Chemistry and physics are two sciences that are hard to connect. Yet there is significant overlap in their aims, methods, and theoretical approaches. In this book, the reduction of chemistry to physics is defended from the viewpoint of a naturalised Nagelian reduction, which is based on a close reading of Nagel's original text. This naturalised notion of reduction is capable of characterising the inter-theory relationships between theories of chemistry and theories of physics. The reconsideration of reduction also (...) leads to a new characterisation of chemical theories. This book is primarily aimed at philosophers of chemistry and chemists with an interest in philosophy, but is also of interest to the general philosopher of science. (shrink)

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language.However, the basics of scientific knowledge changed dramatically within the (...) second half of the 20th century.Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. (shrink)

During the twentieth century, the mechanistic worldview came under attack mainly because of the rise of quantum mechanics but some of its basic characteristics survived and are still evident within current science in some form or other. Many scholars have produced interesting studies of such significant mechanistic trends within current physics and biology but very few have bothered to explore the effects of this worldview on current chemistry. This paper makes a contribution to fill this gap. It presents first (...) a brief historical overview of the mechanistic worldview and then examines the present situation within chemistry by referring to current studies in the philosophy of chemistry and determining which trends are still mechanistic in spirit and which are not. (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)

Building upon Nancy Cartwright's discussion of models in How the Laws of Physics Lie, this paper addresses solid state research in transition metal oxides. Historical analysis reveals that in this domain models function both as the culmination of phenomenology and the commencement of theoretical explanation. Those solid state chemists who concentrate on the description of phenomena pertinent to specific elements or compounds assess models according to different standards than those who seek explanation grounded in approximate applications of the Schroedinger equation. (...) Accurate accounts of scientific debate in this field must include both perspectives. (shrink)

Since the early nineteenth century a membrane or wall has been central to the cell’s identity as the elementary unit of life. Yet the literally and metaphorically marginal status of the cell membrane made it the site of clashes over the definition of life and the proper way to study it. In this article I show how the modern cell membrane was conceived of by analogy to the first “artificial cell,” invented in 1864 by the chemist Moritz Traube (1826–1894), and (...) reimagined by the plant physiologist Wilhelm Pfeffer (1845–1920) as a precision osmometer. Pfeffer’s artificial cell osmometer became the conceptual and empirical basis for the law of dilute solutions in physical chemistry, but his use of an artificial analogue to theorize the existence of the plasma membrane as distinct from the cell wall prompted debate over whether biology ought to be more closely unified with the physical sciences, or whether it must remain independent as the science of life. By examining how the histories of plant physiology and physical chemistry intertwined through the artificial cell, I argue that modern biology relocated vitality from protoplasmic living matter to nonliving chemical substances—or, in broader cultural terms, that the disenchantment of life was accompanied by the (re)enchantment of ordinary matter. (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)

The file on this site provides the slides for a lecture given in Hangzhou in May 2018, and the lecture itself is available at the URL beginning 'sms' in the set of links provided in connection with this item. -/- It is commonly assumed that regular physics underpins biology. Here it is proposed, in a synthesis of ideas by various authors, that in reality structures and mechanisms of a biological character underpin the world studied by physicists, in principle supplying detail (...) in the domain that according to regular physics is of an indeterminate character. In regular physics mathematical equations are primary, but this constraint leads to problems with reconciling theory and reality. Biology on the other hand typically does not characterise nature in quantitative terms, instead investigating in detail important complex interrelationships between parts, leading to an understanding of the systems concerned that is in some respects beyond that which prevails in regular physics. It makes contact with quantum physics in various ways, for example in that both involve interactions between observer and observed, an insight that explains what is special about processes involving observation, justifying in the quantum physics context the replacement of the unphysical many-worlds picture by one involving collapse. The link with biology furthermore clarifies Wheeler’s suggestion that a multiplicity of observations can lead to the ‘fabrication of form’, including the insight that this process depends on very specific ‘structures with power’ related to the 'semiotic scaffolding' of the application of sign theory to biology known as biosemiotics. -/- The observer-observed 'circle' of Wheeler and Yardley is a special case of a more general phenomenon, oppositional dynamics, related to the 'intra-action' of Barad's Agential Realism, involving cooperating systems such as mind and matter, abstract and concrete, observer and observed, that preserve their identities while interacting with one another in such a way as to act as a unit. A third system may also be involved, the mediating system of Peirce linking the two together. Such a situation of changing connections and separations may plausibly lead in the future to an understanding of how complex systems are able to evolve to produce 'life, the universe and everything'. -/- (Added 1 July 2018) The general structure proposed here as an alternative to a mathematics-based physics can be usefully characterised by relating it to different disciplines and the specialised concepts utilised therein. In theoretical physics, the test for the correctness of a theory typically involves numerical predictions, corresponding to which theories are expressed in terms of equations, that is to say assertions that two quantities have identical values. Equations have a lesser significance in biology which typically talks in terms of functional mechanisms, dependent for example on details of chemistry and concepts such as genes, natural selection, signals and geometrical or topologically motivated concepts such as the interconnections between systems and the unfolding of DNA. Biosemiotics adds to this the concept of signs and their interpretation, implying novel concepts such as semiotic scaffolding and the semiosphere, code duality, and appreciation of the different types of signs, including symbols and their capacity for abstraction and use in language systems. Circular Theory adds to this picture, as do the ideas of Barad, considerations such as the idea of oppositional dynamics. The proposals in this lecture can be regarded as the idea that concepts such as those deriving from biosemiotics have more general applicability than just conventional biology and may apply, in some circumstances, to nonlinear systems generally, including the domain new to science hypothesised to underlie the phenomena of present-day physics. -/- The task then has to be to restore the mathematical aspect presumed, in this picture, not to be fundamental as it is in conventional theory. Deacon has invoked a complex sequence of evolutionary steps to account for the emergence over time of human language systems, and correspondingly mathematical behaviour can be subsumed under the general evolutionary mechanisms of biosemiotics (cf. also the proposals of Davis and Hersh regarding the nature of mathematics), so that the mathematical behaviour of physical systems is consistent with the proposed scheme. In conclusion, it is suggested that theoretical physicists should cease expecting to find some universal mathematical ‘theory of everything’, and focus instead on understanding in more detail complex systems exhibiting behaviour of a biological character, extending existing understanding. This may in time provide a more fruitful understanding of the natural world than does the regular approach. The essential concepts have an observational basis from both biology and the little-known discipline of cymatics (a discipline concerned with the remarkable patterns that specific waveforms can give rise to), while again computer simulations also offer promise in providing insight into the complex behaviours involved in the above proposals. -/- References -/- Jesper Hoffmeyer, Semiotic Scaffolding of Living Systems. Commens, a Digital Companion to C. S. Peirce (on Commens web site). Terrence Deacon, The Symbolic Species, W.W. Norton & Co. Karen Barad, Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning, Duke University Press. Philip Davis and Reuben Hersh, The Mathematical Experience, Penguin. Ilexa Yardley, Circular Theory. (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)

