Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting (...) physical models of the atoms are characterized by the same interaction energies as the quantum mechanical models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known as a paradox. (shrink)

This chapter describes the theoretical implications of Extended Synthesis and addresses the methodological options available for determining aspects of theoretical structure. It uses a “bottom-up” approach focused on evolutionary theory in particular, as opposed to a “top-down” strategy that attempts to characterize the structure of all scientific theories. The chapter shows that there are multiple stable components contained within a broad representation of evolutionary theory. It suggests that the philosophical analysis offered in the chapter regarding the structure (...) of evolutionary theory assists attempts to recover coherence through the vehicle of an Extended Synthesis. (shrink)

In this paper I aim to defend a twofold thesis. On one hand, I will sup-port, against Perini [7], the indispensability of diagrams when structurally complex biomolecules are concerned, since it is not possible to satisfactorily use linguistic-sentential representations at that domain. On the other hand, even when diagrams are dispensable I will defend than they will generally be more effective than other representations in encoding biomolecular knowledge, relying on Kulvicki-Shimojima’s diagrammatic effectiveness thesis. Finally, I will ground many epistemic (...) virtues of biomolecular diagrams (understandability, explanatory power, prediction and hypothesis evaluation) on their cognitive-computational indispensability and their semantic-epistemic effectiveness. (shrink)

According to the BSM- Supergravitation Unified Theory (BSM-SG), the energy is indispensable feature of matter, while the matter possesses hierarchical levels of organization from a simple to complex forms, with appearance of fields at some levels. Therefore, the energy also follows these levels. At the fundamental level, where the primary energy source exists, the matter is in its primordial form, where two super-dense fundamental particles (FP) exist in a classical pure empty space (not a physical vacuum). They are associated with (...) the Planck scale parameters of frequency and distance and interact by Supergravitational forces. These forces are inverse proportional to the cube of distance at pure empty space and they are based on frequency interactions. Since the two FPs have different intrinsic frequencies, the SG forces appear different for interactions between the like and unlike FPs and may change the sign. This primordial form of matter exists in the super-heavy black holes located in the center of each well formed galaxy. The next upper level of matter organization includes the underlying structure of the physical vacuum, called a Cosmic Lattice, and the structure of elementary particles. They have common substructure elements obtained by specific crystallization process preceding the formation of the observable galaxies. The Cosmic Lattice, forming a space known as a physical vacuum, is responsible for the existence and propagation of the physical fields: electrical, magnetic, Newtonian gravity and inertia. The energy of physical vacuum is in two forms: Static (enormous) and Dynamic (weak). The Static energy is directly related to the Newtonian mass by the Einstein equation E = mc^2 and it is a primary source of the nuclear energy. The Dynamic energy is responsible for the existence of the electric and magnetic fields, the constant speed of light and the quantum mechanical properties of the physical vacuum. The next upper energy level is the dynamical energy of excited atoms and molecules. At this level a hidden energy wells exit, such as the internal energy of the electron and the internal energy of atoms with more than one electron. The next upper energy level is at some organic molecules and particularly in the biomolecules that contain ring atomic structures. In such a structure, some quantum states are not emitted immediately, but rotating in the ring. While in organic molecules the energy stored in such a ring is released by a chemical process, in the long chain molecule of proteins in the living organism the stored energy can be released simultaneously by triggering. A huge number of atomic rings are contained in the DNA strands. The release of the energy stored in DNA, for example, is an avalanche process that causes an emission of entangled photons possessing a strong penetrating capability. A sequence of entangled photons emitted by DNA should carry the genetic information encoded by the cordons. This mechanism, predicted in BSM-SG theory, is very important for intercommunication between the cells of the living organism. The next upper level of energy organization may exist in the brain. The brain is an organ of a most abundant number of atomic rings, while its tissue environment might permit complex energy interactions. The human brain contains billions of atomic rings. The next hypothetical upper level of energy organization is an information field, physically existed outside, but connected with the living brain. It corresponds to a specific field known as aura, while the possibility of its existence is still not accepted by the main stream science. The problem is that this field could not be detected by the currently existing technical means used for EM communications. The BSM-SG predicts that this field might differ from the EM field we use for communication, but it is a subject of a further theoretical development that must be supported by experiments using specifically designed technical means. According to the BSM-SG theory, the energy conversion from the primary energy source to the complex levels of matter and field organization is a permanent syntropic process based on complex resonance interactions. (shrink)

