncertainty, while set theory has evolved with concepts such as fuzzy and neutrosophic sets, which enable the modeling of complex real-world uncertainties by addressing truth, indeterminacy, and falsehood. These advancements, when combined with graph theory, give rise to novel forms of uncertain sets in "graphized" structures, including hypergraphs and superhypergraphs. Innovations such as Neutrosophic Oversets, Undersets, and Offsets, as well as the Nonstandard Real Set, build upon traditional graph concepts, pushing both theoretical and practical boundaries. The synthesis of combinatorics, set theory, and graph theory in this volume provides a robust framework for addressing the complexities and uncertainties inherent in both mathematical and real-world systems, paving the way for future research and application. In the first chapter, “A Review of the Hierarchy of Plithogenic, Neutrosophic, and Fuzzy Graphs: Survey and Applications”, the authors investigate the interrelationships among various graph classes, including Plithogenic graphs, and explore other related structures. Graph theory, a fundamental branch of mathematics, focuses on networks of nodes and edges, studying their paths, structures, and properties. A Fuzzy Graph extends this concept by assigning a membership degree between 0 and 1 to each edge and vertex, representing the level of uncertainty. The Turiyam Neutrosophic Graph is introduced as an extension of both Neutrosophic and Fuzzy Graphs, while Plithogenic graphs offer a potent method for managing uncertainty. The second chapter, “Review of Some Superhypergraph Classes: Directed, Bidirected, Soft, and Rough”, examines advanced graph structures such as directed superhypergraphs, bidirected hypergraphs, soft superhypergraphs, and rough superhypergraphs. Classical graph classes include undirected graphs, where edges lack orientation, and directed graphs, where edges have specific directions. Recent innovations, including bidirected graphs, have sparked ongoing research and significant advancements in the field. Soft Sets and their extension to Soft Graphs provide a flexible framework for managing uncertainty, while Rough Sets and Rough Graphs address uncertainty by using lower and upper approximations to handle imprecise data. Hypergraphs generalize traditional graphs by allowing edges, or hyperedges, to connect more than two vertices. Superhypergraphs further extend this by allowing both vertices and edges to represent subsets, facilitating the modeling of hierarchical and group-based relationships. The third chapter, “Survey of Intersection Graphs, Fuzzy Graphs, and Neutrosophic Graphs”, explores the intersection graph models within the realms of Fuzzy Graphs, Intuitionistic Fuzzy Graphs, Neutrosophic Graphs, Turiyam Neutrosophic Graphs, and Plithogenic Graphs. The chapter highlights their mathematical properties and interrelationships, reflecting the growing number of graph classes being developed in these areas. Intersection graphs, such as Unit Square Graphs, Circle Graphs, and Ray Intersection Graphs, are crucial for understanding complex graph structures in uncertain environments. The fourth chapter, “Fundamental Computational Problems and Algorithms for SuperHyperGraphs”, addresses optimization problems within the SuperHypergraph framework, such as the SuperHypergraph Partition Problem, Reachability, and Minimum Spanning SuperHypertree. The chapter also adapts classical problems like the Traveling Salesman Problem and the Chinese Postman Problem to the SuperHypergraph context, exploring how hypergraphs, which allow hyperedges to connect more than two vertices, can be used to solve complex hierarchical and relational problems. The fifth chapter, “A Short Note on the Basic Graph Construction Algorithm for Plithogenic Graphs”, delves into algorithms designed for Plithogenic Graphs and Intuitionistic Plithogenic Graphs, analyzing their complexity and validity. Plithogenic Graphs model multi-valued attributes by incorporating membership and contradiction functions, offering a nuanced representation of complex relationships. The sixth chapter, “Short Note of Bunch Graph in Fuzzy, Neutrosophic, and Plithogenic Graphs”, generalizes traditional graph theory by representing nodes as groups (bunches) rather than individual entities. This approach enables the modeling of both competition and collaboration within a network. The chapter explores various uncertain models of bunch graphs, including Fuzzy Graphs, Neutrosophic Graphs, Turiyam Neutrosophic Graphs, and Plithogenic Graphs. In the seventh chapter, “A Reconsideration of Advanced Concepts in Neutrosophic Graphs: Smart, Zero Divisor, Layered, Weak, Semi, and Chemical Graphs”, the authors extend several fuzzy graph classes to Neutrosophic graphs and analyze their properties. Neutrosophic Graphs, a generalization of fuzzy graphs, incorporate degrees of truth, indeterminacy, and falsity to model uncertainty more effectively. The eighth chapter, “Short Note of Even-Hole-Graph for Uncertain Graph”, focuses on Even-Hole-Free and Meyniel Graphs analyzed within the frameworks of Fuzzy, Neutrosophic, Turiyam Neutrosophic, and Plithogenic Graphs. The study investigates the structure of these graphs, with an emphasis on their implications for uncertainty modeling. The ninth chapter, “Survey of Planar and Outerplanar Graphs in Fuzzy and Neutrosophic Graphs”, explores planar and outerplanar graphs, as well as apex graphs, within the contexts of fuzzy, neutrosophic, Turiyam Neutrosophic, and plithogenic graphs. The chapter examines how these types of graphs are used to model uncertain parameters and relationships in mathematical and real-world systems. The tenth chapter, “General Plithogenic Soft Rough Graphs and Some Related Graph Classes”, introduces and explores new concepts such as Turiyam Neutrosophic Soft Graphs and General Plithogenic Soft Graphs. The chapter also examines models of uncertain graphs, including Fuzzy, Intuitionistic Fuzzy, Neutrosophic, and Plithogenic Graphs, all designed to handle uncertainty in diverse contexts. The eleventh chapter, “Survey of Trees, Forests, and Paths in Fuzzy and Neutrosophic Graphs”, provides a comprehensive study of Trees, Forests, and Paths within the framework of Fuzzy and Neutrosophic Graphs. This chapter focuses on classifying and analyzing graph structures like trees and paths in uncertain environments, contributing to the ongoing development of graph theory in the context of uncertainty. (shrink)