Suppose one has a system, the infinite set of positive integers, P, and one wants to study the characteristics of a subset (or subsystem) of that system, the infinite subset of odd positives, O, relative to the overall system. In mathematics, this is done by pairing off each odd with a positive, using a function such as O=2P+1. This puts the odds in a one-to-one correspondence with the positives, thereby, showing that the subset of odds and the original set of (...) positives are the same size, or have the same cardinality. This counter-intuitive result ignores the “natural” relationship of one odd for every two positives in the sequence of positive integers, which would suggest that O is one-half the size of P. However, in the set of axioms that constitute mathematics, it is considered valid. Fair enough. In the physical universe (i.e., the starting system), though, relationships between entities matter. In biochemistry, if you start with an organism, say a rat, and you want to study its heart, you can do this by removing some heart cells and studying them in isolation in a cell culture system. But, the results often differ compared to what occurs in the intact animal because studying the isolated cultured cells ignores the relationships in the intact body between the cells, the rest of the heart tissue and the rest of the rat. In chemistry, if a copper atom were studied in isolation, it would never be known that copper atoms in bulk can conduct electricity because the atoms share their electrons. In physics, the relationships between inertial reference frames in relativity, and observer and observed in quantum physics can't be ignored. Relationships matter in the physical world, but the mathematics of infinite sets is still used to describe it. Does this matter? It seems to, at least in physics. Infinities cause numerous problems in theoretical physics such as non-renormalizability and problems in unifying quantum mehanics and general relativity . This suggests that the pairing off method and the mathematics of infinite sets based on it are analogous to a cell culture system or studying a copper atom in isolation if they are used in studying the physical universe because they ignore the inherent relationships between entities. In the real, physical world, the natural, inherent, relationships between entities can't be ignored. Said another way, the set of axioms that constitute abstract mathematics may be similar but not identical to the set of physical axioms by which the real, physical universe runs. This suggests that the results from abstract mathematics about infinities may not apply to or should be modified for use in physics. (shrink)

This book addresses a tightly knit cluster of questions in the philosophy of mind. There is the question: Are mental properties identical with physical properties? An affirmative answer would seem to secure the truth of physicalism regarding the mind, i.e., the belief that all mental phenomena obtain solely in virtue of physical phenomena. If the answer is negative, then the question arises: Can this solely in virtue of relation be understood as some kind of dependence short of identity? (...) And answering this requires answering two further questions. Exactly what sort of dependence on the physical does physicalism require, and what is needed for a property or phenomenon to qualify as physical? -/- It is argued that multiple realizability still provides irresistible proof (especially with the possibility of immaterial realizers) that mental properties are not identical with any properties of physics, chemistry, or biology. After refuting various attempts to formulate nonreductive physicalism with the notion of realization, a new definition of physicalism is offered. This definition shows how it could be that the mental depends solely on the physical even if mental properties are not identical with those of the natural sciences. Yet, it is also argued that the sort of psychophysical dependence described is robust enough that if it were to obtain, then in a plausible and robust sense of ‘physical’, mental properties would still qualify as physical properties. (shrink)