We reconstruct genetic determinism as a reductionist thesis to the effect that the molecular properties of cells can be accounted for to a great extent by their genetic outfit. The non-reductionist arguments offered at this molecular level often use the relationship between structure and function as their point of departure. By contrast, we develop a non-reductionist argument that is confined to the structural characteristics of biomolecules; no appeal to functions is made. We raise two kinds of objections against (...) the reducibility claim underlying genetic determinism. First, some conceptual distinctions at the protein level cannot be captured on a genetic basis. A one-to-many relationship between DNA sequences and proteins emerges from them. Second, the relationship between genes and proteins is characterized by explanatory loops or reciprocal explanatory dependence. The presence of proteins is explained by the transcription from corresponding DNA sequences, and the latter is in turn accounted for by the action of proteins. By contrast, a reductive account requires a unidirectional explanatory dependence. (shrink)

We develop a conceptual and formal clarification of notion of surprise as a belief-based phenomenon by exploring a rich typology. Each kind of surprise is associated with a particular phase of cognitive processing and involves particular kinds of epistemic representations (representations and expectations under scrutiny, implicit beliefs, presuppositions). We define two main kinds of surprise: mismatch-based surprise and astonishment. In the central part of the paper we suggest how a formal model of surprise can be integrated with a formal model (...) of belief change. We investigate the role of surprise in triggering the process of belief reconsideration. There are a number of models of surprise developed in the psychology of emotion. We provide several comparisons of our approach with those models. (shrink)

This article deals with the methodologies commonly used in the framework of the structural approach to social representations. It concerns free and hierarchical evocations, the characterization questionnaire, the similarity analysis, the basic cognitive schemes model, the attribute-challenge technique and the test of context independence. More than a simple review of these methodologies, it offers a critical approach concerning the problems encountered and related to: thresholds or “cutoff points” used to diagnose the structure and the accuracy of the structural diagnosis, (...) grouping methods employed to reduce the corpus of verbal associations, the dilemma between reliability and feasibility, especially in field research, the adequacy and number of modalities of response in the framework of the structural diagnosis. Following this evaluation, this article suggests potential solutions to overcome these methodological limitations. Moreover, as methodological issues are closely related to theoretical questions, the link between social representation theory and identity approaches is discussed. (shrink)

You are, I am sure, just as aware as I am that the operational nodes of a complex problem, the points at which it can be split open to yield nuggets of new insight or achieve lasting advances, often lie in tediously technical details perhaps incomprehensible to all but specialists in the matter and anyways totally lacking in the romance and easy excitement which attract the topic's dilettantes. I would like you to hold fast to this appreciation, for the concerns (...) I shall raise here are technical indeed. They are, however,seminaltechnicalities which, as we seek to fathom them, should fundamentally reshape our comprehension of the logic of confirmation, causal connectedness, and the foundations of statistical inference. In brief, it will be seen that certain powerful everyday intuitions concerning which propositions are confirmationally irrelevant to which others are exceedingly difficult to justify. (shrink)

In our everyday moral deliberations, we attend to two central types of considerations – outcomes and moral rules. How these considerations interrelate is central to the long-standing debate between deontologists and utilitarians. Is the weight we attach to moral rules reducible to their conduciveness to good outcomes (as many utilitarians claim)? Or do we take moral rules to be absolute constraints on action that normatively trump outcomes (as many deontologists claim)? Arguments over these issues characteristically appeal to commonsense intuitions about (...) various cases. As a result, an important portion of the debate involves empirically tractable questions — questions that can be investigated by probing for people’s judgments in cases in which the two types of considerations come into conflict with one another. (shrink)

Spatial mental representations can be derived from linguistic and non‐linguistic sources of information. This study tested whether these representations could be formed from statistical linguistic frequencies of city names, and to what extent participants differed in their performance when they estimated spatial locations from language or maps. In a computational linguistic study, we demonstrated that co‐occurrences of cities in Tolkien’s Lord of the Rings trilogy and The Hobbit predicted the authentic longitude and latitude of those cities in Middle Earth. In (...) a human study, we showed that human spatial estimates of the location of cities were very similar regardless of whether participants read Tolkien’s texts or memorized a map of Middle Earth. However, text‐based location estimates obtained from statistical linguistic frequencies better predicted the human text‐based estimates than the human map‐based estimates. These findings suggest that language encodes spatial structure of cities, and that human cognitive map representations can come from implicit statistical linguistic patterns, from explicit non‐linguistic perceptual information, or from both. (shrink)

This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries (...) to biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science. (shrink)

This paper presents an approach of unsupervised learning of clusters from a citation database, and applies it to a large corpus of articles in philosophy to give an account of the structure of the discipline. Following a list of journals from the PhilPapers-archive, 68,152 records were downloaded from the Reuters Web of Science-Database. Their citation data was processed using dimensionality reduction and clustering. The resulting clusters were identified, and the results are graphically represented. They suggest that the division of (...) analytic and Continental philosophy in the considered timespan is overstated; that analytical, in contrast to Continental philosophy does not form a coherent group in recent philosophy; and that metaphors about the disciplinary structure should focus on the coherence and interconnectedness of a multitude of smaller and larger subfields. (shrink)

