This fine collection of essays by a leading philosopher of science presents a defence of integrative pluralism as the best description for the complexity of scientific inquiry today. The tendency of some scientists to unify science by reducing all theories to a few fundamental laws of the most basic particles that populate our universe is ill-suited to the biological sciences, which study multi-component, multi-level, evolved complex systems. This integrative pluralism is the most efficient way to understand the different (...) and complex processes - historical and interactive - that generate biological phenomena. This book will be of interest to students and professionals in the philosophy of science. (shrink)

Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate. The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms (...) are changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless - in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches. (shrink)

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry. The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study (...) biological problems. In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo. The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology. (shrink)

The complexity of intracellular molecular pathways can be simplified by the use of Network Biology that breaks down the intricacy of biological processes into components and interactions among them. In the paper we show that any complex interactome, that is, a biological network representing protein-protein, protein-DNA and DNA-RNA interactions, can be decomposed into a conjunction of logical theorems expressed in terms of Zsyntax, a formal language which allows representing biological pathways. This result, illustrated with the case (...) study of melanoma network, opens the possibility for a computable model of the cell expressed in a logical language and shows how a formal way of intending philosophy can be useful to cope with the complexity of the biological world. (shrink)

The complexity that we observe in nature can often be explained in terms of cooperative behavior. For example, the major transitions of evolution required the emergence of cooperation among the lower-level units of selection, which led to specialization through division-of-labor ultimately resulting in spontaneous order. There are two aspects to address explaining how such cooperation is sustained: how free-riders are prevented from free-riding on the benefits of cooperative tasks, and just as importantly, how those social benefits arise. We review (...) these problems from an economic perspective, and highlight how ideas from economics can help us to better understand how the benefits of social interactions arise, how they are sustained, and how they affect the underlying social dilemmas. (shrink)

In this paper I discuss how, given the complexity of biological systems, reliance on theoretical models in the development and testing of biological theories leads to an uncomfortable form of anti-realism. I locate the source of this discomfort in the uniqueness and hence diversity of biological phenomena, in contrast with the simplicity and uniformity of the subject matter of physics. I have argued elsewhere that the use of theoretical models creates an unresolvable tension between the explanatory (...) strength and predictive power of hypotheses, and I review this argument again here. My discussion parallels that of Nancy Cartwright, who claims that the use of ceteris paribus laws in physics creates an antagonism between truth and explanation that requires theoretical models to figure centrally in scientific explanation, thereby precluding realism. I argue instead that in biology it is the use of theoretical models that creates this conflict, and conclude that adequate biological explanation cannot rely on the modeling approach alone. Finally, I claim that if we accept the semantic view of theories, which makes theoretical models an integral part of our conception of theories, we must accept anti-realism as well. (shrink)

The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples (...) span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity. (shrink)

In The Evolution of biological complexity, Christoph Adami, Charles Ofria and Travis C. Collier analysed the relationship between evolution by natural selection and the entropy of the genome. There are some similarities between their paper and my own analysis of.

The article analyzes aspects of the relationship between evolution and biological complexity and the attempts made by scholars and theologians to interpret it within the limits of reductionist scientism or theism. For this purpose, firstly, attention is focused on explaining the meaning of the concept of "evolution" and its historical and philosophical transformation in the context of the idea of complexity. Secondly, the notion of complexity in theology is used as evidence to support teleology. This approach (...) is criticized by some scholars who consider evolution as a random prosses. They give it the status of a universal metaphysical assumption in evolution. The scientists and theologists both formulate metaphysical assumptions differently to interpret evolution. (shrink)

1 The Zero-Force Evolutionary Law 2 Randomness, Hierarchy, and Constraint 3 Diversity 4 Complexity 5 Evidence, Predictions, and Tests 6 Philosophical Foundations 7 Implications.

In this article an epistemological framework is proposed in order to integrate the emergentist thought with systemic studies on biological autonomy, which are focused on the role of organization. Particular attention will be paid to the role of the observer’s activity, especially: (a) the different operations he performs in order to identify the pertinent elements at each descriptive level, and (b) the relationships between the different models he builds from them. According to the approach sustained here, organization will be (...) considered as the result of a specific operation of identification of the relational properties of the functional components of a system, which do not necessarily coincide with the intrinsic properties of its structural constituents. Also, an epistemological notion of emergence—that of “complex emergence”—will be introduced, which can be defined as the insufficiency, even in principle, of a single descriptive modality to provide a complete description of certain classes of systems. This integrative framework will allow us to deal with two issues in biological and emergentist studies: (1) distinguishing the autonomy proper of living systems from some physical processes like those of structural stability and pattern generation, and (2) reconsidering the notion of downward causation not as a direct or indirect influence of the whole on its parts, but instead as an epistemological problem of interaction between descriptive domains in which the concept of organization proposed and the observational operations related to it play a crucial role. (shrink)