A widely cited roadblock to bridging ecological psychology and enactivism is that the former identifies with realism and the latter identifies with constructivism, which critics charge is subjectivist. A pragmatic reading, however, suggests non-mental forms of constructivism that simultaneously fit core tenets of enactivism and ecological realism. After advancing a pragmatic version of enactive constructivism that does not obviate realism, I reinforce the position with an empirical illustration: Physarum polycephalum (a slime mold), a communal unicellular organism that leaves slime trails (...) that form chemical barriers that it avoids in foraging explorations. Here, environmental building and sensorimotor engagement are part of the same process with P. polycephalum coordinating around self-created, affordance-bearing geographies, which nonetheless exist independently in ways described by ecological realists. For ecological psychologists, affordances are values, meaning values are external to the perceiver. I argue that agent-enacted values have the same status and thus do not obviate ecological realism or generate subjectivism. The constructivist-realist debate organizes around the emphasis that enactivists and ecological theorists respectively place on the inner constitution of organisms vs. the structure of environments. Building on alimentary themes introduced in the P. polycephalum example and also in Gibson’s work, I go on to consider how environment, brain, visceral systems, and even bacteria within them enter perceptual loops. This highlights almost unfathomable degrees of mutually modulating internal and external synchronization. It also shows instances in which internal conditions alter worldly configurations and invert values, in Gibson’s sense of the term, albeit without implying subjectivism. My aim is to cut across the somatic focus of enactive constructivism and the external environment-oriented emphasis of ecological realism and show that enactivism can enrich ecological accounts of value. (shrink)