Distinctions in fundamentality between different levels of description are central to the viability of contemporary decoherence-based Everettian quantum mechanics (EQM). This approach to quantum theory characteristically combines a determinate fundamental reality (one universal wave function) with an indeterminate emergent reality (multiple decoherent worlds). In this chapter I explore how the Everettian appeal to fundamentality and emergence can be understood within existing metaphysical frameworks, identify grounding and concept fundamentality as promising theoretical tools, and use them to characterize a system of explanatory (...) levels (with associated laws of nature) for EQM. This Everettian level structure encompasses and extends the ‘classical’ levels structure. The ‘classical’ levels of physics, chemistry, biology, etc. are recovered, but they are emergent in character and potentially variable across Everett worlds. EQM invokes an additional fundamental level, not present in the classical levels picture, and a novel potential role for self-location in interlevel metaphysics. When given a modal realist interpretation, EQM also makes trouble for supervenience-based approaches to levels. (shrink)

Strong claims have been made for emergence as a new paradigm for understanding science, consciousness, and religion. Tracing the past history and current definitions of the concept, Clayton assesses the case for emergent phenomena in the natural world and their significance for philosophy and theology. Complex emergent phenomena require irreducible levels of explanation in physics, chemistry and biology. This pattern of emergence suggests a new approach to the problem of consciousness, which is neither reducible to brain states nor proof (...) of a mental substance or soul. Although emergence does not entail classical theism, it is compatible with a variety of religious positions. Clayton concludes with a defence of emergentist panentheism and a Christian constructive theology consistent with the new sciences of emergence. (shrink)

While the appeal of scientific materialism has been weakened by developments in theoretical physics, chemistry and biology, Pythagoreanism still attracts the allegiance of leading scientists and mathematicians. It is this doctrine that process philosophers must confront if they are to successfully defend their metaphysics. Peirce, Bergson and Whitehead were acutely aware of the challenge of Pythagoreanism, and attempted to circumvent it. The problem addressed by each of these thinkers was how to account for the success of mathematical physics if (...) the world consists of creative processes. In this paper I critically examine the nature of the challenge posed by Pythagoreanism to process philosophy and examine the efforts by process philosophers, particularly Whitehead, to overcome it, and offer some suggestions for advancing these efforts. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists (...) by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice. (shrink)

This paper examines a looming reproducibility crisis in the core of the hard sciences. Namely, it concentrates on molecular modeling and simulation (MMS), a family of methods that predict properties of substances through computing interactions on a molecular level and that is widely popular in physics, chemistry, materials science, and engineering. The paper argues that in order to make quantitative predictions, sophisticated models are needed which have to be evaluated with complex simulation procedures that amalgamate theoretical, technological, and social (...) factors – leading to problems with reproducibility. Thus, for methodological reasons, the predictive success causes a reproducibility problem. (shrink)

The five studies of this special section investigate the role of models and similar representational tools in interdisciplinarity. These studies were all written by philosophers of science, who focused on interdisciplinary episodes between disciplines and sub-disciplines ranging from physics, chemistry and biology to the computational sciences, sociology and economics. The reasons we present these divergent studies in a collective form are three. First, we want to establish model-exchange as a kind of interdisciplinary event. The five case studies, which are (...) summarized in Section 2 below, show the relevance of this kind. Arguing for the relative unity of these cases will, we hope, re-orient the current debate over interdisciplinarity so as to reflect more appropriately the importance of this kind. We discuss our view of the current state of the debate in Section 3. The evidence from these cases also helps us to develop a taxonomy of interdisciplinary model exchanges in Section 4da taxonomy, we would like to add, that might be useful for the discussion of interdisciplinary exchanges beyond the context of models and their transfer. The second reason for presenting these studies together is that they provide an important source of evidence for the philosophy of science. Over the last three decades, philosophy of science has increasingly differentiated into philosophies of various disciplines. This differentiation in our view has greatly increased our understanding of the scientific practices of the respective disciplines, including the epistemological and methodological standards and conventions on which these practices are based and by which they are evaluated. But it has also made it harder to compare these practices and standards across disciplines. The studies we present here are case studies of interdisciplinary exchange: they focus on the transfer, collaborative construction or parallel use of models and similar representational tools. They therefore provide a unique opportunity to investigate various disciplinary treatments of the same or at least similar representational tools. This allows the identification and comparison of different disciplinary practices and their underlying conventions as well as of the respective normative standards of their evaluation. By tracing the paths along which models travel between disciplines and research fields we can observe to which extent discipline-external practices associated with an adopted tool are retained or replaced by disciplineinternal practices. This generates invaluable information about both disciplinarity and interdisciplinarity. We develop this argument further in Section 5. The third reason for presenting these studies in collective form is that their philosophical analysis also has important normative implications for the notion of interdisciplinarity itself. Too often in the current (non-philosophical) discourse is interdisciplinarity cast as an exclusively integrative project: interdisciplinary exchange is often claimed to be successful only if the involved disciplines become mutually more integrated as a consequence of this process. In contrast to this, many of the cases presented here show that interdisciplinary exchange can be scientifically highly successful, even if at the end of the exchange disciplinary borders remain fully intact. Indeed, borders can be fruitfully crossed without any integration across these borders. Such considerations of divergence in scientific practices and tools offer arguments against a naïve plea for unitarian or non-pluralist versions of interdisciplinarity. Disciplinary divergences may have their justifications, and attempting exchanges that require the reduction of these divergences may consequently not be justified. We pursue this argument further in Section 6. (shrink)