Ecologist Richard Levins argues population biologists must trade‐off the generality, realism, and precision of their models since biological systems are complex and our limitations are severe. Steven Orzack and Elliott Sober argue that there are cases where these model properties cannot be varied independently of one another. If this is correct, then Levins's thesis that there is a necessary trade‐off between generality, precision, and realism in mathematical models in biology is false. I argue that Orzack and Sober's arguments fail (...) since Levins's thesis concerns the pragmatic features of model building not just the formal properties of models. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools (...) to handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

My paper draws on examples from molecular biology, the details of which I have developed elsewhere (Rheinberger 1992, 1993, 1995, 1997). Here, I can give only a brief outline of my argument. Reduction of complexity is a prerequisite for experimental research. To make sense of the universe of living beings, the modern biologist is bound to divide his world into fragments in which parameters can be defined, quantities measured, qualities identified. Such is the nature of any "experimental system." Ontic (...) complexity has to be reduced in order to make experimental research possible. The complexity of the research object, however, is epistemically retained in the rich context of an experimental landscape, where the eruption of "volcanic systems" can change the scenery dramatically as the result of particular, unprecedented findings. (shrink)

"Both superb and essential... Succi, with clarity and wit, takes us from quarks and Boltzmann to soft matter - precisely the frontier of physics and life." Stuart Kauffman, MacArthur Fellow, Fellow of the Royal Society of Canada, Gold Medal Accademia Lincea We live in a world of utmost complexity, outside and within us. There are thousand of billions of billions of stars out there in the Universe, a hundred times more molecules in a glass of water, and another hundred (...) times more in our body, all working in sync to keep us alive and well. At face value, such numbers spell certain doom for our ability to make any sense at all of the world around and within us. And yet, they don't. Why, and how - this book endeavours to provide an answer to these questions with specific reference to a selected window of the physics-biology interface. The story unfolds over four main Parts. Part I provides an introduction to the main organizational principles which govern the functioning of complex systems in general, such as nonlinearity, nonlocality and ultra-dimensions. Part II deals with thermodynamics, the science of change, starting with its historical foundations laid down in the 19th century, and then moving on to its modern and still open developments in connection with biology and cosmology. Part III deals with the main character of this book, free energy, and the wondrous scenarios opened up by its merger with the modern tools of statistical physics. It also describes the basic facts about soft matter, the state of matter most relevant to biological organisms. Finally, Part IV discusses the connection between time and complexity, and its profound implications on the human condition, i.e. the one-sided nature of time and the awareness of human mortality. It concludes with a few personal considerations about the special place of emotions and humility in science. (shrink)

Michael Nair-Collins and Franklin Miller are right to emphasise that, in order to deliberate responsibly about ethical and legal questions related to brain death and organ donation, it is crucial to answer the question of whether or not ‘brain death’i does indeed mark the biological death of the organism. Nonetheless, I disagree with the authors’ conclusion that brain death does not indicate the death of the human organism. Death can never be defined in merely biological terms, because any (...) biological conception of death relies on metaphysical presuppositions regarding what it means to be an ‘organism as a whole’, rather than an aggregate of cells and tissues. Death is a change in substance —that is, a change from one type of entity to another — not the cessation of all biological life. Organismal death occurs well before all of the organism’s parts irreversibly cease vital activity and decompose into inorganic matter. Biological life in some form can and usually does continue after organismal death at least for a time, with recent evidence indicating that animal cell networks continue to perform complex functions like stress response, immune response and inflammation response up to several days postmortem.1 With external support, many cells and tissues can continue to perform their functions ex vivo for long periods of time or even indefinitely.2 Henrietta Lax died in 1951, but cells derived from her cancerous cervical cells …. (shrink)

A long-standing debate on the causality of levels in biological explanations has divided philosophers into two camps. The reductionist camp insists on the causal primacy of lower, molecular levels, while the critics point out the inescapable shifting, reciprocity, and circularity of levels across biological explanations. We argue, however, that many explanations in biology do not exclusively draw their explanatory power from detailed insights into inter-level interactions; they predominantly require identifying the adequate levels of biological complexity to (...) be explained. Moreover, the main explanatory strategies grounding both theoretical and experimental approaches to one of the central debates in contemporary biology, i.e., on the origin of life, are primarily and sometimes exclusively driven by issues concerning the levels of biochemical complexity, and these only subsequently frame more substantial and detailed accounts of inter-level biochemical interactions. (shrink)

