The 'Conscious Pilot' is a new model of the neural correlate of consciousness (NCC) consistent with the Orch OR model. The basic idea is that spatiotemporal envelopes of dendritic gamma synchrony move through the brain's neuronal networks. The movement is sideways to neurocomputational flow, occurring via dendritic dendritic gap junction electrical synapses. A conscious pilot moving around an airplane while it flies on auto pilot is used as a metaphor for dendritic synchrony moving through the brain's neurocomputational networks, conveying conscious (...) experience and choice to otherwise non conscious cognitive modes. (shrink)

Change in scientific practice and its implications for the status of scientific claims, examined through an analysis of three episodes at a synchrotron laboratory. After World War II, particle physics became a dominant research discipline in American academia. At many universities, alumni of the Manhattan Project and of Los Alamos were granted resources to start programs of high-energy physics built around the promise of a new and more powerful particle accelerator, the synchrotron. The synchrotron was also a source (...) of very intense X-rays, useful for research in solid states physics and in biology. As synchrotron X-ray science grew, the experimental practice of protein crystallography, garnered funding, prestige, and acclaim. In Velvet Revolution at the Synchrotron, Park Doing examines the change in scientific practice at a synchrotron laboratory as biology rose to dominance over physics. He draws on his own observations and experiences at the Cornell University synchrotron, and considers the implications of that change for the status of scientific claims. Velvet Revolution at the Synchrotron is one of the few recent works in the sociology of science that engages specific scientific and technical claims through participant observation--recorded evocatively and engagingly--to address issues in the philosophy of science. Doing argues that bureaucratic change in science is neither "top-down" nor "bottom-up" but rather performed in and realized through recursively related forums of technical assertion and resistance. He considers the relationship of this change to the content of science, and the implications of this relationship for the project of laboratory studies begun in the late 1970s. (shrink)

As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them (...) by microscopic imaging, the different styles of reasoning involved, and the various theoretical, methodological, and axiological differences. I conclude by arguing that, except for the probe microscopes that are used, there is very little in common between the two cases. At the nanoscale, physics and molecular biology seem to meet in a non-unified way. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, (...) we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes (...) a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanics modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent. (shrink)

SynopsisThe response to physics and chemistry which characterized mid-nineteenth century physiology took two major directions. One, found most prominently among the German physiologists, developed explanatory models which had as their fundamental assumption the ultimate reducibility of all biological phenomena to the laws of physics and chemistry. The other, characteristic of the French school of physiology, recognized that physics and chemistry provided potent analytical tools for the exploration of physiological activities, but assumed in the construction of explanatory (...) models that the organism involved special levels of organization and that there must, in consequence, be special biological laws.The roots of this argument about concept formation in physiology are explored in the works of Theodor Schwann, Johannes Müller, François Magendie and Claude Bernard among others. (shrink)

Philosophers intent upon characterizing the difference between physics and biology often seize upon the purported fact that physical explanations conform more closely to the covering law model than biological explanations. Central to this purported difference is the role of laws of nature in the explanations of these two sciences. However, I argue that, although certain important differences between physics and biology can be highlighted by differences between physical and biological explanations, these differences are not differences in (...) the degree to which those explanations conform to the covering law model, which fits biology about as well as it does physics. (shrink)