Climatology is a paradigmatic complex systems science. Understanding the global climate involves tackling problems in physics, chemistry, economics, and many other disciplines. I argue that complex systems like the global climate are characterized by certain dynamical features that explain how those systems change over time. A complex system's dynamics are shaped by the interaction of many different components operating at many different temporal and spatial scales. Examining the multidisciplinary and holistic methods of climatology can help us better understand the (...) nature of complex systems in general. -/- Questions surrounding climate science can be divided into three rough categories: foundational, methodological, and evaluative questions. "How do we know that we can trust science?" is a paradigmatic foundational question (and a surprisingly difficult one to answer). Because the global climate is so complex, questions like "what makes a system complex?" also fall into this category. There are a number of existing definitions of `complexity,' and while all of them capture some aspects of what makes intuitively complex systems distinctive, none is entirely satisfactory. Most existing accounts of complexity have been developed to work with information-theoretic objects (signals, for instance) rather than the physical and social systems studied by scientists. -/- Dynamical complexity, a concept articulated in detail in the first third of the dissertation, is designed to bridge the gap between the mathematics of contemporary complexity theory (in particular the formalism of "effective complexity" developed by Gell-Mann and Lloyd [2003]) and a more general account of the structure of science generally. Dynamical complexity provides a physical interpretation of the formal tools of mathematical complexity theory, and thus can be used as a framework for thinking about general problems in the philosophy of science, including theories, explanation, and lawhood. -/- Methodological questions include questions about how climate science constructs its models, on what basis we trust those models, and how we might improve those models. In order to answer questions about climate modeling, it's important to understand what climate models look like and how they are constructed. Climate model families are significantly more diverse than are the model families of most other sciences (even sciences that study other complex systems). Existing climate models range from basic models that can be solved on paper to staggeringly complicated models that can only be analyzed using the most advanced supercomputers in the world. I introduce some of the central concepts in climatology by demonstrating how one of the most basic climate models might be constructed. I begin with the assumption that the Earth is a simple featureless blackbody which receives energy from the sun and releases it into space, and show how to model that assumption formally. I then gradually add other factors (e.g. albedo and the greenhouse effect) to the model, and show how each addition brings the model's prediction closer to agreement with observation. After constructing this basic model, I describe the so-called "complexity hierarchy" of the rest of climate models, and argue that the sense of "complexity" used in the climate modeling community is related to dynamical complexity. -/- With a clear understanding of the basics of climate modeling in hand, I then argue that foundational issues discussed early in the dissertation suggest that computation plays an irrevocably central role in climate modeling. "Science by simulation" is essential given the complexity of the global climate, but features of the climate system--the presence of non-linearities, feedback loops, and chaotic dynamics--put principled limits on the effectiveness of computational models. This tension is at the root of the staggering pluralism of the climate model hierarchy, and suggests that such pluralism is here to stay, rather than an artifact of our ignorance. Rather than attempting to converge on a single "best fit" climate model, we ought to embrace the diversity of climate models, and view each as a specialized tool designed to predict and explain a rather narrow range of phenomena. Understanding the climate system as a whole requires examining a number of different models, and correlating their outputs. This is the most significant methodological challenge of climatology. -/- Climatology's role contemporary political discourse raises an unusually high number of evaluative questions for a physical science. The two leading approaches to crafting policy surrounding climate change center on mitigation (i.e. stopping the changes from occurring) and adaptation (making post hoc changes to ameliorate the harm caused by those changes). Crafting an effective socio-political response to the threat of anthropogenic climate change, however, requires us to integrate multiple perspectives and values: the proper response will be just as diverse and pluralistic as the climate models themselves, and will incorporate aspects of both approaches. I conclude by offering some concrete recommendations about how to integrate this value pluralism into our socio-political decision making framework. (shrink)

Considers that in ecosystem, landscape and global ecology, an energetics reading of ecological systems is an expression of a cybernetic, systemic and holistic approach. In ecosystem ecology, the Odumian paradigm emphasizes the concept of emergence, but it has not been accompanied by the creation of a method that fully respects the complexity of the objects studied. In landscape ecology, although the emergentist, multi-level, triadic methodology of J.K. Feibleman and D.T. Campbell has gained acceptance, the importance of emergent properties is still (...) undervalued. In global ecology, the Gaia hypothesis is an expression of an organicist metaphor, while the emergentist terminology used is incongruent with the underlying physicalist cybernetics. More generally, an analytico-additional methodology and the reduction of the properties of ecosystems to the laws of physical chemistry render purely formal any assertion about the emergentist and holistic nature of the ecological systems studied. (shrink)

Scientific progress is a hot topic in the philosophy of science. However, as yet we lack a comprehensive philosophical examination of scientific progress. First, the recent debate pays too much attention to the epistemic approach and the semantic approach. Shan’s new functional approach and Dellsén’s noetic approach are still insufficiently assessed. Second, there is little in-depth analysis of the progress in the history of the sciences. Third, many related philosophical issues are still to be explored. For example, what are the (...) implications of scientific progress for the scientific realism/antirealism debate? Is the incommensurability thesis a challenge to scientific progress? What role does aesthetic values play in scientific progress? Does idealisation impede scientific progress? This book fills this gap. It offers a new assessment of the four main approaches to scientific progress (Part I). It also features eight historical case studies to investigate the notion of progress in different disciplines: physics, chemistry, evolutionary biology, seismology, psychology, sociology, economics, and medicine respectively (Part II). It discusses some issues related to scientific progress: scientific realism, incommensurability, values in science, idealisation, scientific speculation, interdisciplinarity, and scientific perspectivalism (Part III). (shrink)