In the present article, a depiction of complexity versus time will be used for the construction of a novel form of a tree of life, called The Pattern of Life, comprising the biological, cultural, and scientific forms of the evolutionary process. This diagram accentuates the implication of the successive modifications of developmental programs, in the cultural and scientific realms coupled to a feedback mechanism that is decisive for the accelerating pace of complexity growth, also suggested to be (...) of support of a cautious prediction of future evolution. (shrink)

This article is about the power of critical thinking through embryos and embryology in bioart. In this instance, critical thinking does not promise revolution or a takedown of bioengineering, but basic empowerment through scientific knowledge. I argue that the use of embryos in Jill Scott’s Somabook (2011) and Adam Zaretsky’s DIY Embryology (2015) constitutes an instance of what Philip Galanter identifies as complexism. In turn, the complexism of embryology reveals two modes of critical thinking. First, embryology distils the awe and (...) wonder that come with basic scientific literacy. In turn, scientific literacy provides agency for individuals through a trifecta of feeling, belief and pragmatism: based on the frisson of curiosity and wonder that comes with recognizing biological complexity, it frees individuals from the bounds of superstition and metaphysics while building a path to fact-based problem solving. Second, as works of art bearing embryos they are part of the politics and history of embryology that emerged in contrast to genetics almost a century ago. Distinct from the coding of genetics as nucleus-centric, separate, homogeneous, a matter of being, and male, embryology was coded as cytoplasmic, interactive, heterogeneous, a matter of becoming, and feminist. (shrink)

The process of condensation of an amorphous solid into a rigid matrix can often trap molecules in reversible binding sites. Exchange of the same molecular species with such sites is known to be sensitive to small chemical differences and to distinguish between enantiomers. In addition to their usefulness in chromatographic processes, such materials can separate, by solid phase extraction, specific compounds from complex mixtures. Furthermore, the trapped molecules can have their reactions guided and catalytically changed. The combination of this spontaneously (...) formed system of templates and catalytic sites may support a type of replication cycle, and suggests some pathways from simple chemistry toward the complexities of biology. © 2005 Wiley Periodicals, Inc. Complexity 11: 30–35, 2005 -/- . (shrink)

This text explores how we understand living and other complex systems. The conventional basis of understanding rests on abstract general theories, but this book proposes conceptual continuity as a new means of comparing systems of divergent complexity and resolving problems in complex systems.

This paper uses some recent ideas in biology as starting point to explore analogous concepts and tendencies in semiotics and biology, leading to reflections on interdisciplinarity itself within the framework of theories of chaos and complexity. It sees affinities between the biological concept of species and the semiotic category of discipline. It finds many suggestive parallels with semiotics from the recently emerging synthesis of evolution and development, built around the discovery of ‘homeobox’ genes which are present in many (...) very different lineages, opening up possibilities for ‘deep’ homologies between species, and providing a powerful model for semiotic homology. (shrink)

It has been suggested that biological theories differ from physical theories because the subject matter of biology differs from the subject matter of physics especially in the fact that living bodies are more complex than nonliving bodies. It is shown that the interactional complexity of living bodies can only be expressed by invoking biological theories. The claim that living bodies are complex is, therefore, ultimately a claim about the nature of scientific theories rather than a claim about (...) the nature of the subject matter of biology resting upon a presystematic judgement. (shrink)

Self-organized criticality (SOC) is based upon the idea that complex behavior can develop spontaneously in certain multi-body systems whose dynamics vary abruptly. This book is a clear and concise introduction to the field of self-organized criticality, and contains an overview of the main research results. The author begins with an examination of what is meant by SOC, and the systems in which it can occur. He then presents and analyzes computer models to describe a number of systems, and he explains (...) the different mathematical formalisms developed to understand SOC. The final chapter assesses the impact of this field of study, and highlights some key areas of new research. The author assumes no previous knowledge of the field, and the book contains several exercises. It will be ideal as a textbook for graduate students taking physics, engineering, or mathematical biology courses in nonlinear science or complexity. (shrink)

Pleiotropy, in which one mutation causes multiple phenotypes, has traditionally been seen as a deviation from the conventional observation in which one gene affects one phenotype. Epistasis, or gene–gene interaction, has also been treated as an exception to the Mendelian one gene–one phenotype paradigm. This simplified perspective belies the pervasive complexity of biology and hinders progress toward a deeper understanding of biological systems. We assert that epistasis and pleiotropy are not isolated occurrences, but ubiquitous and inherent properties of (...) biomolecular networks. These phenomena should not be treated as exceptions, but rather as fundamental components of genetic analyses. A systems level understanding of epistasis and pleiotropy is, therefore, critical to furthering our understanding of human genetics and its contribution to common human disease. Finally, graph theory offers an intuitive and powerful set of tools with which to study the network bases of these important genetic phenomena. (shrink)