For two reasons, physics occupies a preeminent position among the sciences. On the one hand, due to its recognized position as a fundamental science, and on the other hand, due to the characteristic of its obvious certainty of knowledge. For both reasons it is regarded as the paradigm of scientificity par excellence. With its focus on the issue of epistemic certainty, philosophy of science follows in the footsteps of classical epistemology, and this is also the basis of its 'judicial' (...) pretension vis-à-vis physics. Whereas physics is in a strong competitive relationship to philosophy and epistemology with respect to its position as a fundamental science - even on the subject of cognition, as the pretension of 'reductionism' shows. It is the thematic focus on epistemic certainty itself, however, that becomes the root of a profound epistemological misunderstanding of physics. The reason for this is twofold: first, the idea of epistemic certainty as a criterion of 'demarcation' between physics and metaphysics obscures the view of the much deeper heuristic differences between the two kinds of knowledge. The second, related, reason is that epistemology does not ask the question of the reason for the epistemic certainty of physics; instead, it sets itself the task of 'legitimating' physical knowledge, and this, crucially, with reference to the interpretation of the process of cognition. Thus, as a matter of course, all epistemological assumptions about this process – including the common descriptive understanding of knowledge and its ontological premises – flow into the interpretation of physics as a science. Consequently, this undertaking is not only doubtful from the ground up, because it presupposes for its meaningfulness nothing less than certainty of knowledge concerning (the interpretation of) the process of knowledge, thereby relying on mere convictions; moreover, by projecting the descriptive, 'metaphysical' concept of knowledge onto physics, it leads to unsolvable epistemological problems and corresponding resignative conclusions concerning the claim of knowledge of physics. In other words, epistemology itself builds, due to its basic assumptions, a major obstacle for an adequate understanding of physics. Physics' cross-object, deconstructive approach to knowledge implies a completely different, non-descriptive understanding of its concepts, with consequences that extend far beyond itself due to its status as a basic science. (shrink)

The general concept of information does not belong in the category of universal and inexorable physical laws but in the category of initial conditions and boundary conditions. Boundary conditions formed by local structures are often called constraints. Informational structures such as symbol vehicles are a special type of constraint. It should be clear that the concepts of initial conditions and constraints in physics make no sense outside the context of the law-based physical dynamics to which they apply. This is (...) also the case for the concept of information. -/- . (shrink)

In addition to its obvious successes within the kinetic theory the ideal gas law and the modeling assumptions associated with it have been used to treat phenomena in domains as diverse as economics and biology. One reason for this is that it is useful to model these systems using aggregates and statistical relationships. The issue I deal with here is the way R. A. Fisher used the model of an ideal gas as a methodological device for examining the causal role (...) of selection in producing variation in Mendelian populations. The model enabled him to create the kind of population where one could measure the effects of selection in a way that could not be done empirically. Consequently we are able to see how the model of an ideal gas was transformed into a biological model that functioned as an instrument for both investigating nature and developing a new theory of genetics. (shrink)

Exact definitions in physical and biological terms of the coefficients in Volterra's (1926, 1931) original competition equations are indispensable for the understanding of the system. In agreement with Volterra's own, but not quite sufficient specifications, it is tried in this paper to give more precise definitions of the parameters used by Volterra. This leads to some consequences; i.a. that there does not exist a principle of competitive exclusion. In order to allow for competitive exclusion — or for stabilization — (...) the Volterra equations need additional biophysical specifications and mathematical modifications. Some such modifications are proposed, for instance for aggressive interference as a function of population numbers. (shrink)

In the framework of materialism, the major attention is to find general organizational laws stimulated by physical sciences, ignoring the uniqueness of Life. The main goal of materialism is to reduce consciousness to natural processes, which in turn can be translated into the language of math, physics and chemistry. Following this approach, scientists have made several attempts to deny the living organism of its veracity as an immortal soul, in favor of genes, molecules, atoms and so on. However, advancement (...) in various fields of biology has repeatedly given rise to questions against such a denial and has supplied more and more evidence against the completely misleading ideological imposition that living entities are particular states of matter. In the recent past, however, the realization has arisen that cognitive nature of life at all levels has begun presenting significant challenges to the views of materialism in biology and has created a more receptive environment for the soul hypothesis. Therefore, instead of adjudicating different aprioristic claims, the development of an authentic theory of biology needs both proper scientific knowledge and the appropriate tools of philosophical analysis of life. In a recently published paper the first author of present essay made an attempt to highlight a few relevant developments supporting a sentient view of life in scientific research, which has caused a paradigm shift in our understanding of life and its origin [1]. The present essay highlights the uniqueness of biological systems that offers a considerable challenge to the mainstream materialism in biology and proposes the Vedāntic philosophical view as a viable alternative for development of a biological theory worthy of life. (shrink)