We introduce the notion of complexity, first at an intuitive level and then in relatively more concrete terms, explaining the various characteristic features of complex systems with examples. There exists a vast literature on complexity, and our exposition is intended to be an elementary introduction, meant for a broad audience. -/- Briefly, a complex system is one whose description involves a hierarchy of levels, where each level is made of a large number of components interacting among themselves. The time evolution (...) of such a system is of a complex nature, depending on the interactions among subsystems in the next level below the one under consideration and, at the same time, conditioned by the level above, where the latter sets the context for the evolution. Generally speaking, the interactions among the constituents of the various levels lead to a dynamics characterized by numerous characteristic scales, each level having its own set of scales. What is more, a level commonly exhibits ‘emergent properties’ that cannot be derived from considerations relating to its component systems taken in isolation or to those in a different contextual setting. In the dynamic evolution of some particular level, there occurs a self-organized emergence of a higher level and the process is repeated at still higher levels. -/- The interaction and self-organization of the components of a complex system follow the principle commonly expressed by saying that the ‘whole is different from the sum of the parts’. In the case of systems whose behavior can be expressed mathematically in terms of differential equations this means that the interactions are nonlinear in nature. -/- While all of the above features are not universally exhibited by complex systems, these are nevertheless indicative of a broad commonness relative to which individual systems can be described and analyzed. There exist measures of complexity which, once again, are not of universal applicability, being more heuristic than exact. The present state of knowledge and understanding of complex systems is itself an emerging one. Still, a large number of results on various systems can be related to their complex character, making complexity an immensely fertile concept in the study of natural, biological, and social phenomena. -/- All this puts a very definite limitation on the complete description of a complex system as a whole since such a system can be precisely described only contextually, relative to some particular level, where emergent properties rule out an exact description of more than one levels within a common framework. -/- We discuss the implications of these observations in the context of our conception of the so-called noumenal reality that has a mind-independent existence and is perceived by us in the form of the phenomenal reality. The latter is derived from the former by means of our perceptions and interpretations, and our efforts at sorting out and making sense of the bewildering complexity of reality takes the form of incessant processes of inference that lead to theories. Strictly speaking, theories apply to models that are constructed as idealized versions of parts of reality, within which inferences and abstractions can be carried out meaningfully, enabling us to construct the theories. -/- There exists a correspondence between the phenomenal and the noumenal realities in terms of events and their correlations, where these are experienced as the complex behavior of systems or entities of various descriptions. The infinite diversity of behavior of systems in the phenomenal world are explained within specified contexts by theories. The latter are constructs generated in our ceaseless attempts at interpreting the world, and the question arises as to whether these are reflections of `laws of nature' residing in the noumenal world. This is a fundamental concern of scientific realism, within the fold of which there exists a trend towards the assumption that theories express truths about the noumenal reality. We examine this assumption (referred to as a ‘point of view’ in the present essay) closely and indicate that an alternative point of view is also consistent within the broad framework of scientific realism. This is the view that theories are domain-specific and contextual, and that these are arrived at by independent processes of inference and abstractions in the various domains of experience. Theories in contiguous domains of experience dovetail and interpenetrate with one another, and bear the responsibility of correctly explaining our observations within these domains. -/- With accumulating experience, theories get revised and the network of our theories of the world acquires a complex structure, exhibiting a complex evolution. There exists a tendency within the fold of scientific realism of interpreting this complex evolution in rather simple terms, where one assumes (this, again, is a point of view) that theories tend more and more closely to truths about Nature and, what is more, progress towards an all-embracing ‘ultimate theory’ -- a foundational one in respect of all our inquiries into nature. We examine this point of view closely and outline the alternative view -- one broadly consistent with scientific realism -- that there is no ‘ultimate’ law of nature, that theories do not correspond to truths inherent in reality, and that successive revisions in theory do not lead monotonically to some ultimate truth. Instead, the theories generated in succession are incommensurate with each other, testifying to the fact that a theory gives us a perspective view of some part of reality, arrived at contextually. Instead of resembling a monotonically converging series successive theories are analogous to asymptotic series. -/- Before we summarize all the above considerations, we briefly address the issue of the complexity of the {\it human mind} -- one as pervasive as the complexity of Nature at large. The complexity of the mind is related to the complexity of the underlying neuronal organization in the brain, which operates within a larger biological context, its activities being modulated by other physiological systems, notably the one involving a host of chemical messengers. The mind, with no materiality of its own, is nevertheless emergent from the activity of interacting neuronal assemblies in the brain. As in the case of reality at large, there can be no ultimate theory of the mind, from which one can explain and predict the entire spectrum of human behavior, which is an infinitely rich and diverse one. (shrink)