With the advent of new technology and imaging techniques that measure brain activity and with the development of the computer as a model for human thinking, it is not surprising to find many authors currently addressing issues regarding brain function and themind/body problem. What is perhaps surprising, given the absence of these techniques at the time, is that Merleau-Ponty addresses these same issues with a rigor and insight that equals, and perhaps even exceeds, most current philosophical studies. Merleau-Ponty’s frequently ignored (...) early work, The Structure of Behavior, contains a wealth of analysis still relevant to current biological and neurophysiological studies and to the philosophical consequences frequently drawn from them. Merleau-Ponty critically addresses not only theories that attempt to understand human behavior as the linear calculation of discrete physiological events but also theories that would explain human behavior simply by appealing to abstract conceptual analysis. His theory of emergent materialism focuses on the human body as a concrete organic whole that can be reduced neither to linear physical events nor to abstract conceptual relations. Understanding the human being requires a theory that recognizes the human body as an original whole, that is, that recognizes a body that intimately integrates mind and matter. It is this theory that Merleau-Ponty first articulates in The Structure of Behavior. It is the main themes of this theory that I will attempt to reveal here. (shrink)

I examine the influence of James B. Conant on the writing of Kuhn’s Structure of Scientific Revolutions. By clarifying Conant’s influence on Kuhn, I also clarify the influence that others had on Kuhn’s thinking. And by identifying the various influences that Conant had on Kuhn’s view of science, I identify Kuhn’s most original contributions in Structure. On the one hand, I argue that much of the framework and many of the concepts that figure in Structure were part (...) of Conant’s picture of science, a picture that figured prominently in the general education natural science courses that Conant taught at Harvard. On the other hand, I show that Kuhn’s Structure contains important contributions that do not figure in Conant’s picture of science. I argue that the following three themes in Structure do not originate with Conant: (1) the concept of “normal science”; (2) “the problem of scientific revolutions,” that is, the apparent threat posed by radical changes of theory in science; and (3) Kuhn’s emphasis on the social dimensions of science, specifically the social structure of research communities. (shrink)

This article proposes a way of understanding Kantianism, act-utilitarianism and some other important ethical theories according to which they are all versions of the same kind of theory, sharing a common structure. I argue that this is a profitable way to understand the theories discussed. It is charitable to the theories concerned; it emphasizes the common ground between them; it gives us insights into the differences between them; and it provides a method for generating new ethical theories worth studying. (...) The article briefly discusses the relationship between these ideas and some other recent proposals that emphasize the common ground between Kantianism and versions of consequentialism. (shrink)

A wave of recent philosophical work on practical rationality is organized by the following implicit argument: Practical reasoning is figuring out what to do; to do is to act; so the forms of practical inference can be derived from the structure or features of action. Now it is not as though earlier work, in analytic philosophy, had failed to register the connection between action and practical rationality; in fact, practical reasoning was usually picked out as, roughly, reasoning directed toward (...) action. But for much of the twentieth century, attention moved quickly away from this initial delineation of the subject area, to the interplay of beliefs and desires within the mind (Humean theories, including their Davidsonian and Williamsian variants), or to procedures for checking that a plan of action was supported by sufficient yet consistent reasons (Kantian theories), or to the ultrarefined sensibilities of the practically intelligent reasoner (Aristotelian theories). The hallmark of the emerging family of treatments to be surveyed here is, first, the sustained attention paid to answering the question, "What does it take to be an action (at all)?", and second, the use made of a distinction between full-fledged action and its lesser relatives. (Characterizations and terminology vary, but often the less robust alternative is called "mere activity" or "mere behavior".) Very schematically, these arguments for a theory of practical reasoning try to show that reasons brought to bear on choice must have some particular logical form, if action is not to lapse into something less than that. (shrink)

Science and the Structure of Ethics Abraham Edel I. The Nature and Complexity of the Problem. Issues in the "Relation of Science and Ethics" Traditional ...

The Normative Structure of Responsibility deals with responsibility in legal, moral, and linguistic contexts. The book builds on conceptual analysis and data from everyday language, ethics, and the law in order to defend the thesis that responsibility is fundamentally normative, that is, it cannot be reduced to purely descriptive factors. The book is divided in three parts: the first part draws a conceptual map of various responsibility concepts, conceptions and conditions and their interaction with different kinds of rules; the (...) second part engages with arguments in favour of a descriptive understanding of responsibility based on ethics, neuroscience, and metaphysics and argues against it; the third part investigates the language of responsibility and its use in formal and informal contexts. (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special (...) role of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)