In classical physics, the world is considered as a matter-based reality, the arrangement of whose parts in time is uniquely determined by certain dynamic laws. By contrast, modern quantum physics reveals that matter is not composed of matter, but reality is merely potentiality. The world has a holistic structure, which is based on fundamental relations and not material objects, admitting more open, indeterministic developments. In this more flexible causal framework, inanimate and animate matter are not to be considered (...) as fundamentally different but as different order structures of the same immaterial entity. In a stable configuration, effectively all the uncertainties are statistically averaged out, thus the unique and deterministic behavior of ordinary inanimate matter is exhibited; whereas in the case of statically unstable but dynamically stable configurations, the “lively” features of the underlying quantum structure have a chance to surface to the mesocopic level and to be connected with what we observe as the phenomenon of life. This supposition can be more explicitly treated and clarified by identifying the electric dipole moment of biomolecules as the ordering parameter of the corresponding macroquantum system. This has important consequences for biology and medicine. In particular, it suggests the existence of a quantum-based “software,” essential perhaps for the logistics of biological processes, which are hidden behind the matter/energy-based “hardware” that alone is considered in the conventional approach. In medicine it opens an opportunity to build bridges between conventional medicine based essentially on the classical paradigm, and the various forms of complementary medicine, which have strong affinities with the new features of the modern holistic worldview. (shrink)

Full applicability of physics to human biology does not necessarily imply that one can uncover a comprehensive, algorithmic correlation between physical brain states and corresponding mental states. The argument takes into account that information processing is finite in principle in a finite world. Presumbly the brain-mind-relation cannot be resolved in all essential aspects, particularly when high degrees of abstraction or self-analytical processes are involved. Our conjecture plausibly unifies the universal validity of physics and a logical limitation of human (...) thought, and it does not regard consciousness -the most basic human experience - as a marginal phenomenon. (shrink)

Papers by Andreas Bartels, Ansgar Beckermann, Frédéric Bouchard, Thomas Breuer, Bruno Eckhardt, Bruce Glymour, Claus Kiefer, Roberta Millstein and Alexander Rosenberg.

We summarise the contributions to the discussion and the links between them. The complex relationship between the physical and biological sciences demonstrates three “axes of tension”: the role of simulation, the interplay between levels of explanation, and the generality of “laws”. We identify examples of true synergy between approaches that genuinely explore new research territory, and underscore the contemporary value of the type of discussions contained in this volume.

In this philosophical paper, we explore computational and biological analogies to address the fine-tuning problem in cosmology. We first clarify what it means for physical constants or initial conditions to be fine-tuned. We review important distinctions such as the dimensionless and dimensional physical constants, and the classification of constants proposed by Lévy-Leblond. Then we explore how two great analogies, computational and biological, can give new insights into our problem. This paper includes a preliminary study to examine the two (...) analogies. Importantly, analogies are both useful and fundamental cognitive tools, but can also be misused or misinterpreted. The idea that our universe might be modelled as a computational entity is analysed, and we discuss the distinction between physical laws and initial conditions using algorithmic information theory. Smolin introduced the theory of "cosmological natural selection" with a biological analogy in mind. We examine an extension of. (shrink)

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical (...) practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences. (shrink)

This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. (...) Quantitative scientists are joining biological departments and collaborations between physicists and biologists are particularly vigorous. This state of affairs raises a number of questions, such as: What are the circumstances under which physicists approach biological problems in systems biology? What kind of interdisciplinary challenges must be tackled? The paper suggests that, concerning physicists’ move to work on biological systems, there are common reasons to move, the transition must be understood in terms of degrees, physicists have a rationale for simplifying systems, and distinct conceptions of model and modeling strategies are recurrent. We identified problems regarding linguistic clarity and integration of epistemological aims. We conclude that cultural unconformities within the systems biology community have important consequences to the flow of scientific knowledge. (shrink)