Development and Evolution surveys and illuminates the key themes of rapidly changing fields and areas of controversy that the redefining the theory and philosophy of biology. It continues Stanley Salthe's investigation of evolutionary theory, begun in his influential book Evolving Hierarchical Systems, while negating the implicit philosophical mechanisms of much of that work. Here Salthe attempts to reinitiate a theory of biology from the perspective of development rather than from that of evolution, recognizing the applicability of general systems thinking to (...) biological and social phenomena and pointing towards a non-Darwinian and even a postmodern biology. (shrink)

Autophagy and YAP1‐WWTR1/TAZ signalling are tightly linked in a complex control system of forward and feedback pathways which determine different cellular outcomes in differing cell types at different time‐points after perturbations. Here we extend our previous experimental and modelling approaches to consider two possibilities. First, we have performed additional mathematical modelling to explore how the autophagy‐YAP1 crosstalk may be controlled by posttranslational modifications of components of the pathways. Second, since analogous contrasting results have also been reported for autophagy as a (...) regulator of other transduction pathways engaged in tumorigenesis (Wnt/β‐catenin, TGF‐β/Smads, NF‐kB or XIAP/cIAPs), we have considered if such discrepancies may be explicable through situations involving competing pathways and feedback loops in different cell types, analogous to the autophagy‐YAP/TAZ situation. Since distinct posttranslational modifications dominate those pathways in distinct cells, these need to be understood to enable appropriate cell type‐specific therapeutic strategies for cancers and other diseases. (shrink)

Self-organized complexity in the physical, biological, and social sciences Donald L Turcotte*f and John B. Rundle* *Department of Earth and Atmospheric ...

Protein ubiquitination constitutes a post‐translational modification mediated by ubiquitin ligases whereby ubiquitinated substrates are degraded through the proteasomal or lysosomal pathways, or acquire novel molecular functions according to their “ubiquitin codes.” Dysfunction of the ubiquitination process in cells causes various diseases such as cancers along with neurodegenerative, auto‐immune/inflammatory, and metabolic diseases. KCTD10 functions as a substrate recognition receptor for cullin‐3 (CUL3), a scaffold protein in RING‐type ubiquitin ligase complexes. Recently, studies by ourselves and others have identified new substrates that are (...) ubiquitinated by the CUL3/KCTD10 ubiquitin ligase complex. Moreover, the type of polyubiquitination (e.g., K27‐, K48‐, or K63‐chain) of various substrates (e.g., RhoB, CEP97, EIF3D, and TRIF) mediated by KCTD10 underlies its divergent roles in endothelial barrier formation, primary cilium formation, plasma membrane dynamics, cell proliferation, and immune response. Here, the physiological functions of KCTD10 are summarized and potential mechanisms are proposed. (shrink)

Any living system possesses internal embedded description and exists as a superposition of different potential realisations, which are reduced in interaction with the environment. This reduction cannot be recursively deduced from the state in time present, it includes unpredictable choice and needs to be modelled also from the state in time future. Such non-recursive establishment of emerging configuration, after its memorisation via formation of reflective loop (sign-creating activity), becomes the inherited recursive action. It leads to increase of complexity of (...) the embedded description, which constitutes the rules of generative grammar defining possible directions of open evolutionary process. The states in time future can be estimated from the point of their perfection, which represents the final cause in the Aristotelian sense and may possess a selective advantage. The limits of unfolding of the reflective process, such as the golden ratio and the golden wurf are considered as the canons of perfection established in the evolutionary process. (shrink)

Any living system possesses internal embedded description and exists as a superposition of different potential realisations, which are reduced in interaction with the environment. This reduction cannot be recursively deduced from the state in time present, it includes unpredictable choice and needs to be modelled also from the state in time future. Such non-recursive establishment of emerging configuration, after its memorisation via formation of reflective loop (sign-creating activity), becomes the inherited recursive action. It leads to increase of complexity of (...) the embedded description, which constitutes the rules of generative grammar defining possible directions of open evolutionary process. The states in time future can be estimated from the point of their perfection, which represents the final cause in the Aristotelian sense and may possess a selective advantage. The limits of unfolding of the reflective process, such as the golden ratio and the golden wurf are considered as the canons of perfection established in the evolutionary process. (shrink)

Systems architecture and its associated parallel biology generate architectural forms that are both green and surreal by nature. The connection between systems architecture and Leo Lionni's fantastic book Parallel Botany are considered as architects are now starting to have the ability to create great works of biological parallelism using technologies that are highly sur real, they are on top of the real.