The scientific successes of the last 400 years strongly suggest a picture on which our scientific theories exhibit a layered structure of dependence and determination. Economics is dependent on and determined by psychology; psychology in its turn is, plausibly, dependent on and determined by biology; and so it goes. It is tempting to explain this layered structure of dependence and determination among our theories by appeal to a corresponding layered structure of dependence and determination among the entities (...) putatively treated by those theories. In this paper, I argue that we can resist this temptation: we can explain the sense in which, e.g., the biological truths are dependent on and determined by chemical truths without appealing to properly biological or chemical entities. This opens the door to a view on which, though there are more truths than just the purely physical truths, there are no entities, states, or properties other than the purely physical entities, states, and properties. I argue that some familiar strategies to explicate the idea of a layered structure of theories by appeal to reduction, ground, and truthmaking encounter difficulties. I then show how these difficulties point the way to a more satisfactory treatment which appeals to something very close to the notion of ground. Finally, I show how this treatment provides a theoretical setting in which we might fruitfully frame debates about which entities there really are. (shrink)

It is arguably the case that olfactory system contains two senses that share the same type of stimuli, sensory transduction mechanism, and processing centers. Yet, orthonasal and retronasal olfaction differ in their types of perceptible objects as individuated by their sensory qualities. What will be explored in this paper is how the account of orthonasal smell developed in the Molecular Structure Theory of smell can be expanded for retronasal olfaction (Young, 2016, 2019a-b, 2020). By considering the object of olfactory (...) perception to be the molecular structure of chemical compounds composing odor plumes, Molecular Structure Theory provides a means for determining an odor’s olfactory quality, how odors can be identified and individuated, and how we perceive smellscapes. Surveying the differences between orthonasal and retronasal olfaction provides the basis for the central argument of the paper that the perceptible objects we refer to as smells and individuated on the basis of their olfactory qualities are only relative to orthonasal olfaction. Retronasal olfaction it is speculatively concluded might play an essential role in our perception of flavorful objects. (shrink)

Science frequently gives us multiple, compatible ways of solving the same problem or formulating the same theory. These compatible formulations change our understanding of the world, despite providing the same explanations. According to what I call "conceptualism," reformulations change our understanding by clarifying the epistemic structure of theories. I illustrate conceptualism by analyzing a typical example of symmetry-based reformulation in chemical physics. This case study poses a problem for "explanationism," the rival thesis that differences in understanding require ontic (...) explanatory differences. To defend conceptualism, I consider how prominent accounts of explanation might accommodate this case study. I argue that either they do not succeed, or they generate a skeptical challenge. (shrink)

Space exploration and the search for a better understanding of life have never been entirely separate from one another. This is not simply a matter of policy, a decision by political administrations to combine the two. Rather, it is a matter of the ways in which both draw upon the same scientific culture and upon overlapping societal influences. Some of the latter are the political influences of particular times and particular places, others are of a far broader nature. Progress in (...) one field has tended to be combined with advances in the other. It is a familiar point that, in the very year that NASA was founded, i.e. 1958, the American molecular biologist Joshua Lederberg won a Nobel Prize for his discovery that bacteria can exchange genetic material (a process now known as ‘bacterial conjugation’). This, in turn, was only six years after the classicMiller-Urey experiment to replicate the production of some of the chemical precursors of life. And the Miller-Urey experiment, in turn, overlapped in time with the work of Watson, Crick and Rosalind Franklin in England, on the structure of DNA. Major breakthroughs came in both fields (activity in space and research into life) within the same time-frame, and drew upon at least some of the same background influences and interests. When Lederberg went on to work with NASA on the early programs to look for life on Mars, the progression was, in an everyday sense, natural. Interest in space and interest in life went together. They have always tended to do so. (shrink)