This paper investigates a well-known case of simultaneous discovery in twentieth-century chemistry, the origins of the concept of hybridisation, in the light of Kuhn's insights. There has been no ambiguity as to who discovered this concept, when it was "rst in print, and how important it was. The full-#edged form of the concept was published in 1931 independently by two American scientists John C. Slater (1900}1976) and Linus Pauling (1901}1994), although both of them had made their ideas public earlier: (...) Slater at the American Physical Society meetings in 1930, and Pauling in the Proceedings of the National Academy of Sciences in 1928. Slater and Pauling both argued for the necessity of using an s orbital as well as three p orbitals in the carbon atom in order to explain carbon's four valences and the tetrahedral structure of methane. The metaphor &hybridisation' for denoting this mix of s and p orbitals was "rst used by Robert S. Mulliken and J. H. Van Vleck before gaining currency with the scienti"c community around 1935.2 The concept of hybridisation was indeed indispensable for extending the quantum-mechanical interpretation of the chemical bond as an electron pairing from diatomic molecules to polyatomic ones. To be sure, the emergence of hybridisation attests to scientists' growing interest in exploring the borderland between physics and chemistry, a trend that led to the creation of physical chemistry in the late nineteenth century and of chemical physics and quantum chemistry in the 1920s and 30s. Slater and Pauling themselves experienced and on many occasions talked about the fruitfulness of interdisciplinary research; and historians have legitimately illuminated their works by examining them in this broad context.3 Yet the careful analysis of their research notes and published papers reveals that Slater and Pauling were working in quite disparate disciplinary traditions, with di!erent approaches, for di!erent audiences, and towards di!erent goals. The aim of this paper is to explore their di!erent routes to a common destination*hybridisation*and thereby to explicate tensions existing between physics and chemistry amidst the institutional and conceptual overlapping of the two disciplines. (shrink)

Since 2004, it has been mandated by law that all Danish undergraduate university programmes have to include a compulsory course on the philosophy of science for that particular program. At the Faculty of Science and Technology, Aarhus University, the responsibility for designing and running such courses were given to the Centre for Science Studies, where a series of courses were developed aiming at the various bachelor educations of the Faculty. Since 2005, the Centre has been running a dozen different courses (...) ranging from mathematics, computer science, physics, chemistry over medical chemistry, biology, molecular biology to sports science, geology, molecular medicine, nano science, and engineering. -/- We have adopted a teaching philosophy of using historical and contemporary case studies to anchor broader philosophical discussions in the particular subject discipline under consideration. Thus, the courses are tailored to the interests of the students of the particular programme whilst aiming for broader and important philosophical themes as well as addressing the specific mandated requirements to integrate philosophy, some introductory ethics, and some institutional history. These are multiple and diverse purposes which cannot be met except by compromise. -/- In this short presentation, we discuss our ambitions for using case studies to discuss philosophical issues and the relation between the specific philosophical discussions in the disciplines and the broader themes of philosophy of science. We give examples of the cases chosen to discuss various issues of scientific knowledge, the role of experiments, the relations between mathematics and science, and the issues of responsibility and trust in scientific results. Finally, we address the issue of how and why science students can be interested in and benefit from mandatory courses in the philosophy of their subject. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, (...) mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

There is a common argument form in the metaphysics of natural laws literature: a theory of natural law is attacked by offering a claim L as a law of scientific field F (physics, chemistry, biology, etc.), and from this law metaphysical implications contrary to the theory are drawn. Quite often however, L would not be regarded as a law by a scientist of F. Roberts' "measurability account of laws" offers a new and interesting way to more reliably identify the (...) laws of a field F and to eliminate the L that are not laws of F from the literature. (shrink)

Throughout history, a relatively small number of individuals have made a profound and lasting impact on science and society. Despite long-standing, multi-disciplinary interests in understanding careers of elite scientists, there have been limited attempts for a quantitative, career-level analysis. Here, we leverage a comprehensive dataset we assembled, allowing us to trace the entire career histories of nearly all Nobel laureates in physics, chemistry, and physiology or medicine over the past century. We find that, although Nobel laureates were energetic producers (...) from the outset, producing works that garner unusually high impact, their careers before winning the prize follow relatively similar patterns as ordinary scientists, being characterized by hot streaks and increasing reliance on collaborations. We also uncovered notable variations along their careers, often associated with the Nobel prize, including shifting coauthorship structure in the prize-winning work, and a significant but temporary dip in the impact of work they produce after winning the Nobel. Together, these results document quantitative patterns governing the careers of scientific elites, offering an empirical basis for a deeper understanding of the hallmarks of exceptional careers in science. (shrink)

Marie Curie is the first scientist woman awarded the Nobel Prize in Physics (1903) and another in Chemistry (1911). Her life and her work summarize the tenacity, effort and passion for knowing aspects related to the reality of a new physical-chemical phenomenon: radioactivity. In this semblance, in addition to the scientific aspect, the human aspect that accompanies and sometimes overshadows the lives of great men is shown.

In Metaphysics A.4, Aristotle provides crucial information about fundamental aspects of the chemistry and microphysics of the atomic theory of Leucippus and Democritus of Abdera. Besides the plenum and the void, which he identifies as the elements of the atomic theory, he presents what he himself names as differences. These fundamental differences are named so because they ought to be responsible for the emergence of all other differences in the physical world, and especially the ones that hit our (...) senses. Aristotle provides a list of three differences both in what is recognized as autochthonous terminology from Leucippus and Democritus, and in a translation to terms apparently more intelligible to Aristotelian listeners. Among those differences there is one in particular that is harder to comprehend than the other ones: rhysmos. Aristotle’s translation of rhysmos into schēma has led most interpreters to acknowledge that it referred solely to atoms individually, while the other two differences would refer to relations between atoms. In this paper, I want to propose an interpretation in which rhysmos actually refers to several aspects of the chemistry and microphysics of the atomic theory. (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)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence of molecular structure (...) cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

Are physics and chemistry sufficient to provide a basis for a theory of everything? The worldview of materialist naturalism that forms the foundation of NeoDarwinian evolution, Big Bang cosmogony, and molecular biology in general has been subjected to challenge for its monumental failure to explain life, consciousness and other mind-related aspects of reality. Two recent books, Why Evolution is True by Jerry Coyne [1], and Thomas Nagel’s Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature Is Almost Certainly (...) False [2], both authors being atheists, reflect the deep rift we find, not only in the religious conflict between creation and evolution, but in the fundamental awareness we all have that we are more than just molecular matter. This common sense understanding can only escape the notice of a particularly shallow ideological dogmatism that insists it has all the answers based solely on its unprecedented technological success. Science has come to represent two different things: (a) a body of knowledge, and (b) a method for acquiring knowledge. The problem arises when it is forgotten that there is no independent body of knowledge for science apart from its method – it keeps changing according to the results of the latest findings of the scientific method. The method is not to be abandoned because of those who would like to replace it with a fixed body of knowledge, which then becomes ideology. If biogenesis is hypothesized as the law of Nature, and we observe that life comes from pre-existing life in all our experience, while the hypothesis of abiogenesis, that life comes from matter, is never backed by any observation, then according to the scientific method—which one is to be accepted as true scientific knowledge? Obviously, the one backed by empirical observation. It is necessary to get free of ideological “knowledge,” and return to science as a method for gathering evidence that may lead to conclusions beyond the material naturalist view of Nature, and conforms to what we experience and rationally understand about the world in which we live. (shrink)

Compared to its sister disciplines—philosophy of physics and philosophy of biology—philosophy of chemistry remains a relatively young field of philosophical endeavour. Having originated in the late...

In learning chemistry at the entry level, many learners labor under misconceptions about the subject matter that are so fundamental that they are typically never addressed. A fundamental misconception in chemistry appears to arise from an adding of existing phenomenal concepts to newly-acquired chemical concepts, so that beginning learners think of chemical entities as themselves having the very same ‘macro’ properties that we observe through the senses. Those who teach or practice chemistry never acquire these misconceptions because (...) they were able to naturally pick up the nature of the subject to begin with. But as a result, they remain unaware of the foundational assumptions and understanding that they operate with and that many beginning learners persistently lack. Thus, a systematic picture of the workings of chemical theory as they relate to observable phenomena needs to be elucidated so that the attention of chemical educators is drawn to the fundamental understanding of the subject that they already possess and that beginning learners of chemistry lack, so that beginning learners can be given the opportunity to gain an understanding of how chemical explanations are in general related to observable phenomena. The ‘layered’ way in which chemical and physical entities are related to each other within chemical theory can also be clarified in this way. To afford this picture, the philosophical concepts of supervenience and emergence are explained and applied to chemistry, as philosophers of chemistry have already done. The result provides a model for teaching chemistry that, if consistently applied, has the potential to greatly enhance fundamental understanding of the subject matter. (shrink)

This inaugural lecture, delivered on 17 November 2021 at the University of Neuchâtel, addresses the question: Are material objects analyzable into more basic constituents and, if so, what are they? It might appear that this question is more appropriately settled by empirical means as utilized in the natural sciences. For example, we learn from physics and chemistry that water is composed of H2O-molecules and that hydrogen and oxygen atoms themselves are composed of smaller parts, such as protons, which are (...) in turn composed of yet smaller parts, such as quarks, and so on. While the question at the center of this lecture might thus appear to fall more appropriately into the empirical domain of natural science, I argue that metaphysics in fact has an important role to play in determining how best to answer the question before us. More concretely, I propose that the Aristotelian doctrine of hylomorphism, when appropriately interpreted, provides the best metaphysical answer to the question of whether and how material objects are analyzable into more basic constituents. Hylomorphism holds that those entities to which this doctrine applies are, in some sense, compounds of matter (“hylē”) and form (“morphē” or “eidos”). Thus, the title of this lecture, “Form, Matter, Substance”, refers to the claim that lies at the center of the doctrine of hylomorphism, as applied to the domain of material objects, namely that sensible substances are the result of combining matter and form in the right sort of way; or, for short, “form + matter = substance”. I begin in Section II by providing some historical background which brings out Aristotle’s motivations for proposing the doctrine of hylomorphism in the context of his analysis of change. Section III turns to some of the main features of the contemporary hylomorphic theory I have defended especially in Koslicki (2008) and Koslicki (2018). Section IV discusses some challenging questions concerning artifacts which arise for both hylomorphic and other approaches to the metaphysics of concrete particular objects. Section V concludes by summarizing why, as contemporary metaphysicians, we should prefer a hylomorphic theory over its competitors as an analysis of concrete particular objects that is compatible with our current scientific understanding of the world. (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)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize (...) some fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)