This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. (...) Quantitative scientists are joining biological departments and collaborations between physicists and biologists are particularly vigorous. This state of affairs raises a number of questions, such as: What are the circumstances under which physicists approach biological problems in systems biology? What kind of interdisciplinary challenges must be tackled? The paper suggests that, concerning physicists’ move to work on biological systems, there are common reasons to move, the transition must be understood in terms of degrees, physicists have a rationale for simplifying systems, and distinct conceptions of model and modeling strategies are recurrent. We identified problems regarding linguistic clarity and integration of epistemological aims. We conclude that cultural unconformities within the systems biology community have important consequences to the flow of scientific knowledge. (shrink)

The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation (...) is realized is named the symbol-matter problem. (4) A necessary physical condition is that all informational vehicles are material boundary conditions or constraints acting on the lawful dynamics of local systems. It is useful to define a dependency hierarchy of information types: (1) syntactic information (i.e., communication theory), (2) heritable information acquired by variation and natural selection, (3) non-heritable learned or creative information, and (4) measured physical information in the context of natural laws. High information storage capacity is most reliably implemented by discrete linear sequences of non-dynamic vehicles, while the execution of information for control and construction is a non-holonomic dynamic process. The first epistemic cut occurs in self-replication. The first interpretation of base sequence information is by protein folding; the last interpretation of base sequence information is by natural selection. Evolution has evolved senses and nervous systems that acquire non-heritable information, and only very recently after billions of years, the competence for human language. Genetic and human languages are the only known complete general purpose languages. They have fundamental properties in common, but are entirely different in their acquisition, storage and interpretation. (shrink)

This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary skills. (...) Quantitative scientists are joining biological departments and collaborations between physicists and biologists are particularly vigorous. This state of affairs raises a number of questions, such as: What are the circumstances under which physicists approach biological problems in systems biology? What kind of interdisciplinary challenges must be tackled? The paper suggests that, concerning physicists’ move to work on biological systems, there are common reasons to move, the transition must be understood in terms of degrees, physicists have a rationale for simplifying systems, and distinct conceptions of model and modeling strategies are recurrent. We identified problems regarding linguistic clarity and integration of epistemological aims. We conclude that cultural unconformities within the systems biology community have important consequences to the flow of scientific knowledge. (shrink)

Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of (...) the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this talk is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupre has recently noted that there exists a ‘General Problem of Biological Individuality’ which relates to the issue of how one divides ‘massively integrated and interconnected’ systems into discrete components. In response Dupre advocates a form of ‘Promiscuous Realism’ that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupre and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology. (shrink)

Originally published in 1979. This reprints the revised and expanded edition of 1996. In this volume, physicists, biologists and chemists, who have been involved in some of the most exciting discoveries in modern scientific thought explore issues which have shaped modern physics and which hint at what may form the next scientific revolution. The major issues discussed are the understanding of time and space, quantum and relativity theories and recent attempts to unite them and related questions in theoretical biology.

The known facts of quantum physics and biology strongly suggest the following hypotheses: atoms and the fundamental particles have a rudimentary degree of consciousness, volition, or self-activity; the basic features of quantum mechanics are a result of this fact; the quantum mechanical wave properties of matter are actually the conscious properties of matter; and living organisms are a direct result of these properties of matter. These hypotheses are tested by using them to make detailed predictions of new facts, and (...) then by showing that the predictions can be verified. The hypotheses are used to predict successfully that the quantum wave properties of matter are strongly predominant in proteins, to explain the presence and relative abundance of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur in proteins, and to explain diffraction phenomena, the behavior of helium II, the exclusion principle, and causality and determinism in modern science, thus closely relating physics and biology. (shrink)