The concept of fields available in physics will be considered for application to unravel the mysteries of form, structure and function of human consciousness and mind. The sameness of functions of human consciousness and mind in language acquisition and communication and also acquiring knowledge of various kinds and its will be discussed. In the light of this the limitations of concepts of pure physics and modern physics probes will be discussed. -/- The information and ideas available in the Upanishads (...) in the form of Brahmajnaana will be applied to understand the physical nature of human consciousness and mind and their functions. This information and translation into modern and cognitive scientific terms would be correlated with brainwaves concept of modern physiology. The physiochemical, physical and chemical natures of experiences, purport, meanings, ideas, thoughts and expressions will be presented based on Upanishadic insight thus acquired. The advantage of this alternative probe, method and model to understand the functions of human consciousness and mind will be demonstrated. -/- This model of human consciousness and mental functions is also correlated to brain wave EEG frequency changes. -/- . (shrink)

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies (...) consortia and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

A cause may influence its effect via multiple paths. Paradigmatically (Hesslow [1974]), taking birth control pills both decreases one’s risk of thrombosis by preventing pregnancy and increases it by producing a blood chemical. Building on Pearl ([2001]), I explicate the notion of a path-specific effect. Roughly, a path-specific effect of C on E via path P is the degree to which a change in C would change E were they to be transmitted only via P. Facts about such effects (...) may be gleaned from the structural equations commonly used to represent the causal relationships among variables. I contrast my analysis of the Hesslow case with those given by theorists of probabilistic causality, who mistakenly link it to issues of causal heterogeneity, token-causation and indeterminism. The reason probabilistic theories misdiagnose this case is that they pay inadequate attention to the structural relationships among variables. (shrink)

In this paper, I defend the agent/patient distinction against critics who argue that causal interactions are symmetrical. Specifically, I argue that there is a widespread type of causal interaction between distinct entities, resulting in a type of ontological asymmetry that provides principled grounds for distinguishing agents from patients. The type of interaction where the asymmetry is found is when one of the entities undergoes a change in kind, structure, powers, or intrinsic properties as a result of the interaction while (...) the other does not. Interactions of this type are widespread in molecular biology and chemistry. I focus specifically on (i) the actions of enzymes on substrates and (ii) water molecules breaking the bonds of polarized molecules. Finally, I respond to objections by laying out and to a limited extent defending three commitments of my account: emergent entities and powers, realism about chemical kinds or structures, and the assumption of the agent/patient distinction in functional attributions in biology. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward (...) a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

Origin of life on earth transpired once and from then on, it emerges as an endless eternal process. Matter and energy are constants of the cosmos and the hypothesis is that the origin of life is a moment when these constants intertwined or interacted. Energy from the cosmos interacted with inorganic matter to support matter with retention of this riveted energy, as energy to be circulated within the primitive channelized structures to conserve energy by the materialization of the proton homeostasis (...) mechanisms developed from the obtainable inorganic matter. The driver for these processes as we now confirm, exists in the quantum world and through quantum phenomenal processes could have combined these constants to create the magic of life. Primitive earth was a chemical reactive system that triggered a macromolecular evolution by means of open thermodynamic systems, driven by cyclic gradients of temperature, electromagnetic radiation and chemical potentials which sustained life and proto-consciousness in the first life forms driven by the quantum processes. The origin of life is always an intriguing topic but the purpose for finding the cause should never be inclined towards obliterating it; for if that is the case, the further we seek, the farther it will go. (shrink)