The exploration of chemical periodicity over the past 250 years led to the development of the Periodic System of Elements and demonstrates the value of vague ideas that ignored early scientific anomalies and instead allowed for extended periods of normal science where new methodologies and concepts are developed. The basic chemical element provides this exploration with direction and explanation and has shown to be a central and historically adaptable concept for a theory of matter far from the reductionist frontier. This (...) is explored in the histories of Prout’s hypothesis, Döbereiner Triads, element inversions necessary when ordering chemical elements by atomic weights, and van den Broeck’s ad-hoc proposal to switch to nuclear charges instead. The development of more accurate methods to determine atomic weights, Rayleigh and Ramsey’s gas separation and analytical techniques, Moseley’s X-ray spectroscopy to identify chemical elements, and more recent accelerator-based cold fusion methods to create new elements at the end of the Periodic Table point to the importance of methodological development complementing conceptual advances. I propose to frame the crossover from physics to chemistry not as a loss of accuracy and precision but as an increased application of vague concepts such as similarity which permit classification. This approach provides epistemic flexibility to adapt to scientific anomalies and the continued growth of chemical compound space and rejects the Procrustean philosophy of reductionist physics. Furthermore, it establishes chemistry with its explanatory and operational autonomy epitomized by the periodic system of elements as a gateway to other experimental sciences. (shrink)

Ground offers the hope of vindicating and illuminating an classic philosophical idea: the layered conception, according to which reality is structured by relations of dependence, with physical phenomena on the bottom, upon which chemistry, then biology, and psychology reside. However, ground can only make good on this promise if it is appropriately formally behaved. The paradigm of good formal behavior can be found in the currently dominant grounding orthodoxy, which holds that ground is transitive, antisymmetric, irreflexive, and foundational. (...) However, heretics have recently challenged the orthodoxy. In this paper, I examine ground’s ability to vindicate the layered conception upon various relaxations of the orthodox assumptions. I argue that highly unorthodox views of ground can still vindicate the layered conception and that, in some ways, the heretical views enable ground to better serve as a guide to reality’s layering than do orthodox views of ground. (shrink)

Effective Field Theory (EFT) is the successful paradigm underlying modern theoretical physics, including the "Core Theory" of the Standard Model of particle physics plus Einstein's general relativity. I will argue that EFT grants us a unique insight: each EFT model comes with a built-in specification of its domain of applicability. Hence, once a model is tested within some domain (of energies and interaction strengths), we can be confident that it will continue to be accurate within that domain. Currently, the Core (...) Theory has been tested in regimes that include all of the energy scales relevant to the physics of everyday life (biology, chemistry, technology, etc.). Therefore, we have reason to be confident that the laws of physics underlying the phenomena of everyday life are completely known. (shrink)

The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim (...) that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity. (shrink)

Jerrold J. Katz often explained his semantic theory by way of an analogy with physical atomism and an attendant analogy with chemistry. In this chapter, I track the origin and uses of these analogies by Katz, both in explaining and defending his decompositional semantic theory, through the various phases of his work throughout his career.

When philosophers discuss the possibility of machines making scientific discoveries, they typically focus on discoveries in physics, biology, chemistry and mathematics. Observing the rapid increase of computer-use in science, however, it becomes natural to ask whether there are any scientific domains out of reach for machine discovery. For example, could machines also make discoveries in qualitative social science? Is there something about humans that makes us uniquely suited to studying humans? Is there something about machines that would bar them (...) from such activity? A close look at the methodology of interpretive social science reveals several abilities necessary to make a social scientific discovery, and one capacity necessary to possess any of them is imagination. For machines to make discoveries in social science, therefore, they must possess imagination algorithms. (shrink)

In this dissertation I achieve the following: (1) I present motivating criteria for a general comprehensive theory of scientific explanation. I review historical approaches to modeling explanation in light of these criteria. (2) I present New Mechanist Explanation ("NME") as the leading candidate for a contemporary, complete theory of scientific explanation. (3) I present constraints on the applicability of New Mechanism in modeling biology, chemistry, and physics. I argue for the unsuitability of NME as a candidate for a general (...) theory of explanation due to its significant omissions of explanatory content and subsequent incompleteness. (4) I present arguments for the indispensable explanatory power of mathematics in science, noting that much of NME's failures are owed to its poor integration of mathematical explanation as applied to science. (5) I propose a Rational-Relational theory of explanation(“RRE”). I present RRE in detail and demonstrate it as a true working general theory of explanation which best meets the motivating criteria presented in (1). I disambiguate RRE from structural explanation ("SE"). I show that historical models of explanation, including the deductive nomological (DNE) model, statistical relevance ("SRE") model, structural model (SE) and unification model ("UE") may be successfully treated as sub-classes of explanation within the scope of RRE. I provide a rubric for selecting amongst sub-theories of explanation under RRE in the purpose of highlighting particular features of relational explanations. (6) In conclusion, I argue that philosophers of science should move forward using RRE as a general model of scientific explanation as a working alternative to the incomplete model of NME. (shrink)