The relation between body and mind is one of the oldest riddles that has puzzled mankind. That material and mental events may interact is accepted even by the law: our mental capacity to concentrate on the task can be seriously reduced by drugs. Physical and chemical processes may act upon the mind; and when we are writing a difficult letter, our mind acts upon our body and, through a chain of physical events, upon the mind of the recipient of (...) the letter. This is what the authors of this book call the 'interaction of mental and physical events'. We know very little about this interaction; and according to recent philosophical fashions this is explained by the alleged fact that we have brains but no thoughts. The authors of this book stress that they cannot solve the body mind problem; but they hope that they have been able to shed new light on it. Eccles especially with his theory that the brain is a detector and amplifier; a theory that has given rise to important new developments, including new and exciting experiments; and Popper with his highly controversial theory of 'World 3'. They show that certain fashionable solutions which have been offered fail to understand the seriousness of the problems of the emergence of life, or consciousness and of the creativity of our minds. In Part I, Popper discusses the philosophical issue between dualist or even pluralist interaction on the one side, and materialism and parallelism on the other. There is also a historical review of these issues. In Part II, Eccles examines the mind from the neurological standpoint: the structure of the brain and its functional performance under normal as well as abnormal circumstances. The result is a radical and intriguing hypothesis on the interaction between mental events and detailed neurological occurrences in the cerebral cortex. Part III, based on twelve recorded conversations, reflects the exciting exchange between the authors as they attempt to come to terms with their opinions. (shrink)

In this paper, we will explore the relation between molecular structure and functions displayed by biochemical molecules in complex physiological processes by using tools from the philosophy of science and the philosophy of scientific practice. We will argue that biochemical functions are weakly emergent from molecular structure by using an account of weak. In order to explore this thesis, we will consider the role of vitamin B12 in contributing to the process of erythropoiesis. The structure of the (...) paper is the following: First, we will consider biochemical functions and why they cannot be easily reduced to their chemical realisers. We will suggest weak emergence as an alternative while also accounting for the relevance of the context, in our case, systemic and organisational. The paper will conclude by considering (1) how the usage of tools from the philosophy of science, such as weak emergence, can aid our understanding of the relations between the components of complex phenomena, such as erythropoiesis, and (2) how the philosophy of scientific practice sheds light on the explanatory role of processes that are dynamically stabilised and the different levels of organisation implied. (shrink)

To this day, a hundred and fifty years after Mendeleev's discovery, the overal structure of the periodic system remains unaccounted for in quantum-mechanical terms. Given this dire situation, a handful of scientists in the 1970s embarked on a quest for the symmetries that lie hidden in the periodic table. Their goal was to explain the table's structure in group-theoretical terms. We argue that this symmetry program required an important paradigm shift in the understanding of the nature of (...) class='Hi'>chemical elements. The idea, in essence, consisted of treating the chemical elements, not as particles, but as states of a superparticle. We show that the inspiration for this came from elementary particle physics, and in particular from Heisenberg's suggestion to treat the proton and neutron as different states of the nucleon. We provide a careful study of Heisenberg's last paper on the nature of elementary particles, and explain why the Democritean picture of matter no longer applied in modern physics and a Platonic symmetry-based picture was called for instead. We show how Heisenberg's Platonic philosophy came to dominate the field of elementary particle physics, and how it found its culmination point in Gell-Mann's classification of the hadrons in the eightfold way. We argue that it was the success of Heisenberg's approach in elementary particle physics that sparked the group-theoretical approach to the periodic table. We explain how it was applied to the set of chemical elements via a critical examination of the work of the Russian mathematician Abram Ilyich Fet the Turkish-American physicist Asim Orhan Barut, before giving some final reflections. (shrink)

This paper connects information with computation and cognition via concept of agents that appear at variety of levels of organization of physical/chemical/cognitive systems – from elementary particles to atoms, molecules, life-like chemical systems, to cognitive systems starting with living cells, up to organisms and ecologies. In order to obtain this generalized framework, concepts of information, computation and cognition are generalized. In this framework, nature can be seen as informational structure with computational dynamics, where an (info-computational) agent is (...) needed for the potential information of the world to actualize. Starting from the definition of information as the difference in one physical system that makes a difference in another physical system – which combines Bateson and Hewitt’s definitions, the argument is advanced for natural computation as a computational model of the dynamics of the physical world, where information processing is constantly going on, on a variety of levels of organization. This setting helps us to elucidate the relationships between computation, information, agency and cognition, within the common conceptual framework, with special relevance for biology and robotics. (shrink)