This article’s purpose is to defend the depiction of ordinary-sized physical objects as mereological aggregates (MAs), to clarify what the ontology of an MA is, and to show why mereological essentialism (ME) applies to MAs that seem to be ubiquitous if we are to adopt what Frank Jackson calls “Serious Metaphysics” and refuse to broaden our ontology beyond what is (allegedly) bequeathed to us by physics and chemistry. To accomplish this goal, first, I clarify certain background issues that (...) inform what follows and I identify certain constraints that relate to the contemporary ambivalence towards ME. Second, I present a primer on Husserlian mereology that provides a superior account of parts and wholes than the inadequate approach identified in the previous section. Third, I will offer a defense of ME as the correct approach to providing an ontological account of MAs. Finally, I will evaluate two defeaters against my thesis. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...) employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent observations (...) show that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative. (shrink)

Arthur Clark and Michael Kube–McDowell (“The Triger”, 2000) suggested the sci-fi idea about the direct transformation from a chemical substance to another by the action of a newly physical, “Trigger” field. Karl Brohier, a Nobel Prize winner, who is a dramatic persona in the novel, elaborates a new theory, re-reading and re-writing Pauling’s “The Nature of the Chemical Bond”; according to Brohier: “Information organizes and differentiates energy. It regularizes and stabilizes matter. Information propagates through matter-energy and mediates the interactions (...) of matter-energy.” Dr Horton, his collaborator in the novel replies: “If the universe consists of energy and information, then the Trigger somehow alters the information envelope of certain substances –“. “Alters it, scrambles it, overwhelms it, destabilizes it” Brohier adds. There is a scientific debate whether or how far chemistry is fundamentally reducible to quantum mechanics. Nevertheless, the fact that many essential chemical properties and reactions are at least partly representable in terms of quantum mechanics is doubtless. For the quantum mechanics itself has been reformulated as a theory of a special kind of information, quantum information, chemistry might be in turn interpreted in the same terms. Wave function, the fundamental concept of quantum mechanics, can be equivalently defined as a series of qubits, eventually infinite. A qubit, being defined as the normed superposition of the two orthogonal subspaces of the complex Hilbert space, can be interpreted as a generalization of the standard bit of information as to infinite sets or series. All “forces” in the Standard model, which are furthermore essential for chemical transformations, are groups [U(1),SU(2),SU(3)] of the transformations of the complex Hilbert space and thus, of series of qubits. One can suggest that any chemical substances and changes are fundamentally representable as quantum information and its transformations. If entanglement is interpreted as a physical field, though any group above seems to be unattachable to it, it might be identified as the “Triger field”. It might cause a direct transformation of any chemical substance by from a remote distance. Is this possible in principle? (shrink)

The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of (...) its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

In his book, History as a Science and the System of the Sciences, Thomas Seebohm articulates the view that history can serve to mediate between the sciences of explanation and the sciences of interpretation, that is, between the natural sciences and the human sciences. Among other things, Seebohm analyzes history from a phenomenological perspective to reveal the material foundations of the historical human sciences in the lifeworld. As a preliminary to his analyses, Seebohm examines the formal and material presuppositions of (...) phenomenological epistemology, as well as the emergence of the human sciences and the traditional distinctions and divisions that are made between the natural and the human sciences. -/- As part of this examination, Seebohm devotes a section to discussing Husserl’s formal mereology because he understands that a reflective analysis of the foundations of the historical sciences requires a reflective analysis of the objects of the historical sciences, that is, of concrete organic wholes (i.e., social groups) and of their parts. Seebohm concludes that Husserl’s mereological ontology needs to be altered with regard to the historical sciences because the relations between organic wholes and their parts are not summative relations. Seebohm’s conclusion is relevant for the issue of the reducibility of organic wholes such as social groups to their parts and for the issue of the reducibility of the historical sciences to the lower-order sciences, that is, to the sciences concerned with lower-order ontologies. -/- In this paper, I propose to extend Seebohm’s conclusion to the ontology of chemical wholes as object of quantum chemistry and to argue that Husserl’s formal mereology is descriptively inadequate for this regional ontology as well. This may seem surprising at first, since the objects studied by quantum chemists are not organic wholes. However, my discussion of atoms and molecules as they are understood in quantum chemistry will show that Husserl’s classical summative and extensional mereology does not accurately capture the relations between chemical wholes and their parts. This conclusion is relevant for the question of the reducibility of chemical wholes to their parts and of the reducibility of chemistry to physics, issues that have been of central importance within the philosophy of chemistry for the past several decades. (